LMU BioDB 2017 - User contributions [en]

Aporras1 Individual Assessment and Reflection

2017-12-16T00:18:53Z

Aporras1: /* Individual Assessment and Reflection */ signature

User page: [[User:Aporras1|Antonio Porras]]

Assignment page: [[GRNsight_Gene_Page_Project_Deliverables|Deliverables Page]]

Group page: [[JASPAR_the_Friendly_Ghost|JASPAR the Friendly Ghost]]

==Individual Assessment and Reflection==

=== Statement of Work ===

'''1. Describe exactly what you did on the project.'''

As data analyst I was responsible for performing statistical analysis on dZAP1 expression data provided by [[User:kdahlquist|Dr. Dahlquist]]'s lab. During Week 8 I completed the ANOVA test along with calculating Benjamini-Hochberg corrected p value and the Bonferroni-corrected p-value. The first calculation was less stringent compared to the Bonferroni but both were useful in terms of improving the confidence in the data. The precise steps and outline of what I completed can be found in my [[Aporras1_Week_8]] journal.

Moving into Week 10, I performed STEM high level analysis on the ANOVA data in order to generate gene clusters which presented similar expression over the course of the experiment. Seven significant clusters were generated and the GOlists & genelists were saved and uploaded to the wiki for later analysis. I read and interpreted 6 GOlist terms found in the GOlist of Profile 22 and attempted to understand why the cell would be changing expression in genes associated with certain cell processes. The precise steps and outline of what I completed can be found in my [[Aporras1_Week_10]] journal.

In Week 11, I worked alongside [[User:Qlanners|Quinn Lanners]] to perform a literature search on yeast and cold shock to gain brief exposure to journal articles in this area of research and search engine qualities. The precise steps and outline can be found in my [[Aporras1_Week_11]] journal. The following week [[User:Qlanners|Quinn Lanners]] and I did more in-depth research on the specific journal article: Genome-wide analysis of the yeast transcriptome upon heat and cold shock (Becerra et al., 2003). We outlined the introduction, methods, procedure, analysis tools, and overall findings of the article before creating and presenting a presentation to the class which can be found in my [[Aporras1_Week_12]] journal along with the specific outline and approach to interpretation of their data.

In Week 14 and Week 15 I continued work from the Week 10 data analysis and selected profile 22 of dZAP1 from STEM analysis. I then generated a list of significant transcription factors which targeted genes within the genelist provided by STEM and further used those transcription factors to create a regulatory network. This network was actually determined to be too large and [[User:kdahlquist|Dr. Dahlquist]] trimmed down the network to 15 transcription factors. The network was then put into GRNsight to visualize the regulation pathways. MATLAB was also used to generate an output which would allow for GRNsight to display the direction of regulation and the magnitude with colors and bold/thin regulation arrows. A more detailed outline for the process can be found in my [[Aporras1_Week_14]] journal.

Once I completed all the analysis, I then put the data onto the deliverables page, presentation, and the final paper along with my analysis. These files can be found in [[JASPAR_the_Friendly_Ghost_Final_Deliverables]]. I was primarily responsible for maintaining extreme care with the files and keeping a very well-kept record of data. In addition I worked closely with [[User:Qlanners|Quinn Lanners]] to complete the final paper and aid in any way possible once I completed my data calculations and subsequent analysis. A more detailed outline for the process can be found in my [[Aporras1_Week_15]] journal.

=== Assessment of Project ===

'''2. Give an objective assessment of the success of your project workflow and teamwork.'''

I would say the overall project workflow and teamwork was fairly cohesive considering our different academic backgrounds and schedules. Given this time of the year, with final exams, we did very well to meet outside of class and work in the lab while communicating constantly. My workflow didn't impede the workflow of anyone else throughout the project and it was definitely a good feeling to have throughout working on the project as I attempted to complete everything ahead of time and work on group deliverables before my own.

'''3. What worked and what didn't work?'''

What didn't work was, or at least I didn't fully accept, was the need for both a paper and a presentation. I felt as though it became repetitive when examining both the paper and the introduction. With regards to the team, there weren't any aspects that didn't work, except I wish I would have had a better understanding of the role of the coders and their work through JASPAR. It took a lot of curiosity and asking to figure it out rather than being explained it in the beginning.

'''4. What would you do differently if you could do it all over again?'''

I definitely wish I had the same good data record keeping skills that I have currently because it would have saved a lot of time throughout the semester.

'''5. Evaluate your team’s portion of the GRNsight Gene Page Project and Group Report in the following areas:'''

'''* Content: What is the quality of the work?'''

From my understanding of the coders, they put their best foot forward in terms of working in a new area in which they hadn't worked in before. As data analyst I had context and prior understanding of my analysis but for them they had to work with a completely new database, JASPAR. Quinn created a structure by which every aspect was planned out and made it easy to keep track of deadlines and goals. Overall, while also considering the amount of time spent throughout these last few weeks and paying attention to very specific details, JASPAR the Friendly Ghost did their best to complete what was assigned. Again, while paying attention to copious details.

'''* Organization: Comment on the organization of the project and of your group's wiki pages.'''

As I mentioned earlier, Quinn structured the page easily so that even I could go ahead and add sections because we all understood the intuitive layout. I kept detailed file records and explained any changes I made to the data while also maintaining a detailed electronic notebook every single week.

'''* Completeness: Did your team achieve all of the project objectives? Why or why not?'''

To the best of my knowledge, we did. We would go through the deliverables page line by line checking tasks off in order to ensure that our product was as complete as it could be. Of course its not perfect, but considering the amount of details and time given, we put a significant amount of time into the project and displaying documentation throughout.

=== Reflection on the Process ===

'''What did you learn?'''

'''With your head (biological or computer science principles)'''

I definitely have much better data management than I did at the beginning of the course and the ability to organize thoughts for someone else to read and replicate the processes I completed throughout the semester. Ultimately, synthesizing replicable data and thus very detailed step by step notes. In terms of biology I didn't take as much because we didn't go very much in depth but now I have a better understanding of how to interpret more intricate data sets and understand the context at least in respect to microarray data.

'''With your heart (personal qualities and teamwork qualities that make things work or not work)?'''

Simply working hard.. and early! It made a huge difference in my workflow to finish assignments ahead of time (prior journal entries may not display this). Instead of waiting for deadlines I found an ethic to attack them to account for time where I was met with difficulties or setbacks (e.g. having to trim down my regulation network) and these setbacks didn't do as much damage because I met them so early before the deadline.

'''With your hands (technical skills)?'''

I've been around computers for a very long time so I didn't really gain any technical skills besides knowing how I work best. I came to the lab because the screens were bigger and I usually used two monitors to save time going in between the assignment Page, individual page, and datasets. This greatly improved my workflow and provided structure which I thrive from.

'''What lesson will you take away from this project that you will still use a year from now?'''

Recognizing how I work best. As soon as I recognized how I work best (e.g. working with multiple monitors or working on assignments early) I was able to improve my efficiency as the assignments got more difficult. Lastly, data management and organization. Organization with respect to files made the process much easier than if I hadn't learned to be descriptive with file names or have multiple backups and a notepad with a filename and description. These organizational techniques were vital and will be useful in future environments where data is often more digital than it is paper.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 16:18, 15 December 2017 (PST)

==Acknowledgements==
#Copied the structure of the sections in my assessment and reflection from the [[GRNsight_Gene_Page_Project_Deliverables|Deliverables Page]].
#Worked alongside [[User:Qlanners|Quinn Lanners]] in Week 11 and 12 and subsequently Weeks 14 and 15 to complete the assignment.
#The [[JASPAR the Friendly Ghost]] team members including [[User:Qlanners|Quinn Lanners]], [[User:Simonwro120|Simon Wroblewski]], and [[User:Ebachour|Eddie Bachoura]].
#Received assistance in completing the assignments from [[User:kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dionisio]].
#The entire class members who I had the opportunity to work alongside.
#LMU Biology and Computer Science Departments for the resources throughout the semester.

'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.'''

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 16:00, 15 December 2017 (PST)

==References==
# Dahlquist, K. D., Dionisio, J. D. N., Fitzpatrick, B. G., Anguiano, N. A., Varshneya, A., Southwick, B. J., & Samdarshi, M. (2016). GRNsight: a web application and service for visualizing models of small-to medium-scale gene regulatory networks. PeerJ Computer Science, 2, e85.
# LMU BioDB 2017. (2017). GRNsight Gene Page Project Deliverables. Retrieved December 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/GRNsight_Gene_Page_Project_Deliverables
# LMU BioDB 2017. (2017). Aporras1 Week 8. Retrieved December 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Aporras1_Week_8
# LMU BioDB 2017. (2017). Aporras1 Week 10. Retrieved December 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Aporras1_Week_10
# LMU BioDB 2017. (2017). Aporras1 Week 11. Retrieved December 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Aporras1_Week_11
# LMU BioDB 2017. (2017). Aporras1 Week 12. Retrieved December 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Aporras1_Week_12
# LMU BioDB 2017. (2017). Aporras1 Week 14. Retrieved December 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Aporras1_Week_14
# LMU BioDB 2017. (2017). Aporras1 Week 15. Retrieved December 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Aporras1_Week_15
# Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.

[[Category:Journal Entry]]

Aporras1 Week 15

2017-12-16T00:16:59Z

Aporras1: /* Deliverables Checklist */ removed note

User page: [[User:Aporras1|Antonio Porras]]

Team page: [[JASPAR the Friendly Ghost|JASPAR The Friendly Ghost]]

Assignment page: [[Week 15|Week 15]]

==Electronic Notebook==
# Network was determined to be too big.
#* Began process of deleting the least significant
# Re-downloaded [[Media:AP YEASTRACT Transcription Factors.xlsx]] and found the transcription factors which I used in [[Aporras1_Week_14]] ranked from highest % in user set to lowest:
#**GLN3
#**HAP4
#**Ace2p
#**Sfp1p
#**Bas1p
#**Msn2p
#**Yap1p
#**Ash1p
#**Gcn4p
#**Msn4p
#**Abf1p
#**Cst6p
#**Sok2p
#**Rpn4p
#**Hsf1p
#**Zap1p
#**Cin5p
#**Aft1p
#**Spt23p
#**Pdr1p
#**Met4p
#**Arr1p

===ARR1 deletion===
# Moved "network" workbook to a new file found in [[Media:Trimming Network transcription factor deletions dZAP1.zip]]: Network ARR1 deletion.xlsx
# Began by deleting ARR1 in worksheet "Network ARR1 deletion"
#* Deleted row 5 and column E containing ARR1 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network ARR1 deletion.xlsx" file that has the "network" worksheet.
# Network remained too large.

===MET4 deletion===
# Moved "network" workbook from Network ARR1 deletion.xlsx to a new file found in [[Media:Trimming Network transcription factor deletions dZAP1.zip]]: Network MET4 deletion.xlsx
# Began by deleting MET4 in worksheet "network MET4 deletion"
#* Deleted row 13 and column M containing MET4 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network MET4 deletion" file that has the "network" worksheet.
# Network remained too large.

===PDR1 deletion===
# Moved "network" workbook from Network MET4 deletion.xlsx to a new file found in [[Media:Trimming Network transcription factor deletions dZAP1.zip]]: Network PDR1 deletion.xlsx
# Began by deleting PDR1 in worksheet "network PDR1 deletion"
#* Deleted row 15 and column O containing PDR1 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network PDR1 deletion" file that has the "network" worksheet.
# Network remained too large.

===SPT23 & BAS1 deletion===
# Moved "network" workbook from Network PDR1 deletion.xlsx to a new file found in folder [[Media:Trimming Network transcription factor deletions dZAP1.zip]]: Network SPT23 deletion.xlsx
# Began by deleting PDR1 in worksheet "network SPT23 deletion"
#* Deleted row 19 and column S containing SPT23 data.
#*BAS1 transcription factor became disconnected.
#*Deleted row 6 and column F containing BAS1 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network SPT23 deletion" file that has the "network" worksheet.
# Network remained too large.

===Network Files After Trimming===

[[Media:Trimming Network transcription factor deletions dZAP1.zip]]

Files were not necessary in the final GRNsight visualization, but rather for documentation on work performed before being provided by [[User:Kdahlquist|Dr. Dahlquist]].

Antonio, I finished paring down the network. Here is the final file (renamed): [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx | 15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]]. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:55, 6 December 2017 (PST)''

===GRNsight Visualization===
# Downloaded [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]] provided by [[User:Kdahlquist|Dr. Dahlquist]].
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx" file that has the "network" worksheet. Moved the nodes (genes) around until I created a layout I liked, ordering alphabetically, and took a screenshot of the results and saved the screenshot as:[[Media:GRNsight Visualization of 15-gene 44-edge teamJASPAR Sigmoid estimation.PNG]]

===GRNsight Regulation MATLAB Output===
# Used [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]] and allowed [[User:Kdahlquist|Dr. Dahlquist]] to run MATLAB.
#* Once it was completed, saved the output workbook as:[[Media:15-gene 44-edge teamJASPAR Sigmoid estimation output.xlsx]]
#* Saved the images and uploaded them to the wiki as:[[Media:Output Images from 15-gene 44-edge teamJASPAR Sigmoid estimation.zip]]
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "15-gene_44-edge_teamJASPAR_Sigmoid_estimation_output.xlsx" file that had the "network" worksheet. Moved the nodes (genes) around until I created a layout I liked, ordering alphabetically, and took a screenshot of the results and saved the screenshot as:[[Media:GRNsight Regulation Magnitude Visualization of 15-gene 44-edge teamJASPAR Sigmoid estimation.PNG]]

===Edits to Organization of Files===
# In [[Week 10|Week 10]] the powerpoint STEM screenshots, GOlists, and genelists were all zipped in [[Media:AP dZAP1 STEM Profiles and Powerpoint.zip]] and the deliverables, in [[GRNsight Gene Page Project Deliverables|Project Deliverables]], asked for two separate files.
#* Removed the powerpoint with the p-values and STEM screenshots. Zipped the powerpoint and uploaded it to the wiki as a new file found in the deliverables: [[Media:AP dZAP1 STEM Screenshots & p-values.zip]].
#* Removed the golists and genelists .txt files into a new folder and zipped the folder before uploading it as a new file found in the deliverables: [[Media:AP dZAP1 GOlist and genelist for profiles.zip]]

===Deliverables Checklist===
# Excel spreadsheet with ANOVA results/stem formatting (''.xlsx'')
#*[[Media:AP dZAP1 stem.xlsx]]
# PowerPoint of screenshots of stem results (''.pptx'')
#* [[Media:AP dZAP1 STEM Screenshots & p-values.zip]]
# Gene List and GO List files from each significant profile (''.txt'' compressed together in a ''.zip'' file)
#* [[Media:AP dZAP1 GOlist and genelist for profiles.zip]]
# YEASTRACT "rank by TF" results (''.xlsx'')
#* [[Media:AP YEASTRACT Transcription Factors.xlsx]]
# GRNmap input workbook (with network adjacency matrix, ''.xlsx'')
#* [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]]
# GRNmap output workbook (''.xlsx'')
#* [[Media:15-gene 44-edge teamJASPAR Sigmoid estimation output.xlsx]]
#* Expression vs Time Images generated from MATLAB
#** [[Media:Output Images from 15-gene 44-edge teamJASPAR Sigmoid estimation.zip]]
# Electronic notebook corresponding to these the microarray results files ([[Week 8]], [[Week 10]], & [[Week 14]]) support ''reproducible research'' so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results.
#* Summary for [[Aporras1_Week_8]]: In week 8, performed statistical analysis on the deletion ZAP1 using provided ANOVA. Specfically, Bonferroni & p value correction and Benjamini & Hochberg p value was calculated. The data examined the time intervals of 15 minutes, 30 minutes, 60 minutes, 90 minutes, and 120 minutes during cold shock.
#** Electronic notebook found in "Electronic Notebook" section of [[Aporras1_Week_8]]
#* Summary for [[Aporras1_Week_10]]: Used the data from [[Aporras1_Week_8]] to perform STEM clustering on dZAP1. Selected profile 22 because it had a very low p value and a high amount of genes (2E-157 and 252 respectively). Selected 6 GO terms from profile 22's GOlist to define and analyze in terms of why the cell would change the expression of the genes associated with the GO terms.
#** Electronic notebook found in "Electronic Notebook" section of [[Aporras1_Week_10]]
#* Summary for [[Aporras1_Week_14]]: Made edits to [[Aporras1_Week_8]] and [[Aporras1_Week_10]] according to feedback from [[User:Kdahlquist|Dr. Dahlquist]] & [[User:Dondi|Dr. Dionisio]]. Used the profile 22 genelist and ranked transcription factors with YEASTRACT by significance and selected the most significant ones with low P-values. Generated a regulation matrix using YEASTRACT and created an adjacency matrix with a network to visualize with GRNsight. The network was trimmed down to 15 genes and MATLAB was used to generate an output. Both the output and the original network were visualized with GRNsight.
#** Electronic notebook found in "Electronic Notebook" section of [[Aporras1_Week_14]].

==Final Powerpoint Presentation==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf]]

==Final Paper/Group Report==
[[Media:JASPAR Final Paper.pdf|JASPAR the Friendly Ghost Final Group Report]]

==Acknowledgements==
# Worked alongside [[User:Qlanners|Quinn Lanners]] to begin gathering deliverables.
# Copied the formatting and text from [[GRNsight_Gene_Page_Project_Deliverables]] checklist in my checklist category.
# Received file used for GRNsight visualization, received in class direction and instruction from [[User:Kdahlquist|Dr. Dahlquist]].
# Met up with group members in [[JASPAR the Friendly Ghost]] after the Thursday 12/01/2017 class and outside of class 12/09/2017 to discuss an outline of what needed to be completed and to work on the presentation.

'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.'''

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 16:11, 7 December 2017 (PST)

==References==
#Dahlquist, K. D., Dionisio, J. D. N., Fitzpatrick, B. G., Anguiano, N. A., Varshneya, A., Southwick, B. J., & Samdarshi, M. (2016). GRNsight: a web application and service for visualizing models of small-to medium-scale gene regulatory networks. PeerJ Computer Science, 2, e85.
# LMU BioDB 2017. (2017). Week 15. Retrieved December 05, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15
# LMU BioDB 2017. (2017). GRNsight Gene Page Project Deliverables. Retrieved December 05, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/GRNsight_Gene_Page_Project_Deliverables
# Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.

[[Category:Journal Entry]]

Aporras1 Week 15

2017-12-16T00:15:18Z

Aporras1: /* Final Paper/Group Report */ changed name displayed

User page: [[User:Aporras1|Antonio Porras]]

Team page: [[JASPAR the Friendly Ghost|JASPAR The Friendly Ghost]]

Assignment page: [[Week 15|Week 15]]

==Electronic Notebook==
# Network was determined to be too big.
#* Began process of deleting the least significant
# Re-downloaded [[Media:AP YEASTRACT Transcription Factors.xlsx]] and found the transcription factors which I used in [[Aporras1_Week_14]] ranked from highest % in user set to lowest:
#**GLN3
#**HAP4
#**Ace2p
#**Sfp1p
#**Bas1p
#**Msn2p
#**Yap1p
#**Ash1p
#**Gcn4p
#**Msn4p
#**Abf1p
#**Cst6p
#**Sok2p
#**Rpn4p
#**Hsf1p
#**Zap1p
#**Cin5p
#**Aft1p
#**Spt23p
#**Pdr1p
#**Met4p
#**Arr1p

===ARR1 deletion===
# Moved "network" workbook to a new file found in [[Media:Trimming Network transcription factor deletions dZAP1.zip]]: Network ARR1 deletion.xlsx
# Began by deleting ARR1 in worksheet "Network ARR1 deletion"
#* Deleted row 5 and column E containing ARR1 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network ARR1 deletion.xlsx" file that has the "network" worksheet.
# Network remained too large.

===MET4 deletion===
# Moved "network" workbook from Network ARR1 deletion.xlsx to a new file found in [[Media:Trimming Network transcription factor deletions dZAP1.zip]]: Network MET4 deletion.xlsx
# Began by deleting MET4 in worksheet "network MET4 deletion"
#* Deleted row 13 and column M containing MET4 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network MET4 deletion" file that has the "network" worksheet.
# Network remained too large.

===PDR1 deletion===
# Moved "network" workbook from Network MET4 deletion.xlsx to a new file found in [[Media:Trimming Network transcription factor deletions dZAP1.zip]]: Network PDR1 deletion.xlsx
# Began by deleting PDR1 in worksheet "network PDR1 deletion"
#* Deleted row 15 and column O containing PDR1 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network PDR1 deletion" file that has the "network" worksheet.
# Network remained too large.

===SPT23 & BAS1 deletion===
# Moved "network" workbook from Network PDR1 deletion.xlsx to a new file found in folder [[Media:Trimming Network transcription factor deletions dZAP1.zip]]: Network SPT23 deletion.xlsx
# Began by deleting PDR1 in worksheet "network SPT23 deletion"
#* Deleted row 19 and column S containing SPT23 data.
#*BAS1 transcription factor became disconnected.
#*Deleted row 6 and column F containing BAS1 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network SPT23 deletion" file that has the "network" worksheet.
# Network remained too large.

===Network Files After Trimming===

[[Media:Trimming Network transcription factor deletions dZAP1.zip]]

Files were not necessary in the final GRNsight visualization, but rather for documentation on work performed before being provided by [[User:Kdahlquist|Dr. Dahlquist]].

Antonio, I finished paring down the network. Here is the final file (renamed): [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx | 15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]]. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:55, 6 December 2017 (PST)''

===GRNsight Visualization===
# Downloaded [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]] provided by [[User:Kdahlquist|Dr. Dahlquist]].
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx" file that has the "network" worksheet. Moved the nodes (genes) around until I created a layout I liked, ordering alphabetically, and took a screenshot of the results and saved the screenshot as:[[Media:GRNsight Visualization of 15-gene 44-edge teamJASPAR Sigmoid estimation.PNG]]

===GRNsight Regulation MATLAB Output===
# Used [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]] and allowed [[User:Kdahlquist|Dr. Dahlquist]] to run MATLAB.
#* Once it was completed, saved the output workbook as:[[Media:15-gene 44-edge teamJASPAR Sigmoid estimation output.xlsx]]
#* Saved the images and uploaded them to the wiki as:[[Media:Output Images from 15-gene 44-edge teamJASPAR Sigmoid estimation.zip]]
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "15-gene_44-edge_teamJASPAR_Sigmoid_estimation_output.xlsx" file that had the "network" worksheet. Moved the nodes (genes) around until I created a layout I liked, ordering alphabetically, and took a screenshot of the results and saved the screenshot as:[[Media:GRNsight Regulation Magnitude Visualization of 15-gene 44-edge teamJASPAR Sigmoid estimation.PNG]]

===Edits to Organization of Files===
# In [[Week 10|Week 10]] the powerpoint STEM screenshots, GOlists, and genelists were all zipped in [[Media:AP dZAP1 STEM Profiles and Powerpoint.zip]] and the deliverables, in [[GRNsight Gene Page Project Deliverables|Project Deliverables]], asked for two separate files.
#* Removed the powerpoint with the p-values and STEM screenshots. Zipped the powerpoint and uploaded it to the wiki as a new file found in the deliverables: [[Media:AP dZAP1 STEM Screenshots & p-values.zip]].
#* Removed the golists and genelists .txt files into a new folder and zipped the folder before uploading it as a new file found in the deliverables: [[Media:AP dZAP1 GOlist and genelist for profiles.zip]]

===Deliverables Checklist===
# Excel spreadsheet with ANOVA results/stem formatting (''.xlsx'')
#*[[Media:AP dZAP1 stem.xlsx]]
# PowerPoint of screenshots of stem results (''.pptx'')
#* [[Media:AP dZAP1 STEM Screenshots & p-values.zip]]
# Gene List and GO List files from each significant profile (''.txt'' compressed together in a ''.zip'' file)
#* [[Media:AP dZAP1 GOlist and genelist for profiles.zip]]
# YEASTRACT "rank by TF" results (''.xlsx'')
#* [[Media:AP YEASTRACT Transcription Factors.xlsx]]
# GRNmap input workbook (with network adjacency matrix, ''.xlsx'')
#* [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]]
# GRNmap output workbook (''.xlsx'')
#* [[Media:15-gene 44-edge teamJASPAR Sigmoid estimation output.xlsx]]
#* Expression vs Time Images generated from MATLAB
#** [[Media:Output Images from 15-gene 44-edge teamJASPAR Sigmoid estimation.zip]]
# Electronic notebook corresponding to these the microarray results files ([[Week 8]], [[Week 10]], & [[Week 14]]) support ''reproducible research'' so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results.
#* Summary for [[Aporras1_Week_8]]: In week 8, performed statistical analysis on the deletion ZAP1 using provided ANOVA. Specfically, Bonferroni & p value correction and Benjamini & Hochberg p value was calculated. The data examined the time intervals of 15 minutes, 30 minutes, 60 minutes, 90 minutes, and 120 minutes during cold shock.
#** Electronic notebook found in "Electronic Notebook" section of [[Aporras1_Week_8]]
#* Summary for [[Aporras1_Week_10]]: Used the data from [[Aporras1_Week_8]] to perform STEM clustering on dZAP1. Selected profile 22 because it had a very low p value and a high amount of genes (2E-157 and 252 respectively). Selected 6 GO terms from profile 22's GOlist to define and analyze in terms of why the cell would change the expression of the genes associated with the GO terms.
#** Electronic notebook found in "Electronic Notebook" section of [[Aporras1_Week_10]]
#* Summary for [[Aporras1_Week_14]]: Made edits to [[Aporras1_Week_8]] and [[Aporras1_Week_10]] according to feedback from [[User:Kdahlquist|Dr. Dahlquist]] & [[User:Dondi|Dr. Dionisio]]. Used the profile 22 genelist and ranked transcription factors with YEASTRACT by significance and selected the most significant ones with low P-values. Generated a regulation matrix using YEASTRACT and created an adjacency matrix with a network to visualize with GRNsight. The network was trimmed down to 15 genes and MATLAB was used to generate an output. Both the output and the original network were visualized with GRNsight.
#** Electronic notebook found in "Electronic Notebook" section of [[Aporras1_Week_14]].
#* Note: make a summary and provide links to individual pages with electronic notebooks.

==Final Powerpoint Presentation==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf]]

==Final Paper/Group Report==
[[Media:JASPAR Final Paper.pdf|JASPAR the Friendly Ghost Final Group Report]]

==Acknowledgements==
# Worked alongside [[User:Qlanners|Quinn Lanners]] to begin gathering deliverables.
# Copied the formatting and text from [[GRNsight_Gene_Page_Project_Deliverables]] checklist in my checklist category.
# Received file used for GRNsight visualization, received in class direction and instruction from [[User:Kdahlquist|Dr. Dahlquist]].
# Met up with group members in [[JASPAR the Friendly Ghost]] after the Thursday 12/01/2017 class and outside of class 12/09/2017 to discuss an outline of what needed to be completed and to work on the presentation.

'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.'''

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 16:11, 7 December 2017 (PST)

==References==
#Dahlquist, K. D., Dionisio, J. D. N., Fitzpatrick, B. G., Anguiano, N. A., Varshneya, A., Southwick, B. J., & Samdarshi, M. (2016). GRNsight: a web application and service for visualizing models of small-to medium-scale gene regulatory networks. PeerJ Computer Science, 2, e85.
# LMU BioDB 2017. (2017). Week 15. Retrieved December 05, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15
# LMU BioDB 2017. (2017). GRNsight Gene Page Project Deliverables. Retrieved December 05, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/GRNsight_Gene_Page_Project_Deliverables
# Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.

[[Category:Journal Entry]]

Ebachour Week 15

2017-12-16T00:10:42Z

Aporras1: reformatted location of final paper

==Deliverables==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf|JASPAR the Friendly Ghost Final Group Presentation]] | December 11, 2017 
[[Media:README.txt|JASPAR The Friendly Ghost Group Readme]] | December 15, 2017 
[[Media:Api.txt|JASPAR The Friendly Ghost Group Code]] | December 15, 2017 
[[Media:JASPAR Final Paper.pdf|JASPAR the Friendly Ghost Final Group Report]] | December 15, 2017

==Individual Assessment and Reflection / Electronic Journal==

=== Statement of Work ===

There were a number of steps that the coders team members completed throughout this assignment. Before the coders moved their focus to the bulk of the GRNsight part of this project, they were asked to gain some background knowledge on the field of web development. They read “Chapter 6: How Are Apps Made?” in Paul Ford’s What is Code? which is an article from 2015 that covers most of the bases of the software development industry. They were asked to thoroughly read this chapter and then present to their class what it entailed. This chapter was specific to all of the tools that the coders used in development, highlighting some important tools at the time. After covering all of the background knowledge, the coders then began the introduction phase to the new project. Often when being assigned to a new project, software engineers are given an introduction to the code base so that they may understand how everything functions within the project before they begin their work. This project was no different, as the professor gave a quick introduction along with a manual which illustrated the relevant folders within the code bank that would be used for this feature. After JASPAR’s fellow team members forked GRNsight, the JASPAR team start by setting up a local version of GRNsight and making sure that everything was properly functioning. After this step, they began to acquaint themselves with GRNsight and understand their job in the implementation of this new feature. At this point, as as displayed in Figure C, the coders moved from the immersion phase (green) and into the intermediate phase (yellow).

The intermediate phase was where most of the progress was made towards finishing their part of the feature. They started by creating the branch that would be solely for JASPAR team progress, as well as the new files that would contain their soon-to-be-written code. At this point the coders were all setup on the GRNsight side and were ready to move to learning about the JASPAR database and how it worked. The majority of this part was spent reading the JASPAR database documentation which clearly states how the database API calls work; specifically URL, return values, and headers. JASPAR was effective in laying out their different API calls and explaining what each call did. This made it much easier for the coders to decipher which of the calls was best for retrieving the information that they needed (JASPAR API).
After studying JASPAR, and deciding which calls were to be use, the coders then moved on to implementing the first of the API calls. The first call used the inputted gene symbol to search the JASPAR database and retrieve a list of search results, from which they retrieved the matrix ID from the first result. The second call retrieves the object of gene information associated with that gene symbol. It used the matrix ID that was retrieved from the first call and returned the object with all of the information that JASPAR has for this gene, if any at all. At this point, as they were testing their code, they were getting something called an “Access-Control-Allow-Origin” error which is usually caused by an APIs lack of support for Cross-Origin Resource Sharing(CORS), but when they went and checked the websites overview page, they found that the API specifically stated that they supported CORS (API Overview). After reading this on the API Overview page of JASPAR, the coders began to believe that this error was due to miscoding of the getJasparInfo() function, but after studying the code and testing the API calls through the JASPAR interface, they realized that this issue was not due to the structure of their code, but in fact was due to JASPAR and the fact that they don’t support CORS. At this point, the JASPAR team met with the professor and decided that the best solution would be to implement a relay controller that would handle all traffic from JASPAR to GRNsight. Once the relay controller was done being integrated with the server-side of GRNsight, the API calls began working properly, which corresponded with the end of the intermediate phase of this project (Figure C).

The next phase of the project was the finishing touches (red) phase, which was where the coders spent most of their time interacting with the other teams working on this feature, to make sure that all of the pieces were working together properly (Figure C). The first step was to make sure that the JASPAR information, that the biologists on the integration team were requiring for the final page, was properly being organized and returned so that the information was useful on the page. This required taking the object returned from the second API call and properly “filing” the relevant fields into their spots within the master object. At this point, all that was left to do was to pass the information onto the page design and integration team so that they knew what to expect when calling the JASPAR function, so that they could properly put it on the page, which then marked the end of the coders work on this GRNsight feature, as displayed in Figure C.

=== Assessment of Project ===

* Give an objective assessment of the success of your project workflow and teamwork.
*: Our team worked pretty well together to finish both the paper and the powerpoint together, but this was mainly due to good leadership from Quinn. He kept us up to date and he is the only reason this assignment was even remotely tolerable.
* What worked and what didn't work?
*: Everything worked really well. We had good communication and, although arranging meetup times was difficult, we still met three times out of class to work on the presentation.
* Evaluate your team’s portion of the GRNsight Gene Page Project and Group Report in the following areas:
*# Content: What is the quality of the work?
*#: For the code specifically, everything was very well done, very clean and readable.
*# Organization: Comment on the organization of the project and of your group's wiki pages.
*#: Quinn did a very good job of making our team page. I didn't really have much of a part in it but it looks really good.
*# Completeness: Did your team achieve all of the project objectives? Why or why not?
*#: Yes we completed every single task. Even though they were all just very repetitive.

=== Reflection on the Process ===

* What did you learn?
** With your head (biological or computer science principles)
**: I learned a lot from the Computer Science portions of the class because it was building on my knowledge base of frameworks and software design and engineering.
** With your heart (personal qualities and teamwork qualities that make things work or not work)?
**: I don't like biology, not because the subject isn't of interest (it is), but because of the way things are done in the Biology department. I just find it much more preferable to learn how I do in my major classes.
** With your hands (technical skills)?
**: Maybe I can type faster after all of the writing you guys made me do.

=Acknowledgements=
Copied the structure of the sections in my assessment and reflection from the [[GRNsight_Gene_Page_Project_Deliverables|Deliverables Page]].
I worked with my homework partner in class. We also met face-to-face one time outside of class. We texted outside of class and met to work on the presentation part of the assignment together. 
'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.''' 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 13:29, 15 December 2017 (PST)

=References=
* LMU BioDB 2017. (2017). Week 15. Retrieved November 20, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15

{{Template:Ebachour}}

JASPAR the Friendly Ghost Final Deliverables

2017-12-16T00:07:34Z

Aporras1: editing head for signatures

==Group Report==
[[Media:JASPAR Final Paper.pdf|JASPAR the Friendly Ghost Group Report]]

==Individual statements of work, assessments, reflections==
[[QLanners_individual_statement|Quinn Lanners]] | [[Aporras1_Individual_Assessment_and_Reflection|Antonio Porras]] | [[Ebachour_Week_15|Edward Bachoura]] | [[simonwro120 individual statement|Simon Wroblewski]]

==Group PowerPoint presentation==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf | Final Group Presentation (pdf)]] | December 11, 2017
==Code==
[[Media:Api.txt|JASPAR team's code (as well as hAPI's code)]] | December 15, 2017 
==README that summarizes the functionality of your team's new feature==
[[Media:README.txt|Readme.txt]] | December 15, 2017 
==Excel spreadsheet with ANOVA results/stem formatting==
[[Media:AP dZAP1 stem.xlsx]]
==PowerPoint of screenshots of stem results==
[[Media:AP dZAP1 STEM Screenshots & p-values.zip]]
==Gene List and GO List files from each significant profile==
[[Media:AP dZAP1 GOlist and genelist for profiles.zip]]
==YEASTRACT "rank by TF" results==
[[Media:AP YEASTRACT Transcription Factors.xlsx]]
==GRNmap input workbook==
[[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]]
==GRNmap output workbook==
[[Media:15-gene 44-edge teamJASPAR Sigmoid estimation output.xlsx]]
*Expression vs. Time Images generated from MATLAB: [[Media:Output Images from 15-gene 44-edge teamJASPAR Sigmoid estimation.zip]]
==Electronic notebooks corresponding to the microarray results files==
#[[Aporras1 Week 8]]
#[[Aporras1 Week 10]]
#[[Aporras1 Week 14]]
#[[Aporras1 Week 15]]

==Team Links==

{{Template:JASPAR the Friendly Ghost Links}}
==Team Signatures==
*[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 20:49, 13 December 2017 (PST) 
*[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:48, 15 December 2017 (PST)
*[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 15:55, 15 December 2017 (PST)
*[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 15:57, 15 December 2017 (PST)

==Class Links==

{{Template:GRNsight Gene Page Project Links}}

QLanners Week 15

2017-12-16T00:04:02Z

Aporras1: /* Deliverables */ fixing formatting

==Deliverables==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf|JASPAR the Friendly Ghost Final Group Presentation]] | December 11, 2017

[[Media:JASPAR_Final_Paper.pdf]] | December 15, 2017

==Electronic Notebook==
On Tuesday December 5th, Antonio and I spent the beginning of class going through each part of deliverables, determining how to most effectively split up the work. We made a quick outline of each deliverable and who will be working on each below:

#Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents)
#*Quinn will take care of ensuring all deliverables are organized and delivered properly.
#Group Report (.doc, .docx or .pdf file)
#*''The group report will be a collaborative effort, this outline is just to outline who will probably be contributing most to each section''
##Abstract
##*Primarily Quinn - with input from everyone
##Intro
##*Primarily Quinn
##Materials and Methods
##*Primarily Antonio, Eddie, and Simon
##Results
##*Primarily Antonio, Eddie, and Simon
##Discussion
##*All members
##Conclusions
##*All members
##Acknowledgements
##*All members
##References
##*All members
#Individual statements of work, assessments, reflections (wiki page, .doc, .docx, .pdf, or e-mailed to both Dr. Dahlquist and Dr. Dionisio)
#*Each member will complete this task individually
#Group PowerPoint presentation (given on Tuesday, December 12, .ppt, .pptx or .pdf file)
#*All members. Antonio and Quinn will start on this, but all will work to complete. Then practice will be done as full team.
#Code (GitHub pull request) ''Each team should coordinate in performing a final integration and integration testing iteration (see Coder milestone for details) which the Interaction and Integration team then submits to the original GRNsight GitHub repository as a single, unified pull request from the class project’s fork''
#*Eddie and Simon
#Supply a README that summarizes the functionality of your team's new feature (.txt or .md, one README per team)
#*Eddie and Simon (Quinn help if needed)
#Excel spreadsheet with ANOVA results/stem formatting (.xlsx)
#*Antonio
#PowerPoint of screenshots of stem results (.pptx)
#*Antonio
#Gene List and GO List files from each significant profile (.txt compressed together in a .zip file)
#*Antonio
#YEASTRACT "rank by TF" results (.xlsx)
#*Antonio
#GRNmap input workbook (with network adjacency matrix, .xlsx)
#*Antonio
#GRNmap output workbook (.xlsx)
#*Antonio
#Electronic notebook corresponding to these the microarray results files (Week 8, Week 10, and Weeks 11-15) support reproducible research so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results.
#*Antonio

On Thursday, December 7th, the other project managers and I collaborated to create a modified outline for the Group Report. After proposing our modified paper outline to Dr. Dondi and Dr. Dahlquist, a new outline for this final paper was agreed upon. The following image is an outline for this new Group Report: 
[[File:Biological databases paper outline.jpg | 300px]]
 

Along with creating these modified guidelines, I created a Google document and a Google slides for the final group report and group presentation respectively. I started by creating an outline for the presentation, adding titles to a number of slides and working to make a descriptive table of contents.

On Friday, December 8th, I used [https://www.lucidchart.com Lucid Chart] to make my flow chart for my methods. I also shared this link with my team members, as the website application is very nice for making clean and easy to read flowcharts. Along with creating the flowchart, I began work on the final paper, typing up the introduction section and my methods section for project manager/QA.

On Saturday, December 9th, our group all met in the computer lab to work on the final presentation. We determined how we would organize the slides, and then spent a few hours working together to get all of the necessary information into the presentation. Any work that was not completed was delegated out at the end of the meeting.

On Monday, December 11th, our group met again for two hours to go through the presentation one last time and run through a few practice rounds as a group. After this meeting, I spent the evening making a few last corrections to the presentation, and then uploaded the final presentation pdf to our team page and each team members page. I also started my final statement page later this night, getting about a third of the way through it.

On Tuesday, December 12th, we met as a group one last time before class to run through the presentation one more time. We then gave our presentation to the class. After class, we stayed after for a little to ensure that everyone knew what they had to get done by Friday at 4:00 PM.

On Thursday, December 14th, I worked to finish up my [[QLanners_individual_statement|statement of work page]] and also worked on completing the conclusion section of the group paper. I continued to stay in contact with my team members through our group message to ensure that everyone was aware of what they had to get done and was going to be able to complete their assigned sections by tonight (as we wanted to allow for Friday afternoon to make any last minute corrections). 

Fields unable to retrieve. (This list is incomplete, as I tried to connect with Eddie and John through text on multiple occasions, but never got any responses):
*Similar Proteins (UniProt)

==Acknowledgements==
*All of the [[JASPAR_the_Friendly_Ghost|JASPAR the Friendly Ghost]] team members for the collaborative effort.
*[[User:Cazinge|Eddie A]] and [[User:Johnllopez616|John Lopez]] for providing me information on what (if any) fields were unretrievable from certain databases.
*[[User:Kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dondi]] for their help and guidance throughout the semester.
'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.''' 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 11:11, 14 December 2017 (PST)

==References==
LMU BioDB 2017. (2017). Week 15. Retrieved December 5, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15 
Lucid Chart. (2017). Retrieved on December 8, 2017, from https://www.lucidchart.com 

==Links==
{{Template:QLannersLinks}}

QLanners Week 15

2017-12-16T00:03:45Z

Aporras1: /* Deliverables */ final paper upload

==Deliverables==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf|JASPAR the Friendly Ghost Final Group Presentation]] | December 11, 2017
[[Media:JASPAR_Final_Paper.pdf]] | December 15, 2017

==Electronic Notebook==
On Tuesday December 5th, Antonio and I spent the beginning of class going through each part of deliverables, determining how to most effectively split up the work. We made a quick outline of each deliverable and who will be working on each below:

#Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents)
#*Quinn will take care of ensuring all deliverables are organized and delivered properly.
#Group Report (.doc, .docx or .pdf file)
#*''The group report will be a collaborative effort, this outline is just to outline who will probably be contributing most to each section''
##Abstract
##*Primarily Quinn - with input from everyone
##Intro
##*Primarily Quinn
##Materials and Methods
##*Primarily Antonio, Eddie, and Simon
##Results
##*Primarily Antonio, Eddie, and Simon
##Discussion
##*All members
##Conclusions
##*All members
##Acknowledgements
##*All members
##References
##*All members
#Individual statements of work, assessments, reflections (wiki page, .doc, .docx, .pdf, or e-mailed to both Dr. Dahlquist and Dr. Dionisio)
#*Each member will complete this task individually
#Group PowerPoint presentation (given on Tuesday, December 12, .ppt, .pptx or .pdf file)
#*All members. Antonio and Quinn will start on this, but all will work to complete. Then practice will be done as full team.
#Code (GitHub pull request) ''Each team should coordinate in performing a final integration and integration testing iteration (see Coder milestone for details) which the Interaction and Integration team then submits to the original GRNsight GitHub repository as a single, unified pull request from the class project’s fork''
#*Eddie and Simon
#Supply a README that summarizes the functionality of your team's new feature (.txt or .md, one README per team)
#*Eddie and Simon (Quinn help if needed)
#Excel spreadsheet with ANOVA results/stem formatting (.xlsx)
#*Antonio
#PowerPoint of screenshots of stem results (.pptx)
#*Antonio
#Gene List and GO List files from each significant profile (.txt compressed together in a .zip file)
#*Antonio
#YEASTRACT "rank by TF" results (.xlsx)
#*Antonio
#GRNmap input workbook (with network adjacency matrix, .xlsx)
#*Antonio
#GRNmap output workbook (.xlsx)
#*Antonio
#Electronic notebook corresponding to these the microarray results files (Week 8, Week 10, and Weeks 11-15) support reproducible research so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results.
#*Antonio

On Thursday, December 7th, the other project managers and I collaborated to create a modified outline for the Group Report. After proposing our modified paper outline to Dr. Dondi and Dr. Dahlquist, a new outline for this final paper was agreed upon. The following image is an outline for this new Group Report: 
[[File:Biological databases paper outline.jpg | 300px]]
 

Along with creating these modified guidelines, I created a Google document and a Google slides for the final group report and group presentation respectively. I started by creating an outline for the presentation, adding titles to a number of slides and working to make a descriptive table of contents.

On Friday, December 8th, I used [https://www.lucidchart.com Lucid Chart] to make my flow chart for my methods. I also shared this link with my team members, as the website application is very nice for making clean and easy to read flowcharts. Along with creating the flowchart, I began work on the final paper, typing up the introduction section and my methods section for project manager/QA.

On Saturday, December 9th, our group all met in the computer lab to work on the final presentation. We determined how we would organize the slides, and then spent a few hours working together to get all of the necessary information into the presentation. Any work that was not completed was delegated out at the end of the meeting.

On Monday, December 11th, our group met again for two hours to go through the presentation one last time and run through a few practice rounds as a group. After this meeting, I spent the evening making a few last corrections to the presentation, and then uploaded the final presentation pdf to our team page and each team members page. I also started my final statement page later this night, getting about a third of the way through it.

On Tuesday, December 12th, we met as a group one last time before class to run through the presentation one more time. We then gave our presentation to the class. After class, we stayed after for a little to ensure that everyone knew what they had to get done by Friday at 4:00 PM.

On Thursday, December 14th, I worked to finish up my [[QLanners_individual_statement|statement of work page]] and also worked on completing the conclusion section of the group paper. I continued to stay in contact with my team members through our group message to ensure that everyone was aware of what they had to get done and was going to be able to complete their assigned sections by tonight (as we wanted to allow for Friday afternoon to make any last minute corrections). 

Fields unable to retrieve. (This list is incomplete, as I tried to connect with Eddie and John through text on multiple occasions, but never got any responses):
*Similar Proteins (UniProt)

==Acknowledgements==
*All of the [[JASPAR_the_Friendly_Ghost|JASPAR the Friendly Ghost]] team members for the collaborative effort.
*[[User:Cazinge|Eddie A]] and [[User:Johnllopez616|John Lopez]] for providing me information on what (if any) fields were unretrievable from certain databases.
*[[User:Kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dondi]] for their help and guidance throughout the semester.
'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.''' 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 11:11, 14 December 2017 (PST)

==References==
LMU BioDB 2017. (2017). Week 15. Retrieved December 5, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15 
Lucid Chart. (2017). Retrieved on December 8, 2017, from https://www.lucidchart.com 

==Links==
{{Template:QLannersLinks}}

JASPAR the Friendly Ghost

2017-12-16T00:02:33Z

Aporras1: /* Acknowledgements */ periods

==GRNsight Gene Page Project Deliverables==
[[JASPAR_the_Friendly_Ghost_Final_Deliverables|JASPAR the Friendly Ghost Final GRNsight Deliverables Page]]
==Working Deliverables==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf|Final Group Presentation]] | December 11, 2017 
[[Media:Genome-wide_analysis_of_the_yeast_transcriptome_upon_heat_and_cold_shock._QL_AP.zip|Antonio and Quinn Journal Club Presentation]] | November 21, 2017 
[[Media:e_and_s_presentation_2.pdf|Eddie and Simon Chapter 6 Presentation]] | November 14, 2017 
[https://github.com/bhamilton18/GRNsight GitHub fork] 
[https://github.com/bhamilton18/GRNsight/tree/gene-database-apis GitHub api branch] (in collaboration with [[Gene_hAPI|Gene_hAPI team]]) 
[[Media:README.txt|Readme.txt]] | December 15, 2017 
[[Media:Api.txt|Our code for this feature (also hAPI team's code)]] | December 15, 2017 

==Working Files==

===Antonio's Working Files===
# Gene list for profile 22 of dZAP1 Excel file: [[Media:AP dZAP1 profile22 genelist.xlsx]]
# YEASTRACT Transcription Factor Data: [[Media:AP YEASTRACT Transcription Factors.xlsx]]
# YEASTRACT Regulation Matrix Profile: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix: [[Media:AP Adjacency Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix with Network for GRNsight: [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]]

==Calendar==
{| class ="wikitable"
|+November & December
|-
|Sunday
|Monday
|Tuesday
|Wednesday
|Thursday
|Friday
|Saturday
|-
|
|
|
|'''1'''
|'''2'''
|'''3'''
|'''4'''
|-
|'''5'''
|'''6'''
|'''7'''
|'''8'''
|'''9'''
|'''10'''
|'''11'''
|-
|'''12'''
|'''13'''
|'''14''' C: PPT Presentation PM/DA: Journal Articles
|'''15'''
|'''16'''
|'''17'''
|'''18'''
|-
|'''19'''
|'''20'''
|'''21''' C: Complete setup steps (Milestones 1-3) PM/DA: Journal Club Presentations
|'''22''' ''Thanksgiving Break''
|'''23''' ''Thanksgiving Break''
|'''24''' ''Thanksgiving Break''
|'''25'''
|-
|'''26'''
|'''27'''
|'''28''' C: Fimilariaze self with file structure PM: Chose application data fields from JASPAR DA: Review ANOVA Results
|'''29'''
|'''30''' C: Tests for API PM: Share info to be used from JASPAR with other teams DA: Determine transcription factors, develop candidate gene reg network, and fix edits from week 8 & 10
|'''1'''
|'''2'''
|-
|'''3'''
|'''4'''
|'''5''' C: Retrieval code for API PM: Begin Final Group Paper and PPT DA:Model gene reg network Visualize Results
|'''6'''
|'''7''' C: Review and Test Code PM: Review and Test code PM&DA:Work on Paper and PPT
|'''8'''
|'''9''' Complete Group PPT
|-
|'''10''' Practice Group Presentation
|'''11''' Final group Presentation ''2:00-4:00PM''
|'''12'''
|'''13''' Final Group Paper Completely Written
|'''14''' Edit Final Group Paper
|'''15''' All deliverables due ''4:30PM''
|'''16'''
|}

==Executive Summaries==

===Week 11===

====Quinn's Executive Summary====
Created citations for two entries in the annotated bibliography for papers that report microarray data from yeast subjected to cold shock: 
Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6 
Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301 
Also completed a search activity to compare the results found from PubMed, GoogleScholar, and Web of Science using both basic and advanced search tools. 
Individual Journal Page: [[QLanners Week 11]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Executive Summary====
For this assignment, I spent most of my time reading and re-reading Paul Ford's article on how apps are made. It was chapter 6 in a larger work called ''What is Code?'' After absorbing the information laid out in this chapter, Eddie and I made a presentation about it. The presentation summarizes the article, which is about technique, methods, practices, and tools that expedite and simplify the programming process. In addition to making the presentation, I finished my 10 terms and made an outline for the article on my individual journal page. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 13:45, 14 November 2017 (PST)

====Antonio's Executive Summary====

Created two citations for the bibliography for the following articles:

#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.

I also completed the basic keyword searches on PubMed, Google Scholar, and Web of Science along with the advanced searches and the respective results. Lastly, I completed the prospective searches and collected the results of how many articles the article cites and how many articles cite the article. Totaling to the 3 articles.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 15:51, 14 November 2017 (PST)

Individual Journal Week 11: [[Aporras1_Week_11|Aporras1 Week 11]]

====Eddie Bachoura's Executive Summary====
This week, I spent my time for this class reading the Paul Ford article, chapter 6, which was about how to write applications and the modern practices and tools which are used to aid in cutting down some of the tedious nature of coding. Then, Simon and I spent the rest of the time working on our presentation. Team's progress: I believe that Simon and I worked well this weekend. The only issue that I found was that we didn't start until pretty late (Monday), but that was all at my own fault because I wasn't here for this weekend. We should fix that by starting earlier next weekend!

Individual Journal Week 11: [[Ebachour_Week_11|Eddie Bachoura Week 11]] 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:29, 13 November 2017 (PST)

===Week 12===

====Quinn's Executive Summary====
Worked closely with Antonio to summarize the results of the journal article Becerra et al. (2003) into a journal club presentation. In order to do so, we both completed the outline provided on the [[Week_12|Week 12]] assignment page on our wiki. We then took this information and used it to create our journal club presentations, which we practiced together and will share in class on Tuesday, November 21. 
Individual Journal Page: [[QLanners Week 12]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Executive Summary====
This week, I met with my coding partner [[User:Ebachour|Eddie Bachoura]] and he helped me clone the code that [[User:Bhamilton18|Blair Hamilton]] forked from the master branch.
After that, Eddie and I helped put together a list of milestones with dates that they should be completed. Using that, Quinn was able to put together a calendar like scheduale for our team to refer to. The last thing I did was open up the cloned files from Blair's fork on my text editor so that I could familiarize myself with the code. 
Individual Journal Page: [[simonwro120 Week 12]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:44, 20 November 2017 (PST)

====Antonio's Executive Summary====
Worked throughout the assignment with Quinn to complete the powerpoint presentation on the journal article: ''Genome-wide analysis of the yeast transcriptome upon heat and cold shock''. We both worked closely together on the outline of the article while maintaining our own style of completing the outline. We then practiced our presentation once the information was finalized and are looking forward to sharing on Tuesday the 21st of November.

Individual journal page: [[Aporras1_Week_12|Aporras 1 Week 12]]

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:19, 20 November 2017 (PST)
====Eddie Bachoura's Executive Summary====
This week, most of my time was spent setting up the branch on github and then getting my local version up and running so that I can write and test code on my own laptop. After that, I helped Simon out with doing the same. I also sent Quinn a list of our milestones for this project, as well as letting him know which ones were already completed. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 19:09, 20 November 2017 (PST) 
Week 12 Journal Page: [[ebachour_Week_12| Edward Bachoura]]

===Week 14===

====Quinn's Executive Summary====
This week, I worked closely with the other QAs and [[User:Kdahlquist|Dr. Dahlquist]] to determine what information should be pulled from each of the five databases. I then communicated this information to our coders. Along with this task, I worked communicated closely with both the data analyst and the coders to ensure that they were on track, and to make modifications to their respective milestones on the team calender. Finally, I added additional team milestones to the calendar to reflect all of the steps that need to be taken to complete the deliverables that we have due at the end of the semester. All of this progress can be seen in my [[QLanners_Week_14|individual weekly journal]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Executive Summary====
This week our coding group hit a bit of wall, not just for one, but for multiple reasons. One reason was caused by the fact that one of the coding group members worked in a language that would not be compatible with GRNsight. Another problem our coding group encountered was caused by a complexity in the the JASPAR API relating CORS (Cross-Oirgin Resource Sharing). Although these complications did occur, both me and Eddie B. know where the API guidelines are for JASPAR and what content we need to produce. In addition to that, an api file has been made as well which will be augmented soon. 
Individual Journal Page: [[simonwro120 Week 14]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:45, 4 December 2017 (PST)

====Antonio's Executive Summary====
This week, I made edits to both my individual [[Aporras1 Week 8]] and [[Aporras1 Week 10]] pages based from feedback received from [[User:Kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dionisio]]. The outline for these edits can be found on my [[Aporras1 Week 14]] page along with the continuation of the [[Week 10|Week 10]] assignment. In this continuation, I selected transcription factors from [[Media:AP dZAP1 profile22 genelist.xlsx]] and put them into YEASTRACT to find the most significant ones and found 49 significant transcription factors found in [[Media:AP YEASTRACT Transcription Factors.xlsx]]. Then I selected 22 of the most significant, 2 additional ones (HAP4 and GLN3) as instructed, to put back into YEASTRACT and create a regulation matrix uploaded as: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]. I then created a "network" worksheet, found in [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]], from the matrix and used GRNsight to generate a regulation network visualization: [[Media:AP Regulation Matrix profile22 GRNsight Network.PNG]]. These media downloads can also be found on my [[Aporras1 Week 14|Week 14]] journal entry in the
"Deliverables" section.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:31, 3 December 2017 (PST)

====Eddie's Executive Summary====
We've been working on JASPAR since the last assignment. As of this week, I am mostly sure that we have the two API calls that we need in order to be able to retrieve any Yeast gene database entry on JASPAR, using the gene ID. I would say that we are already done, but it seems that there are some access complications. I have a feeling it has something to do with CORS and I did some research to try to dix the issue. I found one work around, using a chrome extension, that allows me to bypass the issue, but I'm not sure that this solution will translate well to the actual GRNsight server, but I will discuss with Dondi tomorrow. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:25, 4 December 2017 (PST)

===Week 15===

====Quinn's Executive Summary====
This week, I worked closely will all of my teammates to coordinate the completion of all of the final deliverables. I met in person with my teammates on three seperate occasions to work on the final presentation. Furthermore, I delegated the tasks for our final group paper and completed my sections of the paper, along with running through the paper to ensure that we had met all of the requirements. Finally, I ensured that all of our group's deliverables were uploaded to the team page on time. 
All of this is outlined in depth on my [[QLanners_Week_15|individual weekly journal]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:13, 14 December 2017 (PST)

====Simon's Executive Summary====

====Antonio's Executive Summary====
I spent most of my efforts in the beginning of the week trimming down the network because it was too large. Once this was completed I was able to use MATLAB with the help of [[User:kdahlquist|Dr. Dahlquist]] and generate an output to put into GRNsight to visualize the regulation network with magnitude and direction of regulation. Once this was completed I began spending time on the presentation and the project deliverables. Gathering the deliverables, working on the presentation, and working on the final paper had many points of crossover which I became very familiar with my data and analysis. Once the presentation was completed, I spent the rest of my efforts checking off requirements for the deliverables on the team page and requirements for the paper to ensure it would be turned in on time. This work can be found in my [[Aporras1_Week_15|Week 15]] individual page along with details in terms of the progress throughout the week.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 10:38, 15 December 2017 (PST)

====Eddie's Executive Summary====
The beginning of this week was spent finishing our feature. We ran into some issues, but we worked it out with King Dondi. Once we were done with the feature, we spent some time making sure that the other teams knew what to expect from JASPAR specifically, so that they could properly put it on the final page product. After we were done with this part of the assignment, we then began to work on the power point presentation. We all worked together at first and then split off to work on our specific parts. We presented, and still didn't celebrate because we had to write an essay. The essay was a lot of repetition and formalities.
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 13:13, 15 December 2017 (PST)

==Weekly Reflections==

===Week 11===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a good job of staying on task and working together to make sure that we both understood the whole assignment. So there was good communication between the Bibliography group.
#What didn't work?
#*I felt a bit disconnected with my other teammates Eddie and Simon. There was not very good communication with them about whether they needed any help and if they were on progress.
#What to improve upon going forward?
#*Going forward all of the members of the team need to do a better job of communicating. Also, we need to do a better job of properly communicating about how to fill out the team page ahead of time, so that we aren't frantically figuring that out last second. I will work to fix this by initiating communication earlier on in the week.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*Both me and Eddie were able to put together a powerpoint and present in time for the presentation date
#What didn't work?
#*Due to traveling, Eddie could not be back in LA to help with the project until Monday, which did not give us much time, resulting in our presentation being a bit late as far as submission on our wiki pages.
#How will to improve upon going forward?
#*Going forward I'd like to start early and finish early, that way we can be prepared for any unexpected complications. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
1. What worked? Quinn and I were able to get our work done on time without overlap. We communicated well.

2. What didn't work? Nothing specific prevented us from working efficiently.

3. What will I do next to fix what didn't work? Complete work ahead of time to be more thorough. Maintain a growth mindset.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:06, 20 November 2017 (PST)

====Eddie's Reflection====
Found in Week 11 summary ^^^

===Week 12===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a very good job of working ahead and getting our presentation done in a timely manner. In this way, we were able to ask the instructors any questions we had as they came up, and also allowed for ample time to practice.
#What didn't work?
#*Once again, I felt a bit disconnected from my other partners Eddie and Simon. While I texted Eddie a couple times about their progress, I still never got a chance to see exactly what they were doing.
#What to improve upon going forward?
#*While I feel like this will start to come together once we all start working on our assigned portion of the project together, we still do need to improve our communication between the coders and the PM/DA. In order to do so, I will make sure to continue to check base with each team member each day in class, and also text in the group message when I have questions for the whole team.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*With Eddie's help, we were both able to set up GRNsight on our laptops.
#What didn't work?
#*Nothing in specific stopped us from working efficiently.
#How will to improve upon going forward?
#*Going forward I'd like to get my summaries in earlier, as well as my individual page and reflections. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
#What worked?
#*Worked closely with Quinn and we kept regular contact through text as we worked through the assignment. Troubleshooting was easy as we were both very capable to take initiative and work to finish the presentation earlier rather than later in the time given.
#What didn't work?
#*I could definitely improve on mastering certain aspects of the assignment. I didn't really communicate with Eddie or Simon but I'd attribute that to having different assignments and parts to complete rather than a team issue.
#What to will I do next to fix what didn't work?
#*Communicate more. I'm hoping we'll have opportunities to work more closely together in the future.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:12, 20 November 2017 (PST)

====Eddie's Reflection====
# What worked?
#: Our work session was successful in setting up GRNsight on my laptop (again) and on Simon's.
# What didn't work?
#: Nothing :D
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 21:47, 20 November 2017 (PST)

===Week 14===

====Quinn's Reflection====
#What Worked?
#*This week our team did a much better job of communicating and keeping each other in the loop. Also, the collaboration between all of the QAs was a very effective way to determine which information should be pulled from each database
#What didn't work?
#*I was still a bit confused as to how all of the teams should be working together as we approach the end of the semester
#What will I do next to fix what didn't work>
#*I will make sure to ask about this concern in the next stand up review between the QAs. This will help clear this question up for me and the rest of the class. 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Reflection====
#What Worked?
#*Our class was able to produce a solid list of data items, specified to each database. This meant that as a coder for the JASPAR team, I knew which pieces of data to retrireve and produce from the JASPAR database.
#What didn't work?
#*There were some complications with the language some of the new code was written. There was also a problem with the JASPAR API relating to CORS (Cross-Oirgin Resource Sharing).
#What will I do next to fix what didn't work?
#*I hope to be more knowledgeable about these type of things in reference to computer science.
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:57, 4 December 2017 (PST)

====Antonio's Reflection====
# What worked? This week, I worked ahead and was able to complete, at least to my knowledge, this week's assignment ahead of time rather than waiting until the last minute. It was extremely helpful to have a group chat with the other data analysts as we had questions throughout the assignment.
# What didn't work? Everything seems to have run smoothly except I don't really know what the coders are assigned to do and most likely because it goes over my head.
# What will I do next to fix what didn't work? Try to see what the coders are doing, mostly out of curiosity.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:36, 3 December 2017 (PST)

====Eddie's Reflection====
#What worked?
#* We were able to figure out exactly how to extract the info we needed from JASPAR.
#What didn't work?
#* We originally had our own branch, but that didn't work out too well and it didn't make much sense when we were working in parallel to the gene-database-apis branch.
#How will to improve upon going forward?
#* We decided to merge our two branch which helped with this and kept us on the same page. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:25, 4 December 2017 (PST)

===Week 15===

====Quinn's Reflection====
#What worked?
#*We worked very well as a team on the final group presentation, meeting in person on multiple occasions to ensure that we were covering all of the content and everyone knew what they were going to say. This also allowed for this deliverable to be completed with plenty of time.
#What didn't work?
#*The final paper was a bit of a struggle with how busy everyone was towards the end of final week. It was incredibly hard to find any times to meet in person to collaborate, so we were forced to communicate through solely group texts to complete the paper. While we still were able to finish it, the collaboration was not as solid as it had been for the presentation (due to the fact that everyone was so busy)
#What will I do next time to fix what didn't work?
#*While there won't be a next time for this particular project, I will take note for future projects of how hard it is to find time for collaboration during busy times of the year and plan around this fact. 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:13, 14 December 2017 (PST)

====Simon's Reflection====

====Antonio's Reflection====
# What worked?
#* As a group, we worked very cohesively. The presentation and paper was especially important in terms of everyone being on the same page so we were able to meet on the weekend and outside of class prior to presenting and completing the paper.
# What didn't work?
#* The paper was very time consuming during the finals week and there was no shortage of material which needed to be covered and discussed. As a lab TA, I was able to work on my data analyst sections while editing formatting issues that arose but wish there were more details regarding formatting. We had to work on the paper through google doc which wasn't ideal but considering everyone's busy schedule it was the only option we had and communicated through text in addition.
# What will I do next time?
#* As with everything, finish with PLENTY of time. I've been able to significantly improve in this aspect over the course of the semester but having more time to complete assignments in case problems arise is always an advantage.

====Eddie's Reflection====
# What worked?
#* In my opinion, we worked really well as a group to finish the powerpoint ahead of time and start the presentation earlier than some of the other time. This had nothing to do with me, but my teammates were very on top of this whole assignment.
# What didn't work?
#* It was completely unfair how much time we had to spend on this project, especially during the week before and of finals week. And on top of that we are turning in a 40 page paper on our work on the project. Everything worked efficiently within our group and we still struggled with finishing the assignment so it must've been something wrong with the expectations of us for this assignment.
# What will I do next time?
#* I would like to say start earlier, but in all honesty, with all of my other classes and the other assignments that this class was throwing at us, I don't think that was very possible.
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 13:09, 15 December 2017 (PST)

==Acknowledgements==
# A huge thank you to both [[User:kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dionisio]] for taking the time to teach this course and support us, the students, throughout the semester's challenges.
# The [[JASPAR_the_Friendly_Ghost|JASPAR The Friendly Ghost]] team for working as a cohesive unit.
# The Department of Biology at LMU.
# The Department of Computer Science at LMU.
# The entire class composed of students who we worked alongside throughout the semester.

==References==
===Week 11===
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#Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301
#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.
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#Hybridization. (2008). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Hybridization
#Kondo K, Inouye M. 1991. Cold-induction of yeast NSR1 protein and its role in pre-rRNA processing. J Biol Chem 267: 16 259–16 265.
#Kowalski LR, Kondo K, Inouye M. 1995. Cold-shock induction of a family of TIP1-related proteins associated with the membrane in Saccharomyces cerevisiae. Mol Microbiol 15: 341 – 353.
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Mai B, Breeden L. 1997. Xbp1, a stress-upregulated transcrip- tional repressor of the Saccharomyces cerevisae Swi4/Mbp1 family. Mol Cell Biol 17: 6491–6501.
#(n.d.). Retrieved November 19, 2017, from http://fg.cns.utexas.edu/fg/protocol%3A_YPD_plates.html
#(n.d.). Retrieved November 20, 2017, from https://www.nature.com/scitable/definition/diploid-310
#Oligonucleotide. (2014). ''News Medical Life Sciences''. Retrieved on November 19, 2017 from https://www.news-medical.net/life-sciences/What-is-an-Oligonucleotide.aspx
#Polypropylene. (n.d.). ''Dictionary.com''. Retrieved on November 19, 2017 from http://www.dictionary.com/browse/polypropylene
#Putative. (2014). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Putative
#Study.com. (2017). What is Annealing? - Definition, Biology & Process | Study.com. [online] Available at: http://study.com/academy/lesson/what-is-annealing-definition-biology-process.html [Accessed 21 Nov. 2017].
#Transcriptome. (n.d.). ''Nature''. Retrieved on November 19, 2017 from https://www.nature.com/scitable/definition/transcriptome-296
#Yelland, P. M. (2010). An introduction to correspondence analysis. Math. J, 12, 1-23.
#Young, F.W. (1999). Principle Components. ''forrest.psych.unc.edu''. Retrieved on November 19, 2017 from http://forrest.psych.unc.edu/research/vista-frames/help/lecturenotes/lecture13/biplot.html
#Zhang L, Ohta A, Horiuchi H, Takagi M, Imai R. 2001. Multiple mechanisms regulate expression of low temperature responsive (LOT) genes in Saccharomyces cerevisiae. Biochem Biophys Res Commun 283: 531 – 535.

===Week 14===
#Dahlquist, K. D., Dionisio, J. D. N., Fitzpatrick, B. G., Anguiano, N. A., Varshneya, A., Southwick, B. J., & Samdarshi, M. (2016). GRNsight: a web application and service for visualizing models of small-to medium-scale gene regulatory networks. PeerJ Computer Science, 2, e85.
#Ensembl. (2017). "Gene: HSF1". Retrieved November 28, 2017, from https://www.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YGL073W;r=VII:368753-371254;t=YGL073W 
#JASPAR. (2017). "Detailed information of matrix profile MA0319.1". Retrieved on November 28, 2017, from http://jaspar.genereg.net/matrix/MA0319.1/ 
#LMU BioDB 2017. (2017). Week 8. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_8
#LMU BioDB 2017. (2017). Week 10. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10
#LMU BioDB 2017. (2017). Week 14. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14 
#NCBI. (2017). "HSF1 stress-responsive transcription factor HSF1 [ Saccharomyces cerevisiae S288C ]". Retrieved November 28, 2017, from https://www.ncbi.nlm.nih.gov/gene/852806 
#Saccharomyces Genome Database. (2017). "HSF1 / YGL073W Overview". Retrieved November 28, 2017, from https://www.yeastgenome.org/locus/S000003041 
#Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.
#UniProt. (2017). "UniProtKB - P10961 (HSF_YEAST)". Retrieved November 28, 2017 from http://www.uniprot.org/uniprot/P10961

===Week 15===
#Dahlquist, K. D., Dionisio, J. D. N., Fitzpatrick, B. G., Anguiano, N. A., Varshneya, A., Southwick, B. J., & Samdarshi, M. (2016). GRNsight: a web application and service for visualizing models of small-to medium-scale gene regulatory networks. PeerJ Computer Science, 2, e85.
# LMU BioDB 2017. (2017). Week 15. Retrieved December 05, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15
# LMU BioDB 2017. (2017). GRNsight Gene Page Project Deliverables. Retrieved December 05, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/GRNsight_Gene_Page_Project_Deliverables
# Lucid Chart. (2017). Retrieved on December 8, 2017, from https://www.lucidchart.com
# Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.

==Team Links==

{{Template:JASPAR the Friendly Ghost Links}}

==Class Links==

{{Template:GRNsight Gene Page Project Links}}

Aporras1 Individual Assessment and Reflection

2017-12-16T00:00:26Z

Aporras1: /* Acknowledgements */ signature and final acknowledgements

User page: [[User:Aporras1|Antonio Porras]]

Assignment page: [[GRNsight_Gene_Page_Project_Deliverables|Deliverables Page]]

Group page: [[JASPAR_the_Friendly_Ghost|JASPAR the Friendly Ghost]]

==Individual Assessment and Reflection==

=== Statement of Work ===

'''1. Describe exactly what you did on the project.'''

As data analyst I was responsible for performing statistical analysis on dZAP1 expression data provided by [[User:kdahlquist|Dr. Dahlquist]]'s lab. During Week 8 I completed the ANOVA test along with calculating Benjamini-Hochberg corrected p value and the Bonferroni-corrected p-value. The first calculation was less stringent compared to the Bonferroni but both were useful in terms of improving the confidence in the data. The precise steps and outline of what I completed can be found in my [[Aporras1_Week_8]] journal.

Moving into Week 10, I performed STEM high level analysis on the ANOVA data in order to generate gene clusters which presented similar expression over the course of the experiment. Seven significant clusters were generated and the GOlists & genelists were saved and uploaded to the wiki for later analysis. I read and interpreted 6 GOlist terms found in the GOlist of Profile 22 and attempted to understand why the cell would be changing expression in genes associated with certain cell processes. The precise steps and outline of what I completed can be found in my [[Aporras1_Week_10]] journal.

In Week 11, I worked alongside [[User:Qlanners|Quinn Lanners]] to perform a literature search on yeast and cold shock to gain brief exposure to journal articles in this area of research and search engine qualities. The precise steps and outline can be found in my [[Aporras1_Week_11]] journal. The following week [[User:Qlanners|Quinn Lanners]] and I did more in-depth research on the specific journal article: Genome-wide analysis of the yeast transcriptome upon heat and cold shock (Becerra et al., 2003). We outlined the introduction, methods, procedure, analysis tools, and overall findings of the article before creating and presenting a presentation to the class which can be found in my [[Aporras1_Week_12]] journal along with the specific outline and approach to interpretation of their data.

In Week 14 and Week 15 I continued work from the Week 10 data analysis and selected profile 22 of dZAP1 from STEM analysis. I then generated a list of significant transcription factors which targeted genes within the genelist provided by STEM and further used those transcription factors to create a regulatory network. This network was actually determined to be too large and [[User:kdahlquist|Dr. Dahlquist]] trimmed down the network to 15 transcription factors. The network was then put into GRNsight to visualize the regulation pathways. MATLAB was also used to generate an output which would allow for GRNsight to display the direction of regulation and the magnitude with colors and bold/thin regulation arrows. A more detailed outline for the process can be found in my [[Aporras1_Week_14]] journal.

Once I completed all the analysis, I then put the data onto the deliverables page, presentation, and the final paper along with my analysis. These files can be found in [[JASPAR_the_Friendly_Ghost_Final_Deliverables]]. I was primarily responsible for maintaining extreme care with the files and keeping a very well-kept record of data. In addition I worked closely with [[User:Qlanners|Quinn Lanners]] to complete the final paper and aid in any way possible once I completed my data calculations and subsequent analysis. A more detailed outline for the process can be found in my [[Aporras1_Week_15]] journal.

=== Assessment of Project ===

'''2. Give an objective assessment of the success of your project workflow and teamwork.'''

I would say the overall project workflow and teamwork was fairly cohesive considering our different academic backgrounds and schedules. Given this time of the year, with final exams, we did very well to meet outside of class and work in the lab while communicating constantly. My workflow didn't impede the workflow of anyone else throughout the project and it was definitely a good feeling to have throughout working on the project as I attempted to complete everything ahead of time and work on group deliverables before my own.

'''3. What worked and what didn't work?'''

What didn't work was, or at least I didn't fully accept, was the need for both a paper and a presentation. I felt as though it became repetitive when examining both the paper and the introduction. With regards to the team, there weren't any aspects that didn't work, except I wish I would have had a better understanding of the role of the coders and their work through JASPAR. It took a lot of curiosity and asking to figure it out rather than being explained it in the beginning.

'''4. What would you do differently if you could do it all over again?'''

I definitely wish I had the same good data record keeping skills that I have currently because it would have saved a lot of time throughout the semester.

'''5. Evaluate your team’s portion of the GRNsight Gene Page Project and Group Report in the following areas:'''

'''* Content: What is the quality of the work?'''

From my understanding of the coders, they put their best foot forward in terms of working in a new area in which they hadn't worked in before. As data analyst I had context and prior understanding of my analysis but for them they had to work with a completely new database, JASPAR. Quinn created a structure by which every aspect was planned out and made it easy to keep track of deadlines and goals. Overall, while also considering the amount of time spent throughout these last few weeks and paying attention to very specific details, JASPAR the Friendly Ghost did their best to complete what was assigned. Again, while paying attention to copious details.

'''* Organization: Comment on the organization of the project and of your group's wiki pages.'''

As I mentioned earlier, Quinn structured the page easily so that even I could go ahead and add sections because we all understood the intuitive layout. I kept detailed file records and explained any changes I made to the data while also maintaining a detailed electronic notebook every single week.

'''* Completeness: Did your team achieve all of the project objectives? Why or why not?'''

To the best of my knowledge, we did. We would go through the deliverables page line by line checking tasks off in order to ensure that our product was as complete as it could be. Of course its not perfect, but considering the amount of details and time given, we put a significant amount of time into the project and displaying documentation throughout.

=== Reflection on the Process ===

'''What did you learn?'''

'''With your head (biological or computer science principles)'''

I definitely have much better data management than I did at the beginning of the course and the ability to organize thoughts for someone else to read and replicate the processes I completed throughout the semester. Ultimately, synthesizing replicable data and thus very detailed step by step notes. In terms of biology I didn't take as much because we didn't go very much in depth but now I have a better understanding of how to interpret more intricate data sets and understand the context at least in respect to microarray data.

'''With your heart (personal qualities and teamwork qualities that make things work or not work)?'''

Simply working hard.. and early! It made a huge difference in my workflow to finish assignments ahead of time (prior journal entries may not display this). Instead of waiting for deadlines I found an ethic to attack them to account for time where I was met with difficulties or setbacks (e.g. having to trim down my regulation network) and these setbacks didn't do as much damage because I met them so early before the deadline.

'''With your hands (technical skills)?'''

I've been around computers for a very long time so I didn't really gain any technical skills besides knowing how I work best. I came to the lab because the screens were bigger and I usually used two monitors to save time going in between the assignment Page, individual page, and datasets. This greatly improved my workflow and provided structure which I thrive from.

'''What lesson will you take away from this project that you will still use a year from now?'''

Recognizing how I work best. As soon as I recognized how I work best (e.g. working with multiple monitors or working on assignments early) I was able to improve my efficiency as the assignments got more difficult. Lastly, data management and organization. Organization with respect to files made the process much easier than if I hadn't learned to be descriptive with file names or have multiple backups and a notepad with a filename and description. These organizational techniques were vital and will be useful in future environments where data is often more digital than it is paper.

==Acknowledgements==
#Copied the structure of the sections in my assessment and reflection from the [[GRNsight_Gene_Page_Project_Deliverables|Deliverables Page]].
#Worked alongside [[User:Qlanners|Quinn Lanners]] in Week 11 and 12 and subsequently Weeks 14 and 15 to complete the assignment.
#The [[JASPAR the Friendly Ghost]] team members including [[User:Qlanners|Quinn Lanners]], [[User:Simonwro120|Simon Wroblewski]], and [[User:Ebachour|Eddie Bachoura]].
#Received assistance in completing the assignments from [[User:kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dionisio]].
#The entire class members who I had the opportunity to work alongside.
#LMU Biology and Computer Science Departments for the resources throughout the semester.

'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.'''

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 16:00, 15 December 2017 (PST)

==References==
# Dahlquist, K. D., Dionisio, J. D. N., Fitzpatrick, B. G., Anguiano, N. A., Varshneya, A., Southwick, B. J., & Samdarshi, M. (2016). GRNsight: a web application and service for visualizing models of small-to medium-scale gene regulatory networks. PeerJ Computer Science, 2, e85.
# LMU BioDB 2017. (2017). GRNsight Gene Page Project Deliverables. Retrieved December 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/GRNsight_Gene_Page_Project_Deliverables
# LMU BioDB 2017. (2017). Aporras1 Week 8. Retrieved December 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Aporras1_Week_8
# LMU BioDB 2017. (2017). Aporras1 Week 10. Retrieved December 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Aporras1_Week_10
# LMU BioDB 2017. (2017). Aporras1 Week 11. Retrieved December 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Aporras1_Week_11
# LMU BioDB 2017. (2017). Aporras1 Week 12. Retrieved December 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Aporras1_Week_12
# LMU BioDB 2017. (2017). Aporras1 Week 14. Retrieved December 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Aporras1_Week_14
# LMU BioDB 2017. (2017). Aporras1 Week 15. Retrieved December 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Aporras1_Week_15
# Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.

[[Category:Journal Entry]]

Ebachour Week 15

2017-12-15T23:58:47Z

Aporras1: final paper/group report

==Deliverables==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf|JASPAR the Friendly Ghost Final Group Presentation]] | December 11, 2017 
[[Media:README.txt|JASPAR The Friendly Ghost Group Readme]] | December 15, 2017 
[[Media:Api.txt|JASPAR The Friendly Ghost Group Code]] | December 15, 2017 

==Individual Assessment and Reflection / Electronic Journal==

=== Statement of Work ===

There were a number of steps that the coders team members completed throughout this assignment. Before the coders moved their focus to the bulk of the GRNsight part of this project, they were asked to gain some background knowledge on the field of web development. They read “Chapter 6: How Are Apps Made?” in Paul Ford’s What is Code? which is an article from 2015 that covers most of the bases of the software development industry. They were asked to thoroughly read this chapter and then present to their class what it entailed. This chapter was specific to all of the tools that the coders used in development, highlighting some important tools at the time. After covering all of the background knowledge, the coders then began the introduction phase to the new project. Often when being assigned to a new project, software engineers are given an introduction to the code base so that they may understand how everything functions within the project before they begin their work. This project was no different, as the professor gave a quick introduction along with a manual which illustrated the relevant folders within the code bank that would be used for this feature. After JASPAR’s fellow team members forked GRNsight, the JASPAR team start by setting up a local version of GRNsight and making sure that everything was properly functioning. After this step, they began to acquaint themselves with GRNsight and understand their job in the implementation of this new feature. At this point, as as displayed in Figure C, the coders moved from the immersion phase (green) and into the intermediate phase (yellow).

The intermediate phase was where most of the progress was made towards finishing their part of the feature. They started by creating the branch that would be solely for JASPAR team progress, as well as the new files that would contain their soon-to-be-written code. At this point the coders were all setup on the GRNsight side and were ready to move to learning about the JASPAR database and how it worked. The majority of this part was spent reading the JASPAR database documentation which clearly states how the database API calls work; specifically URL, return values, and headers. JASPAR was effective in laying out their different API calls and explaining what each call did. This made it much easier for the coders to decipher which of the calls was best for retrieving the information that they needed (JASPAR API).
After studying JASPAR, and deciding which calls were to be use, the coders then moved on to implementing the first of the API calls. The first call used the inputted gene symbol to search the JASPAR database and retrieve a list of search results, from which they retrieved the matrix ID from the first result. The second call retrieves the object of gene information associated with that gene symbol. It used the matrix ID that was retrieved from the first call and returned the object with all of the information that JASPAR has for this gene, if any at all. At this point, as they were testing their code, they were getting something called an “Access-Control-Allow-Origin” error which is usually caused by an APIs lack of support for Cross-Origin Resource Sharing(CORS), but when they went and checked the websites overview page, they found that the API specifically stated that they supported CORS (API Overview). After reading this on the API Overview page of JASPAR, the coders began to believe that this error was due to miscoding of the getJasparInfo() function, but after studying the code and testing the API calls through the JASPAR interface, they realized that this issue was not due to the structure of their code, but in fact was due to JASPAR and the fact that they don’t support CORS. At this point, the JASPAR team met with the professor and decided that the best solution would be to implement a relay controller that would handle all traffic from JASPAR to GRNsight. Once the relay controller was done being integrated with the server-side of GRNsight, the API calls began working properly, which corresponded with the end of the intermediate phase of this project (Figure C).

The next phase of the project was the finishing touches (red) phase, which was where the coders spent most of their time interacting with the other teams working on this feature, to make sure that all of the pieces were working together properly (Figure C). The first step was to make sure that the JASPAR information, that the biologists on the integration team were requiring for the final page, was properly being organized and returned so that the information was useful on the page. This required taking the object returned from the second API call and properly “filing” the relevant fields into their spots within the master object. At this point, all that was left to do was to pass the information onto the page design and integration team so that they knew what to expect when calling the JASPAR function, so that they could properly put it on the page, which then marked the end of the coders work on this GRNsight feature, as displayed in Figure C.

=== Assessment of Project ===

* Give an objective assessment of the success of your project workflow and teamwork.
*: Our team worked pretty well together to finish both the paper and the powerpoint together, but this was mainly due to good leadership from Quinn. He kept us up to date and he is the only reason this assignment was even remotely tolerable.
* What worked and what didn't work?
*: Everything worked really well. We had good communication and, although arranging meetup times was difficult, we still met three times out of class to work on the presentation.
* Evaluate your team’s portion of the GRNsight Gene Page Project and Group Report in the following areas:
*# Content: What is the quality of the work?
*#: For the code specifically, everything was very well done, very clean and readable.
*# Organization: Comment on the organization of the project and of your group's wiki pages.
*#: Quinn did a very good job of making our team page. I didn't really have much of a part in it but it looks really good.
*# Completeness: Did your team achieve all of the project objectives? Why or why not?
*#: Yes we completed every single task. Even though they were all just very repetitive.

=== Reflection on the Process ===

* What did you learn?
** With your head (biological or computer science principles)
**: I learned a lot from the Computer Science portions of the class because it was building on my knowledge base of frameworks and software design and engineering.
** With your heart (personal qualities and teamwork qualities that make things work or not work)?
**: I don't like biology, not because the subject isn't of interest (it is), but because of the way things are done in the Biology department. I just find it much more preferable to learn how I do in my major classes.
** With your hands (technical skills)?
**: Maybe I can type faster after all of the writing you guys made me do.

===Final Paper/Group Report===
[[Media:JASPAR Final Paper.pdf]]

=Acknowledgements=
Copied the structure of the sections in my assessment and reflection from the [[GRNsight_Gene_Page_Project_Deliverables|Deliverables Page]].
I worked with my homework partner in class. We also met face-to-face one time outside of class. We texted outside of class and met to work on the presentation part of the assignment together. 
'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.''' 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 13:29, 15 December 2017 (PST)

=References=
* LMU BioDB 2017. (2017). Week 15. Retrieved November 20, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15

{{Template:Ebachour}}

Simonwro120 Week 15

2017-12-15T23:56:50Z

Aporras1: final paper upload

='''Electronic Notebook'''=
=Template for Links=
{{simonwro120}}
==Deliverables==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf|JASPAR the Friendly Ghost Final Group Presentation]] | December 11, 2017
===Tuesday (12/5/17)===
*Worked with Eddie on setting up GRNsight locally on my computer, allowing for edits/changes without altering the master version of the application
**Blair H. forked the master version of GRNsight from Dr. Dionisio's repository and the rest of the coders cloned that repository from her fork
**Became familiar with the GRNsight code for future implementation.
===Thursday (12/7/17)===
*Worked with Eddie B. and Dr. Dionisio on the API requests. Attempting to create a solution to the CORS (Cross Origin Resource Sharing) issue that was involved with the JASPAR database
*Near the end of class, Quinn, Antonio, Eddie and myself all exchanged e-mails so that we could all start working on both the powerpoint and paper in a collaborative manner
*Eddie and Dr. Dionisio created a workaround for this problem by implementing a relay controller later on that week
===Monday (12/11/17)===
*Finalized all the slides for the JASPAR powerpoint presentation, planned roles, speaking order, and general flow
*Uploaded the powerpoint to our team page, deliverables page, and individual page
===Tuesday (12/11/17)===
*Met before class to drill through the presentation a couple times to make sure all things were in check
===Deliverable Checklist===
# Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents)
#*Project Manager (Quinn) will ensure that all the deliverables are organized and delivered properly and on time
# Group Report (''.doc'', ''.docx'' or ''.pdf'' file)
#*'''Outline'''
##Abstract
##*Primarily Quinn - Additional input/information from the entire group as well
##Intro
##*Primarily Quinn - Additional input/information from the entire group to facilitate flow
##Materials and Methods
##*Primarily Antonio, Eddie, and Simon
##Results
##*Primarily Antonio, Eddie, and Simon
##Discussion
##*All members
##Conclusions
##*All members
##Acknowledgements
##*All members
##References
##*All members
#Individual statements of work, assessments, reflections (wiki page, ''.doc'', ''.docx'', ''.pdf'', or e-mailed to both Dr. Dahlquist and Dr. Dionisio)
#*Team members should complete this task individually
#Group PowerPoint presentation (given on Tuesday, December 12, ''.ppt'', ''.pptx'' or ''.pdf'' file)
#*Separate sections were completed by different members of the group initially
#*Merged separated sections together to create a coherent and informative powerpoint presentation
#*Practiced verbal presentation until it was executed smoothly
#Code (GitHub pull request)
#*As stated previously, Blair forked from Dondi, and the rest of the class coned that forked repository.
#Supply a README that summarizes the functionality of your team's new feature (''.txt'' or ''.md'', ''one README per team'')
#*Coders should create this explanatory file, project manager may have some input as well
#Excel spreadsheet with ANOVA results/stem formatting (''.xlsx'')
#PowerPoint of screenshots of stem results (''.pptx'')
#Gene List and GO List files from each significant profile (''.txt'' compressed together in a ''.zip'' file)
#YEASTRACT "rank by TF" results (''.xlsx'')
#GRNmap input workbook (with network adjacency matrix, ''.xlsx'')
#GRNmap output workbook (''.xlsx'')
#Electronic notebook corresponding to these the microarray results files ([[Week 8]], [[Week 10]], and Weeks 11-15) support ''reproducible research'' so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results.
#*Deliverables 7 - 13 came from our Data Analyst's (Antonio) hard work

=Final Paper/Group Report=
[[Media:JASPAR Final Paper.pdf]]

== Acknowledgements ==
*I worked with my homework partners, Eddie Bachoura, Quinn Lanners, and Antonio on this assignment.
*Both Eddie B. and I worked primarily together to complete the list of deliverables expected from the "Coders" group.
*I'd also like to acknowledge the help both Dondi and Dr. Dahlquist for their detailed instructions on completing this assignment.
*While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]])

== References ==
#LMU BioDB 2017. (2017). Retrieved December 7, 2017, from [https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15 https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15]
#LMU BioDB 2017. (2017). Retrieved December 7, 2017, from [https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/JASPAR_the_Friendly_Ghost#Eddie.27s_Reflection_3 https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/JASPAR_the_Friendly_Ghost#Eddie.27s_Reflection_3]
#API Overview. (2017). Retrieved December 5, 2017, from [http://jaspar.genereg.net/api/overview#cors-requests http://jaspar.genereg.net/api/overview#cors-requests]
#JASPAR RESTful API. (2017). Retrieved December 5, 2017, from [http://jaspar.genereg.net/api/ http://jaspar.genereg.net/api/]

JASPAR the Friendly Ghost Final Deliverables

2017-12-15T23:55:27Z

Aporras1: /* Team Signatures */ antonio's signature

==Group Report==
[[Media:JASPAR Final Paper.pdf|JASPAR the Friendly Ghost Group Report]]

==Individual statements of work, assessments, reflections==
[[QLanners_individual_statement|Quinn Lanners]] | [[Aporras1_Individual_Assessment_and_Reflection|Antonio Porras]] | [[Ebachour_Week_15|Edward Bachoura]] | [[simonwro120 individual statement|Simon Wroblewski]]

==Group PowerPoint presentation==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf | Final Group Presentation (pdf)]] | December 11, 2017
==Code==
[[Media:Api.txt|JASPAR team's code (as well as hAPI's code)]] | December 15, 2017 
==README that summarizes the functionality of your team's new feature==
[[Media:README.txt|Readme.txt]] | December 15, 2017 
==Excel spreadsheet with ANOVA results/stem formatting==
[[Media:AP dZAP1 stem.xlsx]]
==PowerPoint of screenshots of stem results==
[[Media:AP dZAP1 STEM Screenshots & p-values.zip]]
==Gene List and GO List files from each significant profile==
[[Media:AP dZAP1 GOlist and genelist for profiles.zip]]
==YEASTRACT "rank by TF" results==
[[Media:AP YEASTRACT Transcription Factors.xlsx]]
==GRNmap input workbook==
[[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]]
==GRNmap output workbook==
[[Media:15-gene 44-edge teamJASPAR Sigmoid estimation output.xlsx]]
*Expression vs. Time Images generated from MATLAB: [[Media:Output Images from 15-gene 44-edge teamJASPAR Sigmoid estimation.zip]]
==Electronic notebooks corresponding to the microarray results files==
#[[Aporras1 Week 8]]
#[[Aporras1 Week 10]]
#[[Aporras1 Week 14]]
#[[Aporras1 Week 15]]

==Team Links==

{{Template:JASPAR the Friendly Ghost Links}}
===Team Signatures===
*[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 20:49, 13 December 2017 (PST) 
*[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:48, 15 December 2017 (PST)
*[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 15:55, 15 December 2017 (PST)

==Class Links==

{{Template:GRNsight Gene Page Project Links}}

JASPAR the Friendly Ghost Final Deliverables

2017-12-15T23:54:45Z

Aporras1: /* Group Report */ report link

==Group Report==
[[Media:JASPAR Final Paper.pdf|JASPAR the Friendly Ghost Group Report]]

==Individual statements of work, assessments, reflections==
[[QLanners_individual_statement|Quinn Lanners]] | [[Aporras1_Individual_Assessment_and_Reflection|Antonio Porras]] | [[Ebachour_Week_15|Edward Bachoura]] | [[simonwro120 individual statement|Simon Wroblewski]]

==Group PowerPoint presentation==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf | Final Group Presentation (pdf)]] | December 11, 2017
==Code==
[[Media:Api.txt|JASPAR team's code (as well as hAPI's code)]] | December 15, 2017 
==README that summarizes the functionality of your team's new feature==
[[Media:README.txt|Readme.txt]] | December 15, 2017 
==Excel spreadsheet with ANOVA results/stem formatting==
[[Media:AP dZAP1 stem.xlsx]]
==PowerPoint of screenshots of stem results==
[[Media:AP dZAP1 STEM Screenshots & p-values.zip]]
==Gene List and GO List files from each significant profile==
[[Media:AP dZAP1 GOlist and genelist for profiles.zip]]
==YEASTRACT "rank by TF" results==
[[Media:AP YEASTRACT Transcription Factors.xlsx]]
==GRNmap input workbook==
[[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]]
==GRNmap output workbook==
[[Media:15-gene 44-edge teamJASPAR Sigmoid estimation output.xlsx]]
*Expression vs. Time Images generated from MATLAB: [[Media:Output Images from 15-gene 44-edge teamJASPAR Sigmoid estimation.zip]]
==Electronic notebooks corresponding to the microarray results files==
#[[Aporras1 Week 8]]
#[[Aporras1 Week 10]]
#[[Aporras1 Week 14]]
#[[Aporras1 Week 15]]

==Team Links==

{{Template:JASPAR the Friendly Ghost Links}}
===Team Signatures===
*[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 20:49, 13 December 2017 (PST) 
*[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:48, 15 December 2017 (PST)

==Class Links==

{{Template:GRNsight Gene Page Project Links}}

Aporras1 Week 15

2017-12-15T23:53:46Z

Aporras1: final paper

User page: [[User:Aporras1|Antonio Porras]]

Team page: [[JASPAR the Friendly Ghost|JASPAR The Friendly Ghost]]

Assignment page: [[Week 15|Week 15]]

==Electronic Notebook==
# Network was determined to be too big.
#* Began process of deleting the least significant
# Re-downloaded [[Media:AP YEASTRACT Transcription Factors.xlsx]] and found the transcription factors which I used in [[Aporras1_Week_14]] ranked from highest % in user set to lowest:
#**GLN3
#**HAP4
#**Ace2p
#**Sfp1p
#**Bas1p
#**Msn2p
#**Yap1p
#**Ash1p
#**Gcn4p
#**Msn4p
#**Abf1p
#**Cst6p
#**Sok2p
#**Rpn4p
#**Hsf1p
#**Zap1p
#**Cin5p
#**Aft1p
#**Spt23p
#**Pdr1p
#**Met4p
#**Arr1p

===ARR1 deletion===
# Moved "network" workbook to a new file found in [[Media:Trimming Network transcription factor deletions dZAP1.zip]]: Network ARR1 deletion.xlsx
# Began by deleting ARR1 in worksheet "Network ARR1 deletion"
#* Deleted row 5 and column E containing ARR1 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network ARR1 deletion.xlsx" file that has the "network" worksheet.
# Network remained too large.

===MET4 deletion===
# Moved "network" workbook from Network ARR1 deletion.xlsx to a new file found in [[Media:Trimming Network transcription factor deletions dZAP1.zip]]: Network MET4 deletion.xlsx
# Began by deleting MET4 in worksheet "network MET4 deletion"
#* Deleted row 13 and column M containing MET4 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network MET4 deletion" file that has the "network" worksheet.
# Network remained too large.

===PDR1 deletion===
# Moved "network" workbook from Network MET4 deletion.xlsx to a new file found in [[Media:Trimming Network transcription factor deletions dZAP1.zip]]: Network PDR1 deletion.xlsx
# Began by deleting PDR1 in worksheet "network PDR1 deletion"
#* Deleted row 15 and column O containing PDR1 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network PDR1 deletion" file that has the "network" worksheet.
# Network remained too large.

===SPT23 & BAS1 deletion===
# Moved "network" workbook from Network PDR1 deletion.xlsx to a new file found in folder [[Media:Trimming Network transcription factor deletions dZAP1.zip]]: Network SPT23 deletion.xlsx
# Began by deleting PDR1 in worksheet "network SPT23 deletion"
#* Deleted row 19 and column S containing SPT23 data.
#*BAS1 transcription factor became disconnected.
#*Deleted row 6 and column F containing BAS1 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network SPT23 deletion" file that has the "network" worksheet.
# Network remained too large.

===Network Files After Trimming===

[[Media:Trimming Network transcription factor deletions dZAP1.zip]]

Files were not necessary in the final GRNsight visualization, but rather for documentation on work performed before being provided by [[User:Kdahlquist|Dr. Dahlquist]].

Antonio, I finished paring down the network. Here is the final file (renamed): [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx | 15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]]. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:55, 6 December 2017 (PST)''

===GRNsight Visualization===
# Downloaded [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]] provided by [[User:Kdahlquist|Dr. Dahlquist]].
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx" file that has the "network" worksheet. Moved the nodes (genes) around until I created a layout I liked, ordering alphabetically, and took a screenshot of the results and saved the screenshot as:[[Media:GRNsight Visualization of 15-gene 44-edge teamJASPAR Sigmoid estimation.PNG]]

===GRNsight Regulation MATLAB Output===
# Used [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]] and allowed [[User:Kdahlquist|Dr. Dahlquist]] to run MATLAB.
#* Once it was completed, saved the output workbook as:[[Media:15-gene 44-edge teamJASPAR Sigmoid estimation output.xlsx]]
#* Saved the images and uploaded them to the wiki as:[[Media:Output Images from 15-gene 44-edge teamJASPAR Sigmoid estimation.zip]]
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "15-gene_44-edge_teamJASPAR_Sigmoid_estimation_output.xlsx" file that had the "network" worksheet. Moved the nodes (genes) around until I created a layout I liked, ordering alphabetically, and took a screenshot of the results and saved the screenshot as:[[Media:GRNsight Regulation Magnitude Visualization of 15-gene 44-edge teamJASPAR Sigmoid estimation.PNG]]

===Edits to Organization of Files===
# In [[Week 10|Week 10]] the powerpoint STEM screenshots, GOlists, and genelists were all zipped in [[Media:AP dZAP1 STEM Profiles and Powerpoint.zip]] and the deliverables, in [[GRNsight Gene Page Project Deliverables|Project Deliverables]], asked for two separate files.
#* Removed the powerpoint with the p-values and STEM screenshots. Zipped the powerpoint and uploaded it to the wiki as a new file found in the deliverables: [[Media:AP dZAP1 STEM Screenshots & p-values.zip]].
#* Removed the golists and genelists .txt files into a new folder and zipped the folder before uploading it as a new file found in the deliverables: [[Media:AP dZAP1 GOlist and genelist for profiles.zip]]

===Deliverables Checklist===
# Excel spreadsheet with ANOVA results/stem formatting (''.xlsx'')
#*[[Media:AP dZAP1 stem.xlsx]]
# PowerPoint of screenshots of stem results (''.pptx'')
#* [[Media:AP dZAP1 STEM Screenshots & p-values.zip]]
# Gene List and GO List files from each significant profile (''.txt'' compressed together in a ''.zip'' file)
#* [[Media:AP dZAP1 GOlist and genelist for profiles.zip]]
# YEASTRACT "rank by TF" results (''.xlsx'')
#* [[Media:AP YEASTRACT Transcription Factors.xlsx]]
# GRNmap input workbook (with network adjacency matrix, ''.xlsx'')
#* [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]]
# GRNmap output workbook (''.xlsx'')
#* [[Media:15-gene 44-edge teamJASPAR Sigmoid estimation output.xlsx]]
#* Expression vs Time Images generated from MATLAB
#** [[Media:Output Images from 15-gene 44-edge teamJASPAR Sigmoid estimation.zip]]
# Electronic notebook corresponding to these the microarray results files ([[Week 8]], [[Week 10]], & [[Week 14]]) support ''reproducible research'' so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results.
#* Summary for [[Aporras1_Week_8]]: In week 8, performed statistical analysis on the deletion ZAP1 using provided ANOVA. Specfically, Bonferroni & p value correction and Benjamini & Hochberg p value was calculated. The data examined the time intervals of 15 minutes, 30 minutes, 60 minutes, 90 minutes, and 120 minutes during cold shock.
#** Electronic notebook found in "Electronic Notebook" section of [[Aporras1_Week_8]]
#* Summary for [[Aporras1_Week_10]]: Used the data from [[Aporras1_Week_8]] to perform STEM clustering on dZAP1. Selected profile 22 because it had a very low p value and a high amount of genes (2E-157 and 252 respectively). Selected 6 GO terms from profile 22's GOlist to define and analyze in terms of why the cell would change the expression of the genes associated with the GO terms.
#** Electronic notebook found in "Electronic Notebook" section of [[Aporras1_Week_10]]
#* Summary for [[Aporras1_Week_14]]: Made edits to [[Aporras1_Week_8]] and [[Aporras1_Week_10]] according to feedback from [[User:Kdahlquist|Dr. Dahlquist]] & [[User:Dondi|Dr. Dionisio]]. Used the profile 22 genelist and ranked transcription factors with YEASTRACT by significance and selected the most significant ones with low P-values. Generated a regulation matrix using YEASTRACT and created an adjacency matrix with a network to visualize with GRNsight. The network was trimmed down to 15 genes and MATLAB was used to generate an output. Both the output and the original network were visualized with GRNsight.
#** Electronic notebook found in "Electronic Notebook" section of [[Aporras1_Week_14]].
#* Note: make a summary and provide links to individual pages with electronic notebooks.

==Final Powerpoint Presentation==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf]]

==Final Paper/Group Report==
[[Media:JASPAR Final Paper.pdf]]

==Acknowledgements==
# Worked alongside [[User:Qlanners|Quinn Lanners]] to begin gathering deliverables.
# Copied the formatting and text from [[GRNsight_Gene_Page_Project_Deliverables]] checklist in my checklist category.
# Received file used for GRNsight visualization, received in class direction and instruction from [[User:Kdahlquist|Dr. Dahlquist]].
# Met up with group members in [[JASPAR the Friendly Ghost]] after the Thursday 12/01/2017 class and outside of class 12/09/2017 to discuss an outline of what needed to be completed and to work on the presentation.

'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.'''

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 16:11, 7 December 2017 (PST)

==References==
#Dahlquist, K. D., Dionisio, J. D. N., Fitzpatrick, B. G., Anguiano, N. A., Varshneya, A., Southwick, B. J., & Samdarshi, M. (2016). GRNsight: a web application and service for visualizing models of small-to medium-scale gene regulatory networks. PeerJ Computer Science, 2, e85.
# LMU BioDB 2017. (2017). Week 15. Retrieved December 05, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15
# LMU BioDB 2017. (2017). GRNsight Gene Page Project Deliverables. Retrieved December 05, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/GRNsight_Gene_Page_Project_Deliverables
# Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.

[[Category:Journal Entry]]

File:JASPAR Final Paper.pdf

2017-12-15T23:52:55Z

Aporras1: Final draft of the JASPAR the Friendly Ghost group report.

Final draft of the JASPAR the Friendly Ghost group report.

Aporras1 Individual Assessment and Reflection

2017-12-15T22:15:46Z

Aporras1: jaspar link

User page: [[User:Aporras1|Antonio Porras]]

Assignment page: [[GRNsight_Gene_Page_Project_Deliverables|Deliverables Page]]

Group page: [[JASPAR_the_Friendly_Ghost|JASPAR the Friendly Ghost]]

==Individual Assessment and Reflection==

=== Statement of Work ===

'''1. Describe exactly what you did on the project.'''

As data analyst I was responsible for performing statistical analysis on dZAP1 expression data provided by [[User:kdahlquist|Dr. Dahlquist]]'s lab. During Week 8 I completed the ANOVA test along with calculating Benjamini-Hochberg corrected p value and the Bonferroni-corrected p-value. The first calculation was less stringent compared to the Bonferroni but both were useful in terms of improving the confidence in the data. The precise steps and outline of what I completed can be found in my [[Aporras1_Week_8]] journal.

Moving into Week 10, I performed STEM high level analysis on the ANOVA data in order to generate gene clusters which presented similar expression over the course of the experiment. Seven significant clusters were generated and the GOlists & genelists were saved and uploaded to the wiki for later analysis. I read and interpreted 6 GOlist terms found in the GOlist of Profile 22 and attempted to understand why the cell would be changing expression in genes associated with certain cell processes. The precise steps and outline of what I completed can be found in my [[Aporras1_Week_10]] journal.

In Week 11, I worked alongside [[User:Qlanners|Quinn Lanners]] to perform a literature search on yeast and cold shock to gain brief exposure to journal articles in this area of research and search engine qualities. The precise steps and outline can be found in my [[Aporras1_Week_11]] journal. The following week [[User:Qlanners|Quinn Lanners]] and I did more in-depth research on the specific journal article: Genome-wide analysis of the yeast transcriptome upon heat and cold shock (Becerra et al., 2003). We outlined the introduction, methods, procedure, analysis tools, and overall findings of the article before creating and presenting a presentation to the class which can be found in my [[Aporras1_Week_12]] journal along with the specific outline and approach to interpretation of their data.

In Week 14 and Week 15 I continued work from the Week 10 data analysis and selected profile 22 of dZAP1 from STEM analysis. I then generated a list of significant transcription factors which targeted genes within the genelist provided by STEM and further used those transcription factors to create a regulatory network. This network was actually determined to be too large and [[User:kdahlquist|Dr. Dahlquist]] trimmed down the network to 15 transcription factors. The network was then put into GRNsight to visualize the regulation pathways. MATLAB was also used to generate an output which would allow for GRNsight to display the direction of regulation and the magnitude with colors and bold/thin regulation arrows. A more detailed outline for the process can be found in my [[Aporras1_Week_14]] journal.

Once I completed all the analysis, I then put the data onto the deliverables page, presentation, and the final paper along with my analysis. These files can be found in [[JASPAR_the_Friendly_Ghost_Final_Deliverables]]. I was primarily responsible for maintaining extreme care with the files and keeping a very well-kept record of data. In addition I worked closely with [[User:Qlanners|Quinn Lanners]] to complete the final paper and aid in any way possible once I completed my data calculations and subsequent analysis. A more detailed outline for the process can be found in my [[Aporras1_Week_15]] journal.

=== Assessment of Project ===

'''2. Give an objective assessment of the success of your project workflow and teamwork.'''

I would say the overall project workflow and teamwork was fairly cohesive considering our different academic backgrounds and schedules. Given this time of the year, with final exams, we did very well to meet outside of class and work in the lab while communicating constantly. My workflow didn't impede the workflow of anyone else throughout the project and it was definitely a good feeling to have throughout working on the project as I attempted to complete everything ahead of time and work on group deliverables before my own.

'''3. What worked and what didn't work?'''

What didn't work was, or at least I didn't fully accept, was the need for both a paper and a presentation. I felt as though it became repetitive when examining both the paper and the introduction. With regards to the team, there weren't any aspects that didn't work, except I wish I would have had a better understanding of the role of the coders and their work through JASPAR. It took a lot of curiosity and asking to figure it out rather than being explained it in the beginning.

'''4. What would you do differently if you could do it all over again?'''

I definitely wish I had the same good data record keeping skills that I have currently because it would have saved a lot of time throughout the semester.

'''5. Evaluate your team’s portion of the GRNsight Gene Page Project and Group Report in the following areas:'''

'''* Content: What is the quality of the work?'''

From my understanding of the coders, they put their best foot forward in terms of working in a new area in which they hadn't worked in before. As data analyst I had context and prior understanding of my analysis but for them they had to work with a completely new database, JASPAR. Quinn created a structure by which every aspect was planned out and made it easy to keep track of deadlines and goals. Overall, while also considering the amount of time spent throughout these last few weeks and paying attention to very specific details, JASPAR the Friendly Ghost did their best to complete what was assigned. Again, while paying attention to copious details.

'''* Organization: Comment on the organization of the project and of your group's wiki pages.'''

As I mentioned earlier, Quinn structured the page easily so that even I could go ahead and add sections because we all understood the intuitive layout. I kept detailed file records and explained any changes I made to the data while also maintaining a detailed electronic notebook every single week.

'''* Completeness: Did your team achieve all of the project objectives? Why or why not?'''

To the best of my knowledge, we did. We would go through the deliverables page line by line checking tasks off in order to ensure that our product was as complete as it could be. Of course its not perfect, but considering the amount of details and time given, we put a significant amount of time into the project and displaying documentation throughout.

=== Reflection on the Process ===

'''What did you learn?'''

'''With your head (biological or computer science principles)'''

I definitely have much better data management than I did at the beginning of the course and the ability to organize thoughts for someone else to read and replicate the processes I completed throughout the semester. Ultimately, synthesizing replicable data and thus very detailed step by step notes. In terms of biology I didn't take as much because we didn't go very much in depth but now I have a better understanding of how to interpret more intricate data sets and understand the context at least in respect to microarray data.

'''With your heart (personal qualities and teamwork qualities that make things work or not work)?'''

Simply working hard.. and early! It made a huge difference in my workflow to finish assignments ahead of time (prior journal entries may not display this). Instead of waiting for deadlines I found an ethic to attack them to account for time where I was met with difficulties or setbacks (e.g. having to trim down my regulation network) and these setbacks didn't do as much damage because I met them so early before the deadline.

'''With your hands (technical skills)?'''

I've been around computers for a very long time so I didn't really gain any technical skills besides knowing how I work best. I came to the lab because the screens were bigger and I usually used two monitors to save time going in between the assignment Page, individual page, and datasets. This greatly improved my workflow and provided structure which I thrive from.

'''What lesson will you take away from this project that you will still use a year from now?'''

Recognizing how I work best. As soon as I recognized how I work best (e.g. working with multiple monitors or working on assignments early) I was able to improve my efficiency as the assignments got more difficult. Lastly, data management and organization. Organization with respect to files made the process much easier than if I hadn't learned to be descriptive with file names or have multiple backups and a notepad with a filename and description. These organizational techniques were vital and will be useful in future environments where data is often more digital than it is paper.

==Acknowledgements==
#Copied the structure of the sections in my assessment and reflection from the [[GRNsight_Gene_Page_Project_Deliverables|Deliverables Page]].
#Worked alongside [[User:Qlanners|Quinn Lanners]] in Week 11 and 12 and subsequently Weeks 14 and 15 to complete the assignment.
#The [[JASPAR the Friendly Ghost]] team members including [[User:Qlanners|Quinn Lanners]], [[User:Simonwro120|Simon Wroblewski]], and [[User:Ebachour|Eddie Bachoura]].
#Received assistance in completing the assignments from [[User:kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dionisio]].

==References==
# Dahlquist, K. D., Dionisio, J. D. N., Fitzpatrick, B. G., Anguiano, N. A., Varshneya, A., Southwick, B. J., & Samdarshi, M. (2016). GRNsight: a web application and service for visualizing models of small-to medium-scale gene regulatory networks. PeerJ Computer Science, 2, e85.
# LMU BioDB 2017. (2017). GRNsight Gene Page Project Deliverables. Retrieved December 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/GRNsight_Gene_Page_Project_Deliverables
# LMU BioDB 2017. (2017). Aporras1 Week 8. Retrieved December 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Aporras1_Week_8
# LMU BioDB 2017. (2017). Aporras1 Week 10. Retrieved December 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Aporras1_Week_10
# LMU BioDB 2017. (2017). Aporras1 Week 11. Retrieved December 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Aporras1_Week_11
# LMU BioDB 2017. (2017). Aporras1 Week 12. Retrieved December 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Aporras1_Week_12
# LMU BioDB 2017. (2017). Aporras1 Week 14. Retrieved December 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Aporras1_Week_14
# LMU BioDB 2017. (2017). Aporras1 Week 15. Retrieved December 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Aporras1_Week_15
# Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.

[[Category:Journal Entry]]

Aporras1 Individual Assessment and Reflection

2017-12-15T22:14:41Z

Aporras1: /* Acknowledgements */ typo fix dondi

User page: [[User:Aporras1|Antonio Porras]]

Assignment page: [[GRNsight_Gene_Page_Project_Deliverables|Deliverables Page]]

==Individual Assessment and Reflection==

=== Statement of Work ===

'''1. Describe exactly what you did on the project.'''

As data analyst I was responsible for performing statistical analysis on dZAP1 expression data provided by [[User:kdahlquist|Dr. Dahlquist]]'s lab. During Week 8 I completed the ANOVA test along with calculating Benjamini-Hochberg corrected p value and the Bonferroni-corrected p-value. The first calculation was less stringent compared to the Bonferroni but both were useful in terms of improving the confidence in the data. The precise steps and outline of what I completed can be found in my [[Aporras1_Week_8]] journal.

Moving into Week 10, I performed STEM high level analysis on the ANOVA data in order to generate gene clusters which presented similar expression over the course of the experiment. Seven significant clusters were generated and the GOlists & genelists were saved and uploaded to the wiki for later analysis. I read and interpreted 6 GOlist terms found in the GOlist of Profile 22 and attempted to understand why the cell would be changing expression in genes associated with certain cell processes. The precise steps and outline of what I completed can be found in my [[Aporras1_Week_10]] journal.

In Week 11, I worked alongside [[User:Qlanners|Quinn Lanners]] to perform a literature search on yeast and cold shock to gain brief exposure to journal articles in this area of research and search engine qualities. The precise steps and outline can be found in my [[Aporras1_Week_11]] journal. The following week [[User:Qlanners|Quinn Lanners]] and I did more in-depth research on the specific journal article: Genome-wide analysis of the yeast transcriptome upon heat and cold shock (Becerra et al., 2003). We outlined the introduction, methods, procedure, analysis tools, and overall findings of the article before creating and presenting a presentation to the class which can be found in my [[Aporras1_Week_12]] journal along with the specific outline and approach to interpretation of their data.

In Week 14 and Week 15 I continued work from the Week 10 data analysis and selected profile 22 of dZAP1 from STEM analysis. I then generated a list of significant transcription factors which targeted genes within the genelist provided by STEM and further used those transcription factors to create a regulatory network. This network was actually determined to be too large and [[User:kdahlquist|Dr. Dahlquist]] trimmed down the network to 15 transcription factors. The network was then put into GRNsight to visualize the regulation pathways. MATLAB was also used to generate an output which would allow for GRNsight to display the direction of regulation and the magnitude with colors and bold/thin regulation arrows. A more detailed outline for the process can be found in my [[Aporras1_Week_14]] journal.

Once I completed all the analysis, I then put the data onto the deliverables page, presentation, and the final paper along with my analysis. These files can be found in [[JASPAR_the_Friendly_Ghost_Final_Deliverables]]. I was primarily responsible for maintaining extreme care with the files and keeping a very well-kept record of data. In addition I worked closely with [[User:Qlanners|Quinn Lanners]] to complete the final paper and aid in any way possible once I completed my data calculations and subsequent analysis. A more detailed outline for the process can be found in my [[Aporras1_Week_15]] journal.

=== Assessment of Project ===

'''2. Give an objective assessment of the success of your project workflow and teamwork.'''

I would say the overall project workflow and teamwork was fairly cohesive considering our different academic backgrounds and schedules. Given this time of the year, with final exams, we did very well to meet outside of class and work in the lab while communicating constantly. My workflow didn't impede the workflow of anyone else throughout the project and it was definitely a good feeling to have throughout working on the project as I attempted to complete everything ahead of time and work on group deliverables before my own.

'''3. What worked and what didn't work?'''

What didn't work was, or at least I didn't fully accept, was the need for both a paper and a presentation. I felt as though it became repetitive when examining both the paper and the introduction. With regards to the team, there weren't any aspects that didn't work, except I wish I would have had a better understanding of the role of the coders and their work through JASPAR. It took a lot of curiosity and asking to figure it out rather than being explained it in the beginning.

'''4. What would you do differently if you could do it all over again?'''

I definitely wish I had the same good data record keeping skills that I have currently because it would have saved a lot of time throughout the semester.

'''5. Evaluate your team’s portion of the GRNsight Gene Page Project and Group Report in the following areas:'''

'''* Content: What is the quality of the work?'''

From my understanding of the coders, they put their best foot forward in terms of working in a new area in which they hadn't worked in before. As data analyst I had context and prior understanding of my analysis but for them they had to work with a completely new database, JASPAR. Quinn created a structure by which every aspect was planned out and made it easy to keep track of deadlines and goals. Overall, while also considering the amount of time spent throughout these last few weeks and paying attention to very specific details, JASPAR the Friendly Ghost did their best to complete what was assigned. Again, while paying attention to copious details.

'''* Organization: Comment on the organization of the project and of your group's wiki pages.'''

As I mentioned earlier, Quinn structured the page easily so that even I could go ahead and add sections because we all understood the intuitive layout. I kept detailed file records and explained any changes I made to the data while also maintaining a detailed electronic notebook every single week.

'''* Completeness: Did your team achieve all of the project objectives? Why or why not?'''

To the best of my knowledge, we did. We would go through the deliverables page line by line checking tasks off in order to ensure that our product was as complete as it could be. Of course its not perfect, but considering the amount of details and time given, we put a significant amount of time into the project and displaying documentation throughout.

=== Reflection on the Process ===

'''What did you learn?'''

'''With your head (biological or computer science principles)'''

I definitely have much better data management than I did at the beginning of the course and the ability to organize thoughts for someone else to read and replicate the processes I completed throughout the semester. Ultimately, synthesizing replicable data and thus very detailed step by step notes. In terms of biology I didn't take as much because we didn't go very much in depth but now I have a better understanding of how to interpret more intricate data sets and understand the context at least in respect to microarray data.

'''With your heart (personal qualities and teamwork qualities that make things work or not work)?'''

Simply working hard.. and early! It made a huge difference in my workflow to finish assignments ahead of time (prior journal entries may not display this). Instead of waiting for deadlines I found an ethic to attack them to account for time where I was met with difficulties or setbacks (e.g. having to trim down my regulation network) and these setbacks didn't do as much damage because I met them so early before the deadline.

'''With your hands (technical skills)?'''

I've been around computers for a very long time so I didn't really gain any technical skills besides knowing how I work best. I came to the lab because the screens were bigger and I usually used two monitors to save time going in between the assignment Page, individual page, and datasets. This greatly improved my workflow and provided structure which I thrive from.

'''What lesson will you take away from this project that you will still use a year from now?'''

Recognizing how I work best. As soon as I recognized how I work best (e.g. working with multiple monitors or working on assignments early) I was able to improve my efficiency as the assignments got more difficult. Lastly, data management and organization. Organization with respect to files made the process much easier than if I hadn't learned to be descriptive with file names or have multiple backups and a notepad with a filename and description. These organizational techniques were vital and will be useful in future environments where data is often more digital than it is paper.

==Acknowledgements==
#Copied the structure of the sections in my assessment and reflection from the [[GRNsight_Gene_Page_Project_Deliverables|Deliverables Page]].
#Worked alongside [[User:Qlanners|Quinn Lanners]] in Week 11 and 12 and subsequently Weeks 14 and 15 to complete the assignment.
#The [[JASPAR the Friendly Ghost]] team members including [[User:Qlanners|Quinn Lanners]], [[User:Simonwro120|Simon Wroblewski]], and [[User:Ebachour|Eddie Bachoura]].
#Received assistance in completing the assignments from [[User:kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dionisio]].

==References==
# Dahlquist, K. D., Dionisio, J. D. N., Fitzpatrick, B. G., Anguiano, N. A., Varshneya, A., Southwick, B. J., & Samdarshi, M. (2016). GRNsight: a web application and service for visualizing models of small-to medium-scale gene regulatory networks. PeerJ Computer Science, 2, e85.
# LMU BioDB 2017. (2017). GRNsight Gene Page Project Deliverables. Retrieved December 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/GRNsight_Gene_Page_Project_Deliverables
# LMU BioDB 2017. (2017). Aporras1 Week 8. Retrieved December 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Aporras1_Week_8
# LMU BioDB 2017. (2017). Aporras1 Week 10. Retrieved December 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Aporras1_Week_10
# LMU BioDB 2017. (2017). Aporras1 Week 11. Retrieved December 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Aporras1_Week_11
# LMU BioDB 2017. (2017). Aporras1 Week 12. Retrieved December 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Aporras1_Week_12
# LMU BioDB 2017. (2017). Aporras1 Week 14. Retrieved December 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Aporras1_Week_14
# LMU BioDB 2017. (2017). Aporras1 Week 15. Retrieved December 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Aporras1_Week_15
# Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.

[[Category:Journal Entry]]

Aporras1 Individual Assessment and Reflection

2017-12-15T22:14:15Z

Aporras1: /* Acknowledgements */ final acknowledgments

User page: [[User:Aporras1|Antonio Porras]]

Assignment page: [[GRNsight_Gene_Page_Project_Deliverables|Deliverables Page]]

==Individual Assessment and Reflection==

=== Statement of Work ===

'''1. Describe exactly what you did on the project.'''

As data analyst I was responsible for performing statistical analysis on dZAP1 expression data provided by [[User:kdahlquist|Dr. Dahlquist]]'s lab. During Week 8 I completed the ANOVA test along with calculating Benjamini-Hochberg corrected p value and the Bonferroni-corrected p-value. The first calculation was less stringent compared to the Bonferroni but both were useful in terms of improving the confidence in the data. The precise steps and outline of what I completed can be found in my [[Aporras1_Week_8]] journal.

Moving into Week 10, I performed STEM high level analysis on the ANOVA data in order to generate gene clusters which presented similar expression over the course of the experiment. Seven significant clusters were generated and the GOlists & genelists were saved and uploaded to the wiki for later analysis. I read and interpreted 6 GOlist terms found in the GOlist of Profile 22 and attempted to understand why the cell would be changing expression in genes associated with certain cell processes. The precise steps and outline of what I completed can be found in my [[Aporras1_Week_10]] journal.

In Week 11, I worked alongside [[User:Qlanners|Quinn Lanners]] to perform a literature search on yeast and cold shock to gain brief exposure to journal articles in this area of research and search engine qualities. The precise steps and outline can be found in my [[Aporras1_Week_11]] journal. The following week [[User:Qlanners|Quinn Lanners]] and I did more in-depth research on the specific journal article: Genome-wide analysis of the yeast transcriptome upon heat and cold shock (Becerra et al., 2003). We outlined the introduction, methods, procedure, analysis tools, and overall findings of the article before creating and presenting a presentation to the class which can be found in my [[Aporras1_Week_12]] journal along with the specific outline and approach to interpretation of their data.

In Week 14 and Week 15 I continued work from the Week 10 data analysis and selected profile 22 of dZAP1 from STEM analysis. I then generated a list of significant transcription factors which targeted genes within the genelist provided by STEM and further used those transcription factors to create a regulatory network. This network was actually determined to be too large and [[User:kdahlquist|Dr. Dahlquist]] trimmed down the network to 15 transcription factors. The network was then put into GRNsight to visualize the regulation pathways. MATLAB was also used to generate an output which would allow for GRNsight to display the direction of regulation and the magnitude with colors and bold/thin regulation arrows. A more detailed outline for the process can be found in my [[Aporras1_Week_14]] journal.

Once I completed all the analysis, I then put the data onto the deliverables page, presentation, and the final paper along with my analysis. These files can be found in [[JASPAR_the_Friendly_Ghost_Final_Deliverables]]. I was primarily responsible for maintaining extreme care with the files and keeping a very well-kept record of data. In addition I worked closely with [[User:Qlanners|Quinn Lanners]] to complete the final paper and aid in any way possible once I completed my data calculations and subsequent analysis. A more detailed outline for the process can be found in my [[Aporras1_Week_15]] journal.

=== Assessment of Project ===

'''2. Give an objective assessment of the success of your project workflow and teamwork.'''

I would say the overall project workflow and teamwork was fairly cohesive considering our different academic backgrounds and schedules. Given this time of the year, with final exams, we did very well to meet outside of class and work in the lab while communicating constantly. My workflow didn't impede the workflow of anyone else throughout the project and it was definitely a good feeling to have throughout working on the project as I attempted to complete everything ahead of time and work on group deliverables before my own.

'''3. What worked and what didn't work?'''

What didn't work was, or at least I didn't fully accept, was the need for both a paper and a presentation. I felt as though it became repetitive when examining both the paper and the introduction. With regards to the team, there weren't any aspects that didn't work, except I wish I would have had a better understanding of the role of the coders and their work through JASPAR. It took a lot of curiosity and asking to figure it out rather than being explained it in the beginning.

'''4. What would you do differently if you could do it all over again?'''

I definitely wish I had the same good data record keeping skills that I have currently because it would have saved a lot of time throughout the semester.

'''5. Evaluate your team’s portion of the GRNsight Gene Page Project and Group Report in the following areas:'''

'''* Content: What is the quality of the work?'''

From my understanding of the coders, they put their best foot forward in terms of working in a new area in which they hadn't worked in before. As data analyst I had context and prior understanding of my analysis but for them they had to work with a completely new database, JASPAR. Quinn created a structure by which every aspect was planned out and made it easy to keep track of deadlines and goals. Overall, while also considering the amount of time spent throughout these last few weeks and paying attention to very specific details, JASPAR the Friendly Ghost did their best to complete what was assigned. Again, while paying attention to copious details.

'''* Organization: Comment on the organization of the project and of your group's wiki pages.'''

As I mentioned earlier, Quinn structured the page easily so that even I could go ahead and add sections because we all understood the intuitive layout. I kept detailed file records and explained any changes I made to the data while also maintaining a detailed electronic notebook every single week.

'''* Completeness: Did your team achieve all of the project objectives? Why or why not?'''

To the best of my knowledge, we did. We would go through the deliverables page line by line checking tasks off in order to ensure that our product was as complete as it could be. Of course its not perfect, but considering the amount of details and time given, we put a significant amount of time into the project and displaying documentation throughout.

=== Reflection on the Process ===

'''What did you learn?'''

'''With your head (biological or computer science principles)'''

I definitely have much better data management than I did at the beginning of the course and the ability to organize thoughts for someone else to read and replicate the processes I completed throughout the semester. Ultimately, synthesizing replicable data and thus very detailed step by step notes. In terms of biology I didn't take as much because we didn't go very much in depth but now I have a better understanding of how to interpret more intricate data sets and understand the context at least in respect to microarray data.

'''With your heart (personal qualities and teamwork qualities that make things work or not work)?'''

Simply working hard.. and early! It made a huge difference in my workflow to finish assignments ahead of time (prior journal entries may not display this). Instead of waiting for deadlines I found an ethic to attack them to account for time where I was met with difficulties or setbacks (e.g. having to trim down my regulation network) and these setbacks didn't do as much damage because I met them so early before the deadline.

'''With your hands (technical skills)?'''

I've been around computers for a very long time so I didn't really gain any technical skills besides knowing how I work best. I came to the lab because the screens were bigger and I usually used two monitors to save time going in between the assignment Page, individual page, and datasets. This greatly improved my workflow and provided structure which I thrive from.

'''What lesson will you take away from this project that you will still use a year from now?'''

Recognizing how I work best. As soon as I recognized how I work best (e.g. working with multiple monitors or working on assignments early) I was able to improve my efficiency as the assignments got more difficult. Lastly, data management and organization. Organization with respect to files made the process much easier than if I hadn't learned to be descriptive with file names or have multiple backups and a notepad with a filename and description. These organizational techniques were vital and will be useful in future environments where data is often more digital than it is paper.

==Acknowledgements==
#Copied the structure of the sections in my assessment and reflection from the [[GRNsight_Gene_Page_Project_Deliverables|Deliverables Page]].
#Worked alongside [[User:Qlanners|Quinn Lanners]] in Week 11 and 12 and subsequently Weeks 14 and 15 to complete the assignment.
#The [[JASPAR the Friendly Ghost]] team members including [[User:Qlanners|Quinn Lanners]], [[User:Simonwro120|Simon Wroblewski]], and [[User:Ebachour|Eddie Bachoura]].
#Received assistance in completing the assignments from [[User:kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dionision]].

==References==
# Dahlquist, K. D., Dionisio, J. D. N., Fitzpatrick, B. G., Anguiano, N. A., Varshneya, A., Southwick, B. J., & Samdarshi, M. (2016). GRNsight: a web application and service for visualizing models of small-to medium-scale gene regulatory networks. PeerJ Computer Science, 2, e85.
# LMU BioDB 2017. (2017). GRNsight Gene Page Project Deliverables. Retrieved December 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/GRNsight_Gene_Page_Project_Deliverables
# LMU BioDB 2017. (2017). Aporras1 Week 8. Retrieved December 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Aporras1_Week_8
# LMU BioDB 2017. (2017). Aporras1 Week 10. Retrieved December 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Aporras1_Week_10
# LMU BioDB 2017. (2017). Aporras1 Week 11. Retrieved December 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Aporras1_Week_11
# LMU BioDB 2017. (2017). Aporras1 Week 12. Retrieved December 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Aporras1_Week_12
# LMU BioDB 2017. (2017). Aporras1 Week 14. Retrieved December 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Aporras1_Week_14
# LMU BioDB 2017. (2017). Aporras1 Week 15. Retrieved December 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Aporras1_Week_15
# Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.

[[Category:Journal Entry]]

Aporras1 Individual Assessment and Reflection

2017-12-15T22:09:25Z

Aporras1: /* References */ references

User page: [[User:Aporras1|Antonio Porras]]

Assignment page: [[GRNsight_Gene_Page_Project_Deliverables|Deliverables Page]]

==Individual Assessment and Reflection==

=== Statement of Work ===

'''1. Describe exactly what you did on the project.'''

As data analyst I was responsible for performing statistical analysis on dZAP1 expression data provided by [[User:kdahlquist|Dr. Dahlquist]]'s lab. During Week 8 I completed the ANOVA test along with calculating Benjamini-Hochberg corrected p value and the Bonferroni-corrected p-value. The first calculation was less stringent compared to the Bonferroni but both were useful in terms of improving the confidence in the data. The precise steps and outline of what I completed can be found in my [[Aporras1_Week_8]] journal.

Moving into Week 10, I performed STEM high level analysis on the ANOVA data in order to generate gene clusters which presented similar expression over the course of the experiment. Seven significant clusters were generated and the GOlists & genelists were saved and uploaded to the wiki for later analysis. I read and interpreted 6 GOlist terms found in the GOlist of Profile 22 and attempted to understand why the cell would be changing expression in genes associated with certain cell processes. The precise steps and outline of what I completed can be found in my [[Aporras1_Week_10]] journal.

In Week 11, I worked alongside [[User:Qlanners|Quinn Lanners]] to perform a literature search on yeast and cold shock to gain brief exposure to journal articles in this area of research and search engine qualities. The precise steps and outline can be found in my [[Aporras1_Week_11]] journal. The following week [[User:Qlanners|Quinn Lanners]] and I did more in-depth research on the specific journal article: Genome-wide analysis of the yeast transcriptome upon heat and cold shock (Becerra et al., 2003). We outlined the introduction, methods, procedure, analysis tools, and overall findings of the article before creating and presenting a presentation to the class which can be found in my [[Aporras1_Week_12]] journal along with the specific outline and approach to interpretation of their data.

In Week 14 and Week 15 I continued work from the Week 10 data analysis and selected profile 22 of dZAP1 from STEM analysis. I then generated a list of significant transcription factors which targeted genes within the genelist provided by STEM and further used those transcription factors to create a regulatory network. This network was actually determined to be too large and [[User:kdahlquist|Dr. Dahlquist]] trimmed down the network to 15 transcription factors. The network was then put into GRNsight to visualize the regulation pathways. MATLAB was also used to generate an output which would allow for GRNsight to display the direction of regulation and the magnitude with colors and bold/thin regulation arrows. A more detailed outline for the process can be found in my [[Aporras1_Week_14]] journal.

Once I completed all the analysis, I then put the data onto the deliverables page, presentation, and the final paper along with my analysis. These files can be found in [[JASPAR_the_Friendly_Ghost_Final_Deliverables]]. I was primarily responsible for maintaining extreme care with the files and keeping a very well-kept record of data. In addition I worked closely with [[User:Qlanners|Quinn Lanners]] to complete the final paper and aid in any way possible once I completed my data calculations and subsequent analysis. A more detailed outline for the process can be found in my [[Aporras1_Week_15]] journal.

=== Assessment of Project ===

'''2. Give an objective assessment of the success of your project workflow and teamwork.'''

I would say the overall project workflow and teamwork was fairly cohesive considering our different academic backgrounds and schedules. Given this time of the year, with final exams, we did very well to meet outside of class and work in the lab while communicating constantly. My workflow didn't impede the workflow of anyone else throughout the project and it was definitely a good feeling to have throughout working on the project as I attempted to complete everything ahead of time and work on group deliverables before my own.

'''3. What worked and what didn't work?'''

What didn't work was, or at least I didn't fully accept, was the need for both a paper and a presentation. I felt as though it became repetitive when examining both the paper and the introduction. With regards to the team, there weren't any aspects that didn't work, except I wish I would have had a better understanding of the role of the coders and their work through JASPAR. It took a lot of curiosity and asking to figure it out rather than being explained it in the beginning.

'''4. What would you do differently if you could do it all over again?'''

I definitely wish I had the same good data record keeping skills that I have currently because it would have saved a lot of time throughout the semester.

'''5. Evaluate your team’s portion of the GRNsight Gene Page Project and Group Report in the following areas:'''

'''* Content: What is the quality of the work?'''

From my understanding of the coders, they put their best foot forward in terms of working in a new area in which they hadn't worked in before. As data analyst I had context and prior understanding of my analysis but for them they had to work with a completely new database, JASPAR. Quinn created a structure by which every aspect was planned out and made it easy to keep track of deadlines and goals. Overall, while also considering the amount of time spent throughout these last few weeks and paying attention to very specific details, JASPAR the Friendly Ghost did their best to complete what was assigned. Again, while paying attention to copious details.

'''* Organization: Comment on the organization of the project and of your group's wiki pages.'''

As I mentioned earlier, Quinn structured the page easily so that even I could go ahead and add sections because we all understood the intuitive layout. I kept detailed file records and explained any changes I made to the data while also maintaining a detailed electronic notebook every single week.

'''* Completeness: Did your team achieve all of the project objectives? Why or why not?'''

To the best of my knowledge, we did. We would go through the deliverables page line by line checking tasks off in order to ensure that our product was as complete as it could be. Of course its not perfect, but considering the amount of details and time given, we put a significant amount of time into the project and displaying documentation throughout.

=== Reflection on the Process ===

'''What did you learn?'''

'''With your head (biological or computer science principles)'''

I definitely have much better data management than I did at the beginning of the course and the ability to organize thoughts for someone else to read and replicate the processes I completed throughout the semester. Ultimately, synthesizing replicable data and thus very detailed step by step notes. In terms of biology I didn't take as much because we didn't go very much in depth but now I have a better understanding of how to interpret more intricate data sets and understand the context at least in respect to microarray data.

'''With your heart (personal qualities and teamwork qualities that make things work or not work)?'''

Simply working hard.. and early! It made a huge difference in my workflow to finish assignments ahead of time (prior journal entries may not display this). Instead of waiting for deadlines I found an ethic to attack them to account for time where I was met with difficulties or setbacks (e.g. having to trim down my regulation network) and these setbacks didn't do as much damage because I met them so early before the deadline.

'''With your hands (technical skills)?'''

I've been around computers for a very long time so I didn't really gain any technical skills besides knowing how I work best. I came to the lab because the screens were bigger and I usually used two monitors to save time going in between the assignment Page, individual page, and datasets. This greatly improved my workflow and provided structure which I thrive from.

'''What lesson will you take away from this project that you will still use a year from now?'''

Recognizing how I work best. As soon as I recognized how I work best (e.g. working with multiple monitors or working on assignments early) I was able to improve my efficiency as the assignments got more difficult. Lastly, data management and organization. Organization with respect to files made the process much easier than if I hadn't learned to be descriptive with file names or have multiple backups and a notepad with a filename and description. These organizational techniques were vital and will be useful in future environments where data is often more digital than it is paper.

==Acknowledgements==
#Copied the structure of the sections in my assessment and reflection from the [[GRNsight_Gene_Page_Project_Deliverables|Deliverables Page]].

==References==
# Dahlquist, K. D., Dionisio, J. D. N., Fitzpatrick, B. G., Anguiano, N. A., Varshneya, A., Southwick, B. J., & Samdarshi, M. (2016). GRNsight: a web application and service for visualizing models of small-to medium-scale gene regulatory networks. PeerJ Computer Science, 2, e85.
# LMU BioDB 2017. (2017). GRNsight Gene Page Project Deliverables. Retrieved December 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/GRNsight_Gene_Page_Project_Deliverables
# LMU BioDB 2017. (2017). Aporras1 Week 8. Retrieved December 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Aporras1_Week_8
# LMU BioDB 2017. (2017). Aporras1 Week 10. Retrieved December 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Aporras1_Week_10
# LMU BioDB 2017. (2017). Aporras1 Week 11. Retrieved December 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Aporras1_Week_11
# LMU BioDB 2017. (2017). Aporras1 Week 12. Retrieved December 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Aporras1_Week_12
# LMU BioDB 2017. (2017). Aporras1 Week 14. Retrieved December 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Aporras1_Week_14
# LMU BioDB 2017. (2017). Aporras1 Week 15. Retrieved December 15, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Aporras1_Week_15
# Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.

[[Category:Journal Entry]]

Aporras1 Individual Assessment and Reflection

2017-12-15T22:03:17Z

Aporras1: /* Reflection on the Process */ formatting

Aporras1 Individual Assessment and Reflection

2017-12-15T22:02:49Z

Aporras1: /* Reflection on the Process */ reflection

User page: [[User:Aporras1|Antonio Porras]]

Assignment page: [[GRNsight_Gene_Page_Project_Deliverables|Deliverables Page]]

==Individual Assessment and Reflection==

=== Statement of Work ===

'''1. Describe exactly what you did on the project.'''

As data analyst I was responsible for performing statistical analysis on dZAP1 expression data provided by [[User:kdahlquist|Dr. Dahlquist]]'s lab. During Week 8 I completed the ANOVA test along with calculating Benjamini-Hochberg corrected p value and the Bonferroni-corrected p-value. The first calculation was less stringent compared to the Bonferroni but both were useful in terms of improving the confidence in the data. The precise steps and outline of what I completed can be found in my [[Aporras1_Week_8]] journal.

Moving into Week 10, I performed STEM high level analysis on the ANOVA data in order to generate gene clusters which presented similar expression over the course of the experiment. Seven significant clusters were generated and the GOlists & genelists were saved and uploaded to the wiki for later analysis. I read and interpreted 6 GOlist terms found in the GOlist of Profile 22 and attempted to understand why the cell would be changing expression in genes associated with certain cell processes. The precise steps and outline of what I completed can be found in my [[Aporras1_Week_10]] journal.

In Week 11, I worked alongside [[User:Qlanners|Quinn Lanners]] to perform a literature search on yeast and cold shock to gain brief exposure to journal articles in this area of research and search engine qualities. The precise steps and outline can be found in my [[Aporras1_Week_11]] journal. The following week [[User:Qlanners|Quinn Lanners]] and I did more in-depth research on the specific journal article: Genome-wide analysis of the yeast transcriptome upon heat and cold shock (Becerra et al., 2003). We outlined the introduction, methods, procedure, analysis tools, and overall findings of the article before creating and presenting a presentation to the class which can be found in my [[Aporras1_Week_12]] journal along with the specific outline and approach to interpretation of their data.

In Week 14 and Week 15 I continued work from the Week 10 data analysis and selected profile 22 of dZAP1 from STEM analysis. I then generated a list of significant transcription factors which targeted genes within the genelist provided by STEM and further used those transcription factors to create a regulatory network. This network was actually determined to be too large and [[User:kdahlquist|Dr. Dahlquist]] trimmed down the network to 15 transcription factors. The network was then put into GRNsight to visualize the regulation pathways. MATLAB was also used to generate an output which would allow for GRNsight to display the direction of regulation and the magnitude with colors and bold/thin regulation arrows. A more detailed outline for the process can be found in my [[Aporras1_Week_14]] journal.

Once I completed all the analysis, I then put the data onto the deliverables page, presentation, and the final paper along with my analysis. These files can be found in [[JASPAR_the_Friendly_Ghost_Final_Deliverables]]. I was primarily responsible for maintaining extreme care with the files and keeping a very well-kept record of data. In addition I worked closely with [[User:Qlanners|Quinn Lanners]] to complete the final paper and aid in any way possible once I completed my data calculations and subsequent analysis. A more detailed outline for the process can be found in my [[Aporras1_Week_15]] journal.

=== Assessment of Project ===

'''2. Give an objective assessment of the success of your project workflow and teamwork.'''

I would say the overall project workflow and teamwork was fairly cohesive considering our different academic backgrounds and schedules. Given this time of the year, with final exams, we did very well to meet outside of class and work in the lab while communicating constantly. My workflow didn't impede the workflow of anyone else throughout the project and it was definitely a good feeling to have throughout working on the project as I attempted to complete everything ahead of time and work on group deliverables before my own.

'''3. What worked and what didn't work?'''

What didn't work was, or at least I didn't fully accept, was the need for both a paper and a presentation. I felt as though it became repetitive when examining both the paper and the introduction. With regards to the team, there weren't any aspects that didn't work, except I wish I would have had a better understanding of the role of the coders and their work through JASPAR. It took a lot of curiosity and asking to figure it out rather than being explained it in the beginning.

'''4. What would you do differently if you could do it all over again?'''

I definitely wish I had the same good data record keeping skills that I have currently because it would have saved a lot of time throughout the semester.

'''5. Evaluate your team’s portion of the GRNsight Gene Page Project and Group Report in the following areas:'''

'''* Content: What is the quality of the work?'''

From my understanding of the coders, they put their best foot forward in terms of working in a new area in which they hadn't worked in before. As data analyst I had context and prior understanding of my analysis but for them they had to work with a completely new database, JASPAR. Quinn created a structure by which every aspect was planned out and made it easy to keep track of deadlines and goals. Overall, while also considering the amount of time spent throughout these last few weeks and paying attention to very specific details, JASPAR the Friendly Ghost did their best to complete what was assigned. Again, while paying attention to copious details.

'''* Organization: Comment on the organization of the project and of your group's wiki pages.'''

As I mentioned earlier, Quinn structured the page easily so that even I could go ahead and add sections because we all understood the intuitive layout. I kept detailed file records and explained any changes I made to the data while also maintaining a detailed electronic notebook every single week.

'''* Completeness: Did your team achieve all of the project objectives? Why or why not?'''

To the best of my knowledge, we did. We would go through the deliverables page line by line checking tasks off in order to ensure that our product was as complete as it could be. Of course its not perfect, but considering the amount of details and time given, we put a significant amount of time into the project and displaying documentation throughout.

=== Reflection on the Process ===

What did you learn?

'''With your head (biological or computer science principles)'''
I definitely have much better data management than I did at the beginning of the course and the ability to organize thoughts for someone else to read and replicate the processes I completed throughout the semester. Ultimately, synthesizing replicable data and thus very detailed step by step notes. In terms of biology I didn't take as much because we didn't go very much in depth but now I have a better understanding of how to interpret more intricate data sets and understand the context at least in respect to microarray data.

'''With your heart (personal qualities and teamwork qualities that make things work or not work)?'''
Simply working hard.. and early! It made a huge difference in my workflow to finish assignments ahead of time (prior journal entries may not display this). Instead of waiting for deadlines I found an ethic to attack them to account for time where I was met with difficulties or setbacks (e.g. having to trim down my regulation network) and these setbacks didn't do as much damage because I met them so early before the deadline.

'''With your hands (technical skills)?'''
I've been around computers for a very long time so I didn't really gain any technical skills besides knowing how I work best. I came to the lab because the screens were bigger and I usually used two monitors to save time going in between the assignment Page, individual page, and datasets. This greatly improved my workflow and provided structure which I thrive from.

'''What lesson will you take away from this project that you will still use a year from now?'''
Recognizing how I work best. As soon as I recognized how I work best (e.g. working with multiple monitors or working on assignments early) I was able to improve my efficiency as the assignments got more difficult. Lastly, data management and organization. Organization with respect to files made the process much easier than if I hadn't learned to be descriptive with file names or have multiple backups and a notepad with a filename and description. These organizational techniques were vital and will be useful in future environments where data is often more digital than it is paper.

==Acknowledgements==
#Copied the structure of the sections in my assessment and reflection from the [[GRNsight_Gene_Page_Project_Deliverables|Deliverables Page]].

==References==

[[Category:Journal Entry]]

Aporras1 Individual Assessment and Reflection

2017-12-15T21:49:50Z

Aporras1: /* Assessment of Project */ formatting numbering and bold

Aporras1 Individual Assessment and Reflection

2017-12-15T21:46:51Z

Aporras1: /* Assessment of Project */ assessment

Aporras1 Individual Assessment and Reflection

2017-12-15T21:32:54Z

Aporras1: /* Statement of Work */ adding more detail and formatting edits

Aporras1 Individual Assessment and Reflection

2017-12-15T21:30:01Z

Aporras1: /* Statement of Work */ statement of work

JASPAR the Friendly Ghost Final Deliverables

2017-12-15T19:00:49Z

Aporras1: /* Individual statements of work, assessments, reflections */ fixed link to individual response

==Group Report==
==Individual statements of work, assessments, reflections==
[[QLanners_individual_statement|Quinn Lanners]] | [[Aporras1_Individual_Assessment_and_Reflection|Antonio Porras]] | [[Ebachour_individual_statement|Edward Bachoura]] | [[simonwro120 individual statement|Simon Wroblewski]]

==Group PowerPoint presentation==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf | Final Group Presentation (pdf)]] | December 11, 2017
==Code==
==README that summarizes the functionality of your team's new feature==
==Excel spreadsheet with ANOVA results/stem formatting==
[[Media:AP dZAP1 stem.xlsx]]
==PowerPoint of screenshots of stem results==
[[Media:AP dZAP1 STEM Screenshots & p-values.zip]]
==Gene List and GO List files from each significant profile==
[[Media:AP dZAP1 GOlist and genelist for profiles.zip]]
==YEASTRACT "rank by TF" results==
[[Media:AP YEASTRACT Transcription Factors.xlsx]]
==GRNmap input workbook==
[[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]]
==GRNmap output workbook==
[[Media:15-gene 44-edge teamJASPAR Sigmoid estimation output.xlsx]]
*Expression vs. Time Images generated from MATLAB: [[Media:Output Images from 15-gene 44-edge teamJASPAR Sigmoid estimation.zip]]
==Electronic notebooks corresponding to the microarray results files==
#[[Aporras1 Week 8]]
#[[Aporras1 Week 10]]
#[[Aporras1 Week 14]]
#[[Aporras1 Week 15]]

==Team Links==

{{Template:JASPAR the Friendly Ghost Links}}
===Team Signatures===
*[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 20:49, 13 December 2017 (PST)

==Class Links==

{{Template:GRNsight Gene Page Project Links}}

JASPAR the Friendly Ghost

2017-12-15T18:55:41Z

Aporras1: /* Week 15 */ antonio's week 15 references

==GRNsight Gene Page Project Deliverables==
[[JASPAR_the_Friendly_Ghost_Final_Deliverables|JASPAR the Friendly Ghost Final GRNsight Deliverables Page]]
==Working Deliverables==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf|Final Group Presentation]] | December 11, 2017 
[[Media:Genome-wide_analysis_of_the_yeast_transcriptome_upon_heat_and_cold_shock._QL_AP.zip|Antonio and Quinn Journal Club Presentation]] | November 21, 2017 
[[Media:e_and_s_presentation_2.pdf|Eddie and Simon Chapter 6 Presentation]] | November 14, 2017 
[https://github.com/bhamilton18/GRNsight GitHub fork] 
[https://github.com/bhamilton18/GRNsight/tree/gene-database-apis GitHub api branch] (in collaboration with [[Gene_hAPI|Gene_hAPI team]])
==Working Files==

===Antonio's Working Files===
# Gene list for profile 22 of dZAP1 Excel file: [[Media:AP dZAP1 profile22 genelist.xlsx]]
# YEASTRACT Transcription Factor Data: [[Media:AP YEASTRACT Transcription Factors.xlsx]]
# YEASTRACT Regulation Matrix Profile: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix: [[Media:AP Adjacency Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix with Network for GRNsight: [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]]

==Calendar==
{| class ="wikitable"
|+November & December
|-
|Sunday
|Monday
|Tuesday
|Wednesday
|Thursday
|Friday
|Saturday
|-
|
|
|
|'''1'''
|'''2'''
|'''3'''
|'''4'''
|-
|'''5'''
|'''6'''
|'''7'''
|'''8'''
|'''9'''
|'''10'''
|'''11'''
|-
|'''12'''
|'''13'''
|'''14''' C: PPT Presentation PM/DA: Journal Articles
|'''15'''
|'''16'''
|'''17'''
|'''18'''
|-
|'''19'''
|'''20'''
|'''21''' C: Complete setup steps (Milestones 1-3) PM/DA: Journal Club Presentations
|'''22''' ''Thanksgiving Break''
|'''23''' ''Thanksgiving Break''
|'''24''' ''Thanksgiving Break''
|'''25'''
|-
|'''26'''
|'''27'''
|'''28''' C: Fimilariaze self with file structure PM: Chose application data fields from JASPAR DA: Review ANOVA Results
|'''29'''
|'''30''' C: Tests for API PM: Share info to be used from JASPAR with other teams DA: Determine transcription factors, develop candidate gene reg network, and fix edits from week 8 & 10
|'''1'''
|'''2'''
|-
|'''3'''
|'''4'''
|'''5''' C: Retrieval code for API PM: Begin Final Group Paper and PPT DA:Model gene reg network Visualize Results
|'''6'''
|'''7''' C: Review and Test Code PM: Review and Test code PM&DA:Work on Paper and PPT
|'''8'''
|'''9''' Complete Group PPT
|-
|'''10''' Practice Group Presentation
|'''11''' Final group Presentation ''2:00-4:00PM''
|'''12'''
|'''13''' Final Group Paper Completely Written
|'''14''' Edit Final Group Paper
|'''15''' All deliverables due ''4:30PM''
|'''16'''
|}

==Executive Summaries==

===Week 11===

====Quinn's Executive Summary====
Created citations for two entries in the annotated bibliography for papers that report microarray data from yeast subjected to cold shock: 
Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6 
Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301 
Also completed a search activity to compare the results found from PubMed, GoogleScholar, and Web of Science using both basic and advanced search tools. 
Individual Journal Page: [[QLanners Week 11]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Executive Summary====
For this assignment, I spent most of my time reading and re-reading Paul Ford's article on how apps are made. It was chapter 6 in a larger work called ''What is Code?'' After absorbing the information laid out in this chapter, Eddie and I made a presentation about it. The presentation summarizes the article, which is about technique, methods, practices, and tools that expedite and simplify the programming process. In addition to making the presentation, I finished my 10 terms and made an outline for the article on my individual journal page. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 13:45, 14 November 2017 (PST)

====Antonio's Executive Summary====

Created two citations for the bibliography for the following articles:

#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.

I also completed the basic keyword searches on PubMed, Google Scholar, and Web of Science along with the advanced searches and the respective results. Lastly, I completed the prospective searches and collected the results of how many articles the article cites and how many articles cite the article. Totaling to the 3 articles.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 15:51, 14 November 2017 (PST)

Individual Journal Week 11: [[Aporras1_Week_11|Aporras1 Week 11]]

====Eddie Bachoura's Executive Summary====
This week, I spent my time for this class reading the Paul Ford article, chapter 6, which was about how to write applications and the modern practices and tools which are used to aid in cutting down some of the tedious nature of coding. Then, Simon and I spent the rest of the time working on our presentation. Team's progress: I believe that Simon and I worked well this weekend. The only issue that I found was that we didn't start until pretty late (Monday), but that was all at my own fault because I wasn't here for this weekend. We should fix that by starting earlier next weekend!

Individual Journal Week 11: [[Ebachour_Week_11|Eddie Bachoura Week 11]] 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:29, 13 November 2017 (PST)

===Week 12===

====Quinn's Executive Summary====
Worked closely with Antonio to summarize the results of the journal article Becerra et al. (2003) into a journal club presentation. In order to do so, we both completed the outline provided on the [[Week_12|Week 12]] assignment page on our wiki. We then took this information and used it to create our journal club presentations, which we practiced together and will share in class on Tuesday, November 21. 
Individual Journal Page: [[QLanners Week 12]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Executive Summary====
This week, I met with my coding partner [[User:Ebachour|Eddie Bachoura]] and he helped me clone the code that [[User:Bhamilton18|Blair Hamilton]] forked from the master branch.
After that, Eddie and I helped put together a list of milestones with dates that they should be completed. Using that, Quinn was able to put together a calendar like scheduale for our team to refer to. The last thing I did was open up the cloned files from Blair's fork on my text editor so that I could familiarize myself with the code. 
Individual Journal Page: [[simonwro120 Week 12]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:44, 20 November 2017 (PST)

====Antonio's Executive Summary====
Worked throughout the assignment with Quinn to complete the powerpoint presentation on the journal article: ''Genome-wide analysis of the yeast transcriptome upon heat and cold shock''. We both worked closely together on the outline of the article while maintaining our own style of completing the outline. We then practiced our presentation once the information was finalized and are looking forward to sharing on Tuesday the 21st of November.

Individual journal page: [[Aporras1_Week_12|Aporras 1 Week 12]]

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:19, 20 November 2017 (PST)
====Eddie Bachoura's Executive Summary====
This week, most of my time was spent setting up the branch on github and then getting my local version up and running so that I can write and test code on my own laptop. After that, I helped Simon out with doing the same. I also sent Quinn a list of our milestones for this project, as well as letting him know which ones were already completed. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 19:09, 20 November 2017 (PST) 
Week 12 Journal Page: [[ebachour_Week_12| Edward Bachoura]]

===Week 14===

====Quinn's Executive Summary====
This week, I worked closely with the other QAs and [[User:Kdahlquist|Dr. Dahlquist]] to determine what information should be pulled from each of the five databases. I then communicated this information to our coders. Along with this task, I worked communicated closely with both the data analyst and the coders to ensure that they were on track, and to make modifications to their respective milestones on the team calender. Finally, I added additional team milestones to the calendar to reflect all of the steps that need to be taken to complete the deliverables that we have due at the end of the semester. All of this progress can be seen in my [[QLanners_Week_14|individual weekly journal]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Executive Summary====
This week our coding group hit a bit of wall, not just for one, but for multiple reasons. One reason was caused by the fact that one of the coding group members worked in a language that would not be compatible with GRNsight. Another problem our coding group encountered was caused by a complexity in the the JASPAR API relating CORS (Cross-Oirgin Resource Sharing). Although these complications did occur, both me and Eddie B. know where the API guidelines are for JASPAR and what content we need to produce. In addition to that, an api file has been made as well which will be augmented soon. 
Individual Journal Page: [[simonwro120 Week 14]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:45, 4 December 2017 (PST)

====Antonio's Executive Summary====
This week, I made edits to both my individual [[Aporras1 Week 8]] and [[Aporras1 Week 10]] pages based from feedback received from [[User:Kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dionisio]]. The outline for these edits can be found on my [[Aporras1 Week 14]] page along with the continuation of the [[Week 10|Week 10]] assignment. In this continuation, I selected transcription factors from [[Media:AP dZAP1 profile22 genelist.xlsx]] and put them into YEASTRACT to find the most significant ones and found 49 significant transcription factors found in [[Media:AP YEASTRACT Transcription Factors.xlsx]]. Then I selected 22 of the most significant, 2 additional ones (HAP4 and GLN3) as instructed, to put back into YEASTRACT and create a regulation matrix uploaded as: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]. I then created a "network" worksheet, found in [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]], from the matrix and used GRNsight to generate a regulation network visualization: [[Media:AP Regulation Matrix profile22 GRNsight Network.PNG]]. These media downloads can also be found on my [[Aporras1 Week 14|Week 14]] journal entry in the
"Deliverables" section.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:31, 3 December 2017 (PST)

====Eddie's Executive Summary====
We've been working on JASPAR since the last assignment. As of this week, I am mostly sure that we have the two API calls that we need in order to be able to retrieve any Yeast gene database entry on JASPAR, using the gene ID. I would say that we are already done, but it seems that there are some access complications. I have a feeling it has something to do with CORS and I did some research to try to dix the issue. I found one work around, using a chrome extension, that allows me to bypass the issue, but I'm not sure that this solution will translate well to the actual GRNsight server, but I will discuss with Dondi tomorrow. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:25, 4 December 2017 (PST)

===Week 15===

====Quinn's Executive Summary====
This week, I worked closely will all of my teammates to coordinate the completion of all of the final deliverables. I met in person with my teammates on three seperate occasions to work on the final presentation. Furthermore, I delegated the tasks for our final group paper and completed my sections of the paper, along with running through the paper to ensure that we had met all of the requirements. Finally, I ensured that all of our group's deliverables were uploaded to the team page on time. 
All of this is outlined in depth on my [[QLanners_Week_15|individual weekly journal]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:13, 14 December 2017 (PST)

====Simon's Executive Summary====

====Antonio's Executive Summary====
I spent most of my efforts in the beginning of the week trimming down the network because it was too large. Once this was completed I was able to use MATLAB with the help of [[User:kdahlquist|Dr. Dahlquist]] and generate an output to put into GRNsight to visualize the regulation network with magnitude and direction of regulation. Once this was completed I began spending time on the presentation and the project deliverables. Gathering the deliverables, working on the presentation, and working on the final paper had many points of crossover which I became very familiar with my data and analysis. Once the presentation was completed, I spent the rest of my efforts checking off requirements for the deliverables on the team page and requirements for the paper to ensure it would be turned in on time. This work can be found in my [[Aporras1_Week_15|Week 15]] individual page along with details in terms of the progress throughout the week.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 10:38, 15 December 2017 (PST)

====Eddie's Executive Summary====

==Weekly Reflections==

===Week 11===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a good job of staying on task and working together to make sure that we both understood the whole assignment. So there was good communication between the Bibliography group.
#What didn't work?
#*I felt a bit disconnected with my other teammates Eddie and Simon. There was not very good communication with them about whether they needed any help and if they were on progress.
#What to improve upon going forward?
#*Going forward all of the members of the team need to do a better job of communicating. Also, we need to do a better job of properly communicating about how to fill out the team page ahead of time, so that we aren't frantically figuring that out last second. I will work to fix this by initiating communication earlier on in the week.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*Both me and Eddie were able to put together a powerpoint and present in time for the presentation date
#What didn't work?
#*Due to traveling, Eddie could not be back in LA to help with the project until Monday, which did not give us much time, resulting in our presentation being a bit late as far as submission on our wiki pages.
#How will to improve upon going forward?
#*Going forward I'd like to start early and finish early, that way we can be prepared for any unexpected complications. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
1. What worked? Quinn and I were able to get our work done on time without overlap. We communicated well.

2. What didn't work? Nothing specific prevented us from working efficiently.

3. What will I do next to fix what didn't work? Complete work ahead of time to be more thorough. Maintain a growth mindset.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:06, 20 November 2017 (PST)

====Eddie's Reflection====
Found in Week 11 summary ^^^

===Week 12===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a very good job of working ahead and getting our presentation done in a timely manner. In this way, we were able to ask the instructors any questions we had as they came up, and also allowed for ample time to practice.
#What didn't work?
#*Once again, I felt a bit disconnected from my other partners Eddie and Simon. While I texted Eddie a couple times about their progress, I still never got a chance to see exactly what they were doing.
#What to improve upon going forward?
#*While I feel like this will start to come together once we all start working on our assigned portion of the project together, we still do need to improve our communication between the coders and the PM/DA. In order to do so, I will make sure to continue to check base with each team member each day in class, and also text in the group message when I have questions for the whole team.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*With Eddie's help, we were both able to set up GRNsight on our laptops.
#What didn't work?
#*Nothing in specific stopped us from working efficiently.
#How will to improve upon going forward?
#*Going forward I'd like to get my summaries in earlier, as well as my individual page and reflections. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
#What worked?
#*Worked closely with Quinn and we kept regular contact through text as we worked through the assignment. Troubleshooting was easy as we were both very capable to take initiative and work to finish the presentation earlier rather than later in the time given.
#What didn't work?
#*I could definitely improve on mastering certain aspects of the assignment. I didn't really communicate with Eddie or Simon but I'd attribute that to having different assignments and parts to complete rather than a team issue.
#What to will I do next to fix what didn't work?
#*Communicate more. I'm hoping we'll have opportunities to work more closely together in the future.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:12, 20 November 2017 (PST)

====Eddie's Reflection====
# What worked?
#: Our work session was successful in setting up GRNsight on my laptop (again) and on Simon's.
# What didn't work?
#: Nothing :D
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 21:47, 20 November 2017 (PST)

===Week 14===

====Quinn's Reflection====
#What Worked?
#*This week our team did a much better job of communicating and keeping each other in the loop. Also, the collaboration between all of the QAs was a very effective way to determine which information should be pulled from each database
#What didn't work?
#*I was still a bit confused as to how all of the teams should be working together as we approach the end of the semester
#What will I do next to fix what didn't work>
#*I will make sure to ask about this concern in the next stand up review between the QAs. This will help clear this question up for me and the rest of the class. 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Reflection====
#What Worked?
#*Our class was able to produce a solid list of data items, specified to each database. This meant that as a coder for the JASPAR team, I knew which pieces of data to retrireve and produce from the JASPAR database.
#What didn't work?
#*There were some complications with the language some of the new code was written. There was also a problem with the JASPAR API relating to CORS (Cross-Oirgin Resource Sharing).
#What will I do next to fix what didn't work?
#*I hope to be more knowledgeable about these type of things in reference to computer science.
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:57, 4 December 2017 (PST)

====Antonio's Reflection====
# What worked? This week, I worked ahead and was able to complete, at least to my knowledge, this week's assignment ahead of time rather than waiting until the last minute. It was extremely helpful to have a group chat with the other data analysts as we had questions throughout the assignment.
# What didn't work? Everything seems to have run smoothly except I don't really know what the coders are assigned to do and most likely because it goes over my head.
# What will I do next to fix what didn't work? Try to see what the coders are doing, mostly out of curiosity.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:36, 3 December 2017 (PST)

====Eddie's Reflection====
#What worked?
#* We were able to figure out exactly how to extract the info we needed from JASPAR.
#What didn't work?
#* We originally had our own branch, but that didn't work out too well and it didn't make much sense when we were working in parallel to the gene-database-apis branch.
#How will to improve upon going forward?
#* We decided to merge our two branch which helped with this and kept us on the same page. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:25, 4 December 2017 (PST)

===Week 15===

====Quinn's Reflection====
#What worked?
#*We worked very well as a team on the final group presentation, meeting in person on multiple occasions to ensure that we were covering all of the content and everyone knew what they were going to say. This also allowed for this deliverable to be completed with plenty of time.
#What didn't work?
#*The final paper was a bit of a struggle with how busy everyone was towards the end of final week. It was incredibly hard to find any times to meet in person to collaborate, so we were forced to communicate through solely group texts to complete the paper. While we still were able to finish it, the collaboration was not as solid as it had been for the presentation (due to the fact that everyone was so busy)
#What will I do next time to fix what didn't work?
#*While there won't be a next time for this particular project, I will take note for future projects of how hard it is to find time for collaboration during busy times of the year and plan around this fact. 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:13, 14 December 2017 (PST)

====Simon's Reflection====

====Antonio's Reflection====
# What worked?
#* As a group, we worked very cohesively. The presentation and paper was especially important in terms of everyone being on the same page so we were able to meet on the weekend and outside of class prior to presenting and completing the paper.
# What didn't work?
#* The paper was very time consuming during the finals week and there was no shortage of material which needed to be covered and discussed. As a lab TA, I was able to work on my data analyst sections while editing formatting issues that arose but wish there were more details regarding formatting. We had to work on the paper through google doc which wasn't ideal but considering everyone's busy schedule it was the only option we had and communicated through text in addition.
# What will I do next time?
#* As with everything, finish with PLENTY of time. I've been able to significantly improve in this aspect over the course of the semester but having more time to complete assignments in case problems arise is always an advantage.

====Eddie's Reflection====

==Acknowledgements==
# A huge thank you to both [[User:kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dionisio]] for taking the time to teach this course and support us, the students, throughout the semester's challenges.
# The [[JASPAR_the_Friendly_Ghost|JASPAR The Friendly Ghost]] team for working as a cohesive unit.
# The Department of Biology at LMU
# The Department of Computer Science at LMU
# The entire class composed of students who we worked alongside throughout the semester.

==References==
===Week 11===
#LMU BioDB 2017. (2017). Week 11. Retrieved November 07, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_11
#Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301
#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.
#Top Integrated Development Environment index. (n.d.). Retrieved November 13, 2017, from http://pypl.github.io/IDE.html
#What is an API?. (2016). Retrieved November 13, 2017, from https://medium.freecodecamp.org/what-is-an-api-in-english-please-b880a3214a82
#What's the difference between an API vs SDK?. (2012). Retrieved November 13, 2017, from https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html
#Xcode. (2017). Retrieved November 13, 2017, from https://itunes.apple.com/us/app/xcode/id497799835
#What Is Code? (2015). Retrieved November 13, 2017, from https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made
#Shrinkwrapped Software. (n.d.). Retrieved November 13, 2017, from http://www.businessdictionary.com/definition/shrinkwrapped-software.html
#Web Application Framework. (2015). Retrieved November 13, 2017, from https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework

===Week 12===
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Anneal. (n.d.). ''Genscript''. Retrieved on November 19, 2017 from https://www.genscript.com/molecular-biology-glossary/11896/anneal
#Assay.(2005). ''Biology-Online''. Retrieved on November 19, 2017 http://www.biology-online.org/dictionary/Assay
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301
#Causton HC, Ren B, Koh SS, et al. 2001. Remodelling of yeast genome expression in response to environmental changes. Mol Biol Cell 12: 323–337.
#Chomczynski, P., & Sacchi, N. (1987). Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Analytical biochemistry, 162(1), 156-159.
#Cluster analysis. BusinessDictionary.com. Retrieved November 19, 2017, from BusinessDictionary.com website: http://www.businessdictionary.com/definition/cluster-analysis.html
#Consensus sequence | Definition of consensus sequence in English by Oxford Dictionaries. (n.d.). Retrieved November 20, 2017, from https://en.oxforddictionaries.com/definition/consensus_sequence
#Cyclins. (n.d.). ''BioNinja''. Retrieved on November 19, 2017 from http://ib.bioninja.com.au/standard-level/topic-1-cell-biology/16-cell-division/cyclins.html
#Differences between in vitro, in vivo, and in silico studies. (n.d.). Retrieved November 20, 2017, from https://mpkb.org/home/patients/assessing_literature/in_vitro_studies
#Donzeau M, Bourdineaud JP, Lauquin GJ. 1996. Regulation by low temperatures and anaerobiosis of a yeast gene specifying a putative GPI-anchored plasma membrane protein. Mol Microbiol 20: 449–459.
#Gasch AP, Spellman PT, Kao CM, et al. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11: 4241–4257.
#Glutathione. (n.d.). Retrieved November 20, 2017, from https://www.merriam-webster.com/dictionary/glutathione
#Haploid. (n.d.). Retrieved November 20, 2017, from http://www.biology-online.org/dictionary/Haploid
#HAW. (2011). Difference Between Haploid and Diploid. ''Difference Between.com''. Retrieved on November 19, 2017 from http://www.differencebetween.com/difference-between-haploid-and-vs-diploid/
#Hybridization. (2008). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Hybridization
#Kondo K, Inouye M. 1991. Cold-induction of yeast NSR1 protein and its role in pre-rRNA processing. J Biol Chem 267: 16 259–16 265.
#Kowalski LR, Kondo K, Inouye M. 1995. Cold-shock induction of a family of TIP1-related proteins associated with the membrane in Saccharomyces cerevisiae. Mol Microbiol 15: 341 – 353.
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Mai B, Breeden L. 1997. Xbp1, a stress-upregulated transcrip- tional repressor of the Saccharomyces cerevisae Swi4/Mbp1 family. Mol Cell Biol 17: 6491–6501.
#(n.d.). Retrieved November 19, 2017, from http://fg.cns.utexas.edu/fg/protocol%3A_YPD_plates.html
#(n.d.). Retrieved November 20, 2017, from https://www.nature.com/scitable/definition/diploid-310
#Oligonucleotide. (2014). ''News Medical Life Sciences''. Retrieved on November 19, 2017 from https://www.news-medical.net/life-sciences/What-is-an-Oligonucleotide.aspx
#Polypropylene. (n.d.). ''Dictionary.com''. Retrieved on November 19, 2017 from http://www.dictionary.com/browse/polypropylene
#Putative. (2014). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Putative
#Study.com. (2017). What is Annealing? - Definition, Biology & Process | Study.com. [online] Available at: http://study.com/academy/lesson/what-is-annealing-definition-biology-process.html [Accessed 21 Nov. 2017].
#Transcriptome. (n.d.). ''Nature''. Retrieved on November 19, 2017 from https://www.nature.com/scitable/definition/transcriptome-296
#Yelland, P. M. (2010). An introduction to correspondence analysis. Math. J, 12, 1-23.
#Young, F.W. (1999). Principle Components. ''forrest.psych.unc.edu''. Retrieved on November 19, 2017 from http://forrest.psych.unc.edu/research/vista-frames/help/lecturenotes/lecture13/biplot.html
#Zhang L, Ohta A, Horiuchi H, Takagi M, Imai R. 2001. Multiple mechanisms regulate expression of low temperature responsive (LOT) genes in Saccharomyces cerevisiae. Biochem Biophys Res Commun 283: 531 – 535.

===Week 14===
#Dahlquist, K. D., Dionisio, J. D. N., Fitzpatrick, B. G., Anguiano, N. A., Varshneya, A., Southwick, B. J., & Samdarshi, M. (2016). GRNsight: a web application and service for visualizing models of small-to medium-scale gene regulatory networks. PeerJ Computer Science, 2, e85.
#Ensembl. (2017). "Gene: HSF1". Retrieved November 28, 2017, from https://www.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YGL073W;r=VII:368753-371254;t=YGL073W 
#JASPAR. (2017). "Detailed information of matrix profile MA0319.1". Retrieved on November 28, 2017, from http://jaspar.genereg.net/matrix/MA0319.1/ 
#LMU BioDB 2017. (2017). Week 8. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_8
#LMU BioDB 2017. (2017). Week 10. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10
#LMU BioDB 2017. (2017). Week 14. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14 
#NCBI. (2017). "HSF1 stress-responsive transcription factor HSF1 [ Saccharomyces cerevisiae S288C ]". Retrieved November 28, 2017, from https://www.ncbi.nlm.nih.gov/gene/852806 
#Saccharomyces Genome Database. (2017). "HSF1 / YGL073W Overview". Retrieved November 28, 2017, from https://www.yeastgenome.org/locus/S000003041 
#Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.
#UniProt. (2017). "UniProtKB - P10961 (HSF_YEAST)". Retrieved November 28, 2017 from http://www.uniprot.org/uniprot/P10961

===Week 15===
#Dahlquist, K. D., Dionisio, J. D. N., Fitzpatrick, B. G., Anguiano, N. A., Varshneya, A., Southwick, B. J., & Samdarshi, M. (2016). GRNsight: a web application and service for visualizing models of small-to medium-scale gene regulatory networks. PeerJ Computer Science, 2, e85.
# LMU BioDB 2017. (2017). Week 15. Retrieved December 05, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15
# LMU BioDB 2017. (2017). GRNsight Gene Page Project Deliverables. Retrieved December 05, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/GRNsight_Gene_Page_Project_Deliverables
# Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.

==Team Links==

{{Template:JASPAR the Friendly Ghost Links}}

==Class Links==

{{Template:GRNsight Gene Page Project Links}}

JASPAR the Friendly Ghost

2017-12-15T18:54:56Z

Aporras1: /* Acknowledgements */ acknowledgements

==GRNsight Gene Page Project Deliverables==
[[JASPAR_the_Friendly_Ghost_Final_Deliverables|JASPAR the Friendly Ghost Final GRNsight Deliverables Page]]
==Working Deliverables==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf|Final Group Presentation]] | December 11, 2017 
[[Media:Genome-wide_analysis_of_the_yeast_transcriptome_upon_heat_and_cold_shock._QL_AP.zip|Antonio and Quinn Journal Club Presentation]] | November 21, 2017 
[[Media:e_and_s_presentation_2.pdf|Eddie and Simon Chapter 6 Presentation]] | November 14, 2017 
[https://github.com/bhamilton18/GRNsight GitHub fork] 
[https://github.com/bhamilton18/GRNsight/tree/gene-database-apis GitHub api branch] (in collaboration with [[Gene_hAPI|Gene_hAPI team]])
==Working Files==

===Antonio's Working Files===
# Gene list for profile 22 of dZAP1 Excel file: [[Media:AP dZAP1 profile22 genelist.xlsx]]
# YEASTRACT Transcription Factor Data: [[Media:AP YEASTRACT Transcription Factors.xlsx]]
# YEASTRACT Regulation Matrix Profile: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix: [[Media:AP Adjacency Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix with Network for GRNsight: [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]]

==Calendar==
{| class ="wikitable"
|+November & December
|-
|Sunday
|Monday
|Tuesday
|Wednesday
|Thursday
|Friday
|Saturday
|-
|
|
|
|'''1'''
|'''2'''
|'''3'''
|'''4'''
|-
|'''5'''
|'''6'''
|'''7'''
|'''8'''
|'''9'''
|'''10'''
|'''11'''
|-
|'''12'''
|'''13'''
|'''14''' C: PPT Presentation PM/DA: Journal Articles
|'''15'''
|'''16'''
|'''17'''
|'''18'''
|-
|'''19'''
|'''20'''
|'''21''' C: Complete setup steps (Milestones 1-3) PM/DA: Journal Club Presentations
|'''22''' ''Thanksgiving Break''
|'''23''' ''Thanksgiving Break''
|'''24''' ''Thanksgiving Break''
|'''25'''
|-
|'''26'''
|'''27'''
|'''28''' C: Fimilariaze self with file structure PM: Chose application data fields from JASPAR DA: Review ANOVA Results
|'''29'''
|'''30''' C: Tests for API PM: Share info to be used from JASPAR with other teams DA: Determine transcription factors, develop candidate gene reg network, and fix edits from week 8 & 10
|'''1'''
|'''2'''
|-
|'''3'''
|'''4'''
|'''5''' C: Retrieval code for API PM: Begin Final Group Paper and PPT DA:Model gene reg network Visualize Results
|'''6'''
|'''7''' C: Review and Test Code PM: Review and Test code PM&DA:Work on Paper and PPT
|'''8'''
|'''9''' Complete Group PPT
|-
|'''10''' Practice Group Presentation
|'''11''' Final group Presentation ''2:00-4:00PM''
|'''12'''
|'''13''' Final Group Paper Completely Written
|'''14''' Edit Final Group Paper
|'''15''' All deliverables due ''4:30PM''
|'''16'''
|}

==Executive Summaries==

===Week 11===

====Quinn's Executive Summary====
Created citations for two entries in the annotated bibliography for papers that report microarray data from yeast subjected to cold shock: 
Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6 
Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301 
Also completed a search activity to compare the results found from PubMed, GoogleScholar, and Web of Science using both basic and advanced search tools. 
Individual Journal Page: [[QLanners Week 11]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Executive Summary====
For this assignment, I spent most of my time reading and re-reading Paul Ford's article on how apps are made. It was chapter 6 in a larger work called ''What is Code?'' After absorbing the information laid out in this chapter, Eddie and I made a presentation about it. The presentation summarizes the article, which is about technique, methods, practices, and tools that expedite and simplify the programming process. In addition to making the presentation, I finished my 10 terms and made an outline for the article on my individual journal page. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 13:45, 14 November 2017 (PST)

====Antonio's Executive Summary====

Created two citations for the bibliography for the following articles:

#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.

I also completed the basic keyword searches on PubMed, Google Scholar, and Web of Science along with the advanced searches and the respective results. Lastly, I completed the prospective searches and collected the results of how many articles the article cites and how many articles cite the article. Totaling to the 3 articles.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 15:51, 14 November 2017 (PST)

Individual Journal Week 11: [[Aporras1_Week_11|Aporras1 Week 11]]

====Eddie Bachoura's Executive Summary====
This week, I spent my time for this class reading the Paul Ford article, chapter 6, which was about how to write applications and the modern practices and tools which are used to aid in cutting down some of the tedious nature of coding. Then, Simon and I spent the rest of the time working on our presentation. Team's progress: I believe that Simon and I worked well this weekend. The only issue that I found was that we didn't start until pretty late (Monday), but that was all at my own fault because I wasn't here for this weekend. We should fix that by starting earlier next weekend!

Individual Journal Week 11: [[Ebachour_Week_11|Eddie Bachoura Week 11]] 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:29, 13 November 2017 (PST)

===Week 12===

====Quinn's Executive Summary====
Worked closely with Antonio to summarize the results of the journal article Becerra et al. (2003) into a journal club presentation. In order to do so, we both completed the outline provided on the [[Week_12|Week 12]] assignment page on our wiki. We then took this information and used it to create our journal club presentations, which we practiced together and will share in class on Tuesday, November 21. 
Individual Journal Page: [[QLanners Week 12]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Executive Summary====
This week, I met with my coding partner [[User:Ebachour|Eddie Bachoura]] and he helped me clone the code that [[User:Bhamilton18|Blair Hamilton]] forked from the master branch.
After that, Eddie and I helped put together a list of milestones with dates that they should be completed. Using that, Quinn was able to put together a calendar like scheduale for our team to refer to. The last thing I did was open up the cloned files from Blair's fork on my text editor so that I could familiarize myself with the code. 
Individual Journal Page: [[simonwro120 Week 12]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:44, 20 November 2017 (PST)

====Antonio's Executive Summary====
Worked throughout the assignment with Quinn to complete the powerpoint presentation on the journal article: ''Genome-wide analysis of the yeast transcriptome upon heat and cold shock''. We both worked closely together on the outline of the article while maintaining our own style of completing the outline. We then practiced our presentation once the information was finalized and are looking forward to sharing on Tuesday the 21st of November.

Individual journal page: [[Aporras1_Week_12|Aporras 1 Week 12]]

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:19, 20 November 2017 (PST)
====Eddie Bachoura's Executive Summary====
This week, most of my time was spent setting up the branch on github and then getting my local version up and running so that I can write and test code on my own laptop. After that, I helped Simon out with doing the same. I also sent Quinn a list of our milestones for this project, as well as letting him know which ones were already completed. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 19:09, 20 November 2017 (PST) 
Week 12 Journal Page: [[ebachour_Week_12| Edward Bachoura]]

===Week 14===

====Quinn's Executive Summary====
This week, I worked closely with the other QAs and [[User:Kdahlquist|Dr. Dahlquist]] to determine what information should be pulled from each of the five databases. I then communicated this information to our coders. Along with this task, I worked communicated closely with both the data analyst and the coders to ensure that they were on track, and to make modifications to their respective milestones on the team calender. Finally, I added additional team milestones to the calendar to reflect all of the steps that need to be taken to complete the deliverables that we have due at the end of the semester. All of this progress can be seen in my [[QLanners_Week_14|individual weekly journal]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Executive Summary====
This week our coding group hit a bit of wall, not just for one, but for multiple reasons. One reason was caused by the fact that one of the coding group members worked in a language that would not be compatible with GRNsight. Another problem our coding group encountered was caused by a complexity in the the JASPAR API relating CORS (Cross-Oirgin Resource Sharing). Although these complications did occur, both me and Eddie B. know where the API guidelines are for JASPAR and what content we need to produce. In addition to that, an api file has been made as well which will be augmented soon. 
Individual Journal Page: [[simonwro120 Week 14]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:45, 4 December 2017 (PST)

====Antonio's Executive Summary====
This week, I made edits to both my individual [[Aporras1 Week 8]] and [[Aporras1 Week 10]] pages based from feedback received from [[User:Kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dionisio]]. The outline for these edits can be found on my [[Aporras1 Week 14]] page along with the continuation of the [[Week 10|Week 10]] assignment. In this continuation, I selected transcription factors from [[Media:AP dZAP1 profile22 genelist.xlsx]] and put them into YEASTRACT to find the most significant ones and found 49 significant transcription factors found in [[Media:AP YEASTRACT Transcription Factors.xlsx]]. Then I selected 22 of the most significant, 2 additional ones (HAP4 and GLN3) as instructed, to put back into YEASTRACT and create a regulation matrix uploaded as: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]. I then created a "network" worksheet, found in [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]], from the matrix and used GRNsight to generate a regulation network visualization: [[Media:AP Regulation Matrix profile22 GRNsight Network.PNG]]. These media downloads can also be found on my [[Aporras1 Week 14|Week 14]] journal entry in the
"Deliverables" section.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:31, 3 December 2017 (PST)

====Eddie's Executive Summary====
We've been working on JASPAR since the last assignment. As of this week, I am mostly sure that we have the two API calls that we need in order to be able to retrieve any Yeast gene database entry on JASPAR, using the gene ID. I would say that we are already done, but it seems that there are some access complications. I have a feeling it has something to do with CORS and I did some research to try to dix the issue. I found one work around, using a chrome extension, that allows me to bypass the issue, but I'm not sure that this solution will translate well to the actual GRNsight server, but I will discuss with Dondi tomorrow. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:25, 4 December 2017 (PST)

===Week 15===

====Quinn's Executive Summary====
This week, I worked closely will all of my teammates to coordinate the completion of all of the final deliverables. I met in person with my teammates on three seperate occasions to work on the final presentation. Furthermore, I delegated the tasks for our final group paper and completed my sections of the paper, along with running through the paper to ensure that we had met all of the requirements. Finally, I ensured that all of our group's deliverables were uploaded to the team page on time. 
All of this is outlined in depth on my [[QLanners_Week_15|individual weekly journal]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:13, 14 December 2017 (PST)

====Simon's Executive Summary====

====Antonio's Executive Summary====
I spent most of my efforts in the beginning of the week trimming down the network because it was too large. Once this was completed I was able to use MATLAB with the help of [[User:kdahlquist|Dr. Dahlquist]] and generate an output to put into GRNsight to visualize the regulation network with magnitude and direction of regulation. Once this was completed I began spending time on the presentation and the project deliverables. Gathering the deliverables, working on the presentation, and working on the final paper had many points of crossover which I became very familiar with my data and analysis. Once the presentation was completed, I spent the rest of my efforts checking off requirements for the deliverables on the team page and requirements for the paper to ensure it would be turned in on time. This work can be found in my [[Aporras1_Week_15|Week 15]] individual page along with details in terms of the progress throughout the week.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 10:38, 15 December 2017 (PST)

====Eddie's Executive Summary====

==Weekly Reflections==

===Week 11===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a good job of staying on task and working together to make sure that we both understood the whole assignment. So there was good communication between the Bibliography group.
#What didn't work?
#*I felt a bit disconnected with my other teammates Eddie and Simon. There was not very good communication with them about whether they needed any help and if they were on progress.
#What to improve upon going forward?
#*Going forward all of the members of the team need to do a better job of communicating. Also, we need to do a better job of properly communicating about how to fill out the team page ahead of time, so that we aren't frantically figuring that out last second. I will work to fix this by initiating communication earlier on in the week.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*Both me and Eddie were able to put together a powerpoint and present in time for the presentation date
#What didn't work?
#*Due to traveling, Eddie could not be back in LA to help with the project until Monday, which did not give us much time, resulting in our presentation being a bit late as far as submission on our wiki pages.
#How will to improve upon going forward?
#*Going forward I'd like to start early and finish early, that way we can be prepared for any unexpected complications. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
1. What worked? Quinn and I were able to get our work done on time without overlap. We communicated well.

2. What didn't work? Nothing specific prevented us from working efficiently.

3. What will I do next to fix what didn't work? Complete work ahead of time to be more thorough. Maintain a growth mindset.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:06, 20 November 2017 (PST)

====Eddie's Reflection====
Found in Week 11 summary ^^^

===Week 12===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a very good job of working ahead and getting our presentation done in a timely manner. In this way, we were able to ask the instructors any questions we had as they came up, and also allowed for ample time to practice.
#What didn't work?
#*Once again, I felt a bit disconnected from my other partners Eddie and Simon. While I texted Eddie a couple times about their progress, I still never got a chance to see exactly what they were doing.
#What to improve upon going forward?
#*While I feel like this will start to come together once we all start working on our assigned portion of the project together, we still do need to improve our communication between the coders and the PM/DA. In order to do so, I will make sure to continue to check base with each team member each day in class, and also text in the group message when I have questions for the whole team.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*With Eddie's help, we were both able to set up GRNsight on our laptops.
#What didn't work?
#*Nothing in specific stopped us from working efficiently.
#How will to improve upon going forward?
#*Going forward I'd like to get my summaries in earlier, as well as my individual page and reflections. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
#What worked?
#*Worked closely with Quinn and we kept regular contact through text as we worked through the assignment. Troubleshooting was easy as we were both very capable to take initiative and work to finish the presentation earlier rather than later in the time given.
#What didn't work?
#*I could definitely improve on mastering certain aspects of the assignment. I didn't really communicate with Eddie or Simon but I'd attribute that to having different assignments and parts to complete rather than a team issue.
#What to will I do next to fix what didn't work?
#*Communicate more. I'm hoping we'll have opportunities to work more closely together in the future.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:12, 20 November 2017 (PST)

====Eddie's Reflection====
# What worked?
#: Our work session was successful in setting up GRNsight on my laptop (again) and on Simon's.
# What didn't work?
#: Nothing :D
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 21:47, 20 November 2017 (PST)

===Week 14===

====Quinn's Reflection====
#What Worked?
#*This week our team did a much better job of communicating and keeping each other in the loop. Also, the collaboration between all of the QAs was a very effective way to determine which information should be pulled from each database
#What didn't work?
#*I was still a bit confused as to how all of the teams should be working together as we approach the end of the semester
#What will I do next to fix what didn't work>
#*I will make sure to ask about this concern in the next stand up review between the QAs. This will help clear this question up for me and the rest of the class. 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Reflection====
#What Worked?
#*Our class was able to produce a solid list of data items, specified to each database. This meant that as a coder for the JASPAR team, I knew which pieces of data to retrireve and produce from the JASPAR database.
#What didn't work?
#*There were some complications with the language some of the new code was written. There was also a problem with the JASPAR API relating to CORS (Cross-Oirgin Resource Sharing).
#What will I do next to fix what didn't work?
#*I hope to be more knowledgeable about these type of things in reference to computer science.
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:57, 4 December 2017 (PST)

====Antonio's Reflection====
# What worked? This week, I worked ahead and was able to complete, at least to my knowledge, this week's assignment ahead of time rather than waiting until the last minute. It was extremely helpful to have a group chat with the other data analysts as we had questions throughout the assignment.
# What didn't work? Everything seems to have run smoothly except I don't really know what the coders are assigned to do and most likely because it goes over my head.
# What will I do next to fix what didn't work? Try to see what the coders are doing, mostly out of curiosity.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:36, 3 December 2017 (PST)

====Eddie's Reflection====
#What worked?
#* We were able to figure out exactly how to extract the info we needed from JASPAR.
#What didn't work?
#* We originally had our own branch, but that didn't work out too well and it didn't make much sense when we were working in parallel to the gene-database-apis branch.
#How will to improve upon going forward?
#* We decided to merge our two branch which helped with this and kept us on the same page. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:25, 4 December 2017 (PST)

===Week 15===

====Quinn's Reflection====
#What worked?
#*We worked very well as a team on the final group presentation, meeting in person on multiple occasions to ensure that we were covering all of the content and everyone knew what they were going to say. This also allowed for this deliverable to be completed with plenty of time.
#What didn't work?
#*The final paper was a bit of a struggle with how busy everyone was towards the end of final week. It was incredibly hard to find any times to meet in person to collaborate, so we were forced to communicate through solely group texts to complete the paper. While we still were able to finish it, the collaboration was not as solid as it had been for the presentation (due to the fact that everyone was so busy)
#What will I do next time to fix what didn't work?
#*While there won't be a next time for this particular project, I will take note for future projects of how hard it is to find time for collaboration during busy times of the year and plan around this fact. 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:13, 14 December 2017 (PST)

====Simon's Reflection====

====Antonio's Reflection====
# What worked?
#* As a group, we worked very cohesively. The presentation and paper was especially important in terms of everyone being on the same page so we were able to meet on the weekend and outside of class prior to presenting and completing the paper.
# What didn't work?
#* The paper was very time consuming during the finals week and there was no shortage of material which needed to be covered and discussed. As a lab TA, I was able to work on my data analyst sections while editing formatting issues that arose but wish there were more details regarding formatting. We had to work on the paper through google doc which wasn't ideal but considering everyone's busy schedule it was the only option we had and communicated through text in addition.
# What will I do next time?
#* As with everything, finish with PLENTY of time. I've been able to significantly improve in this aspect over the course of the semester but having more time to complete assignments in case problems arise is always an advantage.

====Eddie's Reflection====

==Acknowledgements==
# A huge thank you to both [[User:kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dionisio]] for taking the time to teach this course and support us, the students, throughout the semester's challenges.
# The [[JASPAR_the_Friendly_Ghost|JASPAR The Friendly Ghost]] team for working as a cohesive unit.
# The Department of Biology at LMU
# The Department of Computer Science at LMU
# The entire class composed of students who we worked alongside throughout the semester.

==References==
===Week 11===
#LMU BioDB 2017. (2017). Week 11. Retrieved November 07, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_11
#Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301
#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.
#Top Integrated Development Environment index. (n.d.). Retrieved November 13, 2017, from http://pypl.github.io/IDE.html
#What is an API?. (2016). Retrieved November 13, 2017, from https://medium.freecodecamp.org/what-is-an-api-in-english-please-b880a3214a82
#What's the difference between an API vs SDK?. (2012). Retrieved November 13, 2017, from https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html
#Xcode. (2017). Retrieved November 13, 2017, from https://itunes.apple.com/us/app/xcode/id497799835
#What Is Code? (2015). Retrieved November 13, 2017, from https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made
#Shrinkwrapped Software. (n.d.). Retrieved November 13, 2017, from http://www.businessdictionary.com/definition/shrinkwrapped-software.html
#Web Application Framework. (2015). Retrieved November 13, 2017, from https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework

===Week 12===
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Anneal. (n.d.). ''Genscript''. Retrieved on November 19, 2017 from https://www.genscript.com/molecular-biology-glossary/11896/anneal
#Assay.(2005). ''Biology-Online''. Retrieved on November 19, 2017 http://www.biology-online.org/dictionary/Assay
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301
#Causton HC, Ren B, Koh SS, et al. 2001. Remodelling of yeast genome expression in response to environmental changes. Mol Biol Cell 12: 323–337.
#Chomczynski, P., & Sacchi, N. (1987). Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Analytical biochemistry, 162(1), 156-159.
#Cluster analysis. BusinessDictionary.com. Retrieved November 19, 2017, from BusinessDictionary.com website: http://www.businessdictionary.com/definition/cluster-analysis.html
#Consensus sequence | Definition of consensus sequence in English by Oxford Dictionaries. (n.d.). Retrieved November 20, 2017, from https://en.oxforddictionaries.com/definition/consensus_sequence
#Cyclins. (n.d.). ''BioNinja''. Retrieved on November 19, 2017 from http://ib.bioninja.com.au/standard-level/topic-1-cell-biology/16-cell-division/cyclins.html
#Differences between in vitro, in vivo, and in silico studies. (n.d.). Retrieved November 20, 2017, from https://mpkb.org/home/patients/assessing_literature/in_vitro_studies
#Donzeau M, Bourdineaud JP, Lauquin GJ. 1996. Regulation by low temperatures and anaerobiosis of a yeast gene specifying a putative GPI-anchored plasma membrane protein. Mol Microbiol 20: 449–459.
#Gasch AP, Spellman PT, Kao CM, et al. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11: 4241–4257.
#Glutathione. (n.d.). Retrieved November 20, 2017, from https://www.merriam-webster.com/dictionary/glutathione
#Haploid. (n.d.). Retrieved November 20, 2017, from http://www.biology-online.org/dictionary/Haploid
#HAW. (2011). Difference Between Haploid and Diploid. ''Difference Between.com''. Retrieved on November 19, 2017 from http://www.differencebetween.com/difference-between-haploid-and-vs-diploid/
#Hybridization. (2008). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Hybridization
#Kondo K, Inouye M. 1991. Cold-induction of yeast NSR1 protein and its role in pre-rRNA processing. J Biol Chem 267: 16 259–16 265.
#Kowalski LR, Kondo K, Inouye M. 1995. Cold-shock induction of a family of TIP1-related proteins associated with the membrane in Saccharomyces cerevisiae. Mol Microbiol 15: 341 – 353.
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Mai B, Breeden L. 1997. Xbp1, a stress-upregulated transcrip- tional repressor of the Saccharomyces cerevisae Swi4/Mbp1 family. Mol Cell Biol 17: 6491–6501.
#(n.d.). Retrieved November 19, 2017, from http://fg.cns.utexas.edu/fg/protocol%3A_YPD_plates.html
#(n.d.). Retrieved November 20, 2017, from https://www.nature.com/scitable/definition/diploid-310
#Oligonucleotide. (2014). ''News Medical Life Sciences''. Retrieved on November 19, 2017 from https://www.news-medical.net/life-sciences/What-is-an-Oligonucleotide.aspx
#Polypropylene. (n.d.). ''Dictionary.com''. Retrieved on November 19, 2017 from http://www.dictionary.com/browse/polypropylene
#Putative. (2014). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Putative
#Study.com. (2017). What is Annealing? - Definition, Biology & Process | Study.com. [online] Available at: http://study.com/academy/lesson/what-is-annealing-definition-biology-process.html [Accessed 21 Nov. 2017].
#Transcriptome. (n.d.). ''Nature''. Retrieved on November 19, 2017 from https://www.nature.com/scitable/definition/transcriptome-296
#Yelland, P. M. (2010). An introduction to correspondence analysis. Math. J, 12, 1-23.
#Young, F.W. (1999). Principle Components. ''forrest.psych.unc.edu''. Retrieved on November 19, 2017 from http://forrest.psych.unc.edu/research/vista-frames/help/lecturenotes/lecture13/biplot.html
#Zhang L, Ohta A, Horiuchi H, Takagi M, Imai R. 2001. Multiple mechanisms regulate expression of low temperature responsive (LOT) genes in Saccharomyces cerevisiae. Biochem Biophys Res Commun 283: 531 – 535.

===Week 14===
#Dahlquist, K. D., Dionisio, J. D. N., Fitzpatrick, B. G., Anguiano, N. A., Varshneya, A., Southwick, B. J., & Samdarshi, M. (2016). GRNsight: a web application and service for visualizing models of small-to medium-scale gene regulatory networks. PeerJ Computer Science, 2, e85.
#Ensembl. (2017). "Gene: HSF1". Retrieved November 28, 2017, from https://www.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YGL073W;r=VII:368753-371254;t=YGL073W 
#JASPAR. (2017). "Detailed information of matrix profile MA0319.1". Retrieved on November 28, 2017, from http://jaspar.genereg.net/matrix/MA0319.1/ 
#LMU BioDB 2017. (2017). Week 8. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_8
#LMU BioDB 2017. (2017). Week 10. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10
#LMU BioDB 2017. (2017). Week 14. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14 
#NCBI. (2017). "HSF1 stress-responsive transcription factor HSF1 [ Saccharomyces cerevisiae S288C ]". Retrieved November 28, 2017, from https://www.ncbi.nlm.nih.gov/gene/852806 
#Saccharomyces Genome Database. (2017). "HSF1 / YGL073W Overview". Retrieved November 28, 2017, from https://www.yeastgenome.org/locus/S000003041 
#Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.
#UniProt. (2017). "UniProtKB - P10961 (HSF_YEAST)". Retrieved November 28, 2017 from http://www.uniprot.org/uniprot/P10961

===Week 15===

==Team Links==

{{Template:JASPAR the Friendly Ghost Links}}

==Class Links==

{{Template:GRNsight Gene Page Project Links}}

JASPAR the Friendly Ghost

2017-12-15T18:49:43Z

Aporras1: /* Antonio's Reflection */ word choice edit

==GRNsight Gene Page Project Deliverables==
[[JASPAR_the_Friendly_Ghost_Final_Deliverables|JASPAR the Friendly Ghost Final GRNsight Deliverables Page]]
==Working Deliverables==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf|Final Group Presentation]] | December 11, 2017 
[[Media:Genome-wide_analysis_of_the_yeast_transcriptome_upon_heat_and_cold_shock._QL_AP.zip|Antonio and Quinn Journal Club Presentation]] | November 21, 2017 
[[Media:e_and_s_presentation_2.pdf|Eddie and Simon Chapter 6 Presentation]] | November 14, 2017 
[https://github.com/bhamilton18/GRNsight GitHub fork] 
[https://github.com/bhamilton18/GRNsight/tree/gene-database-apis GitHub api branch] (in collaboration with [[Gene_hAPI|Gene_hAPI team]])
==Working Files==

===Antonio's Working Files===
# Gene list for profile 22 of dZAP1 Excel file: [[Media:AP dZAP1 profile22 genelist.xlsx]]
# YEASTRACT Transcription Factor Data: [[Media:AP YEASTRACT Transcription Factors.xlsx]]
# YEASTRACT Regulation Matrix Profile: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix: [[Media:AP Adjacency Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix with Network for GRNsight: [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]]

==Calendar==
{| class ="wikitable"
|+November & December
|-
|Sunday
|Monday
|Tuesday
|Wednesday
|Thursday
|Friday
|Saturday
|-
|
|
|
|'''1'''
|'''2'''
|'''3'''
|'''4'''
|-
|'''5'''
|'''6'''
|'''7'''
|'''8'''
|'''9'''
|'''10'''
|'''11'''
|-
|'''12'''
|'''13'''
|'''14''' C: PPT Presentation PM/DA: Journal Articles
|'''15'''
|'''16'''
|'''17'''
|'''18'''
|-
|'''19'''
|'''20'''
|'''21''' C: Complete setup steps (Milestones 1-3) PM/DA: Journal Club Presentations
|'''22''' ''Thanksgiving Break''
|'''23''' ''Thanksgiving Break''
|'''24''' ''Thanksgiving Break''
|'''25'''
|-
|'''26'''
|'''27'''
|'''28''' C: Fimilariaze self with file structure PM: Chose application data fields from JASPAR DA: Review ANOVA Results
|'''29'''
|'''30''' C: Tests for API PM: Share info to be used from JASPAR with other teams DA: Determine transcription factors, develop candidate gene reg network, and fix edits from week 8 & 10
|'''1'''
|'''2'''
|-
|'''3'''
|'''4'''
|'''5''' C: Retrieval code for API PM: Begin Final Group Paper and PPT DA:Model gene reg network Visualize Results
|'''6'''
|'''7''' C: Review and Test Code PM: Review and Test code PM&DA:Work on Paper and PPT
|'''8'''
|'''9''' Complete Group PPT
|-
|'''10''' Practice Group Presentation
|'''11''' Final group Presentation ''2:00-4:00PM''
|'''12'''
|'''13''' Final Group Paper Completely Written
|'''14''' Edit Final Group Paper
|'''15''' All deliverables due ''4:30PM''
|'''16'''
|}

==Executive Summaries==

===Week 11===

====Quinn's Executive Summary====
Created citations for two entries in the annotated bibliography for papers that report microarray data from yeast subjected to cold shock: 
Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6 
Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301 
Also completed a search activity to compare the results found from PubMed, GoogleScholar, and Web of Science using both basic and advanced search tools. 
Individual Journal Page: [[QLanners Week 11]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Executive Summary====
For this assignment, I spent most of my time reading and re-reading Paul Ford's article on how apps are made. It was chapter 6 in a larger work called ''What is Code?'' After absorbing the information laid out in this chapter, Eddie and I made a presentation about it. The presentation summarizes the article, which is about technique, methods, practices, and tools that expedite and simplify the programming process. In addition to making the presentation, I finished my 10 terms and made an outline for the article on my individual journal page. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 13:45, 14 November 2017 (PST)

====Antonio's Executive Summary====

Created two citations for the bibliography for the following articles:

#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.

I also completed the basic keyword searches on PubMed, Google Scholar, and Web of Science along with the advanced searches and the respective results. Lastly, I completed the prospective searches and collected the results of how many articles the article cites and how many articles cite the article. Totaling to the 3 articles.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 15:51, 14 November 2017 (PST)

Individual Journal Week 11: [[Aporras1_Week_11|Aporras1 Week 11]]

====Eddie Bachoura's Executive Summary====
This week, I spent my time for this class reading the Paul Ford article, chapter 6, which was about how to write applications and the modern practices and tools which are used to aid in cutting down some of the tedious nature of coding. Then, Simon and I spent the rest of the time working on our presentation. Team's progress: I believe that Simon and I worked well this weekend. The only issue that I found was that we didn't start until pretty late (Monday), but that was all at my own fault because I wasn't here for this weekend. We should fix that by starting earlier next weekend!

Individual Journal Week 11: [[Ebachour_Week_11|Eddie Bachoura Week 11]] 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:29, 13 November 2017 (PST)

===Week 12===

====Quinn's Executive Summary====
Worked closely with Antonio to summarize the results of the journal article Becerra et al. (2003) into a journal club presentation. In order to do so, we both completed the outline provided on the [[Week_12|Week 12]] assignment page on our wiki. We then took this information and used it to create our journal club presentations, which we practiced together and will share in class on Tuesday, November 21. 
Individual Journal Page: [[QLanners Week 12]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Executive Summary====
This week, I met with my coding partner [[User:Ebachour|Eddie Bachoura]] and he helped me clone the code that [[User:Bhamilton18|Blair Hamilton]] forked from the master branch.
After that, Eddie and I helped put together a list of milestones with dates that they should be completed. Using that, Quinn was able to put together a calendar like scheduale for our team to refer to. The last thing I did was open up the cloned files from Blair's fork on my text editor so that I could familiarize myself with the code. 
Individual Journal Page: [[simonwro120 Week 12]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:44, 20 November 2017 (PST)

====Antonio's Executive Summary====
Worked throughout the assignment with Quinn to complete the powerpoint presentation on the journal article: ''Genome-wide analysis of the yeast transcriptome upon heat and cold shock''. We both worked closely together on the outline of the article while maintaining our own style of completing the outline. We then practiced our presentation once the information was finalized and are looking forward to sharing on Tuesday the 21st of November.

Individual journal page: [[Aporras1_Week_12|Aporras 1 Week 12]]

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:19, 20 November 2017 (PST)
====Eddie Bachoura's Executive Summary====
This week, most of my time was spent setting up the branch on github and then getting my local version up and running so that I can write and test code on my own laptop. After that, I helped Simon out with doing the same. I also sent Quinn a list of our milestones for this project, as well as letting him know which ones were already completed. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 19:09, 20 November 2017 (PST) 
Week 12 Journal Page: [[ebachour_Week_12| Edward Bachoura]]

===Week 14===

====Quinn's Executive Summary====
This week, I worked closely with the other QAs and [[User:Kdahlquist|Dr. Dahlquist]] to determine what information should be pulled from each of the five databases. I then communicated this information to our coders. Along with this task, I worked communicated closely with both the data analyst and the coders to ensure that they were on track, and to make modifications to their respective milestones on the team calender. Finally, I added additional team milestones to the calendar to reflect all of the steps that need to be taken to complete the deliverables that we have due at the end of the semester. All of this progress can be seen in my [[QLanners_Week_14|individual weekly journal]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Executive Summary====
This week our coding group hit a bit of wall, not just for one, but for multiple reasons. One reason was caused by the fact that one of the coding group members worked in a language that would not be compatible with GRNsight. Another problem our coding group encountered was caused by a complexity in the the JASPAR API relating CORS (Cross-Oirgin Resource Sharing). Although these complications did occur, both me and Eddie B. know where the API guidelines are for JASPAR and what content we need to produce. In addition to that, an api file has been made as well which will be augmented soon. 
Individual Journal Page: [[simonwro120 Week 14]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:45, 4 December 2017 (PST)

====Antonio's Executive Summary====
This week, I made edits to both my individual [[Aporras1 Week 8]] and [[Aporras1 Week 10]] pages based from feedback received from [[User:Kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dionisio]]. The outline for these edits can be found on my [[Aporras1 Week 14]] page along with the continuation of the [[Week 10|Week 10]] assignment. In this continuation, I selected transcription factors from [[Media:AP dZAP1 profile22 genelist.xlsx]] and put them into YEASTRACT to find the most significant ones and found 49 significant transcription factors found in [[Media:AP YEASTRACT Transcription Factors.xlsx]]. Then I selected 22 of the most significant, 2 additional ones (HAP4 and GLN3) as instructed, to put back into YEASTRACT and create a regulation matrix uploaded as: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]. I then created a "network" worksheet, found in [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]], from the matrix and used GRNsight to generate a regulation network visualization: [[Media:AP Regulation Matrix profile22 GRNsight Network.PNG]]. These media downloads can also be found on my [[Aporras1 Week 14|Week 14]] journal entry in the
"Deliverables" section.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:31, 3 December 2017 (PST)

====Eddie's Executive Summary====
We've been working on JASPAR since the last assignment. As of this week, I am mostly sure that we have the two API calls that we need in order to be able to retrieve any Yeast gene database entry on JASPAR, using the gene ID. I would say that we are already done, but it seems that there are some access complications. I have a feeling it has something to do with CORS and I did some research to try to dix the issue. I found one work around, using a chrome extension, that allows me to bypass the issue, but I'm not sure that this solution will translate well to the actual GRNsight server, but I will discuss with Dondi tomorrow. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:25, 4 December 2017 (PST)

===Week 15===

====Quinn's Executive Summary====
This week, I worked closely will all of my teammates to coordinate the completion of all of the final deliverables. I met in person with my teammates on three seperate occasions to work on the final presentation. Furthermore, I delegated the tasks for our final group paper and completed my sections of the paper, along with running through the paper to ensure that we had met all of the requirements. Finally, I ensured that all of our group's deliverables were uploaded to the team page on time. 
All of this is outlined in depth on my [[QLanners_Week_15|individual weekly journal]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:13, 14 December 2017 (PST)

====Simon's Executive Summary====

====Antonio's Executive Summary====
I spent most of my efforts in the beginning of the week trimming down the network because it was too large. Once this was completed I was able to use MATLAB with the help of [[User:kdahlquist|Dr. Dahlquist]] and generate an output to put into GRNsight to visualize the regulation network with magnitude and direction of regulation. Once this was completed I began spending time on the presentation and the project deliverables. Gathering the deliverables, working on the presentation, and working on the final paper had many points of crossover which I became very familiar with my data and analysis. Once the presentation was completed, I spent the rest of my efforts checking off requirements for the deliverables on the team page and requirements for the paper to ensure it would be turned in on time. This work can be found in my [[Aporras1_Week_15|Week 15]] individual page along with details in terms of the progress throughout the week.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 10:38, 15 December 2017 (PST)

====Eddie's Executive Summary====

==Weekly Reflections==

===Week 11===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a good job of staying on task and working together to make sure that we both understood the whole assignment. So there was good communication between the Bibliography group.
#What didn't work?
#*I felt a bit disconnected with my other teammates Eddie and Simon. There was not very good communication with them about whether they needed any help and if they were on progress.
#What to improve upon going forward?
#*Going forward all of the members of the team need to do a better job of communicating. Also, we need to do a better job of properly communicating about how to fill out the team page ahead of time, so that we aren't frantically figuring that out last second. I will work to fix this by initiating communication earlier on in the week.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*Both me and Eddie were able to put together a powerpoint and present in time for the presentation date
#What didn't work?
#*Due to traveling, Eddie could not be back in LA to help with the project until Monday, which did not give us much time, resulting in our presentation being a bit late as far as submission on our wiki pages.
#How will to improve upon going forward?
#*Going forward I'd like to start early and finish early, that way we can be prepared for any unexpected complications. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
1. What worked? Quinn and I were able to get our work done on time without overlap. We communicated well.

2. What didn't work? Nothing specific prevented us from working efficiently.

3. What will I do next to fix what didn't work? Complete work ahead of time to be more thorough. Maintain a growth mindset.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:06, 20 November 2017 (PST)

====Eddie's Reflection====
Found in Week 11 summary ^^^

===Week 12===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a very good job of working ahead and getting our presentation done in a timely manner. In this way, we were able to ask the instructors any questions we had as they came up, and also allowed for ample time to practice.
#What didn't work?
#*Once again, I felt a bit disconnected from my other partners Eddie and Simon. While I texted Eddie a couple times about their progress, I still never got a chance to see exactly what they were doing.
#What to improve upon going forward?
#*While I feel like this will start to come together once we all start working on our assigned portion of the project together, we still do need to improve our communication between the coders and the PM/DA. In order to do so, I will make sure to continue to check base with each team member each day in class, and also text in the group message when I have questions for the whole team.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*With Eddie's help, we were both able to set up GRNsight on our laptops.
#What didn't work?
#*Nothing in specific stopped us from working efficiently.
#How will to improve upon going forward?
#*Going forward I'd like to get my summaries in earlier, as well as my individual page and reflections. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
#What worked?
#*Worked closely with Quinn and we kept regular contact through text as we worked through the assignment. Troubleshooting was easy as we were both very capable to take initiative and work to finish the presentation earlier rather than later in the time given.
#What didn't work?
#*I could definitely improve on mastering certain aspects of the assignment. I didn't really communicate with Eddie or Simon but I'd attribute that to having different assignments and parts to complete rather than a team issue.
#What to will I do next to fix what didn't work?
#*Communicate more. I'm hoping we'll have opportunities to work more closely together in the future.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:12, 20 November 2017 (PST)

====Eddie's Reflection====
# What worked?
#: Our work session was successful in setting up GRNsight on my laptop (again) and on Simon's.
# What didn't work?
#: Nothing :D
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 21:47, 20 November 2017 (PST)

===Week 14===

====Quinn's Reflection====
#What Worked?
#*This week our team did a much better job of communicating and keeping each other in the loop. Also, the collaboration between all of the QAs was a very effective way to determine which information should be pulled from each database
#What didn't work?
#*I was still a bit confused as to how all of the teams should be working together as we approach the end of the semester
#What will I do next to fix what didn't work>
#*I will make sure to ask about this concern in the next stand up review between the QAs. This will help clear this question up for me and the rest of the class. 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Reflection====
#What Worked?
#*Our class was able to produce a solid list of data items, specified to each database. This meant that as a coder for the JASPAR team, I knew which pieces of data to retrireve and produce from the JASPAR database.
#What didn't work?
#*There were some complications with the language some of the new code was written. There was also a problem with the JASPAR API relating to CORS (Cross-Oirgin Resource Sharing).
#What will I do next to fix what didn't work?
#*I hope to be more knowledgeable about these type of things in reference to computer science.
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:57, 4 December 2017 (PST)

====Antonio's Reflection====
# What worked? This week, I worked ahead and was able to complete, at least to my knowledge, this week's assignment ahead of time rather than waiting until the last minute. It was extremely helpful to have a group chat with the other data analysts as we had questions throughout the assignment.
# What didn't work? Everything seems to have run smoothly except I don't really know what the coders are assigned to do and most likely because it goes over my head.
# What will I do next to fix what didn't work? Try to see what the coders are doing, mostly out of curiosity.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:36, 3 December 2017 (PST)

====Eddie's Reflection====
#What worked?
#* We were able to figure out exactly how to extract the info we needed from JASPAR.
#What didn't work?
#* We originally had our own branch, but that didn't work out too well and it didn't make much sense when we were working in parallel to the gene-database-apis branch.
#How will to improve upon going forward?
#* We decided to merge our two branch which helped with this and kept us on the same page. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:25, 4 December 2017 (PST)

===Week 15===

====Quinn's Reflection====
#What worked?
#*We worked very well as a team on the final group presentation, meeting in person on multiple occasions to ensure that we were covering all of the content and everyone knew what they were going to say. This also allowed for this deliverable to be completed with plenty of time.
#What didn't work?
#*The final paper was a bit of a struggle with how busy everyone was towards the end of final week. It was incredibly hard to find any times to meet in person to collaborate, so we were forced to communicate through solely group texts to complete the paper. While we still were able to finish it, the collaboration was not as solid as it had been for the presentation (due to the fact that everyone was so busy)
#What will I do next time to fix what didn't work?
#*While there won't be a next time for this particular project, I will take note for future projects of how hard it is to find time for collaboration during busy times of the year and plan around this fact. 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:13, 14 December 2017 (PST)

====Simon's Reflection====

====Antonio's Reflection====
# What worked?
#* As a group, we worked very cohesively. The presentation and paper was especially important in terms of everyone being on the same page so we were able to meet on the weekend and outside of class prior to presenting and completing the paper.
# What didn't work?
#* The paper was very time consuming during the finals week and there was no shortage of material which needed to be covered and discussed. As a lab TA, I was able to work on my data analyst sections while editing formatting issues that arose but wish there were more details regarding formatting. We had to work on the paper through google doc which wasn't ideal but considering everyone's busy schedule it was the only option we had and communicated through text in addition.
# What will I do next time?
#* As with everything, finish with PLENTY of time. I've been able to significantly improve in this aspect over the course of the semester but having more time to complete assignments in case problems arise is always an advantage.

====Eddie's Reflection====

==Acknowledgements==

==References==
===Week 11===
#LMU BioDB 2017. (2017). Week 11. Retrieved November 07, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_11
#Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301
#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.
#Top Integrated Development Environment index. (n.d.). Retrieved November 13, 2017, from http://pypl.github.io/IDE.html
#What is an API?. (2016). Retrieved November 13, 2017, from https://medium.freecodecamp.org/what-is-an-api-in-english-please-b880a3214a82
#What's the difference between an API vs SDK?. (2012). Retrieved November 13, 2017, from https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html
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#Web Application Framework. (2015). Retrieved November 13, 2017, from https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework

===Week 12===
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Anneal. (n.d.). ''Genscript''. Retrieved on November 19, 2017 from https://www.genscript.com/molecular-biology-glossary/11896/anneal
#Assay.(2005). ''Biology-Online''. Retrieved on November 19, 2017 http://www.biology-online.org/dictionary/Assay
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301
#Causton HC, Ren B, Koh SS, et al. 2001. Remodelling of yeast genome expression in response to environmental changes. Mol Biol Cell 12: 323–337.
#Chomczynski, P., & Sacchi, N. (1987). Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Analytical biochemistry, 162(1), 156-159.
#Cluster analysis. BusinessDictionary.com. Retrieved November 19, 2017, from BusinessDictionary.com website: http://www.businessdictionary.com/definition/cluster-analysis.html
#Consensus sequence | Definition of consensus sequence in English by Oxford Dictionaries. (n.d.). Retrieved November 20, 2017, from https://en.oxforddictionaries.com/definition/consensus_sequence
#Cyclins. (n.d.). ''BioNinja''. Retrieved on November 19, 2017 from http://ib.bioninja.com.au/standard-level/topic-1-cell-biology/16-cell-division/cyclins.html
#Differences between in vitro, in vivo, and in silico studies. (n.d.). Retrieved November 20, 2017, from https://mpkb.org/home/patients/assessing_literature/in_vitro_studies
#Donzeau M, Bourdineaud JP, Lauquin GJ. 1996. Regulation by low temperatures and anaerobiosis of a yeast gene specifying a putative GPI-anchored plasma membrane protein. Mol Microbiol 20: 449–459.
#Gasch AP, Spellman PT, Kao CM, et al. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11: 4241–4257.
#Glutathione. (n.d.). Retrieved November 20, 2017, from https://www.merriam-webster.com/dictionary/glutathione
#Haploid. (n.d.). Retrieved November 20, 2017, from http://www.biology-online.org/dictionary/Haploid
#HAW. (2011). Difference Between Haploid and Diploid. ''Difference Between.com''. Retrieved on November 19, 2017 from http://www.differencebetween.com/difference-between-haploid-and-vs-diploid/
#Hybridization. (2008). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Hybridization
#Kondo K, Inouye M. 1991. Cold-induction of yeast NSR1 protein and its role in pre-rRNA processing. J Biol Chem 267: 16 259–16 265.
#Kowalski LR, Kondo K, Inouye M. 1995. Cold-shock induction of a family of TIP1-related proteins associated with the membrane in Saccharomyces cerevisiae. Mol Microbiol 15: 341 – 353.
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Mai B, Breeden L. 1997. Xbp1, a stress-upregulated transcrip- tional repressor of the Saccharomyces cerevisae Swi4/Mbp1 family. Mol Cell Biol 17: 6491–6501.
#(n.d.). Retrieved November 19, 2017, from http://fg.cns.utexas.edu/fg/protocol%3A_YPD_plates.html
#(n.d.). Retrieved November 20, 2017, from https://www.nature.com/scitable/definition/diploid-310
#Oligonucleotide. (2014). ''News Medical Life Sciences''. Retrieved on November 19, 2017 from https://www.news-medical.net/life-sciences/What-is-an-Oligonucleotide.aspx
#Polypropylene. (n.d.). ''Dictionary.com''. Retrieved on November 19, 2017 from http://www.dictionary.com/browse/polypropylene
#Putative. (2014). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Putative
#Study.com. (2017). What is Annealing? - Definition, Biology & Process | Study.com. [online] Available at: http://study.com/academy/lesson/what-is-annealing-definition-biology-process.html [Accessed 21 Nov. 2017].
#Transcriptome. (n.d.). ''Nature''. Retrieved on November 19, 2017 from https://www.nature.com/scitable/definition/transcriptome-296
#Yelland, P. M. (2010). An introduction to correspondence analysis. Math. J, 12, 1-23.
#Young, F.W. (1999). Principle Components. ''forrest.psych.unc.edu''. Retrieved on November 19, 2017 from http://forrest.psych.unc.edu/research/vista-frames/help/lecturenotes/lecture13/biplot.html
#Zhang L, Ohta A, Horiuchi H, Takagi M, Imai R. 2001. Multiple mechanisms regulate expression of low temperature responsive (LOT) genes in Saccharomyces cerevisiae. Biochem Biophys Res Commun 283: 531 – 535.

===Week 14===
#Dahlquist, K. D., Dionisio, J. D. N., Fitzpatrick, B. G., Anguiano, N. A., Varshneya, A., Southwick, B. J., & Samdarshi, M. (2016). GRNsight: a web application and service for visualizing models of small-to medium-scale gene regulatory networks. PeerJ Computer Science, 2, e85.
#Ensembl. (2017). "Gene: HSF1". Retrieved November 28, 2017, from https://www.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YGL073W;r=VII:368753-371254;t=YGL073W 
#JASPAR. (2017). "Detailed information of matrix profile MA0319.1". Retrieved on November 28, 2017, from http://jaspar.genereg.net/matrix/MA0319.1/ 
#LMU BioDB 2017. (2017). Week 8. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_8
#LMU BioDB 2017. (2017). Week 10. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10
#LMU BioDB 2017. (2017). Week 14. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14 
#NCBI. (2017). "HSF1 stress-responsive transcription factor HSF1 [ Saccharomyces cerevisiae S288C ]". Retrieved November 28, 2017, from https://www.ncbi.nlm.nih.gov/gene/852806 
#Saccharomyces Genome Database. (2017). "HSF1 / YGL073W Overview". Retrieved November 28, 2017, from https://www.yeastgenome.org/locus/S000003041 
#Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.
#UniProt. (2017). "UniProtKB - P10961 (HSF_YEAST)". Retrieved November 28, 2017 from http://www.uniprot.org/uniprot/P10961

===Week 15===

==Team Links==

{{Template:JASPAR the Friendly Ghost Links}}

==Class Links==

{{Template:GRNsight Gene Page Project Links}}

JASPAR the Friendly Ghost

2017-12-15T18:48:41Z

Aporras1: /* Week 15 */ antonio's reflection

==GRNsight Gene Page Project Deliverables==
[[JASPAR_the_Friendly_Ghost_Final_Deliverables|JASPAR the Friendly Ghost Final GRNsight Deliverables Page]]
==Working Deliverables==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf|Final Group Presentation]] | December 11, 2017 
[[Media:Genome-wide_analysis_of_the_yeast_transcriptome_upon_heat_and_cold_shock._QL_AP.zip|Antonio and Quinn Journal Club Presentation]] | November 21, 2017 
[[Media:e_and_s_presentation_2.pdf|Eddie and Simon Chapter 6 Presentation]] | November 14, 2017 
[https://github.com/bhamilton18/GRNsight GitHub fork] 
[https://github.com/bhamilton18/GRNsight/tree/gene-database-apis GitHub api branch] (in collaboration with [[Gene_hAPI|Gene_hAPI team]])
==Working Files==

===Antonio's Working Files===
# Gene list for profile 22 of dZAP1 Excel file: [[Media:AP dZAP1 profile22 genelist.xlsx]]
# YEASTRACT Transcription Factor Data: [[Media:AP YEASTRACT Transcription Factors.xlsx]]
# YEASTRACT Regulation Matrix Profile: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix: [[Media:AP Adjacency Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix with Network for GRNsight: [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]]

==Calendar==
{| class ="wikitable"
|+November & December
|-
|Sunday
|Monday
|Tuesday
|Wednesday
|Thursday
|Friday
|Saturday
|-
|
|
|
|'''1'''
|'''2'''
|'''3'''
|'''4'''
|-
|'''5'''
|'''6'''
|'''7'''
|'''8'''
|'''9'''
|'''10'''
|'''11'''
|-
|'''12'''
|'''13'''
|'''14''' C: PPT Presentation PM/DA: Journal Articles
|'''15'''
|'''16'''
|'''17'''
|'''18'''
|-
|'''19'''
|'''20'''
|'''21''' C: Complete setup steps (Milestones 1-3) PM/DA: Journal Club Presentations
|'''22''' ''Thanksgiving Break''
|'''23''' ''Thanksgiving Break''
|'''24''' ''Thanksgiving Break''
|'''25'''
|-
|'''26'''
|'''27'''
|'''28''' C: Fimilariaze self with file structure PM: Chose application data fields from JASPAR DA: Review ANOVA Results
|'''29'''
|'''30''' C: Tests for API PM: Share info to be used from JASPAR with other teams DA: Determine transcription factors, develop candidate gene reg network, and fix edits from week 8 & 10
|'''1'''
|'''2'''
|-
|'''3'''
|'''4'''
|'''5''' C: Retrieval code for API PM: Begin Final Group Paper and PPT DA:Model gene reg network Visualize Results
|'''6'''
|'''7''' C: Review and Test Code PM: Review and Test code PM&DA:Work on Paper and PPT
|'''8'''
|'''9''' Complete Group PPT
|-
|'''10''' Practice Group Presentation
|'''11''' Final group Presentation ''2:00-4:00PM''
|'''12'''
|'''13''' Final Group Paper Completely Written
|'''14''' Edit Final Group Paper
|'''15''' All deliverables due ''4:30PM''
|'''16'''
|}

==Executive Summaries==

===Week 11===

====Quinn's Executive Summary====
Created citations for two entries in the annotated bibliography for papers that report microarray data from yeast subjected to cold shock: 
Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6 
Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301 
Also completed a search activity to compare the results found from PubMed, GoogleScholar, and Web of Science using both basic and advanced search tools. 
Individual Journal Page: [[QLanners Week 11]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Executive Summary====
For this assignment, I spent most of my time reading and re-reading Paul Ford's article on how apps are made. It was chapter 6 in a larger work called ''What is Code?'' After absorbing the information laid out in this chapter, Eddie and I made a presentation about it. The presentation summarizes the article, which is about technique, methods, practices, and tools that expedite and simplify the programming process. In addition to making the presentation, I finished my 10 terms and made an outline for the article on my individual journal page. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 13:45, 14 November 2017 (PST)

====Antonio's Executive Summary====

Created two citations for the bibliography for the following articles:

#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.

I also completed the basic keyword searches on PubMed, Google Scholar, and Web of Science along with the advanced searches and the respective results. Lastly, I completed the prospective searches and collected the results of how many articles the article cites and how many articles cite the article. Totaling to the 3 articles.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 15:51, 14 November 2017 (PST)

Individual Journal Week 11: [[Aporras1_Week_11|Aporras1 Week 11]]

====Eddie Bachoura's Executive Summary====
This week, I spent my time for this class reading the Paul Ford article, chapter 6, which was about how to write applications and the modern practices and tools which are used to aid in cutting down some of the tedious nature of coding. Then, Simon and I spent the rest of the time working on our presentation. Team's progress: I believe that Simon and I worked well this weekend. The only issue that I found was that we didn't start until pretty late (Monday), but that was all at my own fault because I wasn't here for this weekend. We should fix that by starting earlier next weekend!

Individual Journal Week 11: [[Ebachour_Week_11|Eddie Bachoura Week 11]] 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:29, 13 November 2017 (PST)

===Week 12===

====Quinn's Executive Summary====
Worked closely with Antonio to summarize the results of the journal article Becerra et al. (2003) into a journal club presentation. In order to do so, we both completed the outline provided on the [[Week_12|Week 12]] assignment page on our wiki. We then took this information and used it to create our journal club presentations, which we practiced together and will share in class on Tuesday, November 21. 
Individual Journal Page: [[QLanners Week 12]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Executive Summary====
This week, I met with my coding partner [[User:Ebachour|Eddie Bachoura]] and he helped me clone the code that [[User:Bhamilton18|Blair Hamilton]] forked from the master branch.
After that, Eddie and I helped put together a list of milestones with dates that they should be completed. Using that, Quinn was able to put together a calendar like scheduale for our team to refer to. The last thing I did was open up the cloned files from Blair's fork on my text editor so that I could familiarize myself with the code. 
Individual Journal Page: [[simonwro120 Week 12]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:44, 20 November 2017 (PST)

====Antonio's Executive Summary====
Worked throughout the assignment with Quinn to complete the powerpoint presentation on the journal article: ''Genome-wide analysis of the yeast transcriptome upon heat and cold shock''. We both worked closely together on the outline of the article while maintaining our own style of completing the outline. We then practiced our presentation once the information was finalized and are looking forward to sharing on Tuesday the 21st of November.

Individual journal page: [[Aporras1_Week_12|Aporras 1 Week 12]]

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:19, 20 November 2017 (PST)
====Eddie Bachoura's Executive Summary====
This week, most of my time was spent setting up the branch on github and then getting my local version up and running so that I can write and test code on my own laptop. After that, I helped Simon out with doing the same. I also sent Quinn a list of our milestones for this project, as well as letting him know which ones were already completed. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 19:09, 20 November 2017 (PST) 
Week 12 Journal Page: [[ebachour_Week_12| Edward Bachoura]]

===Week 14===

====Quinn's Executive Summary====
This week, I worked closely with the other QAs and [[User:Kdahlquist|Dr. Dahlquist]] to determine what information should be pulled from each of the five databases. I then communicated this information to our coders. Along with this task, I worked communicated closely with both the data analyst and the coders to ensure that they were on track, and to make modifications to their respective milestones on the team calender. Finally, I added additional team milestones to the calendar to reflect all of the steps that need to be taken to complete the deliverables that we have due at the end of the semester. All of this progress can be seen in my [[QLanners_Week_14|individual weekly journal]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Executive Summary====
This week our coding group hit a bit of wall, not just for one, but for multiple reasons. One reason was caused by the fact that one of the coding group members worked in a language that would not be compatible with GRNsight. Another problem our coding group encountered was caused by a complexity in the the JASPAR API relating CORS (Cross-Oirgin Resource Sharing). Although these complications did occur, both me and Eddie B. know where the API guidelines are for JASPAR and what content we need to produce. In addition to that, an api file has been made as well which will be augmented soon. 
Individual Journal Page: [[simonwro120 Week 14]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:45, 4 December 2017 (PST)

====Antonio's Executive Summary====
This week, I made edits to both my individual [[Aporras1 Week 8]] and [[Aporras1 Week 10]] pages based from feedback received from [[User:Kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dionisio]]. The outline for these edits can be found on my [[Aporras1 Week 14]] page along with the continuation of the [[Week 10|Week 10]] assignment. In this continuation, I selected transcription factors from [[Media:AP dZAP1 profile22 genelist.xlsx]] and put them into YEASTRACT to find the most significant ones and found 49 significant transcription factors found in [[Media:AP YEASTRACT Transcription Factors.xlsx]]. Then I selected 22 of the most significant, 2 additional ones (HAP4 and GLN3) as instructed, to put back into YEASTRACT and create a regulation matrix uploaded as: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]. I then created a "network" worksheet, found in [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]], from the matrix and used GRNsight to generate a regulation network visualization: [[Media:AP Regulation Matrix profile22 GRNsight Network.PNG]]. These media downloads can also be found on my [[Aporras1 Week 14|Week 14]] journal entry in the
"Deliverables" section.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:31, 3 December 2017 (PST)

====Eddie's Executive Summary====
We've been working on JASPAR since the last assignment. As of this week, I am mostly sure that we have the two API calls that we need in order to be able to retrieve any Yeast gene database entry on JASPAR, using the gene ID. I would say that we are already done, but it seems that there are some access complications. I have a feeling it has something to do with CORS and I did some research to try to dix the issue. I found one work around, using a chrome extension, that allows me to bypass the issue, but I'm not sure that this solution will translate well to the actual GRNsight server, but I will discuss with Dondi tomorrow. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:25, 4 December 2017 (PST)

===Week 15===

====Quinn's Executive Summary====
This week, I worked closely will all of my teammates to coordinate the completion of all of the final deliverables. I met in person with my teammates on three seperate occasions to work on the final presentation. Furthermore, I delegated the tasks for our final group paper and completed my sections of the paper, along with running through the paper to ensure that we had met all of the requirements. Finally, I ensured that all of our group's deliverables were uploaded to the team page on time. 
All of this is outlined in depth on my [[QLanners_Week_15|individual weekly journal]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:13, 14 December 2017 (PST)

====Simon's Executive Summary====

====Antonio's Executive Summary====
I spent most of my efforts in the beginning of the week trimming down the network because it was too large. Once this was completed I was able to use MATLAB with the help of [[User:kdahlquist|Dr. Dahlquist]] and generate an output to put into GRNsight to visualize the regulation network with magnitude and direction of regulation. Once this was completed I began spending time on the presentation and the project deliverables. Gathering the deliverables, working on the presentation, and working on the final paper had many points of crossover which I became very familiar with my data and analysis. Once the presentation was completed, I spent the rest of my efforts checking off requirements for the deliverables on the team page and requirements for the paper to ensure it would be turned in on time. This work can be found in my [[Aporras1_Week_15|Week 15]] individual page along with details in terms of the progress throughout the week.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 10:38, 15 December 2017 (PST)

====Eddie's Executive Summary====

==Weekly Reflections==

===Week 11===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a good job of staying on task and working together to make sure that we both understood the whole assignment. So there was good communication between the Bibliography group.
#What didn't work?
#*I felt a bit disconnected with my other teammates Eddie and Simon. There was not very good communication with them about whether they needed any help and if they were on progress.
#What to improve upon going forward?
#*Going forward all of the members of the team need to do a better job of communicating. Also, we need to do a better job of properly communicating about how to fill out the team page ahead of time, so that we aren't frantically figuring that out last second. I will work to fix this by initiating communication earlier on in the week.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*Both me and Eddie were able to put together a powerpoint and present in time for the presentation date
#What didn't work?
#*Due to traveling, Eddie could not be back in LA to help with the project until Monday, which did not give us much time, resulting in our presentation being a bit late as far as submission on our wiki pages.
#How will to improve upon going forward?
#*Going forward I'd like to start early and finish early, that way we can be prepared for any unexpected complications. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
1. What worked? Quinn and I were able to get our work done on time without overlap. We communicated well.

2. What didn't work? Nothing specific prevented us from working efficiently.

3. What will I do next to fix what didn't work? Complete work ahead of time to be more thorough. Maintain a growth mindset.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:06, 20 November 2017 (PST)

====Eddie's Reflection====
Found in Week 11 summary ^^^

===Week 12===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a very good job of working ahead and getting our presentation done in a timely manner. In this way, we were able to ask the instructors any questions we had as they came up, and also allowed for ample time to practice.
#What didn't work?
#*Once again, I felt a bit disconnected from my other partners Eddie and Simon. While I texted Eddie a couple times about their progress, I still never got a chance to see exactly what they were doing.
#What to improve upon going forward?
#*While I feel like this will start to come together once we all start working on our assigned portion of the project together, we still do need to improve our communication between the coders and the PM/DA. In order to do so, I will make sure to continue to check base with each team member each day in class, and also text in the group message when I have questions for the whole team.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*With Eddie's help, we were both able to set up GRNsight on our laptops.
#What didn't work?
#*Nothing in specific stopped us from working efficiently.
#How will to improve upon going forward?
#*Going forward I'd like to get my summaries in earlier, as well as my individual page and reflections. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
#What worked?
#*Worked closely with Quinn and we kept regular contact through text as we worked through the assignment. Troubleshooting was easy as we were both very capable to take initiative and work to finish the presentation earlier rather than later in the time given.
#What didn't work?
#*I could definitely improve on mastering certain aspects of the assignment. I didn't really communicate with Eddie or Simon but I'd attribute that to having different assignments and parts to complete rather than a team issue.
#What to will I do next to fix what didn't work?
#*Communicate more. I'm hoping we'll have opportunities to work more closely together in the future.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:12, 20 November 2017 (PST)

====Eddie's Reflection====
# What worked?
#: Our work session was successful in setting up GRNsight on my laptop (again) and on Simon's.
# What didn't work?
#: Nothing :D
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 21:47, 20 November 2017 (PST)

===Week 14===

====Quinn's Reflection====
#What Worked?
#*This week our team did a much better job of communicating and keeping each other in the loop. Also, the collaboration between all of the QAs was a very effective way to determine which information should be pulled from each database
#What didn't work?
#*I was still a bit confused as to how all of the teams should be working together as we approach the end of the semester
#What will I do next to fix what didn't work>
#*I will make sure to ask about this concern in the next stand up review between the QAs. This will help clear this question up for me and the rest of the class. 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Reflection====
#What Worked?
#*Our class was able to produce a solid list of data items, specified to each database. This meant that as a coder for the JASPAR team, I knew which pieces of data to retrireve and produce from the JASPAR database.
#What didn't work?
#*There were some complications with the language some of the new code was written. There was also a problem with the JASPAR API relating to CORS (Cross-Oirgin Resource Sharing).
#What will I do next to fix what didn't work?
#*I hope to be more knowledgeable about these type of things in reference to computer science.
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:57, 4 December 2017 (PST)

====Antonio's Reflection====
# What worked? This week, I worked ahead and was able to complete, at least to my knowledge, this week's assignment ahead of time rather than waiting until the last minute. It was extremely helpful to have a group chat with the other data analysts as we had questions throughout the assignment.
# What didn't work? Everything seems to have run smoothly except I don't really know what the coders are assigned to do and most likely because it goes over my head.
# What will I do next to fix what didn't work? Try to see what the coders are doing, mostly out of curiosity.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:36, 3 December 2017 (PST)

====Eddie's Reflection====
#What worked?
#* We were able to figure out exactly how to extract the info we needed from JASPAR.
#What didn't work?
#* We originally had our own branch, but that didn't work out too well and it didn't make much sense when we were working in parallel to the gene-database-apis branch.
#How will to improve upon going forward?
#* We decided to merge our two branch which helped with this and kept us on the same page. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:25, 4 December 2017 (PST)

===Week 15===

====Quinn's Reflection====
#What worked?
#*We worked very well as a team on the final group presentation, meeting in person on multiple occasions to ensure that we were covering all of the content and everyone knew what they were going to say. This also allowed for this deliverable to be completed with plenty of time.
#What didn't work?
#*The final paper was a bit of a struggle with how busy everyone was towards the end of final week. It was incredibly hard to find any times to meet in person to collaborate, so we were forced to communicate through solely group texts to complete the paper. While we still were able to finish it, the collaboration was not as solid as it had been for the presentation (due to the fact that everyone was so busy)
#What will I do next time to fix what didn't work?
#*While there won't be a next time for this particular project, I will take note for future projects of how hard it is to find time for collaboration during busy times of the year and plan around this fact. 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:13, 14 December 2017 (PST)

====Simon's Reflection====

====Antonio's Reflection====
# What worked?
#* As a group, we worked very cohesively. The presentation and paper was especially important in terms of everyone being on the same page so we were able to meet on the weekend and outside of class prior to presenting and completing the paper.
# What didn't work?
#* The paper was very time consuming during the finals week and there was no shortage of material which needed to be covered and discussed. As a lab TA, I was able to work on my data analyst sections while editing formatting issues that arose but wish there were more details regarding formatting. We had to work on the paper through google doc which wasn't ideal but considering everyone's busy schedule it was the only option we had and communicated through text in addition.
# What will I do next time?
#* As with everything, finish with PLENTY of time. I've been able to significantly improve in this aspect over the course of the semester but having more time to complete assignments in case problems arise is always a positive.

====Eddie's Reflection====

==Acknowledgements==

==References==
===Week 11===
#LMU BioDB 2017. (2017). Week 11. Retrieved November 07, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_11
#Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301
#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.
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#Web Application Framework. (2015). Retrieved November 13, 2017, from https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework

===Week 12===
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#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301
#Causton HC, Ren B, Koh SS, et al. 2001. Remodelling of yeast genome expression in response to environmental changes. Mol Biol Cell 12: 323–337.
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#Zhang L, Ohta A, Horiuchi H, Takagi M, Imai R. 2001. Multiple mechanisms regulate expression of low temperature responsive (LOT) genes in Saccharomyces cerevisiae. Biochem Biophys Res Commun 283: 531 – 535.

===Week 14===
#Dahlquist, K. D., Dionisio, J. D. N., Fitzpatrick, B. G., Anguiano, N. A., Varshneya, A., Southwick, B. J., & Samdarshi, M. (2016). GRNsight: a web application and service for visualizing models of small-to medium-scale gene regulatory networks. PeerJ Computer Science, 2, e85.
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#JASPAR. (2017). "Detailed information of matrix profile MA0319.1". Retrieved on November 28, 2017, from http://jaspar.genereg.net/matrix/MA0319.1/ 
#LMU BioDB 2017. (2017). Week 8. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_8
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#LMU BioDB 2017. (2017). Week 14. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14 
#NCBI. (2017). "HSF1 stress-responsive transcription factor HSF1 [ Saccharomyces cerevisiae S288C ]". Retrieved November 28, 2017, from https://www.ncbi.nlm.nih.gov/gene/852806 
#Saccharomyces Genome Database. (2017). "HSF1 / YGL073W Overview". Retrieved November 28, 2017, from https://www.yeastgenome.org/locus/S000003041 
#Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.
#UniProt. (2017). "UniProtKB - P10961 (HSF_YEAST)". Retrieved November 28, 2017 from http://www.uniprot.org/uniprot/P10961

===Week 15===

==Team Links==

{{Template:JASPAR the Friendly Ghost Links}}

==Class Links==

{{Template:GRNsight Gene Page Project Links}}

JASPAR the Friendly Ghost

2017-12-15T18:39:36Z

Aporras1: /* Antonio's Executive Summary */ link to individual journal

==GRNsight Gene Page Project Deliverables==
[[JASPAR_the_Friendly_Ghost_Final_Deliverables|JASPAR the Friendly Ghost Final GRNsight Deliverables Page]]
==Working Deliverables==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf|Final Group Presentation]] | December 11, 2017 
[[Media:Genome-wide_analysis_of_the_yeast_transcriptome_upon_heat_and_cold_shock._QL_AP.zip|Antonio and Quinn Journal Club Presentation]] | November 21, 2017 
[[Media:e_and_s_presentation_2.pdf|Eddie and Simon Chapter 6 Presentation]] | November 14, 2017 
[https://github.com/bhamilton18/GRNsight GitHub fork] 
[https://github.com/bhamilton18/GRNsight/tree/gene-database-apis GitHub api branch] (in collaboration with [[Gene_hAPI|Gene_hAPI team]])
==Working Files==

===Antonio's Working Files===
# Gene list for profile 22 of dZAP1 Excel file: [[Media:AP dZAP1 profile22 genelist.xlsx]]
# YEASTRACT Transcription Factor Data: [[Media:AP YEASTRACT Transcription Factors.xlsx]]
# YEASTRACT Regulation Matrix Profile: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix: [[Media:AP Adjacency Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix with Network for GRNsight: [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]]

==Calendar==
{| class ="wikitable"
|+November & December
|-
|Sunday
|Monday
|Tuesday
|Wednesday
|Thursday
|Friday
|Saturday
|-
|
|
|
|'''1'''
|'''2'''
|'''3'''
|'''4'''
|-
|'''5'''
|'''6'''
|'''7'''
|'''8'''
|'''9'''
|'''10'''
|'''11'''
|-
|'''12'''
|'''13'''
|'''14''' C: PPT Presentation PM/DA: Journal Articles
|'''15'''
|'''16'''
|'''17'''
|'''18'''
|-
|'''19'''
|'''20'''
|'''21''' C: Complete setup steps (Milestones 1-3) PM/DA: Journal Club Presentations
|'''22''' ''Thanksgiving Break''
|'''23''' ''Thanksgiving Break''
|'''24''' ''Thanksgiving Break''
|'''25'''
|-
|'''26'''
|'''27'''
|'''28''' C: Fimilariaze self with file structure PM: Chose application data fields from JASPAR DA: Review ANOVA Results
|'''29'''
|'''30''' C: Tests for API PM: Share info to be used from JASPAR with other teams DA: Determine transcription factors, develop candidate gene reg network, and fix edits from week 8 & 10
|'''1'''
|'''2'''
|-
|'''3'''
|'''4'''
|'''5''' C: Retrieval code for API PM: Begin Final Group Paper and PPT DA:Model gene reg network Visualize Results
|'''6'''
|'''7''' C: Review and Test Code PM: Review and Test code PM&DA:Work on Paper and PPT
|'''8'''
|'''9''' Complete Group PPT
|-
|'''10''' Practice Group Presentation
|'''11''' Final group Presentation ''2:00-4:00PM''
|'''12'''
|'''13''' Final Group Paper Completely Written
|'''14''' Edit Final Group Paper
|'''15''' All deliverables due ''4:30PM''
|'''16'''
|}

==Executive Summaries==

===Week 11===

====Quinn's Executive Summary====
Created citations for two entries in the annotated bibliography for papers that report microarray data from yeast subjected to cold shock: 
Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6 
Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301 
Also completed a search activity to compare the results found from PubMed, GoogleScholar, and Web of Science using both basic and advanced search tools. 
Individual Journal Page: [[QLanners Week 11]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Executive Summary====
For this assignment, I spent most of my time reading and re-reading Paul Ford's article on how apps are made. It was chapter 6 in a larger work called ''What is Code?'' After absorbing the information laid out in this chapter, Eddie and I made a presentation about it. The presentation summarizes the article, which is about technique, methods, practices, and tools that expedite and simplify the programming process. In addition to making the presentation, I finished my 10 terms and made an outline for the article on my individual journal page. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 13:45, 14 November 2017 (PST)

====Antonio's Executive Summary====

Created two citations for the bibliography for the following articles:

#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.

I also completed the basic keyword searches on PubMed, Google Scholar, and Web of Science along with the advanced searches and the respective results. Lastly, I completed the prospective searches and collected the results of how many articles the article cites and how many articles cite the article. Totaling to the 3 articles.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 15:51, 14 November 2017 (PST)

Individual Journal Week 11: [[Aporras1_Week_11|Aporras1 Week 11]]

====Eddie Bachoura's Executive Summary====
This week, I spent my time for this class reading the Paul Ford article, chapter 6, which was about how to write applications and the modern practices and tools which are used to aid in cutting down some of the tedious nature of coding. Then, Simon and I spent the rest of the time working on our presentation. Team's progress: I believe that Simon and I worked well this weekend. The only issue that I found was that we didn't start until pretty late (Monday), but that was all at my own fault because I wasn't here for this weekend. We should fix that by starting earlier next weekend!

Individual Journal Week 11: [[Ebachour_Week_11|Eddie Bachoura Week 11]] 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:29, 13 November 2017 (PST)

===Week 12===

====Quinn's Executive Summary====
Worked closely with Antonio to summarize the results of the journal article Becerra et al. (2003) into a journal club presentation. In order to do so, we both completed the outline provided on the [[Week_12|Week 12]] assignment page on our wiki. We then took this information and used it to create our journal club presentations, which we practiced together and will share in class on Tuesday, November 21. 
Individual Journal Page: [[QLanners Week 12]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Executive Summary====
This week, I met with my coding partner [[User:Ebachour|Eddie Bachoura]] and he helped me clone the code that [[User:Bhamilton18|Blair Hamilton]] forked from the master branch.
After that, Eddie and I helped put together a list of milestones with dates that they should be completed. Using that, Quinn was able to put together a calendar like scheduale for our team to refer to. The last thing I did was open up the cloned files from Blair's fork on my text editor so that I could familiarize myself with the code. 
Individual Journal Page: [[simonwro120 Week 12]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:44, 20 November 2017 (PST)

====Antonio's Executive Summary====
Worked throughout the assignment with Quinn to complete the powerpoint presentation on the journal article: ''Genome-wide analysis of the yeast transcriptome upon heat and cold shock''. We both worked closely together on the outline of the article while maintaining our own style of completing the outline. We then practiced our presentation once the information was finalized and are looking forward to sharing on Tuesday the 21st of November.

Individual journal page: [[Aporras1_Week_12|Aporras 1 Week 12]]

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:19, 20 November 2017 (PST)
====Eddie Bachoura's Executive Summary====
This week, most of my time was spent setting up the branch on github and then getting my local version up and running so that I can write and test code on my own laptop. After that, I helped Simon out with doing the same. I also sent Quinn a list of our milestones for this project, as well as letting him know which ones were already completed. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 19:09, 20 November 2017 (PST) 
Week 12 Journal Page: [[ebachour_Week_12| Edward Bachoura]]

===Week 14===

====Quinn's Executive Summary====
This week, I worked closely with the other QAs and [[User:Kdahlquist|Dr. Dahlquist]] to determine what information should be pulled from each of the five databases. I then communicated this information to our coders. Along with this task, I worked communicated closely with both the data analyst and the coders to ensure that they were on track, and to make modifications to their respective milestones on the team calender. Finally, I added additional team milestones to the calendar to reflect all of the steps that need to be taken to complete the deliverables that we have due at the end of the semester. All of this progress can be seen in my [[QLanners_Week_14|individual weekly journal]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Executive Summary====
This week our coding group hit a bit of wall, not just for one, but for multiple reasons. One reason was caused by the fact that one of the coding group members worked in a language that would not be compatible with GRNsight. Another problem our coding group encountered was caused by a complexity in the the JASPAR API relating CORS (Cross-Oirgin Resource Sharing). Although these complications did occur, both me and Eddie B. know where the API guidelines are for JASPAR and what content we need to produce. In addition to that, an api file has been made as well which will be augmented soon. 
Individual Journal Page: [[simonwro120 Week 14]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:45, 4 December 2017 (PST)

====Antonio's Executive Summary====
This week, I made edits to both my individual [[Aporras1 Week 8]] and [[Aporras1 Week 10]] pages based from feedback received from [[User:Kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dionisio]]. The outline for these edits can be found on my [[Aporras1 Week 14]] page along with the continuation of the [[Week 10|Week 10]] assignment. In this continuation, I selected transcription factors from [[Media:AP dZAP1 profile22 genelist.xlsx]] and put them into YEASTRACT to find the most significant ones and found 49 significant transcription factors found in [[Media:AP YEASTRACT Transcription Factors.xlsx]]. Then I selected 22 of the most significant, 2 additional ones (HAP4 and GLN3) as instructed, to put back into YEASTRACT and create a regulation matrix uploaded as: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]. I then created a "network" worksheet, found in [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]], from the matrix and used GRNsight to generate a regulation network visualization: [[Media:AP Regulation Matrix profile22 GRNsight Network.PNG]]. These media downloads can also be found on my [[Aporras1 Week 14|Week 14]] journal entry in the
"Deliverables" section.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:31, 3 December 2017 (PST)

====Eddie's Executive Summary====
We've been working on JASPAR since the last assignment. As of this week, I am mostly sure that we have the two API calls that we need in order to be able to retrieve any Yeast gene database entry on JASPAR, using the gene ID. I would say that we are already done, but it seems that there are some access complications. I have a feeling it has something to do with CORS and I did some research to try to dix the issue. I found one work around, using a chrome extension, that allows me to bypass the issue, but I'm not sure that this solution will translate well to the actual GRNsight server, but I will discuss with Dondi tomorrow. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:25, 4 December 2017 (PST)

===Week 15===

====Quinn's Executive Summary====
This week, I worked closely will all of my teammates to coordinate the completion of all of the final deliverables. I met in person with my teammates on three seperate occasions to work on the final presentation. Furthermore, I delegated the tasks for our final group paper and completed my sections of the paper, along with running through the paper to ensure that we had met all of the requirements. Finally, I ensured that all of our group's deliverables were uploaded to the team page on time. 
All of this is outlined in depth on my [[QLanners_Week_15|individual weekly journal]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:13, 14 December 2017 (PST)

====Simon's Executive Summary====

====Antonio's Executive Summary====
I spent most of my efforts in the beginning of the week trimming down the network because it was too large. Once this was completed I was able to use MATLAB with the help of [[User:kdahlquist|Dr. Dahlquist]] and generate an output to put into GRNsight to visualize the regulation network with magnitude and direction of regulation. Once this was completed I began spending time on the presentation and the project deliverables. Gathering the deliverables, working on the presentation, and working on the final paper had many points of crossover which I became very familiar with my data and analysis. Once the presentation was completed, I spent the rest of my efforts checking off requirements for the deliverables on the team page and requirements for the paper to ensure it would be turned in on time. This work can be found in my [[Aporras1_Week_15|Week 15]] individual page along with details in terms of the progress throughout the week.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 10:38, 15 December 2017 (PST)

====Eddie's Executive Summary====

==Weekly Reflections==

===Week 11===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a good job of staying on task and working together to make sure that we both understood the whole assignment. So there was good communication between the Bibliography group.
#What didn't work?
#*I felt a bit disconnected with my other teammates Eddie and Simon. There was not very good communication with them about whether they needed any help and if they were on progress.
#What to improve upon going forward?
#*Going forward all of the members of the team need to do a better job of communicating. Also, we need to do a better job of properly communicating about how to fill out the team page ahead of time, so that we aren't frantically figuring that out last second. I will work to fix this by initiating communication earlier on in the week.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*Both me and Eddie were able to put together a powerpoint and present in time for the presentation date
#What didn't work?
#*Due to traveling, Eddie could not be back in LA to help with the project until Monday, which did not give us much time, resulting in our presentation being a bit late as far as submission on our wiki pages.
#How will to improve upon going forward?
#*Going forward I'd like to start early and finish early, that way we can be prepared for any unexpected complications. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
1. What worked? Quinn and I were able to get our work done on time without overlap. We communicated well.

2. What didn't work? Nothing specific prevented us from working efficiently.

3. What will I do next to fix what didn't work? Complete work ahead of time to be more thorough. Maintain a growth mindset.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:06, 20 November 2017 (PST)

====Eddie's Reflection====
Found in Week 11 summary ^^^

===Week 12===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a very good job of working ahead and getting our presentation done in a timely manner. In this way, we were able to ask the instructors any questions we had as they came up, and also allowed for ample time to practice.
#What didn't work?
#*Once again, I felt a bit disconnected from my other partners Eddie and Simon. While I texted Eddie a couple times about their progress, I still never got a chance to see exactly what they were doing.
#What to improve upon going forward?
#*While I feel like this will start to come together once we all start working on our assigned portion of the project together, we still do need to improve our communication between the coders and the PM/DA. In order to do so, I will make sure to continue to check base with each team member each day in class, and also text in the group message when I have questions for the whole team.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*With Eddie's help, we were both able to set up GRNsight on our laptops.
#What didn't work?
#*Nothing in specific stopped us from working efficiently.
#How will to improve upon going forward?
#*Going forward I'd like to get my summaries in earlier, as well as my individual page and reflections. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
#What worked?
#*Worked closely with Quinn and we kept regular contact through text as we worked through the assignment. Troubleshooting was easy as we were both very capable to take initiative and work to finish the presentation earlier rather than later in the time given.
#What didn't work?
#*I could definitely improve on mastering certain aspects of the assignment. I didn't really communicate with Eddie or Simon but I'd attribute that to having different assignments and parts to complete rather than a team issue.
#What to will I do next to fix what didn't work?
#*Communicate more. I'm hoping we'll have opportunities to work more closely together in the future.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:12, 20 November 2017 (PST)

====Eddie's Reflection====
# What worked?
#: Our work session was successful in setting up GRNsight on my laptop (again) and on Simon's.
# What didn't work?
#: Nothing :D
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 21:47, 20 November 2017 (PST)

===Week 14===

====Quinn's Reflection====
#What Worked?
#*This week our team did a much better job of communicating and keeping each other in the loop. Also, the collaboration between all of the QAs was a very effective way to determine which information should be pulled from each database
#What didn't work?
#*I was still a bit confused as to how all of the teams should be working together as we approach the end of the semester
#What will I do next to fix what didn't work>
#*I will make sure to ask about this concern in the next stand up review between the QAs. This will help clear this question up for me and the rest of the class. 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Reflection====
#What Worked?
#*Our class was able to produce a solid list of data items, specified to each database. This meant that as a coder for the JASPAR team, I knew which pieces of data to retrireve and produce from the JASPAR database.
#What didn't work?
#*There were some complications with the language some of the new code was written. There was also a problem with the JASPAR API relating to CORS (Cross-Oirgin Resource Sharing).
#What will I do next to fix what didn't work?
#*I hope to be more knowledgeable about these type of things in reference to computer science.
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:57, 4 December 2017 (PST)

====Antonio's Reflection====
# What worked? This week, I worked ahead and was able to complete, at least to my knowledge, this week's assignment ahead of time rather than waiting until the last minute. It was extremely helpful to have a group chat with the other data analysts as we had questions throughout the assignment.
# What didn't work? Everything seems to have run smoothly except I don't really know what the coders are assigned to do and most likely because it goes over my head.
# What will I do next to fix what didn't work? Try to see what the coders are doing, mostly out of curiosity.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:36, 3 December 2017 (PST)

====Eddie's Reflection====
#What worked?
#* We were able to figure out exactly how to extract the info we needed from JASPAR.
#What didn't work?
#* We originally had our own branch, but that didn't work out too well and it didn't make much sense when we were working in parallel to the gene-database-apis branch.
#How will to improve upon going forward?
#* We decided to merge our two branch which helped with this and kept us on the same page. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:25, 4 December 2017 (PST)

===Week 15===

====Quinn's Reflection====
#What worked?
#*We worked very well as a team on the final group presentation, meeting in person on multiple occasions to ensure that we were covering all of the content and everyone knew what they were going to say. This also allowed for this deliverable to be completed with plenty of time.
#What didn't work?
#*The final paper was a bit of a struggle with how busy everyone was towards the end of final week. It was incredibly hard to find any times to meet in person to collaborate, so we were forced to communicate through solely group texts to complete the paper. While we still were able to finish it, the collaboration was not as solid as it had been for the presentation (due to the fact that everyone was so busy)
#What will I do next time to fix what didn't work?
#*While there won't be a next time for this particular project, I will take note for future projects of how hard it is to find time for collaboration during busy times of the year and plan around this fact. 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:13, 14 December 2017 (PST)

====Simon's Reflection====

====Antonio's Reflection====

====Eddie's Reflection====

==Acknowledgements==

==References==
===Week 11===
#LMU BioDB 2017. (2017). Week 11. Retrieved November 07, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_11
#Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301
#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.
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#Putative. (2014). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Putative
#Study.com. (2017). What is Annealing? - Definition, Biology & Process | Study.com. [online] Available at: http://study.com/academy/lesson/what-is-annealing-definition-biology-process.html [Accessed 21 Nov. 2017].
#Transcriptome. (n.d.). ''Nature''. Retrieved on November 19, 2017 from https://www.nature.com/scitable/definition/transcriptome-296
#Yelland, P. M. (2010). An introduction to correspondence analysis. Math. J, 12, 1-23.
#Young, F.W. (1999). Principle Components. ''forrest.psych.unc.edu''. Retrieved on November 19, 2017 from http://forrest.psych.unc.edu/research/vista-frames/help/lecturenotes/lecture13/biplot.html
#Zhang L, Ohta A, Horiuchi H, Takagi M, Imai R. 2001. Multiple mechanisms regulate expression of low temperature responsive (LOT) genes in Saccharomyces cerevisiae. Biochem Biophys Res Commun 283: 531 – 535.

===Week 14===
#Dahlquist, K. D., Dionisio, J. D. N., Fitzpatrick, B. G., Anguiano, N. A., Varshneya, A., Southwick, B. J., & Samdarshi, M. (2016). GRNsight: a web application and service for visualizing models of small-to medium-scale gene regulatory networks. PeerJ Computer Science, 2, e85.
#Ensembl. (2017). "Gene: HSF1". Retrieved November 28, 2017, from https://www.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YGL073W;r=VII:368753-371254;t=YGL073W 
#JASPAR. (2017). "Detailed information of matrix profile MA0319.1". Retrieved on November 28, 2017, from http://jaspar.genereg.net/matrix/MA0319.1/ 
#LMU BioDB 2017. (2017). Week 8. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_8
#LMU BioDB 2017. (2017). Week 10. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10
#LMU BioDB 2017. (2017). Week 14. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14 
#NCBI. (2017). "HSF1 stress-responsive transcription factor HSF1 [ Saccharomyces cerevisiae S288C ]". Retrieved November 28, 2017, from https://www.ncbi.nlm.nih.gov/gene/852806 
#Saccharomyces Genome Database. (2017). "HSF1 / YGL073W Overview". Retrieved November 28, 2017, from https://www.yeastgenome.org/locus/S000003041 
#Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.
#UniProt. (2017). "UniProtKB - P10961 (HSF_YEAST)". Retrieved November 28, 2017 from http://www.uniprot.org/uniprot/P10961

===Week 15===

==Team Links==

{{Template:JASPAR the Friendly Ghost Links}}

==Class Links==

{{Template:GRNsight Gene Page Project Links}}

JASPAR the Friendly Ghost

2017-12-15T18:38:10Z

Aporras1: /* Antonio's Executive Summary */ exec summ

==GRNsight Gene Page Project Deliverables==
[[JASPAR_the_Friendly_Ghost_Final_Deliverables|JASPAR the Friendly Ghost Final GRNsight Deliverables Page]]
==Working Deliverables==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf|Final Group Presentation]] | December 11, 2017 
[[Media:Genome-wide_analysis_of_the_yeast_transcriptome_upon_heat_and_cold_shock._QL_AP.zip|Antonio and Quinn Journal Club Presentation]] | November 21, 2017 
[[Media:e_and_s_presentation_2.pdf|Eddie and Simon Chapter 6 Presentation]] | November 14, 2017 
[https://github.com/bhamilton18/GRNsight GitHub fork] 
[https://github.com/bhamilton18/GRNsight/tree/gene-database-apis GitHub api branch] (in collaboration with [[Gene_hAPI|Gene_hAPI team]])
==Working Files==

===Antonio's Working Files===
# Gene list for profile 22 of dZAP1 Excel file: [[Media:AP dZAP1 profile22 genelist.xlsx]]
# YEASTRACT Transcription Factor Data: [[Media:AP YEASTRACT Transcription Factors.xlsx]]
# YEASTRACT Regulation Matrix Profile: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix: [[Media:AP Adjacency Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix with Network for GRNsight: [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]]

==Calendar==
{| class ="wikitable"
|+November & December
|-
|Sunday
|Monday
|Tuesday
|Wednesday
|Thursday
|Friday
|Saturday
|-
|
|
|
|'''1'''
|'''2'''
|'''3'''
|'''4'''
|-
|'''5'''
|'''6'''
|'''7'''
|'''8'''
|'''9'''
|'''10'''
|'''11'''
|-
|'''12'''
|'''13'''
|'''14''' C: PPT Presentation PM/DA: Journal Articles
|'''15'''
|'''16'''
|'''17'''
|'''18'''
|-
|'''19'''
|'''20'''
|'''21''' C: Complete setup steps (Milestones 1-3) PM/DA: Journal Club Presentations
|'''22''' ''Thanksgiving Break''
|'''23''' ''Thanksgiving Break''
|'''24''' ''Thanksgiving Break''
|'''25'''
|-
|'''26'''
|'''27'''
|'''28''' C: Fimilariaze self with file structure PM: Chose application data fields from JASPAR DA: Review ANOVA Results
|'''29'''
|'''30''' C: Tests for API PM: Share info to be used from JASPAR with other teams DA: Determine transcription factors, develop candidate gene reg network, and fix edits from week 8 & 10
|'''1'''
|'''2'''
|-
|'''3'''
|'''4'''
|'''5''' C: Retrieval code for API PM: Begin Final Group Paper and PPT DA:Model gene reg network Visualize Results
|'''6'''
|'''7''' C: Review and Test Code PM: Review and Test code PM&DA:Work on Paper and PPT
|'''8'''
|'''9''' Complete Group PPT
|-
|'''10''' Practice Group Presentation
|'''11''' Final group Presentation ''2:00-4:00PM''
|'''12'''
|'''13''' Final Group Paper Completely Written
|'''14''' Edit Final Group Paper
|'''15''' All deliverables due ''4:30PM''
|'''16'''
|}

==Executive Summaries==

===Week 11===

====Quinn's Executive Summary====
Created citations for two entries in the annotated bibliography for papers that report microarray data from yeast subjected to cold shock: 
Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6 
Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301 
Also completed a search activity to compare the results found from PubMed, GoogleScholar, and Web of Science using both basic and advanced search tools. 
Individual Journal Page: [[QLanners Week 11]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Executive Summary====
For this assignment, I spent most of my time reading and re-reading Paul Ford's article on how apps are made. It was chapter 6 in a larger work called ''What is Code?'' After absorbing the information laid out in this chapter, Eddie and I made a presentation about it. The presentation summarizes the article, which is about technique, methods, practices, and tools that expedite and simplify the programming process. In addition to making the presentation, I finished my 10 terms and made an outline for the article on my individual journal page. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 13:45, 14 November 2017 (PST)

====Antonio's Executive Summary====

Created two citations for the bibliography for the following articles:

#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.

I also completed the basic keyword searches on PubMed, Google Scholar, and Web of Science along with the advanced searches and the respective results. Lastly, I completed the prospective searches and collected the results of how many articles the article cites and how many articles cite the article. Totaling to the 3 articles.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 15:51, 14 November 2017 (PST)

Individual Journal Week 11: [[Aporras1_Week_11|Aporras1 Week 11]]

====Eddie Bachoura's Executive Summary====
This week, I spent my time for this class reading the Paul Ford article, chapter 6, which was about how to write applications and the modern practices and tools which are used to aid in cutting down some of the tedious nature of coding. Then, Simon and I spent the rest of the time working on our presentation. Team's progress: I believe that Simon and I worked well this weekend. The only issue that I found was that we didn't start until pretty late (Monday), but that was all at my own fault because I wasn't here for this weekend. We should fix that by starting earlier next weekend!

Individual Journal Week 11: [[Ebachour_Week_11|Eddie Bachoura Week 11]] 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:29, 13 November 2017 (PST)

===Week 12===

====Quinn's Executive Summary====
Worked closely with Antonio to summarize the results of the journal article Becerra et al. (2003) into a journal club presentation. In order to do so, we both completed the outline provided on the [[Week_12|Week 12]] assignment page on our wiki. We then took this information and used it to create our journal club presentations, which we practiced together and will share in class on Tuesday, November 21. 
Individual Journal Page: [[QLanners Week 12]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Executive Summary====
This week, I met with my coding partner [[User:Ebachour|Eddie Bachoura]] and he helped me clone the code that [[User:Bhamilton18|Blair Hamilton]] forked from the master branch.
After that, Eddie and I helped put together a list of milestones with dates that they should be completed. Using that, Quinn was able to put together a calendar like scheduale for our team to refer to. The last thing I did was open up the cloned files from Blair's fork on my text editor so that I could familiarize myself with the code. 
Individual Journal Page: [[simonwro120 Week 12]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:44, 20 November 2017 (PST)

====Antonio's Executive Summary====
Worked throughout the assignment with Quinn to complete the powerpoint presentation on the journal article: ''Genome-wide analysis of the yeast transcriptome upon heat and cold shock''. We both worked closely together on the outline of the article while maintaining our own style of completing the outline. We then practiced our presentation once the information was finalized and are looking forward to sharing on Tuesday the 21st of November.

Individual journal page: [[Aporras1_Week_12|Aporras 1 Week 12]]

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:19, 20 November 2017 (PST)
====Eddie Bachoura's Executive Summary====
This week, most of my time was spent setting up the branch on github and then getting my local version up and running so that I can write and test code on my own laptop. After that, I helped Simon out with doing the same. I also sent Quinn a list of our milestones for this project, as well as letting him know which ones were already completed. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 19:09, 20 November 2017 (PST) 
Week 12 Journal Page: [[ebachour_Week_12| Edward Bachoura]]

===Week 14===

====Quinn's Executive Summary====
This week, I worked closely with the other QAs and [[User:Kdahlquist|Dr. Dahlquist]] to determine what information should be pulled from each of the five databases. I then communicated this information to our coders. Along with this task, I worked communicated closely with both the data analyst and the coders to ensure that they were on track, and to make modifications to their respective milestones on the team calender. Finally, I added additional team milestones to the calendar to reflect all of the steps that need to be taken to complete the deliverables that we have due at the end of the semester. All of this progress can be seen in my [[QLanners_Week_14|individual weekly journal]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Executive Summary====
This week our coding group hit a bit of wall, not just for one, but for multiple reasons. One reason was caused by the fact that one of the coding group members worked in a language that would not be compatible with GRNsight. Another problem our coding group encountered was caused by a complexity in the the JASPAR API relating CORS (Cross-Oirgin Resource Sharing). Although these complications did occur, both me and Eddie B. know where the API guidelines are for JASPAR and what content we need to produce. In addition to that, an api file has been made as well which will be augmented soon. 
Individual Journal Page: [[simonwro120 Week 14]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:45, 4 December 2017 (PST)

====Antonio's Executive Summary====
This week, I made edits to both my individual [[Aporras1 Week 8]] and [[Aporras1 Week 10]] pages based from feedback received from [[User:Kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dionisio]]. The outline for these edits can be found on my [[Aporras1 Week 14]] page along with the continuation of the [[Week 10|Week 10]] assignment. In this continuation, I selected transcription factors from [[Media:AP dZAP1 profile22 genelist.xlsx]] and put them into YEASTRACT to find the most significant ones and found 49 significant transcription factors found in [[Media:AP YEASTRACT Transcription Factors.xlsx]]. Then I selected 22 of the most significant, 2 additional ones (HAP4 and GLN3) as instructed, to put back into YEASTRACT and create a regulation matrix uploaded as: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]. I then created a "network" worksheet, found in [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]], from the matrix and used GRNsight to generate a regulation network visualization: [[Media:AP Regulation Matrix profile22 GRNsight Network.PNG]]. These media downloads can also be found on my [[Aporras1 Week 14|Week 14]] journal entry in the
"Deliverables" section.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:31, 3 December 2017 (PST)

====Eddie's Executive Summary====
We've been working on JASPAR since the last assignment. As of this week, I am mostly sure that we have the two API calls that we need in order to be able to retrieve any Yeast gene database entry on JASPAR, using the gene ID. I would say that we are already done, but it seems that there are some access complications. I have a feeling it has something to do with CORS and I did some research to try to dix the issue. I found one work around, using a chrome extension, that allows me to bypass the issue, but I'm not sure that this solution will translate well to the actual GRNsight server, but I will discuss with Dondi tomorrow. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:25, 4 December 2017 (PST)

===Week 15===

====Quinn's Executive Summary====
This week, I worked closely will all of my teammates to coordinate the completion of all of the final deliverables. I met in person with my teammates on three seperate occasions to work on the final presentation. Furthermore, I delegated the tasks for our final group paper and completed my sections of the paper, along with running through the paper to ensure that we had met all of the requirements. Finally, I ensured that all of our group's deliverables were uploaded to the team page on time. 
All of this is outlined in depth on my [[QLanners_Week_15|individual weekly journal]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:13, 14 December 2017 (PST)

====Simon's Executive Summary====

====Antonio's Executive Summary====
I spent most of my efforts in the beginning of the week trimming down the network because it was too large. Once this was completed I was able to use MATLAB with the help of [[User:kdahlquist|Dr. Dahlquist]] and generate an output to put into GRNsight to visualize the regulation network with magnitude and direction of regulation. Once this was completed I began spending time on the presentation and the project deliverables. Gathering the deliverables, working on the presentation, and working on the final paper had many points of crossover which I became very familiar with my data and analysis. Once the presentation was completed, I spent the rest of my efforts checking off requirements for the deliverables on the team page and requirements for the paper to ensure it would be turned in on time.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 10:38, 15 December 2017 (PST)

====Eddie's Executive Summary====

==Weekly Reflections==

===Week 11===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a good job of staying on task and working together to make sure that we both understood the whole assignment. So there was good communication between the Bibliography group.
#What didn't work?
#*I felt a bit disconnected with my other teammates Eddie and Simon. There was not very good communication with them about whether they needed any help and if they were on progress.
#What to improve upon going forward?
#*Going forward all of the members of the team need to do a better job of communicating. Also, we need to do a better job of properly communicating about how to fill out the team page ahead of time, so that we aren't frantically figuring that out last second. I will work to fix this by initiating communication earlier on in the week.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*Both me and Eddie were able to put together a powerpoint and present in time for the presentation date
#What didn't work?
#*Due to traveling, Eddie could not be back in LA to help with the project until Monday, which did not give us much time, resulting in our presentation being a bit late as far as submission on our wiki pages.
#How will to improve upon going forward?
#*Going forward I'd like to start early and finish early, that way we can be prepared for any unexpected complications. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
1. What worked? Quinn and I were able to get our work done on time without overlap. We communicated well.

2. What didn't work? Nothing specific prevented us from working efficiently.

3. What will I do next to fix what didn't work? Complete work ahead of time to be more thorough. Maintain a growth mindset.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:06, 20 November 2017 (PST)

====Eddie's Reflection====
Found in Week 11 summary ^^^

===Week 12===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a very good job of working ahead and getting our presentation done in a timely manner. In this way, we were able to ask the instructors any questions we had as they came up, and also allowed for ample time to practice.
#What didn't work?
#*Once again, I felt a bit disconnected from my other partners Eddie and Simon. While I texted Eddie a couple times about their progress, I still never got a chance to see exactly what they were doing.
#What to improve upon going forward?
#*While I feel like this will start to come together once we all start working on our assigned portion of the project together, we still do need to improve our communication between the coders and the PM/DA. In order to do so, I will make sure to continue to check base with each team member each day in class, and also text in the group message when I have questions for the whole team.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*With Eddie's help, we were both able to set up GRNsight on our laptops.
#What didn't work?
#*Nothing in specific stopped us from working efficiently.
#How will to improve upon going forward?
#*Going forward I'd like to get my summaries in earlier, as well as my individual page and reflections. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
#What worked?
#*Worked closely with Quinn and we kept regular contact through text as we worked through the assignment. Troubleshooting was easy as we were both very capable to take initiative and work to finish the presentation earlier rather than later in the time given.
#What didn't work?
#*I could definitely improve on mastering certain aspects of the assignment. I didn't really communicate with Eddie or Simon but I'd attribute that to having different assignments and parts to complete rather than a team issue.
#What to will I do next to fix what didn't work?
#*Communicate more. I'm hoping we'll have opportunities to work more closely together in the future.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:12, 20 November 2017 (PST)

====Eddie's Reflection====
# What worked?
#: Our work session was successful in setting up GRNsight on my laptop (again) and on Simon's.
# What didn't work?
#: Nothing :D
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 21:47, 20 November 2017 (PST)

===Week 14===

====Quinn's Reflection====
#What Worked?
#*This week our team did a much better job of communicating and keeping each other in the loop. Also, the collaboration between all of the QAs was a very effective way to determine which information should be pulled from each database
#What didn't work?
#*I was still a bit confused as to how all of the teams should be working together as we approach the end of the semester
#What will I do next to fix what didn't work>
#*I will make sure to ask about this concern in the next stand up review between the QAs. This will help clear this question up for me and the rest of the class. 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Reflection====
#What Worked?
#*Our class was able to produce a solid list of data items, specified to each database. This meant that as a coder for the JASPAR team, I knew which pieces of data to retrireve and produce from the JASPAR database.
#What didn't work?
#*There were some complications with the language some of the new code was written. There was also a problem with the JASPAR API relating to CORS (Cross-Oirgin Resource Sharing).
#What will I do next to fix what didn't work?
#*I hope to be more knowledgeable about these type of things in reference to computer science.
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:57, 4 December 2017 (PST)

====Antonio's Reflection====
# What worked? This week, I worked ahead and was able to complete, at least to my knowledge, this week's assignment ahead of time rather than waiting until the last minute. It was extremely helpful to have a group chat with the other data analysts as we had questions throughout the assignment.
# What didn't work? Everything seems to have run smoothly except I don't really know what the coders are assigned to do and most likely because it goes over my head.
# What will I do next to fix what didn't work? Try to see what the coders are doing, mostly out of curiosity.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:36, 3 December 2017 (PST)

====Eddie's Reflection====
#What worked?
#* We were able to figure out exactly how to extract the info we needed from JASPAR.
#What didn't work?
#* We originally had our own branch, but that didn't work out too well and it didn't make much sense when we were working in parallel to the gene-database-apis branch.
#How will to improve upon going forward?
#* We decided to merge our two branch which helped with this and kept us on the same page. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:25, 4 December 2017 (PST)

===Week 15===

====Quinn's Reflection====
#What worked?
#*We worked very well as a team on the final group presentation, meeting in person on multiple occasions to ensure that we were covering all of the content and everyone knew what they were going to say. This also allowed for this deliverable to be completed with plenty of time.
#What didn't work?
#*The final paper was a bit of a struggle with how busy everyone was towards the end of final week. It was incredibly hard to find any times to meet in person to collaborate, so we were forced to communicate through solely group texts to complete the paper. While we still were able to finish it, the collaboration was not as solid as it had been for the presentation (due to the fact that everyone was so busy)
#What will I do next time to fix what didn't work?
#*While there won't be a next time for this particular project, I will take note for future projects of how hard it is to find time for collaboration during busy times of the year and plan around this fact. 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:13, 14 December 2017 (PST)

====Simon's Reflection====

====Antonio's Reflection====

====Eddie's Reflection====

==Acknowledgements==

==References==
===Week 11===
#LMU BioDB 2017. (2017). Week 11. Retrieved November 07, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_11
#Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301
#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.
#Top Integrated Development Environment index. (n.d.). Retrieved November 13, 2017, from http://pypl.github.io/IDE.html
#What is an API?. (2016). Retrieved November 13, 2017, from https://medium.freecodecamp.org/what-is-an-api-in-english-please-b880a3214a82
#What's the difference between an API vs SDK?. (2012). Retrieved November 13, 2017, from https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html
#Xcode. (2017). Retrieved November 13, 2017, from https://itunes.apple.com/us/app/xcode/id497799835
#What Is Code? (2015). Retrieved November 13, 2017, from https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made
#Shrinkwrapped Software. (n.d.). Retrieved November 13, 2017, from http://www.businessdictionary.com/definition/shrinkwrapped-software.html
#Web Application Framework. (2015). Retrieved November 13, 2017, from https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework

===Week 12===
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Anneal. (n.d.). ''Genscript''. Retrieved on November 19, 2017 from https://www.genscript.com/molecular-biology-glossary/11896/anneal
#Assay.(2005). ''Biology-Online''. Retrieved on November 19, 2017 http://www.biology-online.org/dictionary/Assay
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301
#Causton HC, Ren B, Koh SS, et al. 2001. Remodelling of yeast genome expression in response to environmental changes. Mol Biol Cell 12: 323–337.
#Chomczynski, P., & Sacchi, N. (1987). Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Analytical biochemistry, 162(1), 156-159.
#Cluster analysis. BusinessDictionary.com. Retrieved November 19, 2017, from BusinessDictionary.com website: http://www.businessdictionary.com/definition/cluster-analysis.html
#Consensus sequence | Definition of consensus sequence in English by Oxford Dictionaries. (n.d.). Retrieved November 20, 2017, from https://en.oxforddictionaries.com/definition/consensus_sequence
#Cyclins. (n.d.). ''BioNinja''. Retrieved on November 19, 2017 from http://ib.bioninja.com.au/standard-level/topic-1-cell-biology/16-cell-division/cyclins.html
#Differences between in vitro, in vivo, and in silico studies. (n.d.). Retrieved November 20, 2017, from https://mpkb.org/home/patients/assessing_literature/in_vitro_studies
#Donzeau M, Bourdineaud JP, Lauquin GJ. 1996. Regulation by low temperatures and anaerobiosis of a yeast gene specifying a putative GPI-anchored plasma membrane protein. Mol Microbiol 20: 449–459.
#Gasch AP, Spellman PT, Kao CM, et al. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11: 4241–4257.
#Glutathione. (n.d.). Retrieved November 20, 2017, from https://www.merriam-webster.com/dictionary/glutathione
#Haploid. (n.d.). Retrieved November 20, 2017, from http://www.biology-online.org/dictionary/Haploid
#HAW. (2011). Difference Between Haploid and Diploid. ''Difference Between.com''. Retrieved on November 19, 2017 from http://www.differencebetween.com/difference-between-haploid-and-vs-diploid/
#Hybridization. (2008). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Hybridization
#Kondo K, Inouye M. 1991. Cold-induction of yeast NSR1 protein and its role in pre-rRNA processing. J Biol Chem 267: 16 259–16 265.
#Kowalski LR, Kondo K, Inouye M. 1995. Cold-shock induction of a family of TIP1-related proteins associated with the membrane in Saccharomyces cerevisiae. Mol Microbiol 15: 341 – 353.
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Mai B, Breeden L. 1997. Xbp1, a stress-upregulated transcrip- tional repressor of the Saccharomyces cerevisae Swi4/Mbp1 family. Mol Cell Biol 17: 6491–6501.
#(n.d.). Retrieved November 19, 2017, from http://fg.cns.utexas.edu/fg/protocol%3A_YPD_plates.html
#(n.d.). Retrieved November 20, 2017, from https://www.nature.com/scitable/definition/diploid-310
#Oligonucleotide. (2014). ''News Medical Life Sciences''. Retrieved on November 19, 2017 from https://www.news-medical.net/life-sciences/What-is-an-Oligonucleotide.aspx
#Polypropylene. (n.d.). ''Dictionary.com''. Retrieved on November 19, 2017 from http://www.dictionary.com/browse/polypropylene
#Putative. (2014). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Putative
#Study.com. (2017). What is Annealing? - Definition, Biology & Process | Study.com. [online] Available at: http://study.com/academy/lesson/what-is-annealing-definition-biology-process.html [Accessed 21 Nov. 2017].
#Transcriptome. (n.d.). ''Nature''. Retrieved on November 19, 2017 from https://www.nature.com/scitable/definition/transcriptome-296
#Yelland, P. M. (2010). An introduction to correspondence analysis. Math. J, 12, 1-23.
#Young, F.W. (1999). Principle Components. ''forrest.psych.unc.edu''. Retrieved on November 19, 2017 from http://forrest.psych.unc.edu/research/vista-frames/help/lecturenotes/lecture13/biplot.html
#Zhang L, Ohta A, Horiuchi H, Takagi M, Imai R. 2001. Multiple mechanisms regulate expression of low temperature responsive (LOT) genes in Saccharomyces cerevisiae. Biochem Biophys Res Commun 283: 531 – 535.

===Week 14===
#Dahlquist, K. D., Dionisio, J. D. N., Fitzpatrick, B. G., Anguiano, N. A., Varshneya, A., Southwick, B. J., & Samdarshi, M. (2016). GRNsight: a web application and service for visualizing models of small-to medium-scale gene regulatory networks. PeerJ Computer Science, 2, e85.
#Ensembl. (2017). "Gene: HSF1". Retrieved November 28, 2017, from https://www.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YGL073W;r=VII:368753-371254;t=YGL073W 
#JASPAR. (2017). "Detailed information of matrix profile MA0319.1". Retrieved on November 28, 2017, from http://jaspar.genereg.net/matrix/MA0319.1/ 
#LMU BioDB 2017. (2017). Week 8. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_8
#LMU BioDB 2017. (2017). Week 10. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10
#LMU BioDB 2017. (2017). Week 14. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14 
#NCBI. (2017). "HSF1 stress-responsive transcription factor HSF1 [ Saccharomyces cerevisiae S288C ]". Retrieved November 28, 2017, from https://www.ncbi.nlm.nih.gov/gene/852806 
#Saccharomyces Genome Database. (2017). "HSF1 / YGL073W Overview". Retrieved November 28, 2017, from https://www.yeastgenome.org/locus/S000003041 
#Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.
#UniProt. (2017). "UniProtKB - P10961 (HSF_YEAST)". Retrieved November 28, 2017 from http://www.uniprot.org/uniprot/P10961

===Week 15===

==Team Links==

{{Template:JASPAR the Friendly Ghost Links}}

==Class Links==

{{Template:GRNsight Gene Page Project Links}}

JASPAR the Friendly Ghost

2017-12-15T18:29:29Z

Aporras1: /* References */ week 15 header

==GRNsight Gene Page Project Deliverables==
[[JASPAR_the_Friendly_Ghost_Final_Deliverables|JASPAR the Friendly Ghost Final GRNsight Deliverables Page]]
==Working Deliverables==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf|Final Group Presentation]] | December 11, 2017 
[[Media:Genome-wide_analysis_of_the_yeast_transcriptome_upon_heat_and_cold_shock._QL_AP.zip|Antonio and Quinn Journal Club Presentation]] | November 21, 2017 
[[Media:e_and_s_presentation_2.pdf|Eddie and Simon Chapter 6 Presentation]] | November 14, 2017 
[https://github.com/bhamilton18/GRNsight GitHub fork] 
[https://github.com/bhamilton18/GRNsight/tree/gene-database-apis GitHub api branch] (in collaboration with [[Gene_hAPI|Gene_hAPI team]])
==Working Files==

===Antonio's Working Files===
# Gene list for profile 22 of dZAP1 Excel file: [[Media:AP dZAP1 profile22 genelist.xlsx]]
# YEASTRACT Transcription Factor Data: [[Media:AP YEASTRACT Transcription Factors.xlsx]]
# YEASTRACT Regulation Matrix Profile: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix: [[Media:AP Adjacency Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix with Network for GRNsight: [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]]

==Calendar==
{| class ="wikitable"
|+November & December
|-
|Sunday
|Monday
|Tuesday
|Wednesday
|Thursday
|Friday
|Saturday
|-
|
|
|
|'''1'''
|'''2'''
|'''3'''
|'''4'''
|-
|'''5'''
|'''6'''
|'''7'''
|'''8'''
|'''9'''
|'''10'''
|'''11'''
|-
|'''12'''
|'''13'''
|'''14''' C: PPT Presentation PM/DA: Journal Articles
|'''15'''
|'''16'''
|'''17'''
|'''18'''
|-
|'''19'''
|'''20'''
|'''21''' C: Complete setup steps (Milestones 1-3) PM/DA: Journal Club Presentations
|'''22''' ''Thanksgiving Break''
|'''23''' ''Thanksgiving Break''
|'''24''' ''Thanksgiving Break''
|'''25'''
|-
|'''26'''
|'''27'''
|'''28''' C: Fimilariaze self with file structure PM: Chose application data fields from JASPAR DA: Review ANOVA Results
|'''29'''
|'''30''' C: Tests for API PM: Share info to be used from JASPAR with other teams DA: Determine transcription factors, develop candidate gene reg network, and fix edits from week 8 & 10
|'''1'''
|'''2'''
|-
|'''3'''
|'''4'''
|'''5''' C: Retrieval code for API PM: Begin Final Group Paper and PPT DA:Model gene reg network Visualize Results
|'''6'''
|'''7''' C: Review and Test Code PM: Review and Test code PM&DA:Work on Paper and PPT
|'''8'''
|'''9''' Complete Group PPT
|-
|'''10''' Practice Group Presentation
|'''11''' Final group Presentation ''2:00-4:00PM''
|'''12'''
|'''13''' Final Group Paper Completely Written
|'''14''' Edit Final Group Paper
|'''15''' All deliverables due ''4:30PM''
|'''16'''
|}

==Executive Summaries==

===Week 11===

====Quinn's Executive Summary====
Created citations for two entries in the annotated bibliography for papers that report microarray data from yeast subjected to cold shock: 
Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6 
Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301 
Also completed a search activity to compare the results found from PubMed, GoogleScholar, and Web of Science using both basic and advanced search tools. 
Individual Journal Page: [[QLanners Week 11]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Executive Summary====
For this assignment, I spent most of my time reading and re-reading Paul Ford's article on how apps are made. It was chapter 6 in a larger work called ''What is Code?'' After absorbing the information laid out in this chapter, Eddie and I made a presentation about it. The presentation summarizes the article, which is about technique, methods, practices, and tools that expedite and simplify the programming process. In addition to making the presentation, I finished my 10 terms and made an outline for the article on my individual journal page. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 13:45, 14 November 2017 (PST)

====Antonio's Executive Summary====

Created two citations for the bibliography for the following articles:

#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.

I also completed the basic keyword searches on PubMed, Google Scholar, and Web of Science along with the advanced searches and the respective results. Lastly, I completed the prospective searches and collected the results of how many articles the article cites and how many articles cite the article. Totaling to the 3 articles.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 15:51, 14 November 2017 (PST)

Individual Journal Week 11: [[Aporras1_Week_11|Aporras1 Week 11]]

====Eddie Bachoura's Executive Summary====
This week, I spent my time for this class reading the Paul Ford article, chapter 6, which was about how to write applications and the modern practices and tools which are used to aid in cutting down some of the tedious nature of coding. Then, Simon and I spent the rest of the time working on our presentation. Team's progress: I believe that Simon and I worked well this weekend. The only issue that I found was that we didn't start until pretty late (Monday), but that was all at my own fault because I wasn't here for this weekend. We should fix that by starting earlier next weekend!

Individual Journal Week 11: [[Ebachour_Week_11|Eddie Bachoura Week 11]] 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:29, 13 November 2017 (PST)

===Week 12===

====Quinn's Executive Summary====
Worked closely with Antonio to summarize the results of the journal article Becerra et al. (2003) into a journal club presentation. In order to do so, we both completed the outline provided on the [[Week_12|Week 12]] assignment page on our wiki. We then took this information and used it to create our journal club presentations, which we practiced together and will share in class on Tuesday, November 21. 
Individual Journal Page: [[QLanners Week 12]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Executive Summary====
This week, I met with my coding partner [[User:Ebachour|Eddie Bachoura]] and he helped me clone the code that [[User:Bhamilton18|Blair Hamilton]] forked from the master branch.
After that, Eddie and I helped put together a list of milestones with dates that they should be completed. Using that, Quinn was able to put together a calendar like scheduale for our team to refer to. The last thing I did was open up the cloned files from Blair's fork on my text editor so that I could familiarize myself with the code. 
Individual Journal Page: [[simonwro120 Week 12]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:44, 20 November 2017 (PST)

====Antonio's Executive Summary====
Worked throughout the assignment with Quinn to complete the powerpoint presentation on the journal article: ''Genome-wide analysis of the yeast transcriptome upon heat and cold shock''. We both worked closely together on the outline of the article while maintaining our own style of completing the outline. We then practiced our presentation once the information was finalized and are looking forward to sharing on Tuesday the 21st of November.

Individual journal page: [[Aporras1_Week_12|Aporras 1 Week 12]]

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:19, 20 November 2017 (PST)
====Eddie Bachoura's Executive Summary====
This week, most of my time was spent setting up the branch on github and then getting my local version up and running so that I can write and test code on my own laptop. After that, I helped Simon out with doing the same. I also sent Quinn a list of our milestones for this project, as well as letting him know which ones were already completed. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 19:09, 20 November 2017 (PST) 
Week 12 Journal Page: [[ebachour_Week_12| Edward Bachoura]]

===Week 14===

====Quinn's Executive Summary====
This week, I worked closely with the other QAs and [[User:Kdahlquist|Dr. Dahlquist]] to determine what information should be pulled from each of the five databases. I then communicated this information to our coders. Along with this task, I worked communicated closely with both the data analyst and the coders to ensure that they were on track, and to make modifications to their respective milestones on the team calender. Finally, I added additional team milestones to the calendar to reflect all of the steps that need to be taken to complete the deliverables that we have due at the end of the semester. All of this progress can be seen in my [[QLanners_Week_14|individual weekly journal]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Executive Summary====
This week our coding group hit a bit of wall, not just for one, but for multiple reasons. One reason was caused by the fact that one of the coding group members worked in a language that would not be compatible with GRNsight. Another problem our coding group encountered was caused by a complexity in the the JASPAR API relating CORS (Cross-Oirgin Resource Sharing). Although these complications did occur, both me and Eddie B. know where the API guidelines are for JASPAR and what content we need to produce. In addition to that, an api file has been made as well which will be augmented soon. 
Individual Journal Page: [[simonwro120 Week 14]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:45, 4 December 2017 (PST)

====Antonio's Executive Summary====
This week, I made edits to both my individual [[Aporras1 Week 8]] and [[Aporras1 Week 10]] pages based from feedback received from [[User:Kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dionisio]]. The outline for these edits can be found on my [[Aporras1 Week 14]] page along with the continuation of the [[Week 10|Week 10]] assignment. In this continuation, I selected transcription factors from [[Media:AP dZAP1 profile22 genelist.xlsx]] and put them into YEASTRACT to find the most significant ones and found 49 significant transcription factors found in [[Media:AP YEASTRACT Transcription Factors.xlsx]]. Then I selected 22 of the most significant, 2 additional ones (HAP4 and GLN3) as instructed, to put back into YEASTRACT and create a regulation matrix uploaded as: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]. I then created a "network" worksheet, found in [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]], from the matrix and used GRNsight to generate a regulation network visualization: [[Media:AP Regulation Matrix profile22 GRNsight Network.PNG]]. These media downloads can also be found on my [[Aporras1 Week 14|Week 14]] journal entry in the
"Deliverables" section.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:31, 3 December 2017 (PST)

====Eddie's Executive Summary====
We've been working on JASPAR since the last assignment. As of this week, I am mostly sure that we have the two API calls that we need in order to be able to retrieve any Yeast gene database entry on JASPAR, using the gene ID. I would say that we are already done, but it seems that there are some access complications. I have a feeling it has something to do with CORS and I did some research to try to dix the issue. I found one work around, using a chrome extension, that allows me to bypass the issue, but I'm not sure that this solution will translate well to the actual GRNsight server, but I will discuss with Dondi tomorrow. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:25, 4 December 2017 (PST)

===Week 15===

====Quinn's Executive Summary====
This week, I worked closely will all of my teammates to coordinate the completion of all of the final deliverables. I met in person with my teammates on three seperate occasions to work on the final presentation. Furthermore, I delegated the tasks for our final group paper and completed my sections of the paper, along with running through the paper to ensure that we had met all of the requirements. Finally, I ensured that all of our group's deliverables were uploaded to the team page on time. 
All of this is outlined in depth on my [[QLanners_Week_15|individual weekly journal]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:13, 14 December 2017 (PST)

====Simon's Executive Summary====

====Antonio's Executive Summary====

====Eddie's Executive Summary====

==Weekly Reflections==

===Week 11===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a good job of staying on task and working together to make sure that we both understood the whole assignment. So there was good communication between the Bibliography group.
#What didn't work?
#*I felt a bit disconnected with my other teammates Eddie and Simon. There was not very good communication with them about whether they needed any help and if they were on progress.
#What to improve upon going forward?
#*Going forward all of the members of the team need to do a better job of communicating. Also, we need to do a better job of properly communicating about how to fill out the team page ahead of time, so that we aren't frantically figuring that out last second. I will work to fix this by initiating communication earlier on in the week.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*Both me and Eddie were able to put together a powerpoint and present in time for the presentation date
#What didn't work?
#*Due to traveling, Eddie could not be back in LA to help with the project until Monday, which did not give us much time, resulting in our presentation being a bit late as far as submission on our wiki pages.
#How will to improve upon going forward?
#*Going forward I'd like to start early and finish early, that way we can be prepared for any unexpected complications. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
1. What worked? Quinn and I were able to get our work done on time without overlap. We communicated well.

2. What didn't work? Nothing specific prevented us from working efficiently.

3. What will I do next to fix what didn't work? Complete work ahead of time to be more thorough. Maintain a growth mindset.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:06, 20 November 2017 (PST)

====Eddie's Reflection====
Found in Week 11 summary ^^^

===Week 12===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a very good job of working ahead and getting our presentation done in a timely manner. In this way, we were able to ask the instructors any questions we had as they came up, and also allowed for ample time to practice.
#What didn't work?
#*Once again, I felt a bit disconnected from my other partners Eddie and Simon. While I texted Eddie a couple times about their progress, I still never got a chance to see exactly what they were doing.
#What to improve upon going forward?
#*While I feel like this will start to come together once we all start working on our assigned portion of the project together, we still do need to improve our communication between the coders and the PM/DA. In order to do so, I will make sure to continue to check base with each team member each day in class, and also text in the group message when I have questions for the whole team.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*With Eddie's help, we were both able to set up GRNsight on our laptops.
#What didn't work?
#*Nothing in specific stopped us from working efficiently.
#How will to improve upon going forward?
#*Going forward I'd like to get my summaries in earlier, as well as my individual page and reflections. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
#What worked?
#*Worked closely with Quinn and we kept regular contact through text as we worked through the assignment. Troubleshooting was easy as we were both very capable to take initiative and work to finish the presentation earlier rather than later in the time given.
#What didn't work?
#*I could definitely improve on mastering certain aspects of the assignment. I didn't really communicate with Eddie or Simon but I'd attribute that to having different assignments and parts to complete rather than a team issue.
#What to will I do next to fix what didn't work?
#*Communicate more. I'm hoping we'll have opportunities to work more closely together in the future.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:12, 20 November 2017 (PST)

====Eddie's Reflection====
# What worked?
#: Our work session was successful in setting up GRNsight on my laptop (again) and on Simon's.
# What didn't work?
#: Nothing :D
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 21:47, 20 November 2017 (PST)

===Week 14===

====Quinn's Reflection====
#What Worked?
#*This week our team did a much better job of communicating and keeping each other in the loop. Also, the collaboration between all of the QAs was a very effective way to determine which information should be pulled from each database
#What didn't work?
#*I was still a bit confused as to how all of the teams should be working together as we approach the end of the semester
#What will I do next to fix what didn't work>
#*I will make sure to ask about this concern in the next stand up review between the QAs. This will help clear this question up for me and the rest of the class. 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Reflection====
#What Worked?
#*Our class was able to produce a solid list of data items, specified to each database. This meant that as a coder for the JASPAR team, I knew which pieces of data to retrireve and produce from the JASPAR database.
#What didn't work?
#*There were some complications with the language some of the new code was written. There was also a problem with the JASPAR API relating to CORS (Cross-Oirgin Resource Sharing).
#What will I do next to fix what didn't work?
#*I hope to be more knowledgeable about these type of things in reference to computer science.
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:57, 4 December 2017 (PST)

====Antonio's Reflection====
# What worked? This week, I worked ahead and was able to complete, at least to my knowledge, this week's assignment ahead of time rather than waiting until the last minute. It was extremely helpful to have a group chat with the other data analysts as we had questions throughout the assignment.
# What didn't work? Everything seems to have run smoothly except I don't really know what the coders are assigned to do and most likely because it goes over my head.
# What will I do next to fix what didn't work? Try to see what the coders are doing, mostly out of curiosity.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:36, 3 December 2017 (PST)

====Eddie's Reflection====
#What worked?
#* We were able to figure out exactly how to extract the info we needed from JASPAR.
#What didn't work?
#* We originally had our own branch, but that didn't work out too well and it didn't make much sense when we were working in parallel to the gene-database-apis branch.
#How will to improve upon going forward?
#* We decided to merge our two branch which helped with this and kept us on the same page. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:25, 4 December 2017 (PST)

===Week 15===

====Quinn's Reflection====
#What worked?
#*We worked very well as a team on the final group presentation, meeting in person on multiple occasions to ensure that we were covering all of the content and everyone knew what they were going to say. This also allowed for this deliverable to be completed with plenty of time.
#What didn't work?
#*The final paper was a bit of a struggle with how busy everyone was towards the end of final week. It was incredibly hard to find any times to meet in person to collaborate, so we were forced to communicate through solely group texts to complete the paper. While we still were able to finish it, the collaboration was not as solid as it had been for the presentation (due to the fact that everyone was so busy)
#What will I do next time to fix what didn't work?
#*While there won't be a next time for this particular project, I will take note for future projects of how hard it is to find time for collaboration during busy times of the year and plan around this fact. 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:13, 14 December 2017 (PST)

====Simon's Reflection====

====Antonio's Reflection====

====Eddie's Reflection====

==Acknowledgements==

==References==
===Week 11===
#LMU BioDB 2017. (2017). Week 11. Retrieved November 07, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_11
#Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301
#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.
#Top Integrated Development Environment index. (n.d.). Retrieved November 13, 2017, from http://pypl.github.io/IDE.html
#What is an API?. (2016). Retrieved November 13, 2017, from https://medium.freecodecamp.org/what-is-an-api-in-english-please-b880a3214a82
#What's the difference between an API vs SDK?. (2012). Retrieved November 13, 2017, from https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html
#Xcode. (2017). Retrieved November 13, 2017, from https://itunes.apple.com/us/app/xcode/id497799835
#What Is Code? (2015). Retrieved November 13, 2017, from https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made
#Shrinkwrapped Software. (n.d.). Retrieved November 13, 2017, from http://www.businessdictionary.com/definition/shrinkwrapped-software.html
#Web Application Framework. (2015). Retrieved November 13, 2017, from https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework

===Week 12===
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Anneal. (n.d.). ''Genscript''. Retrieved on November 19, 2017 from https://www.genscript.com/molecular-biology-glossary/11896/anneal
#Assay.(2005). ''Biology-Online''. Retrieved on November 19, 2017 http://www.biology-online.org/dictionary/Assay
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301
#Causton HC, Ren B, Koh SS, et al. 2001. Remodelling of yeast genome expression in response to environmental changes. Mol Biol Cell 12: 323–337.
#Chomczynski, P., & Sacchi, N. (1987). Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Analytical biochemistry, 162(1), 156-159.
#Cluster analysis. BusinessDictionary.com. Retrieved November 19, 2017, from BusinessDictionary.com website: http://www.businessdictionary.com/definition/cluster-analysis.html
#Consensus sequence | Definition of consensus sequence in English by Oxford Dictionaries. (n.d.). Retrieved November 20, 2017, from https://en.oxforddictionaries.com/definition/consensus_sequence
#Cyclins. (n.d.). ''BioNinja''. Retrieved on November 19, 2017 from http://ib.bioninja.com.au/standard-level/topic-1-cell-biology/16-cell-division/cyclins.html
#Differences between in vitro, in vivo, and in silico studies. (n.d.). Retrieved November 20, 2017, from https://mpkb.org/home/patients/assessing_literature/in_vitro_studies
#Donzeau M, Bourdineaud JP, Lauquin GJ. 1996. Regulation by low temperatures and anaerobiosis of a yeast gene specifying a putative GPI-anchored plasma membrane protein. Mol Microbiol 20: 449–459.
#Gasch AP, Spellman PT, Kao CM, et al. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11: 4241–4257.
#Glutathione. (n.d.). Retrieved November 20, 2017, from https://www.merriam-webster.com/dictionary/glutathione
#Haploid. (n.d.). Retrieved November 20, 2017, from http://www.biology-online.org/dictionary/Haploid
#HAW. (2011). Difference Between Haploid and Diploid. ''Difference Between.com''. Retrieved on November 19, 2017 from http://www.differencebetween.com/difference-between-haploid-and-vs-diploid/
#Hybridization. (2008). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Hybridization
#Kondo K, Inouye M. 1991. Cold-induction of yeast NSR1 protein and its role in pre-rRNA processing. J Biol Chem 267: 16 259–16 265.
#Kowalski LR, Kondo K, Inouye M. 1995. Cold-shock induction of a family of TIP1-related proteins associated with the membrane in Saccharomyces cerevisiae. Mol Microbiol 15: 341 – 353.
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Mai B, Breeden L. 1997. Xbp1, a stress-upregulated transcrip- tional repressor of the Saccharomyces cerevisae Swi4/Mbp1 family. Mol Cell Biol 17: 6491–6501.
#(n.d.). Retrieved November 19, 2017, from http://fg.cns.utexas.edu/fg/protocol%3A_YPD_plates.html
#(n.d.). Retrieved November 20, 2017, from https://www.nature.com/scitable/definition/diploid-310
#Oligonucleotide. (2014). ''News Medical Life Sciences''. Retrieved on November 19, 2017 from https://www.news-medical.net/life-sciences/What-is-an-Oligonucleotide.aspx
#Polypropylene. (n.d.). ''Dictionary.com''. Retrieved on November 19, 2017 from http://www.dictionary.com/browse/polypropylene
#Putative. (2014). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Putative
#Study.com. (2017). What is Annealing? - Definition, Biology & Process | Study.com. [online] Available at: http://study.com/academy/lesson/what-is-annealing-definition-biology-process.html [Accessed 21 Nov. 2017].
#Transcriptome. (n.d.). ''Nature''. Retrieved on November 19, 2017 from https://www.nature.com/scitable/definition/transcriptome-296
#Yelland, P. M. (2010). An introduction to correspondence analysis. Math. J, 12, 1-23.
#Young, F.W. (1999). Principle Components. ''forrest.psych.unc.edu''. Retrieved on November 19, 2017 from http://forrest.psych.unc.edu/research/vista-frames/help/lecturenotes/lecture13/biplot.html
#Zhang L, Ohta A, Horiuchi H, Takagi M, Imai R. 2001. Multiple mechanisms regulate expression of low temperature responsive (LOT) genes in Saccharomyces cerevisiae. Biochem Biophys Res Commun 283: 531 – 535.

===Week 14===
#Dahlquist, K. D., Dionisio, J. D. N., Fitzpatrick, B. G., Anguiano, N. A., Varshneya, A., Southwick, B. J., & Samdarshi, M. (2016). GRNsight: a web application and service for visualizing models of small-to medium-scale gene regulatory networks. PeerJ Computer Science, 2, e85.
#Ensembl. (2017). "Gene: HSF1". Retrieved November 28, 2017, from https://www.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YGL073W;r=VII:368753-371254;t=YGL073W 
#JASPAR. (2017). "Detailed information of matrix profile MA0319.1". Retrieved on November 28, 2017, from http://jaspar.genereg.net/matrix/MA0319.1/ 
#LMU BioDB 2017. (2017). Week 8. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_8
#LMU BioDB 2017. (2017). Week 10. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10
#LMU BioDB 2017. (2017). Week 14. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14 
#NCBI. (2017). "HSF1 stress-responsive transcription factor HSF1 [ Saccharomyces cerevisiae S288C ]". Retrieved November 28, 2017, from https://www.ncbi.nlm.nih.gov/gene/852806 
#Saccharomyces Genome Database. (2017). "HSF1 / YGL073W Overview". Retrieved November 28, 2017, from https://www.yeastgenome.org/locus/S000003041 
#Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.
#UniProt. (2017). "UniProtKB - P10961 (HSF_YEAST)". Retrieved November 28, 2017 from http://www.uniprot.org/uniprot/P10961

===Week 15===

==Team Links==

{{Template:JASPAR the Friendly Ghost Links}}

==Class Links==

{{Template:GRNsight Gene Page Project Links}}

JASPAR the Friendly Ghost Final Deliverables

2017-12-14T07:11:42Z

Aporras1: /* Electronic notebooks corresponding to the microarray results files */ links for pages with files

==Group Report==
==Individual statements of work, assessments, reflections==
[[QLanners_individual_statement|Quinn Lanners]] | [[Aporras1 individual statement|Antonio Porras]] | [[Ebachour_individual_statement|Edward Bachoura]] | [[simonwro120 individual statement|Simon Wroblewski]]
==Group PowerPoint presentation==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf | Final Group Presentation (pdf)]] | December 11, 2017
==Code==
==README that summarizes the functionality of your team's new feature==
==Excel spreadsheet with ANOVA results/stem formatting==
[[Media:AP dZAP1 stem.xlsx]]
==PowerPoint of screenshots of stem results==
[[Media:AP dZAP1 STEM Screenshots & p-values.zip]]
==Gene List and GO List files from each significant profile==
[[Media:AP dZAP1 GOlist and genelist for profiles.zip]]
==YEASTRACT "rank by TF" results==
[[Media:AP YEASTRACT Transcription Factors.xlsx]]
==GRNmap input workbook==
[[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]]
==GRNmap output workbook==
[[Media:15-gene 44-edge teamJASPAR Sigmoid estimation output.xlsx]]
*Expression vs. Time Images generated from MATLAB: [[Media:Output Images from 15-gene 44-edge teamJASPAR Sigmoid estimation.zip]]
==Electronic notebooks corresponding to the microarray results files==
#[[Aporras1 Week 8]]
#[[Aporras1 Week 10]]
#[[Aporras1 Week 14]]
#[[Aporras1 Week 15]]

==Team Links==

{{Template:JASPAR the Friendly Ghost Links}}
===Team Signatures===
*[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 20:49, 13 December 2017 (PST)

==Class Links==

{{Template:GRNsight Gene Page Project Links}}

Aporras1 Individual Assessment and Reflection

2017-12-14T06:22:36Z

Aporras1: /* Acknowledgements */ deliverables page mention

User page: [[User:Aporras1|Antonio Porras]]

Assignment page: [[GRNsight_Gene_Page_Project_Deliverables|Deliverables Page]]

==Individual Assessment and Reflection==

=== Statement of Work ===

* Describe exactly what you did on the project.
* Provide references or links to artifacts of your work, such as:
** Wiki pages
** Other files or documents
** Code or scripts

=== Assessment of Project ===

* Give an objective assessment of the success of your project workflow and teamwork.
* What worked and what didn't work?
* What would you do differently if you could do it all over again?
* Evaluate your team’s portion of the GRNsight Gene Page Project and Group Report in the following areas:
*# Content: What is the quality of the work?
*# Organization: Comment on the organization of the project and of your group's wiki pages.
*# Completeness: Did your team achieve all of the project objectives? Why or why not?

=== Reflection on the Process ===

* What did you learn?
** With your head (biological or computer science principles)
** With your heart (personal qualities and teamwork qualities that make things work or not work)?
** With your hands (technical skills)?
* What lesson will you take away from this project that you will still use a year from now?

==Acknowledgements==
#Copied the structure of the sections in my assessment and reflection from the [[GRNsight_Gene_Page_Project_Deliverables|Deliverables Page]].

==References==

[[Category:Journal Entry]]

Aporras1 Individual Assessment and Reflection

2017-12-14T06:21:21Z

Aporras1: /* Individual Assessment and Reflection */ format for reflection from deliverables page

User page: [[User:Aporras1|Antonio Porras]]

Assignment page: [[GRNsight_Gene_Page_Project_Deliverables|Deliverables Page]]

==Individual Assessment and Reflection==

=== Statement of Work ===

* Describe exactly what you did on the project.
* Provide references or links to artifacts of your work, such as:
** Wiki pages
** Other files or documents
** Code or scripts

=== Assessment of Project ===

* Give an objective assessment of the success of your project workflow and teamwork.
* What worked and what didn't work?
* What would you do differently if you could do it all over again?
* Evaluate your team’s portion of the GRNsight Gene Page Project and Group Report in the following areas:
*# Content: What is the quality of the work?
*# Organization: Comment on the organization of the project and of your group's wiki pages.
*# Completeness: Did your team achieve all of the project objectives? Why or why not?

=== Reflection on the Process ===

* What did you learn?
** With your head (biological or computer science principles)
** With your heart (personal qualities and teamwork qualities that make things work or not work)?
** With your hands (technical skills)?
* What lesson will you take away from this project that you will still use a year from now?

==Acknowledgements==

==References==

[[Category:Journal Entry]]

Aporras1 Individual Assessment and Reflection

2017-12-14T06:07:04Z

Aporras1: headers

Template:Aporras1Links

2017-12-14T06:03:57Z

Aporras1: Individual Assessment and Reflection link

Aporras1 Week 15

2017-12-12T07:15:08Z

Aporras1: final powerpoint deliverable

User page: [[User:Aporras1|Antonio Porras]]

Team page: [[JASPAR the Friendly Ghost|JASPAR The Friendly Ghost]]

Assignment page: [[Week 15|Week 15]]

==Electronic Notebook==
# Network was determined to be too big.
#* Began process of deleting the least significant
# Re-downloaded [[Media:AP YEASTRACT Transcription Factors.xlsx]] and found the transcription factors which I used in [[Aporras1_Week_14]] ranked from highest % in user set to lowest:
#**GLN3
#**HAP4
#**Ace2p
#**Sfp1p
#**Bas1p
#**Msn2p
#**Yap1p
#**Ash1p
#**Gcn4p
#**Msn4p
#**Abf1p
#**Cst6p
#**Sok2p
#**Rpn4p
#**Hsf1p
#**Zap1p
#**Cin5p
#**Aft1p
#**Spt23p
#**Pdr1p
#**Met4p
#**Arr1p

===ARR1 deletion===
# Moved "network" workbook to a new file found in [[Media:Trimming Network transcription factor deletions dZAP1.zip]]: Network ARR1 deletion.xlsx
# Began by deleting ARR1 in worksheet "Network ARR1 deletion"
#* Deleted row 5 and column E containing ARR1 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network ARR1 deletion.xlsx" file that has the "network" worksheet.
# Network remained too large.

===MET4 deletion===
# Moved "network" workbook from Network ARR1 deletion.xlsx to a new file found in [[Media:Trimming Network transcription factor deletions dZAP1.zip]]: Network MET4 deletion.xlsx
# Began by deleting MET4 in worksheet "network MET4 deletion"
#* Deleted row 13 and column M containing MET4 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network MET4 deletion" file that has the "network" worksheet.
# Network remained too large.

===PDR1 deletion===
# Moved "network" workbook from Network MET4 deletion.xlsx to a new file found in [[Media:Trimming Network transcription factor deletions dZAP1.zip]]: Network PDR1 deletion.xlsx
# Began by deleting PDR1 in worksheet "network PDR1 deletion"
#* Deleted row 15 and column O containing PDR1 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network PDR1 deletion" file that has the "network" worksheet.
# Network remained too large.

===SPT23 & BAS1 deletion===
# Moved "network" workbook from Network PDR1 deletion.xlsx to a new file found in folder [[Media:Trimming Network transcription factor deletions dZAP1.zip]]: Network SPT23 deletion.xlsx
# Began by deleting PDR1 in worksheet "network SPT23 deletion"
#* Deleted row 19 and column S containing SPT23 data.
#*BAS1 transcription factor became disconnected.
#*Deleted row 6 and column F containing BAS1 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network SPT23 deletion" file that has the "network" worksheet.
# Network remained too large.

===Network Files After Trimming===

[[Media:Trimming Network transcription factor deletions dZAP1.zip]]

Files were not necessary in the final GRNsight visualization, but rather for documentation on work performed before being provided by [[User:Kdahlquist|Dr. Dahlquist]].

Antonio, I finished paring down the network. Here is the final file (renamed): [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx | 15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]]. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:55, 6 December 2017 (PST)''

===GRNsight Visualization===
# Downloaded [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]] provided by [[User:Kdahlquist|Dr. Dahlquist]].
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx" file that has the "network" worksheet. Moved the nodes (genes) around until I created a layout I liked, ordering alphabetically, and took a screenshot of the results and saved the screenshot as:[[Media:GRNsight Visualization of 15-gene 44-edge teamJASPAR Sigmoid estimation.PNG]]

===GRNsight Regulation MATLAB Output===
# Used [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]] and allowed [[User:Kdahlquist|Dr. Dahlquist]] to run MATLAB.
#* Once it was completed, saved the output workbook as:[[Media:15-gene 44-edge teamJASPAR Sigmoid estimation output.xlsx]]
#* Saved the images and uploaded them to the wiki as:[[Media:Output Images from 15-gene 44-edge teamJASPAR Sigmoid estimation.zip]]
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "15-gene_44-edge_teamJASPAR_Sigmoid_estimation_output.xlsx" file that had the "network" worksheet. Moved the nodes (genes) around until I created a layout I liked, ordering alphabetically, and took a screenshot of the results and saved the screenshot as:[[Media:GRNsight Regulation Magnitude Visualization of 15-gene 44-edge teamJASPAR Sigmoid estimation.PNG]]

===Edits to Organization of Files===
# In [[Week 10|Week 10]] the powerpoint STEM screenshots, GOlists, and genelists were all zipped in [[Media:AP dZAP1 STEM Profiles and Powerpoint.zip]] and the deliverables, in [[GRNsight Gene Page Project Deliverables|Project Deliverables]], asked for two separate files.
#* Removed the powerpoint with the p-values and STEM screenshots. Zipped the powerpoint and uploaded it to the wiki as a new file found in the deliverables: [[Media:AP dZAP1 STEM Screenshots & p-values.zip]].
#* Removed the golists and genelists .txt files into a new folder and zipped the folder before uploading it as a new file found in the deliverables: [[Media:AP dZAP1 GOlist and genelist for profiles.zip]]

===Deliverables Checklist===
# Excel spreadsheet with ANOVA results/stem formatting (''.xlsx'')
#*[[Media:AP dZAP1 stem.xlsx]]
# PowerPoint of screenshots of stem results (''.pptx'')
#* [[Media:AP dZAP1 STEM Screenshots & p-values.zip]]
# Gene List and GO List files from each significant profile (''.txt'' compressed together in a ''.zip'' file)
#* [[Media:AP dZAP1 GOlist and genelist for profiles.zip]]
# YEASTRACT "rank by TF" results (''.xlsx'')
#* [[Media:AP YEASTRACT Transcription Factors.xlsx]]
# GRNmap input workbook (with network adjacency matrix, ''.xlsx'')
#* [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]]
# GRNmap output workbook (''.xlsx'')
#* [[Media:15-gene 44-edge teamJASPAR Sigmoid estimation output.xlsx]]
#* Expression vs Time Images generated from MATLAB
#** [[Media:Output Images from 15-gene 44-edge teamJASPAR Sigmoid estimation.zip]]
# Electronic notebook corresponding to these the microarray results files ([[Week 8]], [[Week 10]], & [[Week 14]]) support ''reproducible research'' so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results.
#* Summary for [[Aporras1_Week_8]]: In week 8, performed statistical analysis on the deletion ZAP1 using provided ANOVA. Specfically, Bonferroni & p value correction and Benjamini & Hochberg p value was calculated. The data examined the time intervals of 15 minutes, 30 minutes, 60 minutes, 90 minutes, and 120 minutes during cold shock.
#** Electronic notebook found in "Electronic Notebook" section of [[Aporras1_Week_8]]
#* Summary for [[Aporras1_Week_10]]: Used the data from [[Aporras1_Week_8]] to perform STEM clustering on dZAP1. Selected profile 22 because it had a very low p value and a high amount of genes (2E-157 and 252 respectively). Selected 6 GO terms from profile 22's GOlist to define and analyze in terms of why the cell would change the expression of the genes associated with the GO terms.
#** Electronic notebook found in "Electronic Notebook" section of [[Aporras1_Week_10]]
#* Summary for [[Aporras1_Week_14]]: Made edits to [[Aporras1_Week_8]] and [[Aporras1_Week_10]] according to feedback from [[User:Kdahlquist|Dr. Dahlquist]] & [[User:Dondi|Dr. Dionisio]]. Used the profile 22 genelist and ranked transcription factors with YEASTRACT by significance and selected the most significant ones with low P-values. Generated a regulation matrix using YEASTRACT and created an adjacency matrix with a network to visualize with GRNsight. The network was trimmed down to 15 genes and MATLAB was used to generate an output. Both the output and the original network were visualized with GRNsight.
#** Electronic notebook found in "Electronic Notebook" section of [[Aporras1_Week_14]].
#* Note: make a summary and provide links to individual pages with electronic notebooks.

==Final Powerpoint Presentation==
[[Media:JASPAR The Friendly Ghost Group Presentation.pdf]]

==Acknowledgements==
# Worked alongside [[User:Qlanners|Quinn Lanners]] to begin gathering deliverables.
# Copied the formatting and text from [[GRNsight_Gene_Page_Project_Deliverables]] checklist in my checklist category.
# Received file used for GRNsight visualization, received in class direction and instruction from [[User:Kdahlquist|Dr. Dahlquist]].
# Met up with group members in [[JASPAR the Friendly Ghost]] after the Thursday 12/01/2017 class and outside of class 12/09/2017 to discuss an outline of what needed to be completed and to work on the presentation.

'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.'''

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 16:11, 7 December 2017 (PST)

==References==
#Dahlquist, K. D., Dionisio, J. D. N., Fitzpatrick, B. G., Anguiano, N. A., Varshneya, A., Southwick, B. J., & Samdarshi, M. (2016). GRNsight: a web application and service for visualizing models of small-to medium-scale gene regulatory networks. PeerJ Computer Science, 2, e85.
# LMU BioDB 2017. (2017). Week 15. Retrieved December 05, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15
# LMU BioDB 2017. (2017). GRNsight Gene Page Project Deliverables. Retrieved December 05, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/GRNsight_Gene_Page_Project_Deliverables
# Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.

[[Category:Journal Entry]]

Aporras1 Week 15

2017-12-12T03:37:12Z

Aporras1: /* Acknowledgements */ statement of individual work

User page: [[User:Aporras1|Antonio Porras]]

Team page: [[JASPAR the Friendly Ghost|JASPAR The Friendly Ghost]]

Assignment page: [[Week 15|Week 15]]

==Electronic Notebook==
# Network was determined to be too big.
#* Began process of deleting the least significant
# Re-downloaded [[Media:AP YEASTRACT Transcription Factors.xlsx]] and found the transcription factors which I used in [[Aporras1_Week_14]] ranked from highest % in user set to lowest:
#**GLN3
#**HAP4
#**Ace2p
#**Sfp1p
#**Bas1p
#**Msn2p
#**Yap1p
#**Ash1p
#**Gcn4p
#**Msn4p
#**Abf1p
#**Cst6p
#**Sok2p
#**Rpn4p
#**Hsf1p
#**Zap1p
#**Cin5p
#**Aft1p
#**Spt23p
#**Pdr1p
#**Met4p
#**Arr1p

===ARR1 deletion===
# Moved "network" workbook to a new file found in [[Media:Trimming Network transcription factor deletions dZAP1.zip]]: Network ARR1 deletion.xlsx
# Began by deleting ARR1 in worksheet "Network ARR1 deletion"
#* Deleted row 5 and column E containing ARR1 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network ARR1 deletion.xlsx" file that has the "network" worksheet.
# Network remained too large.

===MET4 deletion===
# Moved "network" workbook from Network ARR1 deletion.xlsx to a new file found in [[Media:Trimming Network transcription factor deletions dZAP1.zip]]: Network MET4 deletion.xlsx
# Began by deleting MET4 in worksheet "network MET4 deletion"
#* Deleted row 13 and column M containing MET4 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network MET4 deletion" file that has the "network" worksheet.
# Network remained too large.

===PDR1 deletion===
# Moved "network" workbook from Network MET4 deletion.xlsx to a new file found in [[Media:Trimming Network transcription factor deletions dZAP1.zip]]: Network PDR1 deletion.xlsx
# Began by deleting PDR1 in worksheet "network PDR1 deletion"
#* Deleted row 15 and column O containing PDR1 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network PDR1 deletion" file that has the "network" worksheet.
# Network remained too large.

===SPT23 & BAS1 deletion===
# Moved "network" workbook from Network PDR1 deletion.xlsx to a new file found in folder [[Media:Trimming Network transcription factor deletions dZAP1.zip]]: Network SPT23 deletion.xlsx
# Began by deleting PDR1 in worksheet "network SPT23 deletion"
#* Deleted row 19 and column S containing SPT23 data.
#*BAS1 transcription factor became disconnected.
#*Deleted row 6 and column F containing BAS1 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network SPT23 deletion" file that has the "network" worksheet.
# Network remained too large.

===Network Files After Trimming===

[[Media:Trimming Network transcription factor deletions dZAP1.zip]]

Files were not necessary in the final GRNsight visualization, but rather for documentation on work performed before being provided by [[User:Kdahlquist|Dr. Dahlquist]].

Antonio, I finished paring down the network. Here is the final file (renamed): [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx | 15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]]. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:55, 6 December 2017 (PST)''

===GRNsight Visualization===
# Downloaded [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]] provided by [[User:Kdahlquist|Dr. Dahlquist]].
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx" file that has the "network" worksheet. Moved the nodes (genes) around until I created a layout I liked, ordering alphabetically, and took a screenshot of the results and saved the screenshot as:[[Media:GRNsight Visualization of 15-gene 44-edge teamJASPAR Sigmoid estimation.PNG]]

===GRNsight Regulation MATLAB Output===
# Used [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]] and allowed [[User:Kdahlquist|Dr. Dahlquist]] to run MATLAB.
#* Once it was completed, saved the output workbook as:[[Media:15-gene 44-edge teamJASPAR Sigmoid estimation output.xlsx]]
#* Saved the images and uploaded them to the wiki as:[[Media:Output Images from 15-gene 44-edge teamJASPAR Sigmoid estimation.zip]]
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "15-gene_44-edge_teamJASPAR_Sigmoid_estimation_output.xlsx" file that had the "network" worksheet. Moved the nodes (genes) around until I created a layout I liked, ordering alphabetically, and took a screenshot of the results and saved the screenshot as:[[Media:GRNsight Regulation Magnitude Visualization of 15-gene 44-edge teamJASPAR Sigmoid estimation.PNG]]

===Edits to Organization of Files===
# In [[Week 10|Week 10]] the powerpoint STEM screenshots, GOlists, and genelists were all zipped in [[Media:AP dZAP1 STEM Profiles and Powerpoint.zip]] and the deliverables, in [[GRNsight Gene Page Project Deliverables|Project Deliverables]], asked for two separate files.
#* Removed the powerpoint with the p-values and STEM screenshots. Zipped the powerpoint and uploaded it to the wiki as a new file found in the deliverables: [[Media:AP dZAP1 STEM Screenshots & p-values.zip]].
#* Removed the golists and genelists .txt files into a new folder and zipped the folder before uploading it as a new file found in the deliverables: [[Media:AP dZAP1 GOlist and genelist for profiles.zip]]

===Deliverables Checklist===
# Excel spreadsheet with ANOVA results/stem formatting (''.xlsx'')
#*[[Media:AP dZAP1 stem.xlsx]]
# PowerPoint of screenshots of stem results (''.pptx'')
#* [[Media:AP dZAP1 STEM Screenshots & p-values.zip]]
# Gene List and GO List files from each significant profile (''.txt'' compressed together in a ''.zip'' file)
#* [[Media:AP dZAP1 GOlist and genelist for profiles.zip]]
# YEASTRACT "rank by TF" results (''.xlsx'')
#* [[Media:AP YEASTRACT Transcription Factors.xlsx]]
# GRNmap input workbook (with network adjacency matrix, ''.xlsx'')
#* [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]]
# GRNmap output workbook (''.xlsx'')
#* [[Media:15-gene 44-edge teamJASPAR Sigmoid estimation output.xlsx]]
#* Expression vs Time Images generated from MATLAB
#** [[Media:Output Images from 15-gene 44-edge teamJASPAR Sigmoid estimation.zip]]
# Electronic notebook corresponding to these the microarray results files ([[Week 8]], [[Week 10]], & [[Week 14]]) support ''reproducible research'' so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results.
#* Summary for [[Aporras1_Week_8]]: In week 8, performed statistical analysis on the deletion ZAP1 using provided ANOVA. Specfically, Bonferroni & p value correction and Benjamini & Hochberg p value was calculated. The data examined the time intervals of 15 minutes, 30 minutes, 60 minutes, 90 minutes, and 120 minutes during cold shock.
#** Electronic notebook found in "Electronic Notebook" section of [[Aporras1_Week_8]]
#* Summary for [[Aporras1_Week_10]]: Used the data from [[Aporras1_Week_8]] to perform STEM clustering on dZAP1. Selected profile 22 because it had a very low p value and a high amount of genes (2E-157 and 252 respectively). Selected 6 GO terms from profile 22's GOlist to define and analyze in terms of why the cell would change the expression of the genes associated with the GO terms.
#** Electronic notebook found in "Electronic Notebook" section of [[Aporras1_Week_10]]
#* Summary for [[Aporras1_Week_14]]: Made edits to [[Aporras1_Week_8]] and [[Aporras1_Week_10]] according to feedback from [[User:Kdahlquist|Dr. Dahlquist]] & [[User:Dondi|Dr. Dionisio]]. Used the profile 22 genelist and ranked transcription factors with YEASTRACT by significance and selected the most significant ones with low P-values. Generated a regulation matrix using YEASTRACT and created an adjacency matrix with a network to visualize with GRNsight. The network was trimmed down to 15 genes and MATLAB was used to generate an output. Both the output and the original network were visualized with GRNsight.
#** Electronic notebook found in "Electronic Notebook" section of [[Aporras1_Week_14]].
#* Note: make a summary and provide links to individual pages with electronic notebooks.

==Acknowledgements==
# Worked alongside [[User:Qlanners|Quinn Lanners]] to begin gathering deliverables.
# Copied the formatting and text from [[GRNsight_Gene_Page_Project_Deliverables]] checklist in my checklist category.
# Received file used for GRNsight visualization, received in class direction and instruction from [[User:Kdahlquist|Dr. Dahlquist]].
# Met up with group members in [[JASPAR the Friendly Ghost]] after the Thursday 12/01/2017 class and outside of class 12/09/2017 to discuss an outline of what needed to be completed and to work on the presentation.

'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.'''

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 16:11, 7 December 2017 (PST)

==References==
#Dahlquist, K. D., Dionisio, J. D. N., Fitzpatrick, B. G., Anguiano, N. A., Varshneya, A., Southwick, B. J., & Samdarshi, M. (2016). GRNsight: a web application and service for visualizing models of small-to medium-scale gene regulatory networks. PeerJ Computer Science, 2, e85.
# LMU BioDB 2017. (2017). Week 15. Retrieved December 05, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15
# LMU BioDB 2017. (2017). GRNsight Gene Page Project Deliverables. Retrieved December 05, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/GRNsight_Gene_Page_Project_Deliverables
# Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.

[[Category:Journal Entry]]

Aporras1 Week 15

2017-12-09T23:33:11Z

Aporras1: /* Deliverables Checklist */ typo fixed

User page: [[User:Aporras1|Antonio Porras]]

Team page: [[JASPAR the Friendly Ghost|JASPAR The Friendly Ghost]]

Assignment page: [[Week 15|Week 15]]

==Electronic Notebook==
# Network was determined to be too big.
#* Began process of deleting the least significant
# Re-downloaded [[Media:AP YEASTRACT Transcription Factors.xlsx]] and found the transcription factors which I used in [[Aporras1_Week_14]] ranked from highest % in user set to lowest:
#**GLN3
#**HAP4
#**Ace2p
#**Sfp1p
#**Bas1p
#**Msn2p
#**Yap1p
#**Ash1p
#**Gcn4p
#**Msn4p
#**Abf1p
#**Cst6p
#**Sok2p
#**Rpn4p
#**Hsf1p
#**Zap1p
#**Cin5p
#**Aft1p
#**Spt23p
#**Pdr1p
#**Met4p
#**Arr1p

===ARR1 deletion===
# Moved "network" workbook to a new file found in [[Media:Trimming Network transcription factor deletions dZAP1.zip]]: Network ARR1 deletion.xlsx
# Began by deleting ARR1 in worksheet "Network ARR1 deletion"
#* Deleted row 5 and column E containing ARR1 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network ARR1 deletion.xlsx" file that has the "network" worksheet.
# Network remained too large.

===MET4 deletion===
# Moved "network" workbook from Network ARR1 deletion.xlsx to a new file found in [[Media:Trimming Network transcription factor deletions dZAP1.zip]]: Network MET4 deletion.xlsx
# Began by deleting MET4 in worksheet "network MET4 deletion"
#* Deleted row 13 and column M containing MET4 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network MET4 deletion" file that has the "network" worksheet.
# Network remained too large.

===PDR1 deletion===
# Moved "network" workbook from Network MET4 deletion.xlsx to a new file found in [[Media:Trimming Network transcription factor deletions dZAP1.zip]]: Network PDR1 deletion.xlsx
# Began by deleting PDR1 in worksheet "network PDR1 deletion"
#* Deleted row 15 and column O containing PDR1 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network PDR1 deletion" file that has the "network" worksheet.
# Network remained too large.

===SPT23 & BAS1 deletion===
# Moved "network" workbook from Network PDR1 deletion.xlsx to a new file found in folder [[Media:Trimming Network transcription factor deletions dZAP1.zip]]: Network SPT23 deletion.xlsx
# Began by deleting PDR1 in worksheet "network SPT23 deletion"
#* Deleted row 19 and column S containing SPT23 data.
#*BAS1 transcription factor became disconnected.
#*Deleted row 6 and column F containing BAS1 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network SPT23 deletion" file that has the "network" worksheet.
# Network remained too large.

===Network Files After Trimming===

[[Media:Trimming Network transcription factor deletions dZAP1.zip]]

Files were not necessary in the final GRNsight visualization, but rather for documentation on work performed before being provided by [[User:Kdahlquist|Dr. Dahlquist]].

Antonio, I finished paring down the network. Here is the final file (renamed): [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx | 15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]]. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:55, 6 December 2017 (PST)''

===GRNsight Visualization===
# Downloaded [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]] provided by [[User:Kdahlquist|Dr. Dahlquist]].
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx" file that has the "network" worksheet. Moved the nodes (genes) around until I created a layout I liked, ordering alphabetically, and took a screenshot of the results and saved the screenshot as:[[Media:GRNsight Visualization of 15-gene 44-edge teamJASPAR Sigmoid estimation.PNG]]

===GRNsight Regulation MATLAB Output===
# Used [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]] and allowed [[User:Kdahlquist|Dr. Dahlquist]] to run MATLAB.
#* Once it was completed, saved the output workbook as:[[Media:15-gene 44-edge teamJASPAR Sigmoid estimation output.xlsx]]
#* Saved the images and uploaded them to the wiki as:[[Media:Output Images from 15-gene 44-edge teamJASPAR Sigmoid estimation.zip]]
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "15-gene_44-edge_teamJASPAR_Sigmoid_estimation_output.xlsx" file that had the "network" worksheet. Moved the nodes (genes) around until I created a layout I liked, ordering alphabetically, and took a screenshot of the results and saved the screenshot as:[[Media:GRNsight Regulation Magnitude Visualization of 15-gene 44-edge teamJASPAR Sigmoid estimation.PNG]]

===Edits to Organization of Files===
# In [[Week 10|Week 10]] the powerpoint STEM screenshots, GOlists, and genelists were all zipped in [[Media:AP dZAP1 STEM Profiles and Powerpoint.zip]] and the deliverables, in [[GRNsight Gene Page Project Deliverables|Project Deliverables]], asked for two separate files.
#* Removed the powerpoint with the p-values and STEM screenshots. Zipped the powerpoint and uploaded it to the wiki as a new file found in the deliverables: [[Media:AP dZAP1 STEM Screenshots & p-values.zip]].
#* Removed the golists and genelists .txt files into a new folder and zipped the folder before uploading it as a new file found in the deliverables: [[Media:AP dZAP1 GOlist and genelist for profiles.zip]]

===Deliverables Checklist===
# Excel spreadsheet with ANOVA results/stem formatting (''.xlsx'')
#*[[Media:AP dZAP1 stem.xlsx]]
# PowerPoint of screenshots of stem results (''.pptx'')
#* [[Media:AP dZAP1 STEM Screenshots & p-values.zip]]
# Gene List and GO List files from each significant profile (''.txt'' compressed together in a ''.zip'' file)
#* [[Media:AP dZAP1 GOlist and genelist for profiles.zip]]
# YEASTRACT "rank by TF" results (''.xlsx'')
#* [[Media:AP YEASTRACT Transcription Factors.xlsx]]
# GRNmap input workbook (with network adjacency matrix, ''.xlsx'')
#* [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]]
# GRNmap output workbook (''.xlsx'')
#* [[Media:15-gene 44-edge teamJASPAR Sigmoid estimation output.xlsx]]
#* Expression vs Time Images generated from MATLAB
#** [[Media:Output Images from 15-gene 44-edge teamJASPAR Sigmoid estimation.zip]]
# Electronic notebook corresponding to these the microarray results files ([[Week 8]], [[Week 10]], & [[Week 14]]) support ''reproducible research'' so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results.
#* Summary for [[Aporras1_Week_8]]: In week 8, performed statistical analysis on the deletion ZAP1 using provided ANOVA. Specfically, Bonferroni & p value correction and Benjamini & Hochberg p value was calculated. The data examined the time intervals of 15 minutes, 30 minutes, 60 minutes, 90 minutes, and 120 minutes during cold shock.
#** Electronic notebook found in "Electronic Notebook" section of [[Aporras1_Week_8]]
#* Summary for [[Aporras1_Week_10]]: Used the data from [[Aporras1_Week_8]] to perform STEM clustering on dZAP1. Selected profile 22 because it had a very low p value and a high amount of genes (2E-157 and 252 respectively). Selected 6 GO terms from profile 22's GOlist to define and analyze in terms of why the cell would change the expression of the genes associated with the GO terms.
#** Electronic notebook found in "Electronic Notebook" section of [[Aporras1_Week_10]]
#* Summary for [[Aporras1_Week_14]]: Made edits to [[Aporras1_Week_8]] and [[Aporras1_Week_10]] according to feedback from [[User:Kdahlquist|Dr. Dahlquist]] & [[User:Dondi|Dr. Dionisio]]. Used the profile 22 genelist and ranked transcription factors with YEASTRACT by significance and selected the most significant ones with low P-values. Generated a regulation matrix using YEASTRACT and created an adjacency matrix with a network to visualize with GRNsight. The network was trimmed down to 15 genes and MATLAB was used to generate an output. Both the output and the original network were visualized with GRNsight.
#** Electronic notebook found in "Electronic Notebook" section of [[Aporras1_Week_14]].
#* Note: make a summary and provide links to individual pages with electronic notebooks.

==Acknowledgements==
# Worked alongside [[User:Qlanners|Quinn Lanners]] to begin gathering deliverables.
# Copied the formatting and text from [[GRNsight_Gene_Page_Project_Deliverables]] checklist in my checklist category.
# Received file used for GRNsight visualization, received in class direction and instruction from [[User:Kdahlquist|Dr. Dahlquist]].
# Met up with group members in [[JASPAR the Friendly Ghost]] after the Thursday 12/01/2017 class and outside of class 12/09/2017 to discuss an outline of what needed to be completed and to work on the presentation.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 16:11, 7 December 2017 (PST)

==References==
#Dahlquist, K. D., Dionisio, J. D. N., Fitzpatrick, B. G., Anguiano, N. A., Varshneya, A., Southwick, B. J., & Samdarshi, M. (2016). GRNsight: a web application and service for visualizing models of small-to medium-scale gene regulatory networks. PeerJ Computer Science, 2, e85.
# LMU BioDB 2017. (2017). Week 15. Retrieved December 05, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15
# LMU BioDB 2017. (2017). GRNsight Gene Page Project Deliverables. Retrieved December 05, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/GRNsight_Gene_Page_Project_Deliverables
# Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.

[[Category:Journal Entry]]

JASPAR the Friendly Ghost Final Deliverables

2017-12-09T23:15:48Z

Aporras1: files from Data analyst

==Group Report==
==Individual statements of work, assessments, reflections==
[[QLanners_individual_statement|Quinn Lanners]] | [[Aporras1 individual statement|Antonio Porras]] | [[Ebachour_individual_statement|Edward Bachoura]] | [[simonwro120 individual statement|Simon Wroblewski]]
==Group PowerPoint presentation==
==Code==
==README that summarizes the functionality of your team's new feature==
==Excel spreadsheet with ANOVA results/stem formatting==
[[Media:AP dZAP1 stem.xlsx]]
==PowerPoint of screenshots of stem results==
[[Media:AP dZAP1 STEM Screenshots & p-values.zip]]
==Gene List and GO List files from each significant profile==
[[Media:AP dZAP1 GOlist and genelist for profiles.zip]]
==YEASTRACT "rank by TF" results==
[[Media:AP YEASTRACT Transcription Factors.xlsx]]
==GRNmap input workbook==
[[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]]
==GRNmap output workbook==
[[Media:15-gene 44-edge teamJASPAR Sigmoid estimation output.xlsx]]
*Expression vs. Time Images generated from MATLAB: [[Media:Output Images from 15-gene 44-edge teamJASPAR Sigmoid estimation.zip]]
==Electronic notebook corresponding to these the microarray results files==

==Team Links==

{{Template:JASPAR the Friendly Ghost Links}}

==Class Links==

{{Template:GRNsight Gene Page Project Links}}

Aporras1 Week 15

2017-12-09T23:15:35Z

Aporras1: /* Deliverables Checklist */ stem file replace

User page: [[User:Aporras1|Antonio Porras]]

Team page: [[JASPAR the Friendly Ghost|JASPAR The Friendly Ghost]]

Assignment page: [[Week 15|Week 15]]

==Electronic Notebook==
# Network was determined to be too big.
#* Began process of deleting the least significant
# Re-downloaded [[Media:AP YEASTRACT Transcription Factors.xlsx]] and found the transcription factors which I used in [[Aporras1_Week_14]] ranked from highest % in user set to lowest:
#**GLN3
#**HAP4
#**Ace2p
#**Sfp1p
#**Bas1p
#**Msn2p
#**Yap1p
#**Ash1p
#**Gcn4p
#**Msn4p
#**Abf1p
#**Cst6p
#**Sok2p
#**Rpn4p
#**Hsf1p
#**Zap1p
#**Cin5p
#**Aft1p
#**Spt23p
#**Pdr1p
#**Met4p
#**Arr1p

===ARR1 deletion===
# Moved "network" workbook to a new file found in [[Media:Trimming Network transcription factor deletions dZAP1.zip]]: Network ARR1 deletion.xlsx
# Began by deleting ARR1 in worksheet "Network ARR1 deletion"
#* Deleted row 5 and column E containing ARR1 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network ARR1 deletion.xlsx" file that has the "network" worksheet.
# Network remained too large.

===MET4 deletion===
# Moved "network" workbook from Network ARR1 deletion.xlsx to a new file found in [[Media:Trimming Network transcription factor deletions dZAP1.zip]]: Network MET4 deletion.xlsx
# Began by deleting MET4 in worksheet "network MET4 deletion"
#* Deleted row 13 and column M containing MET4 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network MET4 deletion" file that has the "network" worksheet.
# Network remained too large.

===PDR1 deletion===
# Moved "network" workbook from Network MET4 deletion.xlsx to a new file found in [[Media:Trimming Network transcription factor deletions dZAP1.zip]]: Network PDR1 deletion.xlsx
# Began by deleting PDR1 in worksheet "network PDR1 deletion"
#* Deleted row 15 and column O containing PDR1 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network PDR1 deletion" file that has the "network" worksheet.
# Network remained too large.

===SPT23 & BAS1 deletion===
# Moved "network" workbook from Network PDR1 deletion.xlsx to a new file found in folder [[Media:Trimming Network transcription factor deletions dZAP1.zip]]: Network SPT23 deletion.xlsx
# Began by deleting PDR1 in worksheet "network SPT23 deletion"
#* Deleted row 19 and column S containing SPT23 data.
#*BAS1 transcription factor became disconnected.
#*Deleted row 6 and column F containing BAS1 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network SPT23 deletion" file that has the "network" worksheet.
# Network remained too large.

===Network Files After Trimming===

[[Media:Trimming Network transcription factor deletions dZAP1.zip]]

Files were not necessary in the final GRNsight visualization, but rather for documentation on work performed before being provided by [[User:Kdahlquist|Dr. Dahlquist]].

Antonio, I finished paring down the network. Here is the final file (renamed): [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx | 15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]]. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:55, 6 December 2017 (PST)''

===GRNsight Visualization===
# Downloaded [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]] provided by [[User:Kdahlquist|Dr. Dahlquist]].
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx" file that has the "network" worksheet. Moved the nodes (genes) around until I created a layout I liked, ordering alphabetically, and took a screenshot of the results and saved the screenshot as:[[Media:GRNsight Visualization of 15-gene 44-edge teamJASPAR Sigmoid estimation.PNG]]

===GRNsight Regulation MATLAB Output===
# Used [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]] and allowed [[User:Kdahlquist|Dr. Dahlquist]] to run MATLAB.
#* Once it was completed, saved the output workbook as:[[Media:15-gene 44-edge teamJASPAR Sigmoid estimation output.xlsx]]
#* Saved the images and uploaded them to the wiki as:[[Media:Output Images from 15-gene 44-edge teamJASPAR Sigmoid estimation.zip]]
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "15-gene_44-edge_teamJASPAR_Sigmoid_estimation_output.xlsx" file that had the "network" worksheet. Moved the nodes (genes) around until I created a layout I liked, ordering alphabetically, and took a screenshot of the results and saved the screenshot as:[[Media:GRNsight Regulation Magnitude Visualization of 15-gene 44-edge teamJASPAR Sigmoid estimation.PNG]]

===Edits to Organization of Files===
# In [[Week 10|Week 10]] the powerpoint STEM screenshots, GOlists, and genelists were all zipped in [[Media:AP dZAP1 STEM Profiles and Powerpoint.zip]] and the deliverables, in [[GRNsight Gene Page Project Deliverables|Project Deliverables]], asked for two separate files.
#* Removed the powerpoint with the p-values and STEM screenshots. Zipped the powerpoint and uploaded it to the wiki as a new file found in the deliverables: [[Media:AP dZAP1 STEM Screenshots & p-values.zip]].
#* Removed the golists and genelists .txt files into a new folder and zipped the folder before uploading it as a new file found in the deliverables: [[Media:AP dZAP1 GOlist and genelist for profiles.zip]]

===Deliverables Checklist===
# Excel spreadsheet with ANOVA results/stem formatting (''.xlsx'')
#* #[[Media:AP dZAP1 stem.xlsx]]
# PowerPoint of screenshots of stem results (''.pptx'')
#* [[Media:AP dZAP1 STEM Screenshots & p-values.zip]]
# Gene List and GO List files from each significant profile (''.txt'' compressed together in a ''.zip'' file)
#* [[Media:AP dZAP1 GOlist and genelist for profiles.zip]]
# YEASTRACT "rank by TF" results (''.xlsx'')
#* [[Media:AP YEASTRACT Transcription Factors.xlsx]]
# GRNmap input workbook (with network adjacency matrix, ''.xlsx'')
#* [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]]
# GRNmap output workbook (''.xlsx'')
#* [[Media:15-gene 44-edge teamJASPAR Sigmoid estimation output.xlsx]]
#* Expression vs Time Images generated from MATLAB
#** [[Media:Output Images from 15-gene 44-edge teamJASPAR Sigmoid estimation.zip]]
# Electronic notebook corresponding to these the microarray results files ([[Week 8]], [[Week 10]], & [[Week 14]]) support ''reproducible research'' so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results.
#* Summary for [[Aporras1_Week_8]]: In week 8, performed statistical analysis on the deletion ZAP1 using provided ANOVA. Specfically, Bonferroni & p value correction and Benjamini & Hochberg p value was calculated. The data examined the time intervals of 15 minutes, 30 minutes, 60 minutes, 90 minutes, and 120 minutes during cold shock.
#** Electronic notebook found in "Electronic Notebook" section of [[Aporras1_Week_8]]
#* Summary for [[Aporras1_Week_10]]: Used the data from [[Aporras1_Week_8]] to perform STEM clustering on dZAP1. Selected profile 22 because it had a very low p value and a high amount of genes (2E-157 and 252 respectively). Selected 6 GO terms from profile 22's GOlist to define and analyze in terms of why the cell would change the expression of the genes associated with the GO terms.
#** Electronic notebook found in "Electronic Notebook" section of [[Aporras1_Week_10]]
#* Summary for [[Aporras1_Week_14]]: Made edits to [[Aporras1_Week_8]] and [[Aporras1_Week_10]] according to feedback from [[User:Kdahlquist|Dr. Dahlquist]] & [[User:Dondi|Dr. Dionisio]]. Used the profile 22 genelist and ranked transcription factors with YEASTRACT by significance and selected the most significant ones with low P-values. Generated a regulation matrix using YEASTRACT and created an adjacency matrix with a network to visualize with GRNsight. The network was trimmed down to 15 genes and MATLAB was used to generate an output. Both the output and the original network were visualized with GRNsight.
#** Electronic notebook found in "Electronic Notebook" section of [[Aporras1_Week_14]].
#* Note: make a summary and provide links to individual pages with electronic notebooks.

==Acknowledgements==
# Worked alongside [[User:Qlanners|Quinn Lanners]] to begin gathering deliverables.
# Copied the formatting and text from [[GRNsight_Gene_Page_Project_Deliverables]] checklist in my checklist category.
# Received file used for GRNsight visualization, received in class direction and instruction from [[User:Kdahlquist|Dr. Dahlquist]].
# Met up with group members in [[JASPAR the Friendly Ghost]] after the Thursday 12/01/2017 class and outside of class 12/09/2017 to discuss an outline of what needed to be completed and to work on the presentation.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 16:11, 7 December 2017 (PST)

==References==
#Dahlquist, K. D., Dionisio, J. D. N., Fitzpatrick, B. G., Anguiano, N. A., Varshneya, A., Southwick, B. J., & Samdarshi, M. (2016). GRNsight: a web application and service for visualizing models of small-to medium-scale gene regulatory networks. PeerJ Computer Science, 2, e85.
# LMU BioDB 2017. (2017). Week 15. Retrieved December 05, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15
# LMU BioDB 2017. (2017). GRNsight Gene Page Project Deliverables. Retrieved December 05, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/GRNsight_Gene_Page_Project_Deliverables
# Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.

[[Category:Journal Entry]]

JASPAR the Friendly Ghost

2017-12-09T23:09:15Z

Aporras1: /* Antonio's Working Files */ removed wrong file

==GRNsight Gene Page Project Deliverables==
[[JASPAR_the_Friendly_Ghost_Final_Deliverables|JASPAR the Friendly Ghost Final GRNsight Deliverables Page]]
==Working Deliverables==
[[Media:Genome-wide_analysis_of_the_yeast_transcriptome_upon_heat_and_cold_shock._QL_AP.zip|Antonio and Quinn Journal Club Presentation]] | November 21, 2017 
[[Media:e_and_s_presentation_2.pdf|Eddie and Simon Chapter 6 Presentation]] | November 14, 2017 
[https://github.com/bhamilton18/GRNsight GitHub fork] 
[https://github.com/bhamilton18/GRNsight/tree/gene-database-apis GitHub api branch] (in collaboration with [[Gene_hAPI|Gene_hAPI team]])
==Working Files==

===Antonio's Working Files===
# Gene list for profile 22 of dZAP1 Excel file: [[Media:AP dZAP1 profile22 genelist.xlsx]]
# YEASTRACT Transcription Factor Data: [[Media:AP YEASTRACT Transcription Factors.xlsx]]
# YEASTRACT Regulation Matrix Profile: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix: [[Media:AP Adjacency Matrix profile22 dZAP1.xlsx]]
# YEASTRACT Adjacency Matrix with Network for GRNsight: [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]]

==Calendar==
{| class ="wikitable"
|+November & December
|-
|Sunday
|Monday
|Tuesday
|Wednesday
|Thursday
|Friday
|Saturday
|-
|
|
|
|'''1'''
|'''2'''
|'''3'''
|'''4'''
|-
|'''5'''
|'''6'''
|'''7'''
|'''8'''
|'''9'''
|'''10'''
|'''11'''
|-
|'''12'''
|'''13'''
|'''14''' C: PPT Presentation PM/DA: Journal Articles
|'''15'''
|'''16'''
|'''17'''
|'''18'''
|-
|'''19'''
|'''20'''
|'''21''' C: Complete setup steps (Milestones 1-3) PM/DA: Journal Club Presentations
|'''22''' ''Thanksgiving Break''
|'''23''' ''Thanksgiving Break''
|'''24''' ''Thanksgiving Break''
|'''25'''
|-
|'''26'''
|'''27'''
|'''28''' C: Fimilariaze self with file structure PM: Chose application data fields from JASPAR DA: Review ANOVA Results
|'''29'''
|'''30''' C: Tests for API PM: Share info to be used from JASPAR with other teams DA: Determine transcription factors, develop candidate gene reg network, and fix edits from week 8 & 10
|'''1'''
|'''2'''
|-
|'''3'''
|'''4'''
|'''5''' C: Retrieval code for API PM: Begin Final Group Paper and PPT DA:Model gene reg network Visualize Results
|'''6'''
|'''7''' C: Review and Test Code PM: Review and Test code PM&DA:Work on Paper and PPT
|'''8'''
|'''9''' Complete Group PPT
|-
|'''10''' Practice Group Presentation
|'''11''' Final group Presentation ''2:00-4:00PM''
|'''12'''
|'''13''' Final Group Paper Completely Written
|'''14''' Edit Final Group Paper
|'''15''' All deliverables due ''4:30PM''
|'''16'''
|}

==Executive Summaries==

===Week 11===

====Quinn's Executive Summary====
Created citations for two entries in the annotated bibliography for papers that report microarray data from yeast subjected to cold shock: 
Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6 
Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301 
Also completed a search activity to compare the results found from PubMed, GoogleScholar, and Web of Science using both basic and advanced search tools. 
Individual Journal Page: [[QLanners Week 11]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Executive Summary====
For this assignment, I spent most of my time reading and re-reading Paul Ford's article on how apps are made. It was chapter 6 in a larger work called ''What is Code?'' After absorbing the information laid out in this chapter, Eddie and I made a presentation about it. The presentation summarizes the article, which is about technique, methods, practices, and tools that expedite and simplify the programming process. In addition to making the presentation, I finished my 10 terms and made an outline for the article on my individual journal page. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 13:45, 14 November 2017 (PST)

====Antonio's Executive Summary====

Created two citations for the bibliography for the following articles:

#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.

I also completed the basic keyword searches on PubMed, Google Scholar, and Web of Science along with the advanced searches and the respective results. Lastly, I completed the prospective searches and collected the results of how many articles the article cites and how many articles cite the article. Totaling to the 3 articles.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 15:51, 14 November 2017 (PST)

Individual Journal Week 11: [[Aporras1_Week_11|Aporras1 Week 11]]

====Eddie Bachoura's Executive Summary====
This week, I spent my time for this class reading the Paul Ford article, chapter 6, which was about how to write applications and the modern practices and tools which are used to aid in cutting down some of the tedious nature of coding. Then, Simon and I spent the rest of the time working on our presentation. Team's progress: I believe that Simon and I worked well this weekend. The only issue that I found was that we didn't start until pretty late (Monday), but that was all at my own fault because I wasn't here for this weekend. We should fix that by starting earlier next weekend!

Individual Journal Week 11: [[Ebachour_Week_11|Eddie Bachoura Week 11]] 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:29, 13 November 2017 (PST)

===Week 12===

====Quinn's Executive Summary====
Worked closely with Antonio to summarize the results of the journal article Becerra et al. (2003) into a journal club presentation. In order to do so, we both completed the outline provided on the [[Week_12|Week 12]] assignment page on our wiki. We then took this information and used it to create our journal club presentations, which we practiced together and will share in class on Tuesday, November 21. 
Individual Journal Page: [[QLanners Week 12]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Executive Summary====
This week, I met with my coding partner [[User:Ebachour|Eddie Bachoura]] and he helped me clone the code that [[User:Bhamilton18|Blair Hamilton]] forked from the master branch.
After that, Eddie and I helped put together a list of milestones with dates that they should be completed. Using that, Quinn was able to put together a calendar like scheduale for our team to refer to. The last thing I did was open up the cloned files from Blair's fork on my text editor so that I could familiarize myself with the code. 
Individual Journal Page: [[simonwro120 Week 12]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:44, 20 November 2017 (PST)

====Antonio's Executive Summary====
Worked throughout the assignment with Quinn to complete the powerpoint presentation on the journal article: ''Genome-wide analysis of the yeast transcriptome upon heat and cold shock''. We both worked closely together on the outline of the article while maintaining our own style of completing the outline. We then practiced our presentation once the information was finalized and are looking forward to sharing on Tuesday the 21st of November.

Individual journal page: [[Aporras1_Week_12|Aporras 1 Week 12]]

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:19, 20 November 2017 (PST)
====Eddie Bachoura's Executive Summary====
This week, most of my time was spent setting up the branch on github and then getting my local version up and running so that I can write and test code on my own laptop. After that, I helped Simon out with doing the same. I also sent Quinn a list of our milestones for this project, as well as letting him know which ones were already completed. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 19:09, 20 November 2017 (PST) 
Week 12 Journal Page: [[ebachour_Week_12| Edward Bachoura]]

===Week 14===

====Quinn's Executive Summary====
This week, I worked closely with the other QAs and [[User:Kdahlquist|Dr. Dahlquist]] to determine what information should be pulled from each of the five databases. I then communicated this information to our coders. Along with this task, I worked communicated closely with both the data analyst and the coders to ensure that they were on track, and to make modifications to their respective milestones on the team calender. Finally, I added additional team milestones to the calendar to reflect all of the steps that need to be taken to complete the deliverables that we have due at the end of the semester. All of this progress can be seen in my [[QLanners_Week_14|individual weekly journal]] 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Executive Summary====
This week our coding group hit a bit of wall, not just for one, but for multiple reasons. One reason was caused by the fact that one of the coding group members worked in a language that would not be compatible with GRNsight. Another problem our coding group encountered was caused by a complexity in the the JASPAR API relating CORS (Cross-Oirgin Resource Sharing). Although these complications did occur, both me and Eddie B. know where the API guidelines are for JASPAR and what content we need to produce. In addition to that, an api file has been made as well which will be augmented soon. 
Individual Journal Page: [[simonwro120 Week 14]] 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:45, 4 December 2017 (PST)

====Antonio's Executive Summary====
This week, I made edits to both my individual [[Aporras1 Week 8]] and [[Aporras1 Week 10]] pages based from feedback received from [[User:Kdahlquist|Dr. Dahlquist]] and [[User:Dondi|Dr. Dionisio]]. The outline for these edits can be found on my [[Aporras1 Week 14]] page along with the continuation of the [[Week 10|Week 10]] assignment. In this continuation, I selected transcription factors from [[Media:AP dZAP1 profile22 genelist.xlsx]] and put them into YEASTRACT to find the most significant ones and found 49 significant transcription factors found in [[Media:AP YEASTRACT Transcription Factors.xlsx]]. Then I selected 22 of the most significant, 2 additional ones (HAP4 and GLN3) as instructed, to put back into YEASTRACT and create a regulation matrix uploaded as: [[Media:AP Regulation Matrix profile22 dZAP1.xlsx]]. I then created a "network" worksheet, found in [[Media:AP Adjacency Matrix profile22 Network dZAP1.xlsx]], from the matrix and used GRNsight to generate a regulation network visualization: [[Media:AP Regulation Matrix profile22 GRNsight Network.PNG]]. These media downloads can also be found on my [[Aporras1 Week 14|Week 14]] journal entry in the
"Deliverables" section.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:31, 3 December 2017 (PST)

====Eddie's Executive Summary====
We've been working on JASPAR since the last assignment. As of this week, I am mostly sure that we have the two API calls that we need in order to be able to retrieve any Yeast gene database entry on JASPAR, using the gene ID. I would say that we are already done, but it seems that there are some access complications. I have a feeling it has something to do with CORS and I did some research to try to dix the issue. I found one work around, using a chrome extension, that allows me to bypass the issue, but I'm not sure that this solution will translate well to the actual GRNsight server, but I will discuss with Dondi tomorrow. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:25, 4 December 2017 (PST)

==Weekly Reflections==

===Week 11===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a good job of staying on task and working together to make sure that we both understood the whole assignment. So there was good communication between the Bibliography group.
#What didn't work?
#*I felt a bit disconnected with my other teammates Eddie and Simon. There was not very good communication with them about whether they needed any help and if they were on progress.
#What to improve upon going forward?
#*Going forward all of the members of the team need to do a better job of communicating. Also, we need to do a better job of properly communicating about how to fill out the team page ahead of time, so that we aren't frantically figuring that out last second. I will work to fix this by initiating communication earlier on in the week.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 00:25, 14 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*Both me and Eddie were able to put together a powerpoint and present in time for the presentation date
#What didn't work?
#*Due to traveling, Eddie could not be back in LA to help with the project until Monday, which did not give us much time, resulting in our presentation being a bit late as far as submission on our wiki pages.
#How will to improve upon going forward?
#*Going forward I'd like to start early and finish early, that way we can be prepared for any unexpected complications. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
1. What worked? Quinn and I were able to get our work done on time without overlap. We communicated well.

2. What didn't work? Nothing specific prevented us from working efficiently.

3. What will I do next to fix what didn't work? Complete work ahead of time to be more thorough. Maintain a growth mindset.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:06, 20 November 2017 (PST)

====Eddie's Reflection====
Found in Week 11 summary ^^^

===Week 12===

====Quinn's Reflection====
#What worked?
#*Antonio and I did a very good job of working ahead and getting our presentation done in a timely manner. In this way, we were able to ask the instructors any questions we had as they came up, and also allowed for ample time to practice.
#What didn't work?
#*Once again, I felt a bit disconnected from my other partners Eddie and Simon. While I texted Eddie a couple times about their progress, I still never got a chance to see exactly what they were doing.
#What to improve upon going forward?
#*While I feel like this will start to come together once we all start working on our assigned portion of the project together, we still do need to improve our communication between the coders and the PM/DA. In order to do so, I will make sure to continue to check base with each team member each day in class, and also text in the group message when I have questions for the whole team.
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 15:12, 20 November 2017 (PST)

====Simon's Reflection====
#What worked?
#*With Eddie's help, we were both able to set up GRNsight on our laptops.
#What didn't work?
#*Nothing in specific stopped us from working efficiently.
#How will to improve upon going forward?
#*Going forward I'd like to get my summaries in earlier, as well as my individual page and reflections. 
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 22:48, 20 November 2017 (PST)

====Antonio's Reflection====
#What worked?
#*Worked closely with Quinn and we kept regular contact through text as we worked through the assignment. Troubleshooting was easy as we were both very capable to take initiative and work to finish the presentation earlier rather than later in the time given.
#What didn't work?
#*I could definitely improve on mastering certain aspects of the assignment. I didn't really communicate with Eddie or Simon but I'd attribute that to having different assignments and parts to complete rather than a team issue.
#What to will I do next to fix what didn't work?
#*Communicate more. I'm hoping we'll have opportunities to work more closely together in the future.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 22:12, 20 November 2017 (PST)

====Eddie's Reflection====
# What worked?
#: Our work session was successful in setting up GRNsight on my laptop (again) and on Simon's.
# What didn't work?
#: Nothing :D
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 21:47, 20 November 2017 (PST)

===Week 14===

====Quinn's Reflection====
#What Worked?
#*This week our team did a much better job of communicating and keeping each other in the loop. Also, the collaboration between all of the QAs was a very effective way to determine which information should be pulled from each database
#What didn't work?
#*I was still a bit confused as to how all of the teams should be working together as we approach the end of the semester
#What will I do next to fix what didn't work>
#*I will make sure to ask about this concern in the next stand up review between the QAs. This will help clear this question up for me and the rest of the class. 
[[User:Qlanners|Qlanners]] ([[User talk:Qlanners|talk]]) 21:05, 4 December 2017 (PST)

====Simon's Reflection====
#What Worked?
#*Our class was able to produce a solid list of data items, specified to each database. This meant that as a coder for the JASPAR team, I knew which pieces of data to retrireve and produce from the JASPAR database.
#What didn't work?
#*There were some complications with the language some of the new code was written. There was also a problem with the JASPAR API relating to CORS (Cross-Oirgin Resource Sharing).
#What will I do next to fix what didn't work?
#*I hope to be more knowledgeable about these type of things in reference to computer science.
[[User:Simonwro120|Simonwro120]] ([[User talk:Simonwro120|talk]]) 21:57, 4 December 2017 (PST)

====Antonio's Reflection====
# What worked? This week, I worked ahead and was able to complete, at least to my knowledge, this week's assignment ahead of time rather than waiting until the last minute. It was extremely helpful to have a group chat with the other data analysts as we had questions throughout the assignment.
# What didn't work? Everything seems to have run smoothly except I don't really know what the coders are assigned to do and most likely because it goes over my head.
# What will I do next to fix what didn't work? Try to see what the coders are doing, mostly out of curiosity.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 18:36, 3 December 2017 (PST)

====Eddie's Reflection====
#What worked?
#* We were able to figure out exactly how to extract the info we needed from JASPAR.
#What didn't work?
#* We originally had our own branch, but that didn't work out too well and it didn't make much sense when we were working in parallel to the gene-database-apis branch.
#How will to improve upon going forward?
#* We decided to merge our two branch which helped with this and kept us on the same page. 
[[User:Ebachour|Ebachour]] ([[User talk:Ebachour|talk]]) 23:25, 4 December 2017 (PST)

==Acknowledgements==

==References==
===Week 11===
#LMU BioDB 2017. (2017). Week 11. Retrieved November 07, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_11
#Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., & Wanner, N.C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. doi: 10.1007/s11538-015-0092-6
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301
#Homma, T., Iwahashi, H., & Komatsu, Y. (2003). Yeast gene expression during growth at low temperature. Cryobiology, 46(3), 230-237.
#Sahara, T., Goda, T., & Ohgiya, S. (2002). Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. Journal of Biological Chemistry, 277(51), 50015-50021.
#Top Integrated Development Environment index. (n.d.). Retrieved November 13, 2017, from http://pypl.github.io/IDE.html
#What is an API?. (2016). Retrieved November 13, 2017, from https://medium.freecodecamp.org/what-is-an-api-in-english-please-b880a3214a82
#What's the difference between an API vs SDK?. (2012). Retrieved November 13, 2017, from https://blogs.vmware.com/vsphere/2012/01/whats-the-difference-between-an-api-vs-sdk.html
#Xcode. (2017). Retrieved November 13, 2017, from https://itunes.apple.com/us/app/xcode/id497799835
#What Is Code? (2015). Retrieved November 13, 2017, from https://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/#how-are-apps-made
#Shrinkwrapped Software. (n.d.). Retrieved November 13, 2017, from http://www.businessdictionary.com/definition/shrinkwrapped-software.html
#Web Application Framework. (2015). Retrieved November 13, 2017, from https://web.archive.org/web/20150723163302/http://docforge.com/wiki/Web_application_framework

===Week 12===
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Anneal. (n.d.). ''Genscript''. Retrieved on November 19, 2017 from https://www.genscript.com/molecular-biology-glossary/11896/anneal
#Assay.(2005). ''Biology-Online''. Retrieved on November 19, 2017 http://www.biology-online.org/dictionary/Assay
#Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301
#Causton HC, Ren B, Koh SS, et al. 2001. Remodelling of yeast genome expression in response to environmental changes. Mol Biol Cell 12: 323–337.
#Chomczynski, P., & Sacchi, N. (1987). Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Analytical biochemistry, 162(1), 156-159.
#Cluster analysis. BusinessDictionary.com. Retrieved November 19, 2017, from BusinessDictionary.com website: http://www.businessdictionary.com/definition/cluster-analysis.html
#Consensus sequence | Definition of consensus sequence in English by Oxford Dictionaries. (n.d.). Retrieved November 20, 2017, from https://en.oxforddictionaries.com/definition/consensus_sequence
#Cyclins. (n.d.). ''BioNinja''. Retrieved on November 19, 2017 from http://ib.bioninja.com.au/standard-level/topic-1-cell-biology/16-cell-division/cyclins.html
#Differences between in vitro, in vivo, and in silico studies. (n.d.). Retrieved November 20, 2017, from https://mpkb.org/home/patients/assessing_literature/in_vitro_studies
#Donzeau M, Bourdineaud JP, Lauquin GJ. 1996. Regulation by low temperatures and anaerobiosis of a yeast gene specifying a putative GPI-anchored plasma membrane protein. Mol Microbiol 20: 449–459.
#Gasch AP, Spellman PT, Kao CM, et al. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11: 4241–4257.
#Glutathione. (n.d.). Retrieved November 20, 2017, from https://www.merriam-webster.com/dictionary/glutathione
#Haploid. (n.d.). Retrieved November 20, 2017, from http://www.biology-online.org/dictionary/Haploid
#HAW. (2011). Difference Between Haploid and Diploid. ''Difference Between.com''. Retrieved on November 19, 2017 from http://www.differencebetween.com/difference-between-haploid-and-vs-diploid/
#Hybridization. (2008). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Hybridization
#Kondo K, Inouye M. 1991. Cold-induction of yeast NSR1 protein and its role in pre-rRNA processing. J Biol Chem 267: 16 259–16 265.
#Kowalski LR, Kondo K, Inouye M. 1995. Cold-shock induction of a family of TIP1-related proteins associated with the membrane in Saccharomyces cerevisiae. Mol Microbiol 15: 341 – 353.
#LMU BioDB 2017. (2017). Week 12. Retrieved November 16, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_12
#Mai B, Breeden L. 1997. Xbp1, a stress-upregulated transcrip- tional repressor of the Saccharomyces cerevisae Swi4/Mbp1 family. Mol Cell Biol 17: 6491–6501.
#(n.d.). Retrieved November 19, 2017, from http://fg.cns.utexas.edu/fg/protocol%3A_YPD_plates.html
#(n.d.). Retrieved November 20, 2017, from https://www.nature.com/scitable/definition/diploid-310
#Oligonucleotide. (2014). ''News Medical Life Sciences''. Retrieved on November 19, 2017 from https://www.news-medical.net/life-sciences/What-is-an-Oligonucleotide.aspx
#Polypropylene. (n.d.). ''Dictionary.com''. Retrieved on November 19, 2017 from http://www.dictionary.com/browse/polypropylene
#Putative. (2014). ''Biology-Online''. Retrieved on November 19, 2017 from http://www.biology-online.org/dictionary/Putative
#Study.com. (2017). What is Annealing? - Definition, Biology & Process | Study.com. [online] Available at: http://study.com/academy/lesson/what-is-annealing-definition-biology-process.html [Accessed 21 Nov. 2017].
#Transcriptome. (n.d.). ''Nature''. Retrieved on November 19, 2017 from https://www.nature.com/scitable/definition/transcriptome-296
#Yelland, P. M. (2010). An introduction to correspondence analysis. Math. J, 12, 1-23.
#Young, F.W. (1999). Principle Components. ''forrest.psych.unc.edu''. Retrieved on November 19, 2017 from http://forrest.psych.unc.edu/research/vista-frames/help/lecturenotes/lecture13/biplot.html
#Zhang L, Ohta A, Horiuchi H, Takagi M, Imai R. 2001. Multiple mechanisms regulate expression of low temperature responsive (LOT) genes in Saccharomyces cerevisiae. Biochem Biophys Res Commun 283: 531 – 535.

===Week 14===
#Dahlquist, K. D., Dionisio, J. D. N., Fitzpatrick, B. G., Anguiano, N. A., Varshneya, A., Southwick, B. J., & Samdarshi, M. (2016). GRNsight: a web application and service for visualizing models of small-to medium-scale gene regulatory networks. PeerJ Computer Science, 2, e85.
#Ensembl. (2017). "Gene: HSF1". Retrieved November 28, 2017, from https://www.ensembl.org/Saccharomyces_cerevisiae/Gene/Summary?db=core;g=YGL073W;r=VII:368753-371254;t=YGL073W 
#JASPAR. (2017). "Detailed information of matrix profile MA0319.1". Retrieved on November 28, 2017, from http://jaspar.genereg.net/matrix/MA0319.1/ 
#LMU BioDB 2017. (2017). Week 8. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_8
#LMU BioDB 2017. (2017). Week 10. Retrieved November 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_10
#LMU BioDB 2017. (2017). Week 14. Retrieved November 28, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14 
#NCBI. (2017). "HSF1 stress-responsive transcription factor HSF1 [ Saccharomyces cerevisiae S288C ]". Retrieved November 28, 2017, from https://www.ncbi.nlm.nih.gov/gene/852806 
#Saccharomyces Genome Database. (2017). "HSF1 / YGL073W Overview". Retrieved November 28, 2017, from https://www.yeastgenome.org/locus/S000003041 
#Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.
#UniProt. (2017). "UniProtKB - P10961 (HSF_YEAST)". Retrieved November 28, 2017 from http://www.uniprot.org/uniprot/P10961

==Team Links==

{{Template:JASPAR the Friendly Ghost Links}}

==Class Links==

{{Template:GRNsight Gene Page Project Links}}

Aporras1 Week 15

2017-12-09T23:05:50Z

Aporras1: /* Deliverables Checklist */ week 14 link

User page: [[User:Aporras1|Antonio Porras]]

Team page: [[JASPAR the Friendly Ghost|JASPAR The Friendly Ghost]]

Assignment page: [[Week 15|Week 15]]

==Electronic Notebook==
# Network was determined to be too big.
#* Began process of deleting the least significant
# Re-downloaded [[Media:AP YEASTRACT Transcription Factors.xlsx]] and found the transcription factors which I used in [[Aporras1_Week_14]] ranked from highest % in user set to lowest:
#**GLN3
#**HAP4
#**Ace2p
#**Sfp1p
#**Bas1p
#**Msn2p
#**Yap1p
#**Ash1p
#**Gcn4p
#**Msn4p
#**Abf1p
#**Cst6p
#**Sok2p
#**Rpn4p
#**Hsf1p
#**Zap1p
#**Cin5p
#**Aft1p
#**Spt23p
#**Pdr1p
#**Met4p
#**Arr1p

===ARR1 deletion===
# Moved "network" workbook to a new file found in [[Media:Trimming Network transcription factor deletions dZAP1.zip]]: Network ARR1 deletion.xlsx
# Began by deleting ARR1 in worksheet "Network ARR1 deletion"
#* Deleted row 5 and column E containing ARR1 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network ARR1 deletion.xlsx" file that has the "network" worksheet.
# Network remained too large.

===MET4 deletion===
# Moved "network" workbook from Network ARR1 deletion.xlsx to a new file found in [[Media:Trimming Network transcription factor deletions dZAP1.zip]]: Network MET4 deletion.xlsx
# Began by deleting MET4 in worksheet "network MET4 deletion"
#* Deleted row 13 and column M containing MET4 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network MET4 deletion" file that has the "network" worksheet.
# Network remained too large.

===PDR1 deletion===
# Moved "network" workbook from Network MET4 deletion.xlsx to a new file found in [[Media:Trimming Network transcription factor deletions dZAP1.zip]]: Network PDR1 deletion.xlsx
# Began by deleting PDR1 in worksheet "network PDR1 deletion"
#* Deleted row 15 and column O containing PDR1 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network PDR1 deletion" file that has the "network" worksheet.
# Network remained too large.

===SPT23 & BAS1 deletion===
# Moved "network" workbook from Network PDR1 deletion.xlsx to a new file found in folder [[Media:Trimming Network transcription factor deletions dZAP1.zip]]: Network SPT23 deletion.xlsx
# Began by deleting PDR1 in worksheet "network SPT23 deletion"
#* Deleted row 19 and column S containing SPT23 data.
#*BAS1 transcription factor became disconnected.
#*Deleted row 6 and column F containing BAS1 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network SPT23 deletion" file that has the "network" worksheet.
# Network remained too large.

===Network Files After Trimming===

[[Media:Trimming Network transcription factor deletions dZAP1.zip]]

Files were not necessary in the final GRNsight visualization, but rather for documentation on work performed before being provided by [[User:Kdahlquist|Dr. Dahlquist]].

Antonio, I finished paring down the network. Here is the final file (renamed): [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx | 15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]]. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:55, 6 December 2017 (PST)''

===GRNsight Visualization===
# Downloaded [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]] provided by [[User:Kdahlquist|Dr. Dahlquist]].
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx" file that has the "network" worksheet. Moved the nodes (genes) around until I created a layout I liked, ordering alphabetically, and took a screenshot of the results and saved the screenshot as:[[Media:GRNsight Visualization of 15-gene 44-edge teamJASPAR Sigmoid estimation.PNG]]

===GRNsight Regulation MATLAB Output===
# Used [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]] and allowed [[User:Kdahlquist|Dr. Dahlquist]] to run MATLAB.
#* Once it was completed, saved the output workbook as:[[Media:15-gene 44-edge teamJASPAR Sigmoid estimation output.xlsx]]
#* Saved the images and uploaded them to the wiki as:[[Media:Output Images from 15-gene 44-edge teamJASPAR Sigmoid estimation.zip]]
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "15-gene_44-edge_teamJASPAR_Sigmoid_estimation_output.xlsx" file that had the "network" worksheet. Moved the nodes (genes) around until I created a layout I liked, ordering alphabetically, and took a screenshot of the results and saved the screenshot as:[[Media:GRNsight Regulation Magnitude Visualization of 15-gene 44-edge teamJASPAR Sigmoid estimation.PNG]]

===Edits to Organization of Files===
# In [[Week 10|Week 10]] the powerpoint STEM screenshots, GOlists, and genelists were all zipped in [[Media:AP dZAP1 STEM Profiles and Powerpoint.zip]] and the deliverables, in [[GRNsight Gene Page Project Deliverables|Project Deliverables]], asked for two separate files.
#* Removed the powerpoint with the p-values and STEM screenshots. Zipped the powerpoint and uploaded it to the wiki as a new file found in the deliverables: [[Media:AP dZAP1 STEM Screenshots & p-values.zip]].
#* Removed the golists and genelists .txt files into a new folder and zipped the folder before uploading it as a new file found in the deliverables: [[Media:AP dZAP1 GOlist and genelist for profiles.zip]]

===Deliverables Checklist===
# Excel spreadsheet with ANOVA results/stem formatting (''.xlsx'')
#* [[Media:AP dZAP1.zip]]
# PowerPoint of screenshots of stem results (''.pptx'')
#* [[Media:AP dZAP1 STEM Screenshots & p-values.zip]]
# Gene List and GO List files from each significant profile (''.txt'' compressed together in a ''.zip'' file)
#* [[Media:AP dZAP1 GOlist and genelist for profiles.zip]]
# YEASTRACT "rank by TF" results (''.xlsx'')
#* [[Media:AP YEASTRACT Transcription Factors.xlsx]]
# GRNmap input workbook (with network adjacency matrix, ''.xlsx'')
#* [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]]
# GRNmap output workbook (''.xlsx'')
#* [[Media:15-gene 44-edge teamJASPAR Sigmoid estimation output.xlsx]]
#* Expression vs Time Images generated from MATLAB
#** [[Media:Output Images from 15-gene 44-edge teamJASPAR Sigmoid estimation.zip]]
# Electronic notebook corresponding to these the microarray results files ([[Week 8]], [[Week 10]], & [[Week 14]]) support ''reproducible research'' so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results.
#* Summary for [[Aporras1_Week_8]]: In week 8, performed statistical analysis on the deletion ZAP1 using provided ANOVA. Specfically, Bonferroni & p value correction and Benjamini & Hochberg p value was calculated. The data examined the time intervals of 15 minutes, 30 minutes, 60 minutes, 90 minutes, and 120 minutes during cold shock.
#** Electronic notebook found in "Electronic Notebook" section of [[Aporras1_Week_8]]
#* Summary for [[Aporras1_Week_10]]: Used the data from [[Aporras1_Week_8]] to perform STEM clustering on dZAP1. Selected profile 22 because it had a very low p value and a high amount of genes (2E-157 and 252 respectively). Selected 6 GO terms from profile 22's GOlist to define and analyze in terms of why the cell would change the expression of the genes associated with the GO terms.
#** Electronic notebook found in "Electronic Notebook" section of [[Aporras1_Week_10]]
#* Summary for [[Aporras1_Week_14]]: Made edits to [[Aporras1_Week_8]] and [[Aporras1_Week_10]] according to feedback from [[User:Kdahlquist|Dr. Dahlquist]] & [[User:Dondi|Dr. Dionisio]]. Used the profile 22 genelist and ranked transcription factors with YEASTRACT by significance and selected the most significant ones with low P-values. Generated a regulation matrix using YEASTRACT and created an adjacency matrix with a network to visualize with GRNsight. The network was trimmed down to 15 genes and MATLAB was used to generate an output. Both the output and the original network were visualized with GRNsight.
#** Electronic notebook found in "Electronic Notebook" section of [[Aporras1_Week_14]].
#* Note: make a summary and provide links to individual pages with electronic notebooks.

==Acknowledgements==
# Worked alongside [[User:Qlanners|Quinn Lanners]] to begin gathering deliverables.
# Copied the formatting and text from [[GRNsight_Gene_Page_Project_Deliverables]] checklist in my checklist category.
# Received file used for GRNsight visualization, received in class direction and instruction from [[User:Kdahlquist|Dr. Dahlquist]].
# Met up with group members in [[JASPAR the Friendly Ghost]] after the Thursday 12/01/2017 class and outside of class 12/09/2017 to discuss an outline of what needed to be completed and to work on the presentation.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 16:11, 7 December 2017 (PST)

==References==
#Dahlquist, K. D., Dionisio, J. D. N., Fitzpatrick, B. G., Anguiano, N. A., Varshneya, A., Southwick, B. J., & Samdarshi, M. (2016). GRNsight: a web application and service for visualizing models of small-to medium-scale gene regulatory networks. PeerJ Computer Science, 2, e85.
# LMU BioDB 2017. (2017). Week 15. Retrieved December 05, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15
# LMU BioDB 2017. (2017). GRNsight Gene Page Project Deliverables. Retrieved December 05, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/GRNsight_Gene_Page_Project_Deliverables
# Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.

[[Category:Journal Entry]]

Aporras1 Week 15

2017-12-09T23:05:10Z

Aporras1: /* Deliverables Checklist */ typo

User page: [[User:Aporras1|Antonio Porras]]

Team page: [[JASPAR the Friendly Ghost|JASPAR The Friendly Ghost]]

Assignment page: [[Week 15|Week 15]]

==Electronic Notebook==
# Network was determined to be too big.
#* Began process of deleting the least significant
# Re-downloaded [[Media:AP YEASTRACT Transcription Factors.xlsx]] and found the transcription factors which I used in [[Aporras1_Week_14]] ranked from highest % in user set to lowest:
#**GLN3
#**HAP4
#**Ace2p
#**Sfp1p
#**Bas1p
#**Msn2p
#**Yap1p
#**Ash1p
#**Gcn4p
#**Msn4p
#**Abf1p
#**Cst6p
#**Sok2p
#**Rpn4p
#**Hsf1p
#**Zap1p
#**Cin5p
#**Aft1p
#**Spt23p
#**Pdr1p
#**Met4p
#**Arr1p

===ARR1 deletion===
# Moved "network" workbook to a new file found in [[Media:Trimming Network transcription factor deletions dZAP1.zip]]: Network ARR1 deletion.xlsx
# Began by deleting ARR1 in worksheet "Network ARR1 deletion"
#* Deleted row 5 and column E containing ARR1 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network ARR1 deletion.xlsx" file that has the "network" worksheet.
# Network remained too large.

===MET4 deletion===
# Moved "network" workbook from Network ARR1 deletion.xlsx to a new file found in [[Media:Trimming Network transcription factor deletions dZAP1.zip]]: Network MET4 deletion.xlsx
# Began by deleting MET4 in worksheet "network MET4 deletion"
#* Deleted row 13 and column M containing MET4 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network MET4 deletion" file that has the "network" worksheet.
# Network remained too large.

===PDR1 deletion===
# Moved "network" workbook from Network MET4 deletion.xlsx to a new file found in [[Media:Trimming Network transcription factor deletions dZAP1.zip]]: Network PDR1 deletion.xlsx
# Began by deleting PDR1 in worksheet "network PDR1 deletion"
#* Deleted row 15 and column O containing PDR1 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network PDR1 deletion" file that has the "network" worksheet.
# Network remained too large.

===SPT23 & BAS1 deletion===
# Moved "network" workbook from Network PDR1 deletion.xlsx to a new file found in folder [[Media:Trimming Network transcription factor deletions dZAP1.zip]]: Network SPT23 deletion.xlsx
# Began by deleting PDR1 in worksheet "network SPT23 deletion"
#* Deleted row 19 and column S containing SPT23 data.
#*BAS1 transcription factor became disconnected.
#*Deleted row 6 and column F containing BAS1 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network SPT23 deletion" file that has the "network" worksheet.
# Network remained too large.

===Network Files After Trimming===

[[Media:Trimming Network transcription factor deletions dZAP1.zip]]

Files were not necessary in the final GRNsight visualization, but rather for documentation on work performed before being provided by [[User:Kdahlquist|Dr. Dahlquist]].

Antonio, I finished paring down the network. Here is the final file (renamed): [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx | 15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]]. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:55, 6 December 2017 (PST)''

===GRNsight Visualization===
# Downloaded [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]] provided by [[User:Kdahlquist|Dr. Dahlquist]].
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx" file that has the "network" worksheet. Moved the nodes (genes) around until I created a layout I liked, ordering alphabetically, and took a screenshot of the results and saved the screenshot as:[[Media:GRNsight Visualization of 15-gene 44-edge teamJASPAR Sigmoid estimation.PNG]]

===GRNsight Regulation MATLAB Output===
# Used [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]] and allowed [[User:Kdahlquist|Dr. Dahlquist]] to run MATLAB.
#* Once it was completed, saved the output workbook as:[[Media:15-gene 44-edge teamJASPAR Sigmoid estimation output.xlsx]]
#* Saved the images and uploaded them to the wiki as:[[Media:Output Images from 15-gene 44-edge teamJASPAR Sigmoid estimation.zip]]
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "15-gene_44-edge_teamJASPAR_Sigmoid_estimation_output.xlsx" file that had the "network" worksheet. Moved the nodes (genes) around until I created a layout I liked, ordering alphabetically, and took a screenshot of the results and saved the screenshot as:[[Media:GRNsight Regulation Magnitude Visualization of 15-gene 44-edge teamJASPAR Sigmoid estimation.PNG]]

===Edits to Organization of Files===
# In [[Week 10|Week 10]] the powerpoint STEM screenshots, GOlists, and genelists were all zipped in [[Media:AP dZAP1 STEM Profiles and Powerpoint.zip]] and the deliverables, in [[GRNsight Gene Page Project Deliverables|Project Deliverables]], asked for two separate files.
#* Removed the powerpoint with the p-values and STEM screenshots. Zipped the powerpoint and uploaded it to the wiki as a new file found in the deliverables: [[Media:AP dZAP1 STEM Screenshots & p-values.zip]].
#* Removed the golists and genelists .txt files into a new folder and zipped the folder before uploading it as a new file found in the deliverables: [[Media:AP dZAP1 GOlist and genelist for profiles.zip]]

===Deliverables Checklist===
# Excel spreadsheet with ANOVA results/stem formatting (''.xlsx'')
#* [[Media:AP dZAP1.zip]]
# PowerPoint of screenshots of stem results (''.pptx'')
#* [[Media:AP dZAP1 STEM Screenshots & p-values.zip]]
# Gene List and GO List files from each significant profile (''.txt'' compressed together in a ''.zip'' file)
#* [[Media:AP dZAP1 GOlist and genelist for profiles.zip]]
# YEASTRACT "rank by TF" results (''.xlsx'')
#* [[Media:AP YEASTRACT Transcription Factors.xlsx]]
# GRNmap input workbook (with network adjacency matrix, ''.xlsx'')
#* [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]]
# GRNmap output workbook (''.xlsx'')
#* [[Media:15-gene 44-edge teamJASPAR Sigmoid estimation output.xlsx]]
#* Expression vs Time Images generated from MATLAB
#** [[Media:Output Images from 15-gene 44-edge teamJASPAR Sigmoid estimation.zip]]
# Electronic notebook corresponding to these the microarray results files ([[Week 8]], [[Week 10]]) support ''reproducible research'' so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results.
#* Summary for [[Aporras1_Week_8]]: In week 8, performed statistical analysis on the deletion ZAP1 using provided ANOVA. Specfically, Bonferroni & p value correction and Benjamini & Hochberg p value was calculated. The data examined the time intervals of 15 minutes, 30 minutes, 60 minutes, 90 minutes, and 120 minutes during cold shock.
#** Electronic notebook found in "Electronic Notebook" section of [[Aporras1_Week_8]]
#* Summary for [[Aporras1_Week_10]]: Used the data from [[Aporras1_Week_8]] to perform STEM clustering on dZAP1. Selected profile 22 because it had a very low p value and a high amount of genes (2E-157 and 252 respectively). Selected 6 GO terms from profile 22's GOlist to define and analyze in terms of why the cell would change the expression of the genes associated with the GO terms.
#** Electronic notebook found in "Electronic Notebook" section of [[Aporras1_Week_10]]
#* Summary for [[Aporras1_Week_14]]: Made edits to [[Aporras1_Week_8]] and [[Aporras1_Week_10]] according to feedback from [[User:Kdahlquist|Dr. Dahlquist]] & [[User:Dondi|Dr. Dionisio]]. Used the profile 22 genelist and ranked transcription factors with YEASTRACT by significance and selected the most significant ones with low P-values. Generated a regulation matrix using YEASTRACT and created an adjacency matrix with a network to visualize with GRNsight. The network was trimmed down to 15 genes and MATLAB was used to generate an output. Both the output and the original network were visualized with GRNsight.
#** Electronic notebook found in "Electronic Notebook" section of [[Aporras1_Week_14]].
#* Note: make a summary and provide links to individual pages with electronic notebooks.

==Acknowledgements==
# Worked alongside [[User:Qlanners|Quinn Lanners]] to begin gathering deliverables.
# Copied the formatting and text from [[GRNsight_Gene_Page_Project_Deliverables]] checklist in my checklist category.
# Received file used for GRNsight visualization, received in class direction and instruction from [[User:Kdahlquist|Dr. Dahlquist]].
# Met up with group members in [[JASPAR the Friendly Ghost]] after the Thursday 12/01/2017 class and outside of class 12/09/2017 to discuss an outline of what needed to be completed and to work on the presentation.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 16:11, 7 December 2017 (PST)

==References==
#Dahlquist, K. D., Dionisio, J. D. N., Fitzpatrick, B. G., Anguiano, N. A., Varshneya, A., Southwick, B. J., & Samdarshi, M. (2016). GRNsight: a web application and service for visualizing models of small-to medium-scale gene regulatory networks. PeerJ Computer Science, 2, e85.
# LMU BioDB 2017. (2017). Week 15. Retrieved December 05, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15
# LMU BioDB 2017. (2017). GRNsight Gene Page Project Deliverables. Retrieved December 05, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/GRNsight_Gene_Page_Project_Deliverables
# Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.

[[Category:Journal Entry]]

Aporras1 Week 15

2017-12-09T23:04:08Z

Aporras1: /* Deliverables Checklist */ summaries for weeks 8 10 and 14

User page: [[User:Aporras1|Antonio Porras]]

Team page: [[JASPAR the Friendly Ghost|JASPAR The Friendly Ghost]]

Assignment page: [[Week 15|Week 15]]

==Electronic Notebook==
# Network was determined to be too big.
#* Began process of deleting the least significant
# Re-downloaded [[Media:AP YEASTRACT Transcription Factors.xlsx]] and found the transcription factors which I used in [[Aporras1_Week_14]] ranked from highest % in user set to lowest:
#**GLN3
#**HAP4
#**Ace2p
#**Sfp1p
#**Bas1p
#**Msn2p
#**Yap1p
#**Ash1p
#**Gcn4p
#**Msn4p
#**Abf1p
#**Cst6p
#**Sok2p
#**Rpn4p
#**Hsf1p
#**Zap1p
#**Cin5p
#**Aft1p
#**Spt23p
#**Pdr1p
#**Met4p
#**Arr1p

===ARR1 deletion===
# Moved "network" workbook to a new file found in [[Media:Trimming Network transcription factor deletions dZAP1.zip]]: Network ARR1 deletion.xlsx
# Began by deleting ARR1 in worksheet "Network ARR1 deletion"
#* Deleted row 5 and column E containing ARR1 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network ARR1 deletion.xlsx" file that has the "network" worksheet.
# Network remained too large.

===MET4 deletion===
# Moved "network" workbook from Network ARR1 deletion.xlsx to a new file found in [[Media:Trimming Network transcription factor deletions dZAP1.zip]]: Network MET4 deletion.xlsx
# Began by deleting MET4 in worksheet "network MET4 deletion"
#* Deleted row 13 and column M containing MET4 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network MET4 deletion" file that has the "network" worksheet.
# Network remained too large.

===PDR1 deletion===
# Moved "network" workbook from Network MET4 deletion.xlsx to a new file found in [[Media:Trimming Network transcription factor deletions dZAP1.zip]]: Network PDR1 deletion.xlsx
# Began by deleting PDR1 in worksheet "network PDR1 deletion"
#* Deleted row 15 and column O containing PDR1 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network PDR1 deletion" file that has the "network" worksheet.
# Network remained too large.

===SPT23 & BAS1 deletion===
# Moved "network" workbook from Network PDR1 deletion.xlsx to a new file found in folder [[Media:Trimming Network transcription factor deletions dZAP1.zip]]: Network SPT23 deletion.xlsx
# Began by deleting PDR1 in worksheet "network SPT23 deletion"
#* Deleted row 19 and column S containing SPT23 data.
#*BAS1 transcription factor became disconnected.
#*Deleted row 6 and column F containing BAS1 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network SPT23 deletion" file that has the "network" worksheet.
# Network remained too large.

===Network Files After Trimming===

[[Media:Trimming Network transcription factor deletions dZAP1.zip]]

Files were not necessary in the final GRNsight visualization, but rather for documentation on work performed before being provided by [[User:Kdahlquist|Dr. Dahlquist]].

Antonio, I finished paring down the network. Here is the final file (renamed): [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx | 15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]]. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:55, 6 December 2017 (PST)''

===GRNsight Visualization===
# Downloaded [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]] provided by [[User:Kdahlquist|Dr. Dahlquist]].
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx" file that has the "network" worksheet. Moved the nodes (genes) around until I created a layout I liked, ordering alphabetically, and took a screenshot of the results and saved the screenshot as:[[Media:GRNsight Visualization of 15-gene 44-edge teamJASPAR Sigmoid estimation.PNG]]

===GRNsight Regulation MATLAB Output===
# Used [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]] and allowed [[User:Kdahlquist|Dr. Dahlquist]] to run MATLAB.
#* Once it was completed, saved the output workbook as:[[Media:15-gene 44-edge teamJASPAR Sigmoid estimation output.xlsx]]
#* Saved the images and uploaded them to the wiki as:[[Media:Output Images from 15-gene 44-edge teamJASPAR Sigmoid estimation.zip]]
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "15-gene_44-edge_teamJASPAR_Sigmoid_estimation_output.xlsx" file that had the "network" worksheet. Moved the nodes (genes) around until I created a layout I liked, ordering alphabetically, and took a screenshot of the results and saved the screenshot as:[[Media:GRNsight Regulation Magnitude Visualization of 15-gene 44-edge teamJASPAR Sigmoid estimation.PNG]]

===Edits to Organization of Files===
# In [[Week 10|Week 10]] the powerpoint STEM screenshots, GOlists, and genelists were all zipped in [[Media:AP dZAP1 STEM Profiles and Powerpoint.zip]] and the deliverables, in [[GRNsight Gene Page Project Deliverables|Project Deliverables]], asked for two separate files.
#* Removed the powerpoint with the p-values and STEM screenshots. Zipped the powerpoint and uploaded it to the wiki as a new file found in the deliverables: [[Media:AP dZAP1 STEM Screenshots & p-values.zip]].
#* Removed the golists and genelists .txt files into a new folder and zipped the folder before uploading it as a new file found in the deliverables: [[Media:AP dZAP1 GOlist and genelist for profiles.zip]]

===Deliverables Checklist===
# Excel spreadsheet with ANOVA results/stem formatting (''.xlsx'')
#* [[Media:AP dZAP1.zip]]
# PowerPoint of screenshots of stem results (''.pptx'')
#* [[Media:AP dZAP1 STEM Screenshots & p-values.zip]]
# Gene List and GO List files from each significant profile (''.txt'' compressed together in a ''.zip'' file)
#* [[Media:AP dZAP1 GOlist and genelist for profiles.zip]]
# YEASTRACT "rank by TF" results (''.xlsx'')
#* [[Media:AP YEASTRACT Transcription Factors.xlsx]]
# GRNmap input workbook (with network adjacency matrix, ''.xlsx'')
#* [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]]
# GRNmap output workbook (''.xlsx'')
#* [[Media:15-gene 44-edge teamJASPAR Sigmoid estimation output.xlsx]]
#* Expression vs Time Images generated from MATLAB
#** [[Media:Output Images from 15-gene 44-edge teamJASPAR Sigmoid estimation.zip]]
# Electronic notebook corresponding to these the microarray results files ([[Week 8]], [[Week 10]], and Weeks 11-15) support ''reproducible research'' so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results.
#* Summary for [[Aporras1_Week_8]]: In week 8, performed statistical analysis on the deletion ZAP1 using provided ANOVA. Specfically, Bonferroni & p value correction and Benjamini & Hochberg p value was calculated. The data examined the time intervals of 15 minutes, 30 minutes, 60 minutes, 90 minutes, and 120 minutes during cold shock.
#** Electronic notebook found in "Electronic Notebook" section of [[Aporras1_Week_8]]
#* Summary for [[Aporras1_Week_10]]: Used the data from [[Aporras1_Week_8]] to perform STEM clustering on dZAP1. Selected profile 22 because it had a very low p value and a high amount of genes (2E-157 and 252 respectively). Selected 6 GO terms from profile 22's GOlist to define and analyze in terms of why the cell would change the expression of the genes associated with the GO terms.
#** Electronic notebook found in "Electronic Notebook" section of [[Aporras1_Week_10]]
#* Summary for [[Aporras1_Week_14]]: Made edits to [[Aporras1_Week_8]] and [[Aporras1_Week_10]] according to feedback from [[User:Kdahlquist|Dr. Dahlquist]] & [[User:Dondi|Dr. Dionisio]]. Used the profile 22 genelist and ranked transcription factors with YEASTRACT by significance and selected the most significant ones with low P-values. Generated a regulation matrix using YEASTRACT and created an adjacency matrix with a network to visualize with GRNsight. The network was trimmed down to 15 genes and MATLAB was used to generate an output. Both the output and the original network were visualized with GRNsight.
#** Electronic notebook found in "Electronic Notebook" section of [[Aporras1_Week_14]].
#* Note: make a summary and provide links to individual pages with electronic notebooks.

==Acknowledgements==
# Worked alongside [[User:Qlanners|Quinn Lanners]] to begin gathering deliverables.
# Copied the formatting and text from [[GRNsight_Gene_Page_Project_Deliverables]] checklist in my checklist category.
# Received file used for GRNsight visualization, received in class direction and instruction from [[User:Kdahlquist|Dr. Dahlquist]].
# Met up with group members in [[JASPAR the Friendly Ghost]] after the Thursday 12/01/2017 class and outside of class 12/09/2017 to discuss an outline of what needed to be completed and to work on the presentation.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 16:11, 7 December 2017 (PST)

==References==
#Dahlquist, K. D., Dionisio, J. D. N., Fitzpatrick, B. G., Anguiano, N. A., Varshneya, A., Southwick, B. J., & Samdarshi, M. (2016). GRNsight: a web application and service for visualizing models of small-to medium-scale gene regulatory networks. PeerJ Computer Science, 2, e85.
# LMU BioDB 2017. (2017). Week 15. Retrieved December 05, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15
# LMU BioDB 2017. (2017). GRNsight Gene Page Project Deliverables. Retrieved December 05, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/GRNsight_Gene_Page_Project_Deliverables
# Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.

[[Category:Journal Entry]]

Aporras1 Week 15

2017-12-09T22:22:56Z

Aporras1: /* References */ removed typo

User page: [[User:Aporras1|Antonio Porras]]

Team page: [[JASPAR the Friendly Ghost|JASPAR The Friendly Ghost]]

Assignment page: [[Week 15|Week 15]]

==Electronic Notebook==
# Network was determined to be too big.
#* Began process of deleting the least significant
# Re-downloaded [[Media:AP YEASTRACT Transcription Factors.xlsx]] and found the transcription factors which I used in [[Aporras1_Week_14]] ranked from highest % in user set to lowest:
#**GLN3
#**HAP4
#**Ace2p
#**Sfp1p
#**Bas1p
#**Msn2p
#**Yap1p
#**Ash1p
#**Gcn4p
#**Msn4p
#**Abf1p
#**Cst6p
#**Sok2p
#**Rpn4p
#**Hsf1p
#**Zap1p
#**Cin5p
#**Aft1p
#**Spt23p
#**Pdr1p
#**Met4p
#**Arr1p

===ARR1 deletion===
# Moved "network" workbook to a new file found in [[Media:Trimming Network transcription factor deletions dZAP1.zip]]: Network ARR1 deletion.xlsx
# Began by deleting ARR1 in worksheet "Network ARR1 deletion"
#* Deleted row 5 and column E containing ARR1 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network ARR1 deletion.xlsx" file that has the "network" worksheet.
# Network remained too large.

===MET4 deletion===
# Moved "network" workbook from Network ARR1 deletion.xlsx to a new file found in [[Media:Trimming Network transcription factor deletions dZAP1.zip]]: Network MET4 deletion.xlsx
# Began by deleting MET4 in worksheet "network MET4 deletion"
#* Deleted row 13 and column M containing MET4 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network MET4 deletion" file that has the "network" worksheet.
# Network remained too large.

===PDR1 deletion===
# Moved "network" workbook from Network MET4 deletion.xlsx to a new file found in [[Media:Trimming Network transcription factor deletions dZAP1.zip]]: Network PDR1 deletion.xlsx
# Began by deleting PDR1 in worksheet "network PDR1 deletion"
#* Deleted row 15 and column O containing PDR1 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network PDR1 deletion" file that has the "network" worksheet.
# Network remained too large.

===SPT23 & BAS1 deletion===
# Moved "network" workbook from Network PDR1 deletion.xlsx to a new file found in folder [[Media:Trimming Network transcription factor deletions dZAP1.zip]]: Network SPT23 deletion.xlsx
# Began by deleting PDR1 in worksheet "network SPT23 deletion"
#* Deleted row 19 and column S containing SPT23 data.
#*BAS1 transcription factor became disconnected.
#*Deleted row 6 and column F containing BAS1 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network SPT23 deletion" file that has the "network" worksheet.
# Network remained too large.

===Network Files After Trimming===

[[Media:Trimming Network transcription factor deletions dZAP1.zip]]

Files were not necessary in the final GRNsight visualization, but rather for documentation on work performed before being provided by [[User:Kdahlquist|Dr. Dahlquist]].

Antonio, I finished paring down the network. Here is the final file (renamed): [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx | 15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]]. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:55, 6 December 2017 (PST)''

===GRNsight Visualization===
# Downloaded [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]] provided by [[User:Kdahlquist|Dr. Dahlquist]].
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx" file that has the "network" worksheet. Moved the nodes (genes) around until I created a layout I liked, ordering alphabetically, and took a screenshot of the results and saved the screenshot as:[[Media:GRNsight Visualization of 15-gene 44-edge teamJASPAR Sigmoid estimation.PNG]]

===GRNsight Regulation MATLAB Output===
# Used [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]] and allowed [[User:Kdahlquist|Dr. Dahlquist]] to run MATLAB.
#* Once it was completed, saved the output workbook as:[[Media:15-gene 44-edge teamJASPAR Sigmoid estimation output.xlsx]]
#* Saved the images and uploaded them to the wiki as:[[Media:Output Images from 15-gene 44-edge teamJASPAR Sigmoid estimation.zip]]
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "15-gene_44-edge_teamJASPAR_Sigmoid_estimation_output.xlsx" file that had the "network" worksheet. Moved the nodes (genes) around until I created a layout I liked, ordering alphabetically, and took a screenshot of the results and saved the screenshot as:[[Media:GRNsight Regulation Magnitude Visualization of 15-gene 44-edge teamJASPAR Sigmoid estimation.PNG]]

===Edits to Organization of Files===
# In [[Week 10|Week 10]] the powerpoint STEM screenshots, GOlists, and genelists were all zipped in [[Media:AP dZAP1 STEM Profiles and Powerpoint.zip]] and the deliverables, in [[GRNsight Gene Page Project Deliverables|Project Deliverables]], asked for two separate files.
#* Removed the powerpoint with the p-values and STEM screenshots. Zipped the powerpoint and uploaded it to the wiki as a new file found in the deliverables: [[Media:AP dZAP1 STEM Screenshots & p-values.zip]].
#* Removed the golists and genelists .txt files into a new folder and zipped the folder before uploading it as a new file found in the deliverables: [[Media:AP dZAP1 GOlist and genelist for profiles.zip]]

===Deliverables Checklist===
# Excel spreadsheet with ANOVA results/stem formatting (''.xlsx'')
#* [[Media:AP dZAP1.zip]]
# PowerPoint of screenshots of stem results (''.pptx'')
#* [[Media:AP dZAP1 STEM Screenshots & p-values.zip]]
# Gene List and GO List files from each significant profile (''.txt'' compressed together in a ''.zip'' file)
#* [[Media:AP dZAP1 GOlist and genelist for profiles.zip]]
# YEASTRACT "rank by TF" results (''.xlsx'')
#* [[Media:AP YEASTRACT Transcription Factors.xlsx]]
# GRNmap input workbook (with network adjacency matrix, ''.xlsx'')
#* [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]]
# GRNmap output workbook (''.xlsx'')
#* [[Media:15-gene 44-edge teamJASPAR Sigmoid estimation output.xlsx]]
#* Expression vs Time Images generated from MATLAB
#** [[Media:Output Images from 15-gene 44-edge teamJASPAR Sigmoid estimation.zip]]
# Electronic notebook corresponding to these the microarray results files ([[Week 8]], [[Week 10]], and Weeks 11-15) support ''reproducible research'' so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results.
#* Note: make a summary and provide links to individual pages with electronic notebooks.

==Acknowledgements==
# Worked alongside [[User:Qlanners|Quinn Lanners]] to begin gathering deliverables.
# Copied the formatting and text from [[GRNsight_Gene_Page_Project_Deliverables]] checklist in my checklist category.
# Received file used for GRNsight visualization, received in class direction and instruction from [[User:Kdahlquist|Dr. Dahlquist]].
# Met up with group members in [[JASPAR the Friendly Ghost]] after the Thursday 12/01/2017 class and outside of class 12/09/2017 to discuss an outline of what needed to be completed and to work on the presentation.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 16:11, 7 December 2017 (PST)

==References==
#Dahlquist, K. D., Dionisio, J. D. N., Fitzpatrick, B. G., Anguiano, N. A., Varshneya, A., Southwick, B. J., & Samdarshi, M. (2016). GRNsight: a web application and service for visualizing models of small-to medium-scale gene regulatory networks. PeerJ Computer Science, 2, e85.
# LMU BioDB 2017. (2017). Week 15. Retrieved December 05, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15
# LMU BioDB 2017. (2017). GRNsight Gene Page Project Deliverables. Retrieved December 05, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/GRNsight_Gene_Page_Project_Deliverables
# Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.

[[Category:Journal Entry]]

Aporras1 Week 15

2017-12-09T22:22:37Z

Aporras1: /* References */ grnsight and yeastract citations

User page: [[User:Aporras1|Antonio Porras]]

Team page: [[JASPAR the Friendly Ghost|JASPAR The Friendly Ghost]]

Assignment page: [[Week 15|Week 15]]

==Electronic Notebook==
# Network was determined to be too big.
#* Began process of deleting the least significant
# Re-downloaded [[Media:AP YEASTRACT Transcription Factors.xlsx]] and found the transcription factors which I used in [[Aporras1_Week_14]] ranked from highest % in user set to lowest:
#**GLN3
#**HAP4
#**Ace2p
#**Sfp1p
#**Bas1p
#**Msn2p
#**Yap1p
#**Ash1p
#**Gcn4p
#**Msn4p
#**Abf1p
#**Cst6p
#**Sok2p
#**Rpn4p
#**Hsf1p
#**Zap1p
#**Cin5p
#**Aft1p
#**Spt23p
#**Pdr1p
#**Met4p
#**Arr1p

===ARR1 deletion===
# Moved "network" workbook to a new file found in [[Media:Trimming Network transcription factor deletions dZAP1.zip]]: Network ARR1 deletion.xlsx
# Began by deleting ARR1 in worksheet "Network ARR1 deletion"
#* Deleted row 5 and column E containing ARR1 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network ARR1 deletion.xlsx" file that has the "network" worksheet.
# Network remained too large.

===MET4 deletion===
# Moved "network" workbook from Network ARR1 deletion.xlsx to a new file found in [[Media:Trimming Network transcription factor deletions dZAP1.zip]]: Network MET4 deletion.xlsx
# Began by deleting MET4 in worksheet "network MET4 deletion"
#* Deleted row 13 and column M containing MET4 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network MET4 deletion" file that has the "network" worksheet.
# Network remained too large.

===PDR1 deletion===
# Moved "network" workbook from Network MET4 deletion.xlsx to a new file found in [[Media:Trimming Network transcription factor deletions dZAP1.zip]]: Network PDR1 deletion.xlsx
# Began by deleting PDR1 in worksheet "network PDR1 deletion"
#* Deleted row 15 and column O containing PDR1 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network PDR1 deletion" file that has the "network" worksheet.
# Network remained too large.

===SPT23 & BAS1 deletion===
# Moved "network" workbook from Network PDR1 deletion.xlsx to a new file found in folder [[Media:Trimming Network transcription factor deletions dZAP1.zip]]: Network SPT23 deletion.xlsx
# Began by deleting PDR1 in worksheet "network SPT23 deletion"
#* Deleted row 19 and column S containing SPT23 data.
#*BAS1 transcription factor became disconnected.
#*Deleted row 6 and column F containing BAS1 data.
# Moved whole spreadsheet to a new worksheet "network"
# Uploaded the file to the wiki page.
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "Network SPT23 deletion" file that has the "network" worksheet.
# Network remained too large.

===Network Files After Trimming===

[[Media:Trimming Network transcription factor deletions dZAP1.zip]]

Files were not necessary in the final GRNsight visualization, but rather for documentation on work performed before being provided by [[User:Kdahlquist|Dr. Dahlquist]].

Antonio, I finished paring down the network. Here is the final file (renamed): [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx | 15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]]. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:55, 6 December 2017 (PST)''

===GRNsight Visualization===
# Downloaded [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]] provided by [[User:Kdahlquist|Dr. Dahlquist]].
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx" file that has the "network" worksheet. Moved the nodes (genes) around until I created a layout I liked, ordering alphabetically, and took a screenshot of the results and saved the screenshot as:[[Media:GRNsight Visualization of 15-gene 44-edge teamJASPAR Sigmoid estimation.PNG]]

===GRNsight Regulation MATLAB Output===
# Used [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]] and allowed [[User:Kdahlquist|Dr. Dahlquist]] to run MATLAB.
#* Once it was completed, saved the output workbook as:[[Media:15-gene 44-edge teamJASPAR Sigmoid estimation output.xlsx]]
#* Saved the images and uploaded them to the wiki as:[[Media:Output Images from 15-gene 44-edge teamJASPAR Sigmoid estimation.zip]]
# Went to the [http://dondi.github.io/GRNsight/ GRNsight] home page.
#* Selected the menu item File > Open and selected "15-gene_44-edge_teamJASPAR_Sigmoid_estimation_output.xlsx" file that had the "network" worksheet. Moved the nodes (genes) around until I created a layout I liked, ordering alphabetically, and took a screenshot of the results and saved the screenshot as:[[Media:GRNsight Regulation Magnitude Visualization of 15-gene 44-edge teamJASPAR Sigmoid estimation.PNG]]

===Edits to Organization of Files===
# In [[Week 10|Week 10]] the powerpoint STEM screenshots, GOlists, and genelists were all zipped in [[Media:AP dZAP1 STEM Profiles and Powerpoint.zip]] and the deliverables, in [[GRNsight Gene Page Project Deliverables|Project Deliverables]], asked for two separate files.
#* Removed the powerpoint with the p-values and STEM screenshots. Zipped the powerpoint and uploaded it to the wiki as a new file found in the deliverables: [[Media:AP dZAP1 STEM Screenshots & p-values.zip]].
#* Removed the golists and genelists .txt files into a new folder and zipped the folder before uploading it as a new file found in the deliverables: [[Media:AP dZAP1 GOlist and genelist for profiles.zip]]

===Deliverables Checklist===
# Excel spreadsheet with ANOVA results/stem formatting (''.xlsx'')
#* [[Media:AP dZAP1.zip]]
# PowerPoint of screenshots of stem results (''.pptx'')
#* [[Media:AP dZAP1 STEM Screenshots & p-values.zip]]
# Gene List and GO List files from each significant profile (''.txt'' compressed together in a ''.zip'' file)
#* [[Media:AP dZAP1 GOlist and genelist for profiles.zip]]
# YEASTRACT "rank by TF" results (''.xlsx'')
#* [[Media:AP YEASTRACT Transcription Factors.xlsx]]
# GRNmap input workbook (with network adjacency matrix, ''.xlsx'')
#* [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]]
# GRNmap output workbook (''.xlsx'')
#* [[Media:15-gene 44-edge teamJASPAR Sigmoid estimation output.xlsx]]
#* Expression vs Time Images generated from MATLAB
#** [[Media:Output Images from 15-gene 44-edge teamJASPAR Sigmoid estimation.zip]]
# Electronic notebook corresponding to these the microarray results files ([[Week 8]], [[Week 10]], and Weeks 11-15) support ''reproducible research'' so that all manipulations of the data and files are documented so that someone else could begin with your starting file, follow the protocol, and obtain your results.
#* Note: make a summary and provide links to individual pages with electronic notebooks.

==Acknowledgements==
# Worked alongside [[User:Qlanners|Quinn Lanners]] to begin gathering deliverables.
# Copied the formatting and text from [[GRNsight_Gene_Page_Project_Deliverables]] checklist in my checklist category.
# Received file used for GRNsight visualization, received in class direction and instruction from [[User:Kdahlquist|Dr. Dahlquist]].
# Met up with group members in [[JASPAR the Friendly Ghost]] after the Thursday 12/01/2017 class and outside of class 12/09/2017 to discuss an outline of what needed to be completed and to work on the presentation.

[[User:Aporras1|Aporras1]] ([[User talk:Aporras1|talk]]) 16:11, 7 December 2017 (PST)

==References==
# #Dahlquist, K. D., Dionisio, J. D. N., Fitzpatrick, B. G., Anguiano, N. A., Varshneya, A., Southwick, B. J., & Samdarshi, M. (2016). GRNsight: a web application and service for visualizing models of small-to medium-scale gene regulatory networks. PeerJ Computer Science, 2, e85.
# LMU BioDB 2017. (2017). Week 15. Retrieved December 05, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_15
# LMU BioDB 2017. (2017). GRNsight Gene Page Project Deliverables. Retrieved December 05, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/GRNsight_Gene_Page_Project_Deliverables
# Teixeira, M. C., Monteiro, P. T., Guerreiro, J. F., Gonçalves, J. P., Mira, N. P., dos Santos, S. C., ... & Madeira, S. C. (2013). The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic acids research, 42(D1), D161-D166.

[[Category:Journal Entry]]

File:AP dZAP1 profile22 genelist.xlsx

2017-12-09T22:09:46Z

Aporras1: Aporras1 uploaded a new version of File:AP dZAP1 profile22 genelist.xlsx

dZAP1 genelist from stem for profile 22 created by Antonio Porras in excel format.