LMU BioDB 2019 - User contributions [en]

File:Crespin AssessmentandReflection.docx

2019-12-13T18:18:15Z

Icrespin: Icrespin uploaded a new version of File:Crespin AssessmentandReflection.docx

== Summary ==
individual info on doc

FunGals

2019-12-13T18:04:10Z

Icrespin: /* Week 15 */ added references

==Effects of the Pesticide Thiuram: Genome-wide Screening of Indicator Genes by Yeast DNA Microarray==

'''Team Information'''
Project Manager: [[User:Marmas|Michael Armas]]
Quality Assurance: [[User:Icrespin| Iliana Crespin]]
Data Analysis: [[User:eyoung20|Emma Young]], [[User:knguye66|Kaitlyn Nguyen]]
Coder: [[User:Marmas|Michael Armas]]

== Methods and Results ==
=== Week 11 ===
====Setting up the Project====
*Selected [[User:Marmas|Michael Armas]] as team's Project Manager.
*Added the name of of selected project manager to the Project Manager guild page and Overview pages.
*Named the team FunGals and created [[FunGals]] home page on the wiki.
*The name of the team home page was the selected team name.

*Created a link to team's page on the course Main page.
*Created a template for FunGal with useful information and links that you will invoke on all pages that you will create for the project.
*Created a category using team name and included it the FunGal template so that it is used on all pages created for the project. Also included the category "Group Projects" in the template. 
*Each person needs to write a short executive summary of that person's progress on the project for the week, with links to the relevant individual journal pages (which will have more detailed information).
*Each team member should reflect on the team's progress '''(Note that you will be directed to add specific information to your team's pages in the individual portion of the assignment for this and future weeks)''':
**What worked? What didn't work? What will I do next to fix what didn't work?
*** Michael Armas: Working with this team is a great pleasure! Everyone on the team is pulling their weight and providing information that contributes to the group work. Next time, as the project manager, I want to be more organized and come up with interim deadlines to make sure we are not cramming right before the actual deadline. In fact, I would have something small due every day than procrastinate until the end. However, with this team, we are making it work and doing exceptional work!
*** Kaitlyn Nguyen: What worked this week is starting the presentation formatting early, thus allocating the rest of the time to "filling in the missing parts" of the powerpoint. What also worked this week was team communication via group-chats. What didn't work this week was starting the individual assignment later, leaving less time to practicing and fully understanding the material from the journal article for the presentation in class. To fix what didn't work, I will start my individual assignment much earlier, to leave the rest of the time to focus on collaborative teamwork and group assignments. [[User:Knguye66|Knguye66]] ([[User talk:Knguye66|talk]]) 23:37, 13 November 2019 (PST)
*** Emma Young: The team seems to work really well together. I think in upcoming weeks we will really thrive in working together. A foundation for communication has already been established and we have already started reviewing each others work and providing constructive criticism and help where it is needed. The main issue this week was a matter of timing. With the amount of work we had to do in the time frame given we were not able to meet up due to busy and conflicting prior engagements. This meant that we did not reach our full potential of working together effectively as a group this week. Next week, we hopefully will be able to set better deadlines and be able to have the ability to plan out time to work on this in a less rushed manner.
*** Iliana Crespin: Overall, this group has been great. Everyone has worked together and understands what must be done. In addition, each member is understanding of the special circumstances before the deadline of this assignment. The only thing that didn't work out was how scattered each of us were because of all the assignments that had to be completed from other classes. In addition, mandated plans (school- or work-related) popped up which made it difficult to contribute equally. For the future, I will make sure to manage my time better, because I have work and school. Therefore, by doing a fair share of certain things before classes/work, I will be able to contribute more.[[User:Icrespin|Icrespin]] ([[User talk:Icrespin|talk]]) 23:46, 13 November 2019 (PST)

====Annotated Bibliography====

#Braconi, D., Bernardini, G., & Santucci, A. (2016). Saccharomyces cerevisiae as a model in ecotoxicological studies: A post-genomics perspective. Journal of Proteomics, 137, 19-34. DOI: 10.1016/j.jprot.2015.09.001
#Hinkle, K. L., & Olsen, D. (2018). Exposure to the lampricide TFM elicits an environmental stress response in yeast. FEMS yeast research, 19(1), foy121. doi: 10.1093/femsyr/foy121
#Iwahashi, Y., Hosoda, H., Park, J. H., Lee, J. H., Suzuki, Y., Kitagawa, E., ... & Iwahashi, H. (2006). Mechanisms of patulin toxicity under conditions that inhibit yeast growth. Journal of agricultural and food chemistry, 54(5), 1936-1942. doi: 10.1021/jf052264g.
#Iwahashi, H., Ishidou, E., Kitagawa, E., & Momose, Y. (2007). Combined Cadmium and Thiuram Show Synergistic Toxicity and Induce Mitochondrial Petite Mutants. Environmental Science & Technology, 41(22), 7941–7946. doi: 10.1021/es071313y
#Iwahashi, H., Ishidou, E., Kitagawa, E., & Momose, Y. (2007). Combined Cadmium and Thiuram Show Synergistic Toxicity and Induce Mitochondrial Petite Mutants. Environmental Science & Technology, 41(22), 7941–7946. doi: 10.1021/es071313y
#Kitagawa, E., Momose, Y., & Iwahashi, H. (2003). Correlation of the Structures of Agricultural Fungicides to Gene Expression in Saccharomyces cerevisiaeupon Exposure to Toxic Doses. Environmental Science & Technology, 37(12), 2788–2793. doi: 10.1021/es026156b
#Lu Yu, Na Guo, Rizeng Meng, Bin Liu, Xudong Tang, Jing Jin, Yumei Cui, Xuming Deng. Allicin-induced global gene expression profile of Saccharomyces cerevisiae. Applied Microbiology and Biotechnology 2010, 88 (1) , 219-229. DOI: 10.1007/s00253-010-2709-x.
#Pierron, A., Mimoun, S., Murate, L. S., Loiseau, N., Lippi, Y., Bracarense, A. P. F., ... & Oswald, I. P. (2016). Intestinal toxicity of the masked mycotoxin deoxynivalenol-3-β-D-glucoside. Archives of toxicology, 90(8), 2037-2046. doi: 10.1007/s00204-015-1592-8

===Week 12/13===
====Milestone 3: Getting the data ready for analysis ====

# As a group Downloaded and examined the microarray dataset, compared it to the samples and experiment described in the journal club article.
#* [https://sgd-prod-upload.s3.amazonaws.com/S000204415/Kitagawa_2002_PMID_12269742.zip Kitagawa et al. (2002)]
#* downloaded and unzipped
#* file was downloaded but was PLC format
#* Mike figured out how to drag and drop it one to excel to open the file
# Along with the QA's, make a "sample-data relationship table" that lists all of the samples (microarray chips), noting the treatment, time point, replicate number, and other information pertaining to each sample.
#* This "Metadata" sheet was created in Excel and is present on the excel work under the week 12/13 data and files.
#* In collaboration with other groups, the Metadata sheet was filled out so that nomenclature is consistent.
# The class collectively came up with consistent column headers that summarized the information
#* As decided by all groups, the format for column headers was yeastStrain_treatmentOrMutation_concentrationAndUnits_dataType_timeAndUnits-replicateNumber.
# Organized the data in a worksheet in an Excel workbook so that:
#* MasterIndex was in the first column, ID was in the second column
#* Data columns were to the right, in increasing chronological order, using the column header pattern that was created.
#* Replicates were grouped together
# Data analysts (DA) [[User:Knguye66|Kaitlyn]] set-up the ANOVA worksheet via referencing [[Week 8]]
#* The steps for the ANOVA: Part I, Benjamini, Bonferroni, and p-value correction, as well as, a quick sanity check were followed.
# DAs [[User:Eyoung20|Eyoung20]] begin setting up for STEM analysis to complete the first stage of milestones and deliverables
# All the calculations were checked by the QA [[User:Icrespin|Iliana]].

*Each team member should reflect on the team's progress '''(Note that you will be directed to add specific information to your team's pages in the individual portion of the assignment for this and future weeks)''':
**What worked? What didn't work? What will I do next to fix what didn't work?
*** Michael Armas: What worked this week was the communication between my guild and me, and my group and me. Everyone was able to help each other out and make sure the project is coming along smoothly. What didn't work this week for me was understanding exactly what I had to do to set up spreadsheets for data analysis. However, thanks to Mihir, I was able to understand how to create a metadata sheet and reach the milestone for this week. Before I leave class from now on, I will reassure myself that I understand the information by asking Dr. Dahlquist the best way to reach the week's milestone.
*** Kaitlyn Nguyen: This week, the pattern and organization to which each group member worked flowed smoothly as every member of the group knew exactly what each person was accomplishing. Having extra time in class and staying after class helped us jump-start on our tasks together and find out what assignments work best for each team member. What didn't work this week was that each milestone and part of this project works chronologically, whereby other members have to wait for the first person to finish his/her task before beginning theirs. As the days and weeks move on, it will be good to continue this method, but switch off on who starts the tasks first for the assignment. [[User:Knguye66|Knguye66]] ([[User talk:Knguye66|talk]]) 18:44, 20 November 2019 (PST)
*** Emma Young: For this week I worked closely with [[User:Knguye66|Kaitlyn]] to start the data analysis for the rest of the project. We worked with the whole team to analyze the data from the journal article and format for the rest of the data analysis. [[User:Marmas|Mike]] worked with the other programers to formulate the metadata sheet and the format for the ANOVA sheet. More details on this can be found in his personal electronic notebook [[Marmas Week 12/13]] Then [[User:Knguye66|Kaitlyn]] worked on the ANOVA analysis of the data. [[User:Icrespin|Iliana]] double checked the the results of the analysis the details can be found in [[Icrespin Journal Week 12/13]]. After the checks were completed and any errors were found, I ran a sanity check on the ANOVA data and then formatted the STEM worksheet for future analysis. The details about what [[User:Knguye66|Kaitlyn] and [[user:eyoung20|I]] did can be found in our shared journal [[Knguye66 Eyoung20 Week 12/13]]. As can be seen in this summary this week your group was really good at communicating and working together to work on this project. We worked really well together this week. One thing that did not work as well was trying to work on the excel spreadsheet online when others were working on it, there was a large lag on the sheet. I think for the next steps I might do the work on a saved downloaded version of the excel sheet and then copy my work to the shared excel. [[User:Eyoung20|Eyoung20]] ([[User talk:Eyoung20|talk]]) 16:36, 25 November 2019 (PST)
*** Iliana Crespin: For this week, it was a better organization on completing the assignment. There is more of a pattern of what should be done throughout each day to prepare for the deadline. What didn't work out for me is still trying to see how a QA can incorporate any work, since my teammates are great. For the next few weeks, I will try to continue double checking the work and contribute more. This contribution can include working with the data analysts and seeing how I can help out a bit more. In addition, texting teammates a bit more to remind any little things that must be due before the deadline. [[User:Icrespin|Icrespin]] ([[User talk:Icrespin|talk]]) 14:48, 21 November 2019 (PST)

===Week 15===
'''Milestone 4'''
#Begin wrapping up with running analysis on the created database using GRNmap
#*Data Analysts: Create GRNmap using individual database from MS Access.
#*Coder: Communicate with the QA to ensure the database is correct and if any changes need to be made
#*QA: Review the database and communicate to the Coder if any changes need to be made.
#Each team member should reflect on the team's progress
#*What worked? What didn't work? What will I do next to fix what didn't work?
#**Michael Armas
#**Kaitlyn Nguyen
#**Emma Young
#**Iliana Crespin: After everything, the team was able to complete all of the necessary items on time. I had an amazing team who went above and beyond on accommodations. There was a lot of communication that allowed us to make sure we were doing our tasks. One thing that didn't work was how I handled each deadline. Due to work circumstances, it was very difficult to do a lot of things, which made me a bit helpless. However, my team members were very flexible. For the future, one thing to work on is time management.[[User:Icrespin|Icrespin]] ([[User talk:Icrespin|talk]]) 19:29, 12 December 2019 (PST)

== Data and Files ==
=== Week 11 ===
* Presentation file: [[Media: Marmas_FunGals_Presentation.pptx|Group Presentation]]
=== Week 12/13 ===
*[[media: Thiuram_yeast_experiment.xlsx|Excel Workbook]]
*[[meda: FunGals_genelist.zip|Genelist from STEM]]
*[[media: FunGals_GOlist.zip|GOlist from STEM]]
*[[media:Data_for_FunGals.pptx|FunGals Data on Powerpoint]]
===Week 15===
*[[Media:Marmas_finalProject_Expression-and-Degradation-rate-database_120319.zip|FunGals Expression Database]]
*[[Media:GRN_Model_Red_from_Matlab.zip|GRN Model Red Profile]]
*[[media:Data_for_FunGals.pptx|FunGals Data on Powerpoint]]

== Milestones ==
{| class="wikitable"
|-
! Tasks to be completed
! Due Date
|-
| Write down Methods and Results for Week 12/13
*Coder/designer: find out the column names and edit them, sample to data relationship table
*Data Analysis: ANOVA analysis and set-up, STEM set-up (will run STEM on Thursday)
*QA: make sure all data in original file actually made it into the database, let coder and analysts know if there are issues
| Thursday, 12:00am, 11/19/19
|-
| Team Journal Assignment, continue writing down Methods and Results for Week 12/13
*Data Analysis: finish editing missing information for ANOVA and (STRAIN) worksheet, run STEM
*Coder and QA: add standard names to genes, make sure all data in original file actually made it into the database, let coder and analysts know if there are issues
| Tuesday, 12:00am, 11/26/19
|-
| Creating the database and running queries, working with all guilds to assure project is in line to be completed
*Data Analysts: Run YEASTRACT and modify GO Terms.
*Coder: Create individual database for the team.
*QA:Design Expression Tables used to create the final individual database.
| Thursday, 12:00am, 11/28/19
|-
|Begin wrapping up with running analysis on the created database using GRNmap
*Data Analysts: Create GRNmap using individual database from MS Access.
*Coder: Communicate with the QA to ensure the database is correct and if any changes need to be made
*QA: Review the database and communicate to the Coder if any changes need to be made.
| Tuesday, 12:00am, 12/03/19
|-
| Wrap up data analysis and individual milestones and begin to gather deliverables for turn-in
*Data Analysts: Provide feedback on the database and its ease-of-use. Work with QA to gather deliverables.
*Coder: Work with the entire guild to properly combine all databases for the entire class to use.
*QA: Work with the coder to finalize the [https://www.quackit.com/microsoft_access/microsoft_access_2016/howto/how_to_create_a_database_diagram_in_access_2016.cfm database schema diagram]
| Thursday, 12:00am, 12/05/19
|-
| Final Presentation
| Tuesday, 12:00am, 12/10/19
|-
| Report submitted
| Friday, 4:00 pm, 12/13/19
|-
|}

==Acknowledgements==
This section is in acknowledgement to partner [[User:Marmas|Michael Armas]], [[User:Icrespin|Iliana Crespin]], [[User:eyoung20|Emma Young]], and [[User:knguye66|Kaitlyn Nguyen]]. I would also like to acknowledge [[User:Kdahlquist|Dr. Dahlquist]] for introducing and teaching the topic and direction of this assignment.

"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
 
[[User:Marmas|Marmas]] ([[User talk:Marmas|talk]]) 23:40, 13 November 2019 (PST)
[[User:Icrespin|Icrespin]] ([[User talk:Icrespin|talk]]) 23:46, 13 November 2019 (PST)

"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
[[User:Eyoung20|Eyoung20]] ([[User talk:Eyoung20|talk]]) 23:57, 13 November 2019 (PST) [[User:Knguye66|Knguye66]] ([[User talk:Knguye66|talk]]) 18:45, 20 November 2019 (PST)

{{FunGals}}

==References==
===Week 11===
*Kitagawa, E., Takahashi, J., Momose, Y., & Iwahashi, H. (2002). Effects of the pesticide thiuram: genome-wide screening of indicator genes by yeast DNA microarray. Environmental science & technology, 36(18), 3908-3915. DOI: 10.1021/es015705v
*Dahlquist, K. (2019, November 7). Week 11. In Wikipedia, Biological Databases. https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_1https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_11
===Week 12/13===
*Dahlquist, K. (2019, November 19). Data Analysis. In Wikipedia, Biological Databases. Retrieved 6:25, November 20, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Data_Analysis
*Dahlquist, K. (2019, November 20). Final Project Deliverables. In Wikipedia, Biological Databases. Retrieved 6:25, November 20, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Final_Project_Deliverables
*Dahlquist, K. (2019, November 19). Week 12/13. In Wikipedia, Biological Databases. Retrieved 6:25, November 20, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13
*Dahlquist, K. (2019, October 17). Week 8. In Wikipedia, Biological Databases. Retrieved 6:30, October 21, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_8
===Week 15===
Dahlquist, K. (2019, November 19). Week 12/13. In Wikipedia, Biological Databases. Retrieved 6:25, November 20, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13

Dahlquist, K. (2019, October 17). Week 8. In Wikipedia, Biological Databases. Retrieved 6:30, October 21, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_8

Final Project. (2019). Deliverables. Retrieved December 10, 2019 from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Final_Project_Deliverables

FunGals. (2019). Home Page. Retrieved December 12, 2019 from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/FunGals

Kitagawa, E., Takahashi, J., Momose, Y., & Iwahashi, H. (2002). Effects of the pesticide thiuram: genome-wide screening of indicator genes by yeast DNA microarray. Environmental science & technology, 36(18), 3908-3915. DOI: 10.1021/es015705v

FunGals Deliverables

2019-12-13T05:34:28Z

Icrespin: /* Acknowledgments */ added acknowledgments

{{template:FunGals}}

==Checklist==
{| class="wikitable"
|-
! Tasks to be completed
! Complete/Incomplete
|-
| Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents)
| '''Complete'''
|-
| Group Report (''.doc'', ''.docx'' or ''.pdf'' file)
| Incomplete
|-
| Individual statements of work, assessments, reflections (wiki page, ''.doc'', ''.docx'', ''.pdf'', or e-mailed to Dr. Dahlquist)
| Incomplete
|-
| Group PowerPoint presentation (given on Tuesday, December 10, ''.ppt'', ''.pptx'' or ''.pdf'' file)
| '''Complete'''
|-
| Sample-data relationship table in Excel (''.xlsx'')
| '''Complete'''
|-
| Excel spreadsheet with ANOVA results/stem formatting (''.xlsx'')
| '''Complete'''
|-
| PowerPoint of ANOVA table, screenshots of stem results (''.pptx''), screenshot of black and white GRNsight input network and colored GRNsight output networks
| Incomplete
|-
| Gene List and GO List files from each significant profile (''.txt'' compressed together in a ''.zip'' file)
| '''Complete'''
|-
| YEASTRACT "rank by TF" results (''.xlsx'')
| '''Complete'''
|-
| GRNmap input workbook (with network adjacency matrix, ''.xlsx'')
| '''Complete'''
|-
| GRNmap output workbook (''.xlsx'') and output plots (''.jpg'') zipped together
| '''Complete'''
|-
| MS Access database, unified by the three teams with expression tables and metadata table(s) created (''.accdb'')
| '''Complete'''
|-
| ReadMe for the database that describes the design of the database, references the sources of the data, and has a [https://www.quackit.com/microsoft_access/microsoft_access_2016/howto/how_to_create_a_database_diagram_in_access_2016.cfm database schema diagram] (''.doc'', ''.docx'', ''.pdf'')
| '''Complete'''
|-
| Query design for populating a GRNmap input workbook from the database (screenshot of MS Access, or SQL code, ''.txt'')
| Incomplete
|-
| Electronic notebook corresponding to these the microarray results files ([[Week 12/13]] and [[Week 15]]) to 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.
| Incomplete
|-
|}

==Data and Files==
*[[Media:Metadata_Sheet_(1).xlsx | Sample-Data Relationship Table (Metadata Sheet)]]
*[[media: Thiuram_yeast_experiment.xlsx| ANOVA Results/STEM formatting (.xlsx)]]
*[[meda: FunGals_genelist.zip|Genelist from STEM]]
*[[media: FunGals_GOlist.zip|GOlist from STEM]]
*[[media:Genelist_combined_profiles_FunGals.xlsx| YEASTRACT Rank by TF - Green and Red Profiles (.xlsx)]]
*[[media:FunGals_Green_Profile_RegulationMatrix_Documented_2019123_2322_1272399515.xlsx| Green Regulation Matrix/network (.xlsx)]]
*[[media:FunGals Green Profile RegulationMatrix Input Workbook.xlsx | Input Workbook for Green profile (.xlsx)]]
*[[media:FunGals Red Profile RegulationMatrix Documented 2019123 2318 1127808084.xlsx| Input Workbook Red network (.xlsx)]]
*[[media:GRNmap FunGals Green profile.zip | Output Workbook & GRNModel from MatLab for Green profile (.zip)]]
*[[Media:GRN_Model_Red_from_Matlab.zip | Output Workbook & GRNModel from MatLab for Red profile (.zip)]]
*[[Media:FunGals_Final_Presentation.pptx | Final Presentation]]

==Individual Assessment and Reflection==

===Michael Armas===

==== 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 Final 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?

===Kaitlyn Nguyen===

==== 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 Final 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?

===Emma Young===

==== 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 Final 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?

===Iliana Crespin===
[[Media:Crespin_AssessmentandReflection.docx| Individual Assessment and Reflection]]

==Acknowledgments==
This section is in acknowledgement to partners Michael Armas, Iliana Crespin, Emma Young, and Kaitlyn Nguyen.

Thank you Dr. Dahlquist for helping us on this project and being able to answer our questions. It was great having you as our professor this semester.

"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."[[User:Icrespin|Icrespin]] ([[User talk:Icrespin|talk]]) 21:34, 12 December 2019 (PST)

==References==
Dahlquist, K. (2019, November 19). Week 12/13. In Wikipedia, Biological Databases. Retrieved 6:25, November 20, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13

Dahlquist, K. (2019, October 17). Week 8. In Wikipedia, Biological Databases. Retrieved 6:30, October 21, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_8

Final Project. (2019). Deliverables. Retrieved December 10, 2019 from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Final_Project_Deliverables

FunGals. (2019). Home Page. Retrieved December 12, 2019 from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/FunGals

Kitagawa, E., Takahashi, J., Momose, Y., & Iwahashi, H. (2002). Effects of the pesticide thiuram: genome-wide screening of indicator genes by yeast DNA microarray. Environmental science & technology, 36(18), 3908-3915. DOI: 10.1021/es015705v

[[Category: Group Projects]]

FunGals Deliverables

2019-12-13T05:31:21Z

Icrespin: /* References */ added references

{{template:FunGals}}

==Checklist==
{| class="wikitable"
|-
! Tasks to be completed
! Complete/Incomplete
|-
| Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents)
| '''Complete'''
|-
| Group Report (''.doc'', ''.docx'' or ''.pdf'' file)
| Incomplete
|-
| Individual statements of work, assessments, reflections (wiki page, ''.doc'', ''.docx'', ''.pdf'', or e-mailed to Dr. Dahlquist)
| Incomplete
|-
| Group PowerPoint presentation (given on Tuesday, December 10, ''.ppt'', ''.pptx'' or ''.pdf'' file)
| '''Complete'''
|-
| Sample-data relationship table in Excel (''.xlsx'')
| '''Complete'''
|-
| Excel spreadsheet with ANOVA results/stem formatting (''.xlsx'')
| '''Complete'''
|-
| PowerPoint of ANOVA table, screenshots of stem results (''.pptx''), screenshot of black and white GRNsight input network and colored GRNsight output networks
| Incomplete
|-
| Gene List and GO List files from each significant profile (''.txt'' compressed together in a ''.zip'' file)
| '''Complete'''
|-
| YEASTRACT "rank by TF" results (''.xlsx'')
| '''Complete'''
|-
| GRNmap input workbook (with network adjacency matrix, ''.xlsx'')
| '''Complete'''
|-
| GRNmap output workbook (''.xlsx'') and output plots (''.jpg'') zipped together
| '''Complete'''
|-
| MS Access database, unified by the three teams with expression tables and metadata table(s) created (''.accdb'')
| '''Complete'''
|-
| ReadMe for the database that describes the design of the database, references the sources of the data, and has a [https://www.quackit.com/microsoft_access/microsoft_access_2016/howto/how_to_create_a_database_diagram_in_access_2016.cfm database schema diagram] (''.doc'', ''.docx'', ''.pdf'')
| '''Complete'''
|-
| Query design for populating a GRNmap input workbook from the database (screenshot of MS Access, or SQL code, ''.txt'')
| Incomplete
|-
| Electronic notebook corresponding to these the microarray results files ([[Week 12/13]] and [[Week 15]]) to 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.
| Incomplete
|-
|}

==Data and Files==
*[[Media:Metadata_Sheet_(1).xlsx | Sample-Data Relationship Table (Metadata Sheet)]]
*[[media: Thiuram_yeast_experiment.xlsx| ANOVA Results/STEM formatting (.xlsx)]]
*[[meda: FunGals_genelist.zip|Genelist from STEM]]
*[[media: FunGals_GOlist.zip|GOlist from STEM]]
*[[media:Genelist_combined_profiles_FunGals.xlsx| YEASTRACT Rank by TF - Green and Red Profiles (.xlsx)]]
*[[media:FunGals_Green_Profile_RegulationMatrix_Documented_2019123_2322_1272399515.xlsx| Green Regulation Matrix/network (.xlsx)]]
*[[media:FunGals Green Profile RegulationMatrix Input Workbook.xlsx | Input Workbook for Green profile (.xlsx)]]
*[[media:FunGals Red Profile RegulationMatrix Documented 2019123 2318 1127808084.xlsx| Input Workbook Red network (.xlsx)]]
*[[media:GRNmap FunGals Green profile.zip | Output Workbook & GRNModel from MatLab for Green profile (.zip)]]
*[[Media:GRN_Model_Red_from_Matlab.zip | Output Workbook & GRNModel from MatLab for Red profile (.zip)]]
*[[Media:FunGals_Final_Presentation.pptx | Final Presentation]]

==Individual Assessment and Reflection==

===Michael Armas===

==== 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 Final 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?

===Kaitlyn Nguyen===

==== 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 Final 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?

===Emma Young===

==== 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 Final 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?

===Iliana Crespin===
[[Media:Crespin_AssessmentandReflection.docx| Individual Assessment and Reflection]]

==Acknowledgments==

==References==
Dahlquist, K. (2019, November 19). Week 12/13. In Wikipedia, Biological Databases. Retrieved 6:25, November 20, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13

Dahlquist, K. (2019, October 17). Week 8. In Wikipedia, Biological Databases. Retrieved 6:30, October 21, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_8

Final Project. (2019). Deliverables. Retrieved December 10, 2019 from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Final_Project_Deliverables

FunGals. (2019). Home Page. Retrieved December 12, 2019 from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/FunGals

Kitagawa, E., Takahashi, J., Momose, Y., & Iwahashi, H. (2002). Effects of the pesticide thiuram: genome-wide screening of indicator genes by yeast DNA microarray. Environmental science & technology, 36(18), 3908-3915. DOI: 10.1021/es015705v

[[Category: Group Projects]]

FunGals Deliverables

2019-12-13T05:24:18Z

Icrespin: /* Iliana Crespin */ added file

File:Crespin AssessmentandReflection.docx

2019-12-13T05:23:24Z

Icrespin: individual info on doc

== Summary ==
individual info on doc

Icrespin Journal Week 15

2019-12-13T04:16:28Z

Icrespin: /* Milestones */ removed some format

==Electronic Lab Notebook==
{{template:Icrespin}}

==Purpose==
The purpose of this week's assignment is to finish the last few deliverables for the final project and complete the Quality Assurance milestones. For this week, the powerpoint presentation would be done and ready to present. Lastly, QA will check to see if everything is ready to be turned in.

==Methods/Results==
===December 3, 2019===
*Worked with Coder to design a database to store the microarray data
*Used MS Access to store
*Reviewed information and created appropriate headings

===December 6, 2019===
*Communicated with coder on things that can be done
*Reviewed metadata that was created by Coder/Designer guild
*Reviewed data to make sure it was correct
*Finished database schema diagram with coder

===December 10, 2019===
*Created and finalized powerpoint presentation
*Checked to make sure slides had the appropriate information
*Worked on final deliverables

==Milestones==
{| class="wikitable"
|-
! Milestones
! Due Date
! Complete/Incomplete
|-
| Annotated Bibliography
*Work on creating a bibliography with other team members
| Tuesday, 12:00am, 11/12/19
| '''COMPLETE'''
|-
| Journal Club Presentation
*Review article and ask any questions that seemed unclear
*Add important slides to powerpoint
*Practice what will be presented to audience
| Thursday, 12:00am, 11/14/19
| '''COMPLETE'''
|-
| Working with Data Analysts to Understand Microarray Dataset
*Review and double check work done by data analysts
*Complete sanity checks to make sure it matches with work
*Add any information needed to make sure everything is fine
| Tuesday, 12:00am, 11/26/19
| '''COMPLETE'''
|-
| Making Sure Expression Data has Both Sytematic Name and Standard Name ID's
*Review information to make sure this is complete
| Tuesday, 12:00am, 11/26/19
| '''COMPLETE'''
|-
| Work with Coder/Designers to Design a Database to Store Time-course Microarray Data from Four Sources
*Add database to Box folder
*Work with Coder to create MS Access database to store yeast time-course microarray
*Review information and determine headings for database
| Tuesday, 12:00am, 12/03/19
| '''COMPLETE'''
|-
| Validation and Quality Assurance on Database
*Review information to make sure it is correct
*Communicate with Coder if something is wrong/missing
| Thursday, 12:00am, 12/06/19
| '''COMPLETE'''
|-
| Final Documentation
*Review database schema diagram with Coder
| Thursday, 12:00am, 12/06/19
| '''COMPLETE'''
|-
| Final Presentation
| Tuesday, 12:00am, 12/10/19
| '''COMPLETE'''
|-
| Report submitted
| Friday, 4:00 pm, 12/13/19
| '''COMPLETE'''
|-
|}

==Data/Files==
*[[Media:FunGals_Final_Presentation.pptx | Final Presentation]]
*[[Media: Thiuram_yeast_experiment.xlsx| ANOVA Results/STEM formatting (.xlsx)]]

==Acknowledgments==
*Thank you to my FunGals partners for helping out and accomplishing their tasks on time. Data/Files were copied and pasted from our FunGals main page.
*Thank you Dr. Dahlquist for checking on our data and answering our questions.
*Thank you other team/guild members for the collaborated work on specific milestones.
*"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."[[User:Icrespin|Icrespin]] ([[User talk:Icrespin|talk]]) 19:11, 12 December 2019 (PST)

==References==
Final Project. (2019). Deliverables. Retrieved December 10, 2019 from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Final_Project_Deliverables

Quality Assurance. (2019). Quality Assurance Main Page. Retrieved December 6, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Quality_Assurance

[[Category: Journal Entry]]
[[Category: Group Projects]]
[[Category: FunGals]]

FunGals

2019-12-13T03:29:00Z

Icrespin: /* Week 15 */ added sign

FunGals

2019-12-13T03:17:35Z

Icrespin: /* Week 15 */ added info to reflection

==Effects of the Pesticide Thiuram: Genome-wide Screening of Indicator Genes by Yeast DNA Microarray==

'''Team Information'''
Project Manager: [[User:Marmas|Michael Armas]]
Quality Assurance: [[User:Icrespin| Iliana Crespin]]
Data Analysis: [[User:eyoung20|Emma Young]], [[User:knguye66|Kaitlyn Nguyen]]
Coder: [[User:Marmas|Michael Armas]]

== Methods and Results ==
=== Week 11 ===
====Setting up the Project====
*Selected [[User:Marmas|Michael Armas]] as team's Project Manager.
*Added the name of of selected project manager to the Project Manager guild page and Overview pages.
*Named the team FunGals and created [[FunGals]] home page on the wiki.
*The name of the team home page was the selected team name.

*Created a link to team's page on the course Main page.
*Created a template for FunGal with useful information and links that you will invoke on all pages that you will create for the project.
*Created a category using team name and included it the FunGal template so that it is used on all pages created for the project. Also included the category "Group Projects" in the template. 
*Each person needs to write a short executive summary of that person's progress on the project for the week, with links to the relevant individual journal pages (which will have more detailed information).
*Each team member should reflect on the team's progress '''(Note that you will be directed to add specific information to your team's pages in the individual portion of the assignment for this and future weeks)''':
**What worked? What didn't work? What will I do next to fix what didn't work?
*** Michael Armas: Working with this team is a great pleasure! Everyone on the team is pulling their weight and providing information that contributes to the group work. Next time, as the project manager, I want to be more organized and come up with interim deadlines to make sure we are not cramming right before the actual deadline. In fact, I would have something small due every day than procrastinate until the end. However, with this team, we are making it work and doing exceptional work!
*** Kaitlyn Nguyen: What worked this week is starting the presentation formatting early, thus allocating the rest of the time to "filling in the missing parts" of the powerpoint. What also worked this week was team communication via group-chats. What didn't work this week was starting the individual assignment later, leaving less time to practicing and fully understanding the material from the journal article for the presentation in class. To fix what didn't work, I will start my individual assignment much earlier, to leave the rest of the time to focus on collaborative teamwork and group assignments. [[User:Knguye66|Knguye66]] ([[User talk:Knguye66|talk]]) 23:37, 13 November 2019 (PST)
*** Emma Young: The team seems to work really well together. I think in upcoming weeks we will really thrive in working together. A foundation for communication has already been established and we have already started reviewing each others work and providing constructive criticism and help where it is needed. The main issue this week was a matter of timing. With the amount of work we had to do in the time frame given we were not able to meet up due to busy and conflicting prior engagements. This meant that we did not reach our full potential of working together effectively as a group this week. Next week, we hopefully will be able to set better deadlines and be able to have the ability to plan out time to work on this in a less rushed manner.
*** Iliana Crespin: Overall, this group has been great. Everyone has worked together and understands what must be done. In addition, each member is understanding of the special circumstances before the deadline of this assignment. The only thing that didn't work out was how scattered each of us were because of all the assignments that had to be completed from other classes. In addition, mandated plans (school- or work-related) popped up which made it difficult to contribute equally. For the future, I will make sure to manage my time better, because I have work and school. Therefore, by doing a fair share of certain things before classes/work, I will be able to contribute more.[[User:Icrespin|Icrespin]] ([[User talk:Icrespin|talk]]) 23:46, 13 November 2019 (PST)

====Annotated Bibliography====

#Braconi, D., Bernardini, G., & Santucci, A. (2016). Saccharomyces cerevisiae as a model in ecotoxicological studies: A post-genomics perspective. Journal of Proteomics, 137, 19-34. DOI: 10.1016/j.jprot.2015.09.001
#Hinkle, K. L., & Olsen, D. (2018). Exposure to the lampricide TFM elicits an environmental stress response in yeast. FEMS yeast research, 19(1), foy121. doi: 10.1093/femsyr/foy121
#Iwahashi, Y., Hosoda, H., Park, J. H., Lee, J. H., Suzuki, Y., Kitagawa, E., ... & Iwahashi, H. (2006). Mechanisms of patulin toxicity under conditions that inhibit yeast growth. Journal of agricultural and food chemistry, 54(5), 1936-1942. doi: 10.1021/jf052264g.
#Iwahashi, H., Ishidou, E., Kitagawa, E., & Momose, Y. (2007). Combined Cadmium and Thiuram Show Synergistic Toxicity and Induce Mitochondrial Petite Mutants. Environmental Science & Technology, 41(22), 7941–7946. doi: 10.1021/es071313y
#Iwahashi, H., Ishidou, E., Kitagawa, E., & Momose, Y. (2007). Combined Cadmium and Thiuram Show Synergistic Toxicity and Induce Mitochondrial Petite Mutants. Environmental Science & Technology, 41(22), 7941–7946. doi: 10.1021/es071313y
#Kitagawa, E., Momose, Y., & Iwahashi, H. (2003). Correlation of the Structures of Agricultural Fungicides to Gene Expression in Saccharomyces cerevisiaeupon Exposure to Toxic Doses. Environmental Science & Technology, 37(12), 2788–2793. doi: 10.1021/es026156b
#Lu Yu, Na Guo, Rizeng Meng, Bin Liu, Xudong Tang, Jing Jin, Yumei Cui, Xuming Deng. Allicin-induced global gene expression profile of Saccharomyces cerevisiae. Applied Microbiology and Biotechnology 2010, 88 (1) , 219-229. DOI: 10.1007/s00253-010-2709-x.
#Pierron, A., Mimoun, S., Murate, L. S., Loiseau, N., Lippi, Y., Bracarense, A. P. F., ... & Oswald, I. P. (2016). Intestinal toxicity of the masked mycotoxin deoxynivalenol-3-β-D-glucoside. Archives of toxicology, 90(8), 2037-2046. doi: 10.1007/s00204-015-1592-8

===Week 12/13===
====Milestone 3: Getting the data ready for analysis ====

# As a group Downloaded and examined the microarray dataset, compared it to the samples and experiment described in the journal club article.
#* [https://sgd-prod-upload.s3.amazonaws.com/S000204415/Kitagawa_2002_PMID_12269742.zip Kitagawa et al. (2002)]
#* downloaded and unzipped
#* file was downloaded but was PLC format
#* Mike figured out how to drag and drop it one to excel to open the file
# Along with the QA's, make a "sample-data relationship table" that lists all of the samples (microarray chips), noting the treatment, time point, replicate number, and other information pertaining to each sample.
#* This "Metadata" sheet was created in Excel and is present on the excel work under the week 12/13 data and files.
#* In collaboration with other groups, the Metadata sheet was filled out so that nomenclature is consistent.
# The class collectively came up with consistent column headers that summarized the information
#* As decided by all groups, the format for column headers was yeastStrain_treatmentOrMutation_concentrationAndUnits_dataType_timeAndUnits-replicateNumber.
# Organized the data in a worksheet in an Excel workbook so that:
#* MasterIndex was in the first column, ID was in the second column
#* Data columns were to the right, in increasing chronological order, using the column header pattern that was created.
#* Replicates were grouped together
# Data analysts (DA) [[User:Knguye66|Kaitlyn]] set-up the ANOVA worksheet via referencing [[Week 8]]
#* The steps for the ANOVA: Part I, Benjamini, Bonferroni, and p-value correction, as well as, a quick sanity check were followed.
# DAs [[User:Eyoung20|Eyoung20]] begin setting up for STEM analysis to complete the first stage of milestones and deliverables
# All the calculations were checked by the QA [[User:Icrespin|Iliana]].

*Each team member should reflect on the team's progress '''(Note that you will be directed to add specific information to your team's pages in the individual portion of the assignment for this and future weeks)''':
**What worked? What didn't work? What will I do next to fix what didn't work?
*** Michael Armas: What worked this week was the communication between my guild and me, and my group and me. Everyone was able to help each other out and make sure the project is coming along smoothly. What didn't work this week for me was understanding exactly what I had to do to set up spreadsheets for data analysis. However, thanks to Mihir, I was able to understand how to create a metadata sheet and reach the milestone for this week. Before I leave class from now on, I will reassure myself that I understand the information by asking Dr. Dahlquist the best way to reach the week's milestone.
*** Kaitlyn Nguyen: This week, the pattern and organization to which each group member worked flowed smoothly as every member of the group knew exactly what each person was accomplishing. Having extra time in class and staying after class helped us jump-start on our tasks together and find out what assignments work best for each team member. What didn't work this week was that each milestone and part of this project works chronologically, whereby other members have to wait for the first person to finish his/her task before beginning theirs. As the days and weeks move on, it will be good to continue this method, but switch off on who starts the tasks first for the assignment. [[User:Knguye66|Knguye66]] ([[User talk:Knguye66|talk]]) 18:44, 20 November 2019 (PST)
*** Emma Young: For this week I worked closely with [[User:Knguye66|Kaitlyn]] to start the data analysis for the rest of the project. We worked with the whole team to analyze the data from the journal article and format for the rest of the data analysis. [[User:Marmas|Mike]] worked with the other programers to formulate the metadata sheet and the format for the ANOVA sheet. More details on this can be found in his personal electronic notebook [[Marmas Week 12/13]] Then [[User:Knguye66|Kaitlyn]] worked on the ANOVA analysis of the data. [[User:Icrespin|Iliana]] double checked the the results of the analysis the details can be found in [[Icrespin Journal Week 12/13]]. After the checks were completed and any errors were found, I ran a sanity check on the ANOVA data and then formatted the STEM worksheet for future analysis. The details about what [[User:Knguye66|Kaitlyn] and [[user:eyoung20|I]] did can be found in our shared journal [[Knguye66 Eyoung20 Week 12/13]]. As can be seen in this summary this week your group was really good at communicating and working together to work on this project. We worked really well together this week. One thing that did not work as well was trying to work on the excel spreadsheet online when others were working on it, there was a large lag on the sheet. I think for the next steps I might do the work on a saved downloaded version of the excel sheet and then copy my work to the shared excel. [[User:Eyoung20|Eyoung20]] ([[User talk:Eyoung20|talk]]) 16:36, 25 November 2019 (PST)
*** Iliana Crespin: For this week, it was a better organization on completing the assignment. There is more of a pattern of what should be done throughout each day to prepare for the deadline. What didn't work out for me is still trying to see how a QA can incorporate any work, since my teammates are great. For the next few weeks, I will try to continue double checking the work and contribute more. This contribution can include working with the data analysts and seeing how I can help out a bit more. In addition, texting teammates a bit more to remind any little things that must be due before the deadline. [[User:Icrespin|Icrespin]] ([[User talk:Icrespin|talk]]) 14:48, 21 November 2019 (PST)

===Week 15===
'''Milestone 4'''
#Begin wrapping up with running analysis on the created database using GRNmap
#*Data Analysts: Create GRNmap using individual database from MS Access.
#*Coder: Communicate with the QA to ensure the database is correct and if any changes need to be made
#*QA: Review the database and communicate to the Coder if any changes need to be made.
#Each team member should reflect on the team's progress
#*What worked? What didn't work? What will I do next to fix what didn't work?
#**Michael Armas
#**Kaitlyn Nguyen
#**Emma Young
#**Iliana Crespin: After everything, the team was able to complete all of the necessary items on time. I had an amazing team who went above and beyond on accommodations. There was a lot of communication that allowed us to make sure we were doing our tasks. One thing that didn't work was how I handled each deadline. Due to work circumstances, it was very difficult to do a lot of things, which made me a bit helpless. However, my team members were very flexible. For the future, one thing to work on is time management.

== Data and Files ==
=== Week 11 ===
* Presentation file: [[Media: Marmas_FunGals_Presentation.pptx|Group Presentation]]
=== Week 12/13 ===
*[[media: Thiuram_yeast_experiment.xlsx|Excel Workbook]]
*[[meda: FunGals_genelist.zip|Genelist from STEM]]
*[[media: FunGals_GOlist.zip|GOlist from STEM]]
*[[media:Data_for_FunGals.pptx|FunGals Data on Powerpoint]]
===Week 15===
*[[Media:Marmas_finalProject_Expression-and-Degradation-rate-database_120319.zip|FunGals Expression Database]]
*[[Media:GRN_Model_Red_from_Matlab.zip|GRN Model Red Profile]]
*[[media:Data_for_FunGals.pptx|FunGals Data on Powerpoint]]

== Milestones ==
{| class="wikitable"
|-
! Tasks to be completed
! Due Date
|-
| Write down Methods and Results for Week 12/13
*Coder/designer: find out the column names and edit them, sample to data relationship table
*Data Analysis: ANOVA analysis and set-up, STEM set-up (will run STEM on Thursday)
*QA: make sure all data in original file actually made it into the database, let coder and analysts know if there are issues
| Thursday, 12:00am, 11/19/19
|-
| Team Journal Assignment, continue writing down Methods and Results for Week 12/13
*Data Analysis: finish editing missing information for ANOVA and (STRAIN) worksheet, run STEM
*Coder and QA: add standard names to genes, make sure all data in original file actually made it into the database, let coder and analysts know if there are issues
| Tuesday, 12:00am, 11/26/19
|-
| Creating the database and running queries, working with all guilds to assure project is in line to be completed
*Data Analysts: Run YEASTRACT and modify GO Terms.
*Coder: Create individual database for the team.
*QA:Design Expression Tables used to create the final individual database.
| Thursday, 12:00am, 11/28/19
|-
|Begin wrapping up with running analysis on the created database using GRNmap
*Data Analysts: Create GRNmap using individual database from MS Access.
*Coder: Communicate with the QA to ensure the database is correct and if any changes need to be made
*QA: Review the database and communicate to the Coder if any changes need to be made.
| Tuesday, 12:00am, 12/03/19
|-
| Wrap up data analysis and individual milestones and begin to gather deliverables for turn-in
*Data Analysts: Provide feedback on the database and its ease-of-use. Work with QA to gather deliverables.
*Coder: Work with the entire guild to properly combine all databases for the entire class to use.
*QA: Work with the coder to finalize the [https://www.quackit.com/microsoft_access/microsoft_access_2016/howto/how_to_create_a_database_diagram_in_access_2016.cfm database schema diagram]
| Thursday, 12:00am, 12/05/19
|-
| Final Presentation
| Tuesday, 12:00am, 12/10/19
|-
| Report submitted
| Friday, 4:00 pm, 12/13/19
|-
|}

==Acknowledgements==
This section is in acknowledgement to partner [[User:Marmas|Michael Armas]], [[User:Icrespin|Iliana Crespin]], [[User:eyoung20|Emma Young]], and [[User:knguye66|Kaitlyn Nguyen]]. I would also like to acknowledge [[User:Kdahlquist|Dr. Dahlquist]] for introducing and teaching the topic and direction of this assignment.

"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
 
[[User:Marmas|Marmas]] ([[User talk:Marmas|talk]]) 23:40, 13 November 2019 (PST)
[[User:Icrespin|Icrespin]] ([[User talk:Icrespin|talk]]) 23:46, 13 November 2019 (PST)

"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
[[User:Eyoung20|Eyoung20]] ([[User talk:Eyoung20|talk]]) 23:57, 13 November 2019 (PST) [[User:Knguye66|Knguye66]] ([[User talk:Knguye66|talk]]) 18:45, 20 November 2019 (PST)

{{FunGals}}

==References==
===Week 11===
*Kitagawa, E., Takahashi, J., Momose, Y., & Iwahashi, H. (2002). Effects of the pesticide thiuram: genome-wide screening of indicator genes by yeast DNA microarray. Environmental science & technology, 36(18), 3908-3915. DOI: 10.1021/es015705v
*Dahlquist, K. (2019, November 7). Week 11. In Wikipedia, Biological Databases. https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_1https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_11
===Week 12/13===
*Dahlquist, K. (2019, November 19). Data Analysis. In Wikipedia, Biological Databases. Retrieved 6:25, November 20, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Data_Analysis
*Dahlquist, K. (2019, November 20). Final Project Deliverables. In Wikipedia, Biological Databases. Retrieved 6:25, November 20, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Final_Project_Deliverables
*Dahlquist, K. (2019, November 19). Week 12/13. In Wikipedia, Biological Databases. Retrieved 6:25, November 20, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13
*Dahlquist, K. (2019, October 17). Week 8. In Wikipedia, Biological Databases. Retrieved 6:30, October 21, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_8
===Week 15===

Icrespin Journal Week 15

2019-12-13T03:12:21Z

Icrespin: /* References */ added references

==Electronic Lab Notebook==
{{template:Icrespin}}

==Purpose==
The purpose of this week's assignment is to finish the last few deliverables for the final project and complete the Quality Assurance milestones. For this week, the powerpoint presentation would be done and ready to present. Lastly, QA will check to see if everything is ready to be turned in.

==Methods/Results==
===December 3, 2019===
*Worked with Coder to design a database to store the microarray data
*Used MS Access to store
*Reviewed information and created appropriate headings

===December 6, 2019===
*Communicated with coder on things that can be done
*Reviewed metadata that was created by Coder/Designer guild
*Reviewed data to make sure it was correct
*Finished database schema diagram with coder

===December 10, 2019===
*Created and finalized powerpoint presentation
*Checked to make sure slides had the appropriate information
*Worked on final deliverables

==Milestones==
{| class="wikitable"
|-
! Milestones
! Due Date
! Complete/Incomplete
|-
| Annotated Bibliography
*Work on creating a bibliography with other team members
| Tuesday, 12:00am, 11/12/19
| '''COMPLETE'''
|-
| Journal Club Presentation
*Review article and ask any questions that seemed unclear
*Add important slides to powerpoint
*Practice what will be presented to audience
| Thursday, 12:00am, 11/14/19
| '''COMPLETE'''
|-
| Working with Data Analysts to Understand Microarray Dataset
*Review and double check work done by data analysts
*Complete sanity checks to make sure it matches with work
*Add any information needed to make sure everything is fine
| Tuesday, 12:00am, 11/26/19
| '''COMPLETE'''
|-
| Making Sure Expression Data has Both Sytematic Name and Standard Name ID's
*Review information to make sure this is complete
| Tuesday, 12:00am, 11/26/19
| '''COMPLETE'''
|-
| Work with Coder/Designers to Design a Database to Store Time-course Microarray Data from Four Sources
*Add database to Box folder
*Work with Coder to create MS Access database to store yeast time-course microarray
*Review information and determine headings for database
| Tuesday, 12:00am, 12/03/19
| '''COMPLETE'''
|-
| Validation and Quality Assurance on Database
*Review information to make sure it is correct
*Communicate with Coder if something is wrong/missing
| Thursday, 12:00am, 12/06/19
| '''COMPLETE'''
|-
| Final Documentation
*Review database schema diagram with Coder
| Thursday, 12:00am, 12/06/19
| '''COMPLETE'''
|-
| Final Presentation
| Tuesday, 12:00am, 12/10/19
| '''COMPLETE'''
|-
| Report submitted
| Friday, 4:00 pm, 12/13/19
| '''INCOMPLETE'''
|-
|}

==Data/Files==
*[[Media:FunGals_Final_Presentation.pptx | Final Presentation]]
*[[Media: Thiuram_yeast_experiment.xlsx| ANOVA Results/STEM formatting (.xlsx)]]

==Acknowledgments==
*Thank you to my FunGals partners for helping out and accomplishing their tasks on time. Data/Files were copied and pasted from our FunGals main page.
*Thank you Dr. Dahlquist for checking on our data and answering our questions.
*Thank you other team/guild members for the collaborated work on specific milestones.
*"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."[[User:Icrespin|Icrespin]] ([[User talk:Icrespin|talk]]) 19:11, 12 December 2019 (PST)

==References==
Final Project. (2019). Deliverables. Retrieved December 10, 2019 from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Final_Project_Deliverables

Quality Assurance. (2019). Quality Assurance Main Page. Retrieved December 6, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Quality_Assurance

[[Category: Journal Entry]]
[[Category: Group Projects]]
[[Category: FunGals]]

Icrespin Journal Week 15

2019-12-13T03:11:18Z

Icrespin: /* Acknowledgments */ added acknowledgements

==Electronic Lab Notebook==
{{template:Icrespin}}

==Purpose==
The purpose of this week's assignment is to finish the last few deliverables for the final project and complete the Quality Assurance milestones. For this week, the powerpoint presentation would be done and ready to present. Lastly, QA will check to see if everything is ready to be turned in.

==Methods/Results==
===December 3, 2019===
*Worked with Coder to design a database to store the microarray data
*Used MS Access to store
*Reviewed information and created appropriate headings

===December 6, 2019===
*Communicated with coder on things that can be done
*Reviewed metadata that was created by Coder/Designer guild
*Reviewed data to make sure it was correct
*Finished database schema diagram with coder

===December 10, 2019===
*Created and finalized powerpoint presentation
*Checked to make sure slides had the appropriate information
*Worked on final deliverables

==Milestones==
{| class="wikitable"
|-
! Milestones
! Due Date
! Complete/Incomplete
|-
| Annotated Bibliography
*Work on creating a bibliography with other team members
| Tuesday, 12:00am, 11/12/19
| '''COMPLETE'''
|-
| Journal Club Presentation
*Review article and ask any questions that seemed unclear
*Add important slides to powerpoint
*Practice what will be presented to audience
| Thursday, 12:00am, 11/14/19
| '''COMPLETE'''
|-
| Working with Data Analysts to Understand Microarray Dataset
*Review and double check work done by data analysts
*Complete sanity checks to make sure it matches with work
*Add any information needed to make sure everything is fine
| Tuesday, 12:00am, 11/26/19
| '''COMPLETE'''
|-
| Making Sure Expression Data has Both Sytematic Name and Standard Name ID's
*Review information to make sure this is complete
| Tuesday, 12:00am, 11/26/19
| '''COMPLETE'''
|-
| Work with Coder/Designers to Design a Database to Store Time-course Microarray Data from Four Sources
*Add database to Box folder
*Work with Coder to create MS Access database to store yeast time-course microarray
*Review information and determine headings for database
| Tuesday, 12:00am, 12/03/19
| '''COMPLETE'''
|-
| Validation and Quality Assurance on Database
*Review information to make sure it is correct
*Communicate with Coder if something is wrong/missing
| Thursday, 12:00am, 12/06/19
| '''COMPLETE'''
|-
| Final Documentation
*Review database schema diagram with Coder
| Thursday, 12:00am, 12/06/19
| '''COMPLETE'''
|-
| Final Presentation
| Tuesday, 12:00am, 12/10/19
| '''COMPLETE'''
|-
| Report submitted
| Friday, 4:00 pm, 12/13/19
| '''INCOMPLETE'''
|-
|}

==Data/Files==
*[[Media:FunGals_Final_Presentation.pptx | Final Presentation]]
*[[Media: Thiuram_yeast_experiment.xlsx| ANOVA Results/STEM formatting (.xlsx)]]

==Acknowledgments==
*Thank you to my FunGals partners for helping out and accomplishing their tasks on time. Data/Files were copied and pasted from our FunGals main page.
*Thank you Dr. Dahlquist for checking on our data and answering our questions.
*Thank you other team/guild members for the collaborated work on specific milestones.
*"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."[[User:Icrespin|Icrespin]] ([[User talk:Icrespin|talk]]) 19:11, 12 December 2019 (PST)

==References==

Icrespin Journal Week 15

2019-12-13T03:09:30Z

Icrespin: /* Data/Files */ added data

==Electronic Lab Notebook==
{{template:Icrespin}}

==Purpose==
The purpose of this week's assignment is to finish the last few deliverables for the final project and complete the Quality Assurance milestones. For this week, the powerpoint presentation would be done and ready to present. Lastly, QA will check to see if everything is ready to be turned in.

==Methods/Results==
===December 3, 2019===
*Worked with Coder to design a database to store the microarray data
*Used MS Access to store
*Reviewed information and created appropriate headings

===December 6, 2019===
*Communicated with coder on things that can be done
*Reviewed metadata that was created by Coder/Designer guild
*Reviewed data to make sure it was correct
*Finished database schema diagram with coder

===December 10, 2019===
*Created and finalized powerpoint presentation
*Checked to make sure slides had the appropriate information
*Worked on final deliverables

==Milestones==
{| class="wikitable"
|-
! Milestones
! Due Date
! Complete/Incomplete
|-
| Annotated Bibliography
*Work on creating a bibliography with other team members
| Tuesday, 12:00am, 11/12/19
| '''COMPLETE'''
|-
| Journal Club Presentation
*Review article and ask any questions that seemed unclear
*Add important slides to powerpoint
*Practice what will be presented to audience
| Thursday, 12:00am, 11/14/19
| '''COMPLETE'''
|-
| Working with Data Analysts to Understand Microarray Dataset
*Review and double check work done by data analysts
*Complete sanity checks to make sure it matches with work
*Add any information needed to make sure everything is fine
| Tuesday, 12:00am, 11/26/19
| '''COMPLETE'''
|-
| Making Sure Expression Data has Both Sytematic Name and Standard Name ID's
*Review information to make sure this is complete
| Tuesday, 12:00am, 11/26/19
| '''COMPLETE'''
|-
| Work with Coder/Designers to Design a Database to Store Time-course Microarray Data from Four Sources
*Add database to Box folder
*Work with Coder to create MS Access database to store yeast time-course microarray
*Review information and determine headings for database
| Tuesday, 12:00am, 12/03/19
| '''COMPLETE'''
|-
| Validation and Quality Assurance on Database
*Review information to make sure it is correct
*Communicate with Coder if something is wrong/missing
| Thursday, 12:00am, 12/06/19
| '''COMPLETE'''
|-
| Final Documentation
*Review database schema diagram with Coder
| Thursday, 12:00am, 12/06/19
| '''COMPLETE'''
|-
| Final Presentation
| Tuesday, 12:00am, 12/10/19
| '''COMPLETE'''
|-
| Report submitted
| Friday, 4:00 pm, 12/13/19
| '''INCOMPLETE'''
|-
|}

==Data/Files==
*[[Media:FunGals_Final_Presentation.pptx | Final Presentation]]
*[[Media: Thiuram_yeast_experiment.xlsx| ANOVA Results/STEM formatting (.xlsx)]]

==Acknowledgments==

==References==

Icrespin Journal Week 15

2019-12-13T03:08:06Z

Icrespin: /* Methods/Results */ added methods

==Electronic Lab Notebook==
{{template:Icrespin}}

==Purpose==
The purpose of this week's assignment is to finish the last few deliverables for the final project and complete the Quality Assurance milestones. For this week, the powerpoint presentation would be done and ready to present. Lastly, QA will check to see if everything is ready to be turned in.

==Methods/Results==
===December 3, 2019===
*Worked with Coder to design a database to store the microarray data
*Used MS Access to store
*Reviewed information and created appropriate headings

===December 6, 2019===
*Communicated with coder on things that can be done
*Reviewed metadata that was created by Coder/Designer guild
*Reviewed data to make sure it was correct
*Finished database schema diagram with coder

===December 10, 2019===
*Created and finalized powerpoint presentation
*Checked to make sure slides had the appropriate information
*Worked on final deliverables

==Milestones==
{| class="wikitable"
|-
! Milestones
! Due Date
! Complete/Incomplete
|-
| Annotated Bibliography
*Work on creating a bibliography with other team members
| Tuesday, 12:00am, 11/12/19
| '''COMPLETE'''
|-
| Journal Club Presentation
*Review article and ask any questions that seemed unclear
*Add important slides to powerpoint
*Practice what will be presented to audience
| Thursday, 12:00am, 11/14/19
| '''COMPLETE'''
|-
| Working with Data Analysts to Understand Microarray Dataset
*Review and double check work done by data analysts
*Complete sanity checks to make sure it matches with work
*Add any information needed to make sure everything is fine
| Tuesday, 12:00am, 11/26/19
| '''COMPLETE'''
|-
| Making Sure Expression Data has Both Sytematic Name and Standard Name ID's
*Review information to make sure this is complete
| Tuesday, 12:00am, 11/26/19
| '''COMPLETE'''
|-
| Work with Coder/Designers to Design a Database to Store Time-course Microarray Data from Four Sources
*Add database to Box folder
*Work with Coder to create MS Access database to store yeast time-course microarray
*Review information and determine headings for database
| Tuesday, 12:00am, 12/03/19
| '''COMPLETE'''
|-
| Validation and Quality Assurance on Database
*Review information to make sure it is correct
*Communicate with Coder if something is wrong/missing
| Thursday, 12:00am, 12/06/19
| '''COMPLETE'''
|-
| Final Documentation
*Review database schema diagram with Coder
| Thursday, 12:00am, 12/06/19
| '''COMPLETE'''
|-
| Final Presentation
| Tuesday, 12:00am, 12/10/19
| '''COMPLETE'''
|-
| Report submitted
| Friday, 4:00 pm, 12/13/19
| '''INCOMPLETE'''
|-
|}

==Data/Files==

==Acknowledgments==

==References==

Icrespin Journal Week 15

2019-12-13T03:03:02Z

Icrespin: /* Milestones */ fixed table

Icrespin Journal Week 15

2019-12-13T03:02:36Z

Icrespin: /* Purpose */ added purpose

FunGals

2019-12-05T23:13:15Z

Icrespin: /* Week 15 */ added info

==Effects of the Pesticide Thiuram: Genome-wide Screening of Indicator Genes by Yeast DNA Microarray==

'''Team Information'''
Project Manager: [[User:Marmas|Michael Armas]]
Quality Assurance: [[User:Icrespin| Iliana Crespin]]
Data Analysis: [[User:eyoung20|Emma Young]], [[User:knguye66|Kaitlyn Nguyen]]
Coder: [[User:Marmas|Michael Armas]]

== Methods and Results ==
=== Week 11 ===
====Setting up the Project====
*Selected [[User:Marmas|Michael Armas]] as team's Project Manager.
*Added the name of of selected project manager to the Project Manager guild page and Overview pages.
*Named the team FunGals and created [[FunGals]] home page on the wiki.
*The name of the team home page was the selected team name.

*Created a link to team's page on the course Main page.
*Created a template for FunGal with useful information and links that you will invoke on all pages that you will create for the project.
*Created a category using team name and included it the FunGal template so that it is used on all pages created for the project. Also included the category "Group Projects" in the template. 
*Each person needs to write a short executive summary of that person's progress on the project for the week, with links to the relevant individual journal pages (which will have more detailed information).
*Each team member should reflect on the team's progress '''(Note that you will be directed to add specific information to your team's pages in the individual portion of the assignment for this and future weeks)''':
**What worked? What didn't work? What will I do next to fix what didn't work?
*** Michael Armas: Working with this team is a great pleasure! Everyone on the team is pulling their weight and providing information that contributes to the group work. Next time, as the project manager, I want to be more organized and come up with interim deadlines to make sure we are not cramming right before the actual deadline. In fact, I would have something small due every day than procrastinate until the end. However, with this team, we are making it work and doing exceptional work!
*** Kaitlyn Nguyen: What worked this week is starting the presentation formatting early, thus allocating the rest of the time to "filling in the missing parts" of the powerpoint. What also worked this week was team communication via group-chats. What didn't work this week was starting the individual assignment later, leaving less time to practicing and fully understanding the material from the journal article for the presentation in class. To fix what didn't work, I will start my individual assignment much earlier, to leave the rest of the time to focus on collaborative teamwork and group assignments. [[User:Knguye66|Knguye66]] ([[User talk:Knguye66|talk]]) 23:37, 13 November 2019 (PST)
*** Emma Young: The team seems to work really well together. I think in upcoming weeks we will really thrive in working together. A foundation for communication has already been established and we have already started reviewing each others work and providing constructive criticism and help where it is needed. The main issue this week was a matter of timing. With the amount of work we had to do in the time frame given we were not able to meet up due to busy and conflicting prior engagements. This meant that we did not reach our full potential of working together effectively as a group this week. Next week, we hopefully will be able to set better deadlines and be able to have the ability to plan out time to work on this in a less rushed manner.
*** Iliana Crespin: Overall, this group has been great. Everyone has worked together and understands what must be done. In addition, each member is understanding of the special circumstances before the deadline of this assignment. The only thing that didn't work out was how scattered each of us were because of all the assignments that had to be completed from other classes. In addition, mandated plans (school- or work-related) popped up which made it difficult to contribute equally. For the future, I will make sure to manage my time better, because I have work and school. Therefore, by doing a fair share of certain things before classes/work, I will be able to contribute more.[[User:Icrespin|Icrespin]] ([[User talk:Icrespin|talk]]) 23:46, 13 November 2019 (PST)

====Annotated Bibliography====

#Braconi, D., Bernardini, G., & Santucci, A. (2016). Saccharomyces cerevisiae as a model in ecotoxicological studies: A post-genomics perspective. Journal of Proteomics, 137, 19-34. DOI: 10.1016/j.jprot.2015.09.001
#Hinkle, K. L., & Olsen, D. (2018). Exposure to the lampricide TFM elicits an environmental stress response in yeast. FEMS yeast research, 19(1), foy121. doi: 10.1093/femsyr/foy121
#Iwahashi, Y., Hosoda, H., Park, J. H., Lee, J. H., Suzuki, Y., Kitagawa, E., ... & Iwahashi, H. (2006). Mechanisms of patulin toxicity under conditions that inhibit yeast growth. Journal of agricultural and food chemistry, 54(5), 1936-1942. doi: 10.1021/jf052264g.
#Iwahashi, H., Ishidou, E., Kitagawa, E., & Momose, Y. (2007). Combined Cadmium and Thiuram Show Synergistic Toxicity and Induce Mitochondrial Petite Mutants. Environmental Science & Technology, 41(22), 7941–7946. doi: 10.1021/es071313y
#Iwahashi, H., Ishidou, E., Kitagawa, E., & Momose, Y. (2007). Combined Cadmium and Thiuram Show Synergistic Toxicity and Induce Mitochondrial Petite Mutants. Environmental Science & Technology, 41(22), 7941–7946. doi: 10.1021/es071313y
#Kitagawa, E., Momose, Y., & Iwahashi, H. (2003). Correlation of the Structures of Agricultural Fungicides to Gene Expression in Saccharomyces cerevisiaeupon Exposure to Toxic Doses. Environmental Science & Technology, 37(12), 2788–2793. doi: 10.1021/es026156b
#Lu Yu, Na Guo, Rizeng Meng, Bin Liu, Xudong Tang, Jing Jin, Yumei Cui, Xuming Deng. Allicin-induced global gene expression profile of Saccharomyces cerevisiae. Applied Microbiology and Biotechnology 2010, 88 (1) , 219-229. DOI: 10.1007/s00253-010-2709-x.
#Pierron, A., Mimoun, S., Murate, L. S., Loiseau, N., Lippi, Y., Bracarense, A. P. F., ... & Oswald, I. P. (2016). Intestinal toxicity of the masked mycotoxin deoxynivalenol-3-β-D-glucoside. Archives of toxicology, 90(8), 2037-2046. doi: 10.1007/s00204-015-1592-8

===Week 12/13===
====Milestone 3: Getting the data ready for analysis ====

# As a group Downloaded and examined the microarray dataset, compared it to the samples and experiment described in the journal club article.
#* [https://sgd-prod-upload.s3.amazonaws.com/S000204415/Kitagawa_2002_PMID_12269742.zip Kitagawa et al. (2002)]
#* downloaded and unzipped
#* file was downloaded but was PLC format
#* Mike figured out how to drag and drop it one to excel to open the file
# Along with the QA's, make a "sample-data relationship table" that lists all of the samples (microarray chips), noting the treatment, time point, replicate number, and other information pertaining to each sample.
#* This "Metadata" sheet was created in Excel and is present on the excel work under the week 12/13 data and files.
#* In collaboration with other groups, the Metadata sheet was filled out so that nomenclature is consistent.
# The class collectively came up with consistent column headers that summarized the information
#* As decided by all groups, the format for column headers was yeastStrain_treatmentOrMutation_concentrationAndUnits_dataType_timeAndUnits-replicateNumber.
# Organized the data in a worksheet in an Excel workbook so that:
#* MasterIndex was in the first column, ID was in the second column
#* Data columns were to the right, in increasing chronological order, using the column header pattern that was created.
#* Replicates were grouped together
# Data analysts (DA) [[User:Knguye66|Kaitlyn]] set-up the ANOVA worksheet via referencing [[Week 8]]
#* The steps for the ANOVA: Part I, Benjamini, Bonferroni, and p-value correction, as well as, a quick sanity check were followed.
# DAs [[User:Eyoung20|Eyoung20]] begin setting up for STEM analysis to complete the first stage of milestones and deliverables
# All the calculations were checked by the QA [[User:Icrespin|Iliana]].

*Each team member should reflect on the team's progress '''(Note that you will be directed to add specific information to your team's pages in the individual portion of the assignment for this and future weeks)''':
**What worked? What didn't work? What will I do next to fix what didn't work?
*** Michael Armas: What worked this week was the communication between my guild and me, and my group and me. Everyone was able to help each other out and make sure the project is coming along smoothly. What didn't work this week for me was understanding exactly what I had to do to set up spreadsheets for data analysis. However, thanks to Mihir, I was able to understand how to create a metadata sheet and reach the milestone for this week. Before I leave class from now on, I will reassure myself that I understand the information by asking Dr. Dahlquist the best way to reach the week's milestone.
*** Kaitlyn Nguyen: This week, the pattern and organization to which each group member worked flowed smoothly as every member of the group knew exactly what each person was accomplishing. Having extra time in class and staying after class helped us jump-start on our tasks together and find out what assignments work best for each team member. What didn't work this week was that each milestone and part of this project works chronologically, whereby other members have to wait for the first person to finish his/her task before beginning theirs. As the days and weeks move on, it will be good to continue this method, but switch off on who starts the tasks first for the assignment. [[User:Knguye66|Knguye66]] ([[User talk:Knguye66|talk]]) 18:44, 20 November 2019 (PST)
*** Emma Young: For this week I worked closely with [[User:Knguye66|Kaitlyn]] to start the data analysis for the rest of the project. We worked with the whole team to analyze the data from the journal article and format for the rest of the data analysis. [[User:Marmas|Mike]] worked with the other programers to formulate the metadata sheet and the format for the ANOVA sheet. More details on this can be found in his personal electronic notebook [[Marmas Week 12/13]] Then [[User:Knguye66|Kaitlyn]] worked on the ANOVA analysis of the data. [[User:Icrespin|Iliana]] double checked the the results of the analysis the details can be found in [[Icrespin Journal Week 12/13]]. After the checks were completed and any errors were found, I ran a sanity check on the ANOVA data and then formatted the STEM worksheet for future analysis. The details about what [[User:Knguye66|Kaitlyn] and [[user:eyoung20|I]] did can be found in our shared journal [[Knguye66 Eyoung20 Week 12/13]]. As can be seen in this summary this week your group was really good at communicating and working together to work on this project. We worked really well together this week. One thing that did not work as well was trying to work on the excel spreadsheet online when others were working on it, there was a large lag on the sheet. I think for the next steps I might do the work on a saved downloaded version of the excel sheet and then copy my work to the shared excel. [[User:Eyoung20|Eyoung20]] ([[User talk:Eyoung20|talk]]) 16:36, 25 November 2019 (PST)
*** Iliana Crespin: For this week, it was a better organization on completing the assignment. There is more of a pattern of what should be done throughout each day to prepare for the deadline. What didn't work out for me is still trying to see how a QA can incorporate any work, since my teammates are great. For the next few weeks, I will try to continue double checking the work and contribute more. This contribution can include working with the data analysts and seeing how I can help out a bit more. In addition, texting teammates a bit more to remind any little things that must be due before the deadline. [[User:Icrespin|Icrespin]] ([[User talk:Icrespin|talk]]) 14:48, 21 November 2019 (PST)

===Week 15===
'''Milestone 4'''
#Begin wrapping up with running analysis on the created database using GRNmap
#*Data Analysts: Create GRNmap using individual database from MS Access.
#*Coder: Communicate with the QA to ensure the database is correct and if any changes need to be made
#*QA: Review the database and communicate to the Coder if any changes need to be made.
#Each team member should reflect on the team's progress
#*What worked? What didn't work? What will I do next to fix what didn't work?
#**Michael Armas
#**Kaitlyn Nguyen
#**Emma Young
#**Iliana Crespin

== Data and Files ==
=== Week 11 ===
* Presentation file: [[Media: Marmas_FunGals_Presentation.pptx|Group Presentation]]
=== Week 12/13 ===
*[[media: Thiuram_yeast_experiment.xlsx|Excel Workbook]]
*[[meda: FunGals_genelist.zip|Genelist from STEM]]
*[[media: FunGals_GOlist.zip|GOlist from STEM]]
===Week 15===
*[[Media:Marmas_finalProject_Expression-and-Degradation-rate-database_120319.zip|FunGals Expression Database]]

== Milestones ==
{| class="wikitable"
|-
! Tasks to be completed
! Due Date
|-
| Write down Methods and Results for Week 12/13
*Coder/designer: find out the column names and edit them, sample to data relationship table
*Data Analysis: ANOVA analysis and set-up, STEM set-up (will run STEM on Thursday)
*QA: make sure all data in original file actually made it into the database, let coder and analysts know if there are issues
| Thursday, 12:00am, 11/19/19
|-
| Team Journal Assignment, continue writing down Methods and Results for Week 12/13
*Data Analysis: finish editing missing information for ANOVA and (STRAIN) worksheet, run STEM
*Coder and QA: add standard names to genes, make sure all data in original file actually made it into the database, let coder and analysts know if there are issues
| Tuesday, 12:00am, 11/26/19
|-
| Creating the database and running queries, working with all guilds to assure project is in line to be completed
*Data Analysts: Run YEASTRACT and modify GO Terms.
*Coder: Create individual database for the team.
*QA:Design Expression Tables used to create the final individual database.
| Thursday, 12:00am, 11/28/19
|-
|Begin wrapping up with running analysis on the created database using GRNmap
*Data Analysts: Create GRNmap using individual database from MS Access.
*Coder: Communicate with the QA to ensure the database is correct and if any changes need to be made
*QA: Review the database and communicate to the Coder if any changes need to be made.
| Tuesday, 12:00am, 12/03/19
|-
| Wrap up data analysis and individual milestones and begin to gather deliverables for turn-in
*Data Analysts: Provide feedback on the database and its ease-of-use. Work with QA to gather deliverables.
*Coder: Work with the entire guild to properly combine all databases for the entire class to use.
*QA: Work with the coder to finalize the [https://www.quackit.com/microsoft_access/microsoft_access_2016/howto/how_to_create_a_database_diagram_in_access_2016.cfm database schema diagram]
| Thursday, 12:00am, 12/05/19
|-
| Final Presentation
| Tuesday, 12:00am, 12/10/19
|-
| Report submitted
| Friday, 4:00 pm, 12/13/19
|-
|}

==Acknowledgements==
This section is in acknowledgement to partner [[User:Marmas|Michael Armas]], [[User:Icrespin|Iliana Crespin]], [[User:eyoung20|Emma Young]], and [[User:knguye66|Kaitlyn Nguyen]]. I would also like to acknowledge [[User:Kdahlquist|Dr. Dahlquist]] for introducing and teaching the topic and direction of this assignment.

"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
 
[[User:Marmas|Marmas]] ([[User talk:Marmas|talk]]) 23:40, 13 November 2019 (PST)
[[User:Icrespin|Icrespin]] ([[User talk:Icrespin|talk]]) 23:46, 13 November 2019 (PST)

"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
[[User:Eyoung20|Eyoung20]] ([[User talk:Eyoung20|talk]]) 23:57, 13 November 2019 (PST) [[User:Knguye66|Knguye66]] ([[User talk:Knguye66|talk]]) 18:45, 20 November 2019 (PST)

{{FunGals}}

==References==
===Week 11===
*Kitagawa, E., Takahashi, J., Momose, Y., & Iwahashi, H. (2002). Effects of the pesticide thiuram: genome-wide screening of indicator genes by yeast DNA microarray. Environmental science & technology, 36(18), 3908-3915. DOI: 10.1021/es015705v
*Dahlquist, K. (2019, November 7). Week 11. In Wikipedia, Biological Databases. https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_1https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_11
===Week 12/13===
*Dahlquist, K. (2019, November 19). Data Analysis. In Wikipedia, Biological Databases. Retrieved 6:25, November 20, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Data_Analysis
*Dahlquist, K. (2019, November 20). Final Project Deliverables. In Wikipedia, Biological Databases. Retrieved 6:25, November 20, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Final_Project_Deliverables
*Dahlquist, K. (2019, November 19). Week 12/13. In Wikipedia, Biological Databases. Retrieved 6:25, November 20, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13
*Dahlquist, K. (2019, October 17). Week 8. In Wikipedia, Biological Databases. Retrieved 6:30, October 21, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_8
===Week 15===

FunGals

2019-12-05T23:12:12Z

Icrespin: /* Week 15 */ added a question

==Effects of the Pesticide Thiuram: Genome-wide Screening of Indicator Genes by Yeast DNA Microarray==

'''Team Information'''
Project Manager: [[User:Marmas|Michael Armas]]
Quality Assurance: [[User:Icrespin| Iliana Crespin]]
Data Analysis: [[User:eyoung20|Emma Young]], [[User:knguye66|Kaitlyn Nguyen]]
Coder: [[User:Marmas|Michael Armas]]

== Methods and Results ==
=== Week 11 ===
====Setting up the Project====
*Selected [[User:Marmas|Michael Armas]] as team's Project Manager.
*Added the name of of selected project manager to the Project Manager guild page and Overview pages.
*Named the team FunGals and created [[FunGals]] home page on the wiki.
*The name of the team home page was the selected team name.

*Created a link to team's page on the course Main page.
*Created a template for FunGal with useful information and links that you will invoke on all pages that you will create for the project.
*Created a category using team name and included it the FunGal template so that it is used on all pages created for the project. Also included the category "Group Projects" in the template. 
*Each person needs to write a short executive summary of that person's progress on the project for the week, with links to the relevant individual journal pages (which will have more detailed information).
*Each team member should reflect on the team's progress '''(Note that you will be directed to add specific information to your team's pages in the individual portion of the assignment for this and future weeks)''':
**What worked? What didn't work? What will I do next to fix what didn't work?
*** Michael Armas: Working with this team is a great pleasure! Everyone on the team is pulling their weight and providing information that contributes to the group work. Next time, as the project manager, I want to be more organized and come up with interim deadlines to make sure we are not cramming right before the actual deadline. In fact, I would have something small due every day than procrastinate until the end. However, with this team, we are making it work and doing exceptional work!
*** Kaitlyn Nguyen: What worked this week is starting the presentation formatting early, thus allocating the rest of the time to "filling in the missing parts" of the powerpoint. What also worked this week was team communication via group-chats. What didn't work this week was starting the individual assignment later, leaving less time to practicing and fully understanding the material from the journal article for the presentation in class. To fix what didn't work, I will start my individual assignment much earlier, to leave the rest of the time to focus on collaborative teamwork and group assignments. [[User:Knguye66|Knguye66]] ([[User talk:Knguye66|talk]]) 23:37, 13 November 2019 (PST)
*** Emma Young: The team seems to work really well together. I think in upcoming weeks we will really thrive in working together. A foundation for communication has already been established and we have already started reviewing each others work and providing constructive criticism and help where it is needed. The main issue this week was a matter of timing. With the amount of work we had to do in the time frame given we were not able to meet up due to busy and conflicting prior engagements. This meant that we did not reach our full potential of working together effectively as a group this week. Next week, we hopefully will be able to set better deadlines and be able to have the ability to plan out time to work on this in a less rushed manner.
*** Iliana Crespin: Overall, this group has been great. Everyone has worked together and understands what must be done. In addition, each member is understanding of the special circumstances before the deadline of this assignment. The only thing that didn't work out was how scattered each of us were because of all the assignments that had to be completed from other classes. In addition, mandated plans (school- or work-related) popped up which made it difficult to contribute equally. For the future, I will make sure to manage my time better, because I have work and school. Therefore, by doing a fair share of certain things before classes/work, I will be able to contribute more.[[User:Icrespin|Icrespin]] ([[User talk:Icrespin|talk]]) 23:46, 13 November 2019 (PST)

====Annotated Bibliography====

#Braconi, D., Bernardini, G., & Santucci, A. (2016). Saccharomyces cerevisiae as a model in ecotoxicological studies: A post-genomics perspective. Journal of Proteomics, 137, 19-34. DOI: 10.1016/j.jprot.2015.09.001
#Hinkle, K. L., & Olsen, D. (2018). Exposure to the lampricide TFM elicits an environmental stress response in yeast. FEMS yeast research, 19(1), foy121. doi: 10.1093/femsyr/foy121
#Iwahashi, Y., Hosoda, H., Park, J. H., Lee, J. H., Suzuki, Y., Kitagawa, E., ... & Iwahashi, H. (2006). Mechanisms of patulin toxicity under conditions that inhibit yeast growth. Journal of agricultural and food chemistry, 54(5), 1936-1942. doi: 10.1021/jf052264g.
#Iwahashi, H., Ishidou, E., Kitagawa, E., & Momose, Y. (2007). Combined Cadmium and Thiuram Show Synergistic Toxicity and Induce Mitochondrial Petite Mutants. Environmental Science & Technology, 41(22), 7941–7946. doi: 10.1021/es071313y
#Iwahashi, H., Ishidou, E., Kitagawa, E., & Momose, Y. (2007). Combined Cadmium and Thiuram Show Synergistic Toxicity and Induce Mitochondrial Petite Mutants. Environmental Science & Technology, 41(22), 7941–7946. doi: 10.1021/es071313y
#Kitagawa, E., Momose, Y., & Iwahashi, H. (2003). Correlation of the Structures of Agricultural Fungicides to Gene Expression in Saccharomyces cerevisiaeupon Exposure to Toxic Doses. Environmental Science & Technology, 37(12), 2788–2793. doi: 10.1021/es026156b
#Lu Yu, Na Guo, Rizeng Meng, Bin Liu, Xudong Tang, Jing Jin, Yumei Cui, Xuming Deng. Allicin-induced global gene expression profile of Saccharomyces cerevisiae. Applied Microbiology and Biotechnology 2010, 88 (1) , 219-229. DOI: 10.1007/s00253-010-2709-x.
#Pierron, A., Mimoun, S., Murate, L. S., Loiseau, N., Lippi, Y., Bracarense, A. P. F., ... & Oswald, I. P. (2016). Intestinal toxicity of the masked mycotoxin deoxynivalenol-3-β-D-glucoside. Archives of toxicology, 90(8), 2037-2046. doi: 10.1007/s00204-015-1592-8

===Week 12/13===
====Milestone 3: Getting the data ready for analysis ====

# As a group Downloaded and examined the microarray dataset, compared it to the samples and experiment described in the journal club article.
#* [https://sgd-prod-upload.s3.amazonaws.com/S000204415/Kitagawa_2002_PMID_12269742.zip Kitagawa et al. (2002)]
#* downloaded and unzipped
#* file was downloaded but was PLC format
#* Mike figured out how to drag and drop it one to excel to open the file
# Along with the QA's, make a "sample-data relationship table" that lists all of the samples (microarray chips), noting the treatment, time point, replicate number, and other information pertaining to each sample.
#* This "Metadata" sheet was created in Excel and is present on the excel work under the week 12/13 data and files.
#* In collaboration with other groups, the Metadata sheet was filled out so that nomenclature is consistent.
# The class collectively came up with consistent column headers that summarized the information
#* As decided by all groups, the format for column headers was yeastStrain_treatmentOrMutation_concentrationAndUnits_dataType_timeAndUnits-replicateNumber.
# Organized the data in a worksheet in an Excel workbook so that:
#* MasterIndex was in the first column, ID was in the second column
#* Data columns were to the right, in increasing chronological order, using the column header pattern that was created.
#* Replicates were grouped together
# Data analysts (DA) [[User:Knguye66|Kaitlyn]] set-up the ANOVA worksheet via referencing [[Week 8]]
#* The steps for the ANOVA: Part I, Benjamini, Bonferroni, and p-value correction, as well as, a quick sanity check were followed.
# DAs [[User:Eyoung20|Eyoung20]] begin setting up for STEM analysis to complete the first stage of milestones and deliverables
# All the calculations were checked by the QA [[User:Icrespin|Iliana]].

*Each team member should reflect on the team's progress '''(Note that you will be directed to add specific information to your team's pages in the individual portion of the assignment for this and future weeks)''':
**What worked? What didn't work? What will I do next to fix what didn't work?
*** Michael Armas: What worked this week was the communication between my guild and me, and my group and me. Everyone was able to help each other out and make sure the project is coming along smoothly. What didn't work this week for me was understanding exactly what I had to do to set up spreadsheets for data analysis. However, thanks to Mihir, I was able to understand how to create a metadata sheet and reach the milestone for this week. Before I leave class from now on, I will reassure myself that I understand the information by asking Dr. Dahlquist the best way to reach the week's milestone.
*** Kaitlyn Nguyen: This week, the pattern and organization to which each group member worked flowed smoothly as every member of the group knew exactly what each person was accomplishing. Having extra time in class and staying after class helped us jump-start on our tasks together and find out what assignments work best for each team member. What didn't work this week was that each milestone and part of this project works chronologically, whereby other members have to wait for the first person to finish his/her task before beginning theirs. As the days and weeks move on, it will be good to continue this method, but switch off on who starts the tasks first for the assignment. [[User:Knguye66|Knguye66]] ([[User talk:Knguye66|talk]]) 18:44, 20 November 2019 (PST)
*** Emma Young: For this week I worked closely with [[User:Knguye66|Kaitlyn]] to start the data analysis for the rest of the project. We worked with the whole team to analyze the data from the journal article and format for the rest of the data analysis. [[User:Marmas|Mike]] worked with the other programers to formulate the metadata sheet and the format for the ANOVA sheet. More details on this can be found in his personal electronic notebook [[Marmas Week 12/13]] Then [[User:Knguye66|Kaitlyn]] worked on the ANOVA analysis of the data. [[User:Icrespin|Iliana]] double checked the the results of the analysis the details can be found in [[Icrespin Journal Week 12/13]]. After the checks were completed and any errors were found, I ran a sanity check on the ANOVA data and then formatted the STEM worksheet for future analysis. The details about what [[User:Knguye66|Kaitlyn] and [[user:eyoung20|I]] did can be found in our shared journal [[Knguye66 Eyoung20 Week 12/13]]. As can be seen in this summary this week your group was really good at communicating and working together to work on this project. We worked really well together this week. One thing that did not work as well was trying to work on the excel spreadsheet online when others were working on it, there was a large lag on the sheet. I think for the next steps I might do the work on a saved downloaded version of the excel sheet and then copy my work to the shared excel. [[User:Eyoung20|Eyoung20]] ([[User talk:Eyoung20|talk]]) 16:36, 25 November 2019 (PST)
*** Iliana Crespin: For this week, it was a better organization on completing the assignment. There is more of a pattern of what should be done throughout each day to prepare for the deadline. What didn't work out for me is still trying to see how a QA can incorporate any work, since my teammates are great. For the next few weeks, I will try to continue double checking the work and contribute more. This contribution can include working with the data analysts and seeing how I can help out a bit more. In addition, texting teammates a bit more to remind any little things that must be due before the deadline. [[User:Icrespin|Icrespin]] ([[User talk:Icrespin|talk]]) 14:48, 21 November 2019 (PST)

===Week 15===
'''Milestone 4'''
#Begin wrapping up with running analysis on the created database using GRNmap
#*Data Analysts: Create GRNmap using individual database from MS Access.
#*Coder: Communicate with the QA to ensure the database is correct and if any changes need to be made
#*QA: Review the database and communicate to the Coder if any changes need to be made.
#Each team member should reflect on the team's progress

== Data and Files ==
=== Week 11 ===
* Presentation file: [[Media: Marmas_FunGals_Presentation.pptx|Group Presentation]]
=== Week 12/13 ===
*[[media: Thiuram_yeast_experiment.xlsx|Excel Workbook]]
*[[meda: FunGals_genelist.zip|Genelist from STEM]]
*[[media: FunGals_GOlist.zip|GOlist from STEM]]
===Week 15===
*[[Media:Marmas_finalProject_Expression-and-Degradation-rate-database_120319.zip|FunGals Expression Database]]

== Milestones ==
{| class="wikitable"
|-
! Tasks to be completed
! Due Date
|-
| Write down Methods and Results for Week 12/13
*Coder/designer: find out the column names and edit them, sample to data relationship table
*Data Analysis: ANOVA analysis and set-up, STEM set-up (will run STEM on Thursday)
*QA: make sure all data in original file actually made it into the database, let coder and analysts know if there are issues
| Thursday, 12:00am, 11/19/19
|-
| Team Journal Assignment, continue writing down Methods and Results for Week 12/13
*Data Analysis: finish editing missing information for ANOVA and (STRAIN) worksheet, run STEM
*Coder and QA: add standard names to genes, make sure all data in original file actually made it into the database, let coder and analysts know if there are issues
| Tuesday, 12:00am, 11/26/19
|-
| Creating the database and running queries, working with all guilds to assure project is in line to be completed
*Data Analysts: Run YEASTRACT and modify GO Terms.
*Coder: Create individual database for the team.
*QA:Design Expression Tables used to create the final individual database.
| Thursday, 12:00am, 11/28/19
|-
|Begin wrapping up with running analysis on the created database using GRNmap
*Data Analysts: Create GRNmap using individual database from MS Access.
*Coder: Communicate with the QA to ensure the database is correct and if any changes need to be made
*QA: Review the database and communicate to the Coder if any changes need to be made.
| Tuesday, 12:00am, 12/03/19
|-
| Wrap up data analysis and individual milestones and begin to gather deliverables for turn-in
*Data Analysts: Provide feedback on the database and its ease-of-use. Work with QA to gather deliverables.
*Coder: Work with the entire guild to properly combine all databases for the entire class to use.
*QA: Work with the coder to finalize the [https://www.quackit.com/microsoft_access/microsoft_access_2016/howto/how_to_create_a_database_diagram_in_access_2016.cfm database schema diagram]
| Thursday, 12:00am, 12/05/19
|-
| Final Presentation
| Tuesday, 12:00am, 12/10/19
|-
| Report submitted
| Friday, 4:00 pm, 12/13/19
|-
|}

==Acknowledgements==
This section is in acknowledgement to partner [[User:Marmas|Michael Armas]], [[User:Icrespin|Iliana Crespin]], [[User:eyoung20|Emma Young]], and [[User:knguye66|Kaitlyn Nguyen]]. I would also like to acknowledge [[User:Kdahlquist|Dr. Dahlquist]] for introducing and teaching the topic and direction of this assignment.

"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
 
[[User:Marmas|Marmas]] ([[User talk:Marmas|talk]]) 23:40, 13 November 2019 (PST)
[[User:Icrespin|Icrespin]] ([[User talk:Icrespin|talk]]) 23:46, 13 November 2019 (PST)

"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
[[User:Eyoung20|Eyoung20]] ([[User talk:Eyoung20|talk]]) 23:57, 13 November 2019 (PST) [[User:Knguye66|Knguye66]] ([[User talk:Knguye66|talk]]) 18:45, 20 November 2019 (PST)

{{FunGals}}

==References==
===Week 11===
*Kitagawa, E., Takahashi, J., Momose, Y., & Iwahashi, H. (2002). Effects of the pesticide thiuram: genome-wide screening of indicator genes by yeast DNA microarray. Environmental science & technology, 36(18), 3908-3915. DOI: 10.1021/es015705v
*Dahlquist, K. (2019, November 7). Week 11. In Wikipedia, Biological Databases. https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_1https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_11
===Week 12/13===
*Dahlquist, K. (2019, November 19). Data Analysis. In Wikipedia, Biological Databases. Retrieved 6:25, November 20, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Data_Analysis
*Dahlquist, K. (2019, November 20). Final Project Deliverables. In Wikipedia, Biological Databases. Retrieved 6:25, November 20, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Final_Project_Deliverables
*Dahlquist, K. (2019, November 19). Week 12/13. In Wikipedia, Biological Databases. Retrieved 6:25, November 20, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13
*Dahlquist, K. (2019, October 17). Week 8. In Wikipedia, Biological Databases. Retrieved 6:30, October 21, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_8
===Week 15===

FunGals

2019-12-05T23:11:23Z

Icrespin: /* Week 15 */ added more info

==Effects of the Pesticide Thiuram: Genome-wide Screening of Indicator Genes by Yeast DNA Microarray==

'''Team Information'''
Project Manager: [[User:Marmas|Michael Armas]]
Quality Assurance: [[User:Icrespin| Iliana Crespin]]
Data Analysis: [[User:eyoung20|Emma Young]], [[User:knguye66|Kaitlyn Nguyen]]
Coder: [[User:Marmas|Michael Armas]]

== Methods and Results ==
=== Week 11 ===
====Setting up the Project====
*Selected [[User:Marmas|Michael Armas]] as team's Project Manager.
*Added the name of of selected project manager to the Project Manager guild page and Overview pages.
*Named the team FunGals and created [[FunGals]] home page on the wiki.
*The name of the team home page was the selected team name.

*Created a link to team's page on the course Main page.
*Created a template for FunGal with useful information and links that you will invoke on all pages that you will create for the project.
*Created a category using team name and included it the FunGal template so that it is used on all pages created for the project. Also included the category "Group Projects" in the template. 
*Each person needs to write a short executive summary of that person's progress on the project for the week, with links to the relevant individual journal pages (which will have more detailed information).
*Each team member should reflect on the team's progress '''(Note that you will be directed to add specific information to your team's pages in the individual portion of the assignment for this and future weeks)''':
**What worked? What didn't work? What will I do next to fix what didn't work?
*** Michael Armas: Working with this team is a great pleasure! Everyone on the team is pulling their weight and providing information that contributes to the group work. Next time, as the project manager, I want to be more organized and come up with interim deadlines to make sure we are not cramming right before the actual deadline. In fact, I would have something small due every day than procrastinate until the end. However, with this team, we are making it work and doing exceptional work!
*** Kaitlyn Nguyen: What worked this week is starting the presentation formatting early, thus allocating the rest of the time to "filling in the missing parts" of the powerpoint. What also worked this week was team communication via group-chats. What didn't work this week was starting the individual assignment later, leaving less time to practicing and fully understanding the material from the journal article for the presentation in class. To fix what didn't work, I will start my individual assignment much earlier, to leave the rest of the time to focus on collaborative teamwork and group assignments. [[User:Knguye66|Knguye66]] ([[User talk:Knguye66|talk]]) 23:37, 13 November 2019 (PST)
*** Emma Young: The team seems to work really well together. I think in upcoming weeks we will really thrive in working together. A foundation for communication has already been established and we have already started reviewing each others work and providing constructive criticism and help where it is needed. The main issue this week was a matter of timing. With the amount of work we had to do in the time frame given we were not able to meet up due to busy and conflicting prior engagements. This meant that we did not reach our full potential of working together effectively as a group this week. Next week, we hopefully will be able to set better deadlines and be able to have the ability to plan out time to work on this in a less rushed manner.
*** Iliana Crespin: Overall, this group has been great. Everyone has worked together and understands what must be done. In addition, each member is understanding of the special circumstances before the deadline of this assignment. The only thing that didn't work out was how scattered each of us were because of all the assignments that had to be completed from other classes. In addition, mandated plans (school- or work-related) popped up which made it difficult to contribute equally. For the future, I will make sure to manage my time better, because I have work and school. Therefore, by doing a fair share of certain things before classes/work, I will be able to contribute more.[[User:Icrespin|Icrespin]] ([[User talk:Icrespin|talk]]) 23:46, 13 November 2019 (PST)

====Annotated Bibliography====

#Braconi, D., Bernardini, G., & Santucci, A. (2016). Saccharomyces cerevisiae as a model in ecotoxicological studies: A post-genomics perspective. Journal of Proteomics, 137, 19-34. DOI: 10.1016/j.jprot.2015.09.001
#Hinkle, K. L., & Olsen, D. (2018). Exposure to the lampricide TFM elicits an environmental stress response in yeast. FEMS yeast research, 19(1), foy121. doi: 10.1093/femsyr/foy121
#Iwahashi, Y., Hosoda, H., Park, J. H., Lee, J. H., Suzuki, Y., Kitagawa, E., ... & Iwahashi, H. (2006). Mechanisms of patulin toxicity under conditions that inhibit yeast growth. Journal of agricultural and food chemistry, 54(5), 1936-1942. doi: 10.1021/jf052264g.
#Iwahashi, H., Ishidou, E., Kitagawa, E., & Momose, Y. (2007). Combined Cadmium and Thiuram Show Synergistic Toxicity and Induce Mitochondrial Petite Mutants. Environmental Science & Technology, 41(22), 7941–7946. doi: 10.1021/es071313y
#Iwahashi, H., Ishidou, E., Kitagawa, E., & Momose, Y. (2007). Combined Cadmium and Thiuram Show Synergistic Toxicity and Induce Mitochondrial Petite Mutants. Environmental Science & Technology, 41(22), 7941–7946. doi: 10.1021/es071313y
#Kitagawa, E., Momose, Y., & Iwahashi, H. (2003). Correlation of the Structures of Agricultural Fungicides to Gene Expression in Saccharomyces cerevisiaeupon Exposure to Toxic Doses. Environmental Science & Technology, 37(12), 2788–2793. doi: 10.1021/es026156b
#Lu Yu, Na Guo, Rizeng Meng, Bin Liu, Xudong Tang, Jing Jin, Yumei Cui, Xuming Deng. Allicin-induced global gene expression profile of Saccharomyces cerevisiae. Applied Microbiology and Biotechnology 2010, 88 (1) , 219-229. DOI: 10.1007/s00253-010-2709-x.
#Pierron, A., Mimoun, S., Murate, L. S., Loiseau, N., Lippi, Y., Bracarense, A. P. F., ... & Oswald, I. P. (2016). Intestinal toxicity of the masked mycotoxin deoxynivalenol-3-β-D-glucoside. Archives of toxicology, 90(8), 2037-2046. doi: 10.1007/s00204-015-1592-8

===Week 12/13===
====Milestone 3: Getting the data ready for analysis ====

# As a group Downloaded and examined the microarray dataset, compared it to the samples and experiment described in the journal club article.
#* [https://sgd-prod-upload.s3.amazonaws.com/S000204415/Kitagawa_2002_PMID_12269742.zip Kitagawa et al. (2002)]
#* downloaded and unzipped
#* file was downloaded but was PLC format
#* Mike figured out how to drag and drop it one to excel to open the file
# Along with the QA's, make a "sample-data relationship table" that lists all of the samples (microarray chips), noting the treatment, time point, replicate number, and other information pertaining to each sample.
#* This "Metadata" sheet was created in Excel and is present on the excel work under the week 12/13 data and files.
#* In collaboration with other groups, the Metadata sheet was filled out so that nomenclature is consistent.
# The class collectively came up with consistent column headers that summarized the information
#* As decided by all groups, the format for column headers was yeastStrain_treatmentOrMutation_concentrationAndUnits_dataType_timeAndUnits-replicateNumber.
# Organized the data in a worksheet in an Excel workbook so that:
#* MasterIndex was in the first column, ID was in the second column
#* Data columns were to the right, in increasing chronological order, using the column header pattern that was created.
#* Replicates were grouped together
# Data analysts (DA) [[User:Knguye66|Kaitlyn]] set-up the ANOVA worksheet via referencing [[Week 8]]
#* The steps for the ANOVA: Part I, Benjamini, Bonferroni, and p-value correction, as well as, a quick sanity check were followed.
# DAs [[User:Eyoung20|Eyoung20]] begin setting up for STEM analysis to complete the first stage of milestones and deliverables
# All the calculations were checked by the QA [[User:Icrespin|Iliana]].

*Each team member should reflect on the team's progress '''(Note that you will be directed to add specific information to your team's pages in the individual portion of the assignment for this and future weeks)''':
**What worked? What didn't work? What will I do next to fix what didn't work?
*** Michael Armas: What worked this week was the communication between my guild and me, and my group and me. Everyone was able to help each other out and make sure the project is coming along smoothly. What didn't work this week for me was understanding exactly what I had to do to set up spreadsheets for data analysis. However, thanks to Mihir, I was able to understand how to create a metadata sheet and reach the milestone for this week. Before I leave class from now on, I will reassure myself that I understand the information by asking Dr. Dahlquist the best way to reach the week's milestone.
*** Kaitlyn Nguyen: This week, the pattern and organization to which each group member worked flowed smoothly as every member of the group knew exactly what each person was accomplishing. Having extra time in class and staying after class helped us jump-start on our tasks together and find out what assignments work best for each team member. What didn't work this week was that each milestone and part of this project works chronologically, whereby other members have to wait for the first person to finish his/her task before beginning theirs. As the days and weeks move on, it will be good to continue this method, but switch off on who starts the tasks first for the assignment. [[User:Knguye66|Knguye66]] ([[User talk:Knguye66|talk]]) 18:44, 20 November 2019 (PST)
*** Emma Young: For this week I worked closely with [[User:Knguye66|Kaitlyn]] to start the data analysis for the rest of the project. We worked with the whole team to analyze the data from the journal article and format for the rest of the data analysis. [[User:Marmas|Mike]] worked with the other programers to formulate the metadata sheet and the format for the ANOVA sheet. More details on this can be found in his personal electronic notebook [[Marmas Week 12/13]] Then [[User:Knguye66|Kaitlyn]] worked on the ANOVA analysis of the data. [[User:Icrespin|Iliana]] double checked the the results of the analysis the details can be found in [[Icrespin Journal Week 12/13]]. After the checks were completed and any errors were found, I ran a sanity check on the ANOVA data and then formatted the STEM worksheet for future analysis. The details about what [[User:Knguye66|Kaitlyn] and [[user:eyoung20|I]] did can be found in our shared journal [[Knguye66 Eyoung20 Week 12/13]]. As can be seen in this summary this week your group was really good at communicating and working together to work on this project. We worked really well together this week. One thing that did not work as well was trying to work on the excel spreadsheet online when others were working on it, there was a large lag on the sheet. I think for the next steps I might do the work on a saved downloaded version of the excel sheet and then copy my work to the shared excel. [[User:Eyoung20|Eyoung20]] ([[User talk:Eyoung20|talk]]) 16:36, 25 November 2019 (PST)
*** Iliana Crespin: For this week, it was a better organization on completing the assignment. There is more of a pattern of what should be done throughout each day to prepare for the deadline. What didn't work out for me is still trying to see how a QA can incorporate any work, since my teammates are great. For the next few weeks, I will try to continue double checking the work and contribute more. This contribution can include working with the data analysts and seeing how I can help out a bit more. In addition, texting teammates a bit more to remind any little things that must be due before the deadline. [[User:Icrespin|Icrespin]] ([[User talk:Icrespin|talk]]) 14:48, 21 November 2019 (PST)

===Week 15===
'''Milestone 4'''
#Begin wrapping up with running analysis on the created database using GRNmap
#*Data Analysts: Create GRNmap using individual database from MS Access.
#*Coder: Communicate with the QA to ensure the database is correct and if any changes need to be made
#*QA: Review the database and communicate to the Coder if any changes need to be made.

== Data and Files ==
=== Week 11 ===
* Presentation file: [[Media: Marmas_FunGals_Presentation.pptx|Group Presentation]]
=== Week 12/13 ===
*[[media: Thiuram_yeast_experiment.xlsx|Excel Workbook]]
*[[meda: FunGals_genelist.zip|Genelist from STEM]]
*[[media: FunGals_GOlist.zip|GOlist from STEM]]
===Week 15===
*[[Media:Marmas_finalProject_Expression-and-Degradation-rate-database_120319.zip|FunGals Expression Database]]

== Milestones ==
{| class="wikitable"
|-
! Tasks to be completed
! Due Date
|-
| Write down Methods and Results for Week 12/13
*Coder/designer: find out the column names and edit them, sample to data relationship table
*Data Analysis: ANOVA analysis and set-up, STEM set-up (will run STEM on Thursday)
*QA: make sure all data in original file actually made it into the database, let coder and analysts know if there are issues
| Thursday, 12:00am, 11/19/19
|-
| Team Journal Assignment, continue writing down Methods and Results for Week 12/13
*Data Analysis: finish editing missing information for ANOVA and (STRAIN) worksheet, run STEM
*Coder and QA: add standard names to genes, make sure all data in original file actually made it into the database, let coder and analysts know if there are issues
| Tuesday, 12:00am, 11/26/19
|-
| Creating the database and running queries, working with all guilds to assure project is in line to be completed
*Data Analysts: Run YEASTRACT and modify GO Terms.
*Coder: Create individual database for the team.
*QA:Design Expression Tables used to create the final individual database.
| Thursday, 12:00am, 11/28/19
|-
|Begin wrapping up with running analysis on the created database using GRNmap
*Data Analysts: Create GRNmap using individual database from MS Access.
*Coder: Communicate with the QA to ensure the database is correct and if any changes need to be made
*QA: Review the database and communicate to the Coder if any changes need to be made.
| Tuesday, 12:00am, 12/03/19
|-
| Wrap up data analysis and individual milestones and begin to gather deliverables for turn-in
*Data Analysts: Provide feedback on the database and its ease-of-use. Work with QA to gather deliverables.
*Coder: Work with the entire guild to properly combine all databases for the entire class to use.
*QA: Work with the coder to finalize the [https://www.quackit.com/microsoft_access/microsoft_access_2016/howto/how_to_create_a_database_diagram_in_access_2016.cfm database schema diagram]
| Thursday, 12:00am, 12/05/19
|-
| Final Presentation
| Tuesday, 12:00am, 12/10/19
|-
| Report submitted
| Friday, 4:00 pm, 12/13/19
|-
|}

==Acknowledgements==
This section is in acknowledgement to partner [[User:Marmas|Michael Armas]], [[User:Icrespin|Iliana Crespin]], [[User:eyoung20|Emma Young]], and [[User:knguye66|Kaitlyn Nguyen]]. I would also like to acknowledge [[User:Kdahlquist|Dr. Dahlquist]] for introducing and teaching the topic and direction of this assignment.

"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
 
[[User:Marmas|Marmas]] ([[User talk:Marmas|talk]]) 23:40, 13 November 2019 (PST)
[[User:Icrespin|Icrespin]] ([[User talk:Icrespin|talk]]) 23:46, 13 November 2019 (PST)

"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
[[User:Eyoung20|Eyoung20]] ([[User talk:Eyoung20|talk]]) 23:57, 13 November 2019 (PST) [[User:Knguye66|Knguye66]] ([[User talk:Knguye66|talk]]) 18:45, 20 November 2019 (PST)

{{FunGals}}

==References==
===Week 11===
*Kitagawa, E., Takahashi, J., Momose, Y., & Iwahashi, H. (2002). Effects of the pesticide thiuram: genome-wide screening of indicator genes by yeast DNA microarray. Environmental science & technology, 36(18), 3908-3915. DOI: 10.1021/es015705v
*Dahlquist, K. (2019, November 7). Week 11. In Wikipedia, Biological Databases. https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_1https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_11
===Week 12/13===
*Dahlquist, K. (2019, November 19). Data Analysis. In Wikipedia, Biological Databases. Retrieved 6:25, November 20, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Data_Analysis
*Dahlquist, K. (2019, November 20). Final Project Deliverables. In Wikipedia, Biological Databases. Retrieved 6:25, November 20, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Final_Project_Deliverables
*Dahlquist, K. (2019, November 19). Week 12/13. In Wikipedia, Biological Databases. Retrieved 6:25, November 20, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13
*Dahlquist, K. (2019, October 17). Week 8. In Wikipedia, Biological Databases. Retrieved 6:30, October 21, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_8
===Week 15===

FunGals

2019-12-05T23:10:29Z

Icrespin: /* Week 15 */ added new milestone

==Effects of the Pesticide Thiuram: Genome-wide Screening of Indicator Genes by Yeast DNA Microarray==

'''Team Information'''
Project Manager: [[User:Marmas|Michael Armas]]
Quality Assurance: [[User:Icrespin| Iliana Crespin]]
Data Analysis: [[User:eyoung20|Emma Young]], [[User:knguye66|Kaitlyn Nguyen]]
Coder: [[User:Marmas|Michael Armas]]

== Methods and Results ==
=== Week 11 ===
====Setting up the Project====
*Selected [[User:Marmas|Michael Armas]] as team's Project Manager.
*Added the name of of selected project manager to the Project Manager guild page and Overview pages.
*Named the team FunGals and created [[FunGals]] home page on the wiki.
*The name of the team home page was the selected team name.

*Created a link to team's page on the course Main page.
*Created a template for FunGal with useful information and links that you will invoke on all pages that you will create for the project.
*Created a category using team name and included it the FunGal template so that it is used on all pages created for the project. Also included the category "Group Projects" in the template. 
*Each person needs to write a short executive summary of that person's progress on the project for the week, with links to the relevant individual journal pages (which will have more detailed information).
*Each team member should reflect on the team's progress '''(Note that you will be directed to add specific information to your team's pages in the individual portion of the assignment for this and future weeks)''':
**What worked? What didn't work? What will I do next to fix what didn't work?
*** Michael Armas: Working with this team is a great pleasure! Everyone on the team is pulling their weight and providing information that contributes to the group work. Next time, as the project manager, I want to be more organized and come up with interim deadlines to make sure we are not cramming right before the actual deadline. In fact, I would have something small due every day than procrastinate until the end. However, with this team, we are making it work and doing exceptional work!
*** Kaitlyn Nguyen: What worked this week is starting the presentation formatting early, thus allocating the rest of the time to "filling in the missing parts" of the powerpoint. What also worked this week was team communication via group-chats. What didn't work this week was starting the individual assignment later, leaving less time to practicing and fully understanding the material from the journal article for the presentation in class. To fix what didn't work, I will start my individual assignment much earlier, to leave the rest of the time to focus on collaborative teamwork and group assignments. [[User:Knguye66|Knguye66]] ([[User talk:Knguye66|talk]]) 23:37, 13 November 2019 (PST)
*** Emma Young: The team seems to work really well together. I think in upcoming weeks we will really thrive in working together. A foundation for communication has already been established and we have already started reviewing each others work and providing constructive criticism and help where it is needed. The main issue this week was a matter of timing. With the amount of work we had to do in the time frame given we were not able to meet up due to busy and conflicting prior engagements. This meant that we did not reach our full potential of working together effectively as a group this week. Next week, we hopefully will be able to set better deadlines and be able to have the ability to plan out time to work on this in a less rushed manner.
*** Iliana Crespin: Overall, this group has been great. Everyone has worked together and understands what must be done. In addition, each member is understanding of the special circumstances before the deadline of this assignment. The only thing that didn't work out was how scattered each of us were because of all the assignments that had to be completed from other classes. In addition, mandated plans (school- or work-related) popped up which made it difficult to contribute equally. For the future, I will make sure to manage my time better, because I have work and school. Therefore, by doing a fair share of certain things before classes/work, I will be able to contribute more.[[User:Icrespin|Icrespin]] ([[User talk:Icrespin|talk]]) 23:46, 13 November 2019 (PST)

====Annotated Bibliography====

#Braconi, D., Bernardini, G., & Santucci, A. (2016). Saccharomyces cerevisiae as a model in ecotoxicological studies: A post-genomics perspective. Journal of Proteomics, 137, 19-34. DOI: 10.1016/j.jprot.2015.09.001
#Hinkle, K. L., & Olsen, D. (2018). Exposure to the lampricide TFM elicits an environmental stress response in yeast. FEMS yeast research, 19(1), foy121. doi: 10.1093/femsyr/foy121
#Iwahashi, Y., Hosoda, H., Park, J. H., Lee, J. H., Suzuki, Y., Kitagawa, E., ... & Iwahashi, H. (2006). Mechanisms of patulin toxicity under conditions that inhibit yeast growth. Journal of agricultural and food chemistry, 54(5), 1936-1942. doi: 10.1021/jf052264g.
#Iwahashi, H., Ishidou, E., Kitagawa, E., & Momose, Y. (2007). Combined Cadmium and Thiuram Show Synergistic Toxicity and Induce Mitochondrial Petite Mutants. Environmental Science & Technology, 41(22), 7941–7946. doi: 10.1021/es071313y
#Iwahashi, H., Ishidou, E., Kitagawa, E., & Momose, Y. (2007). Combined Cadmium and Thiuram Show Synergistic Toxicity and Induce Mitochondrial Petite Mutants. Environmental Science & Technology, 41(22), 7941–7946. doi: 10.1021/es071313y
#Kitagawa, E., Momose, Y., & Iwahashi, H. (2003). Correlation of the Structures of Agricultural Fungicides to Gene Expression in Saccharomyces cerevisiaeupon Exposure to Toxic Doses. Environmental Science & Technology, 37(12), 2788–2793. doi: 10.1021/es026156b
#Lu Yu, Na Guo, Rizeng Meng, Bin Liu, Xudong Tang, Jing Jin, Yumei Cui, Xuming Deng. Allicin-induced global gene expression profile of Saccharomyces cerevisiae. Applied Microbiology and Biotechnology 2010, 88 (1) , 219-229. DOI: 10.1007/s00253-010-2709-x.
#Pierron, A., Mimoun, S., Murate, L. S., Loiseau, N., Lippi, Y., Bracarense, A. P. F., ... & Oswald, I. P. (2016). Intestinal toxicity of the masked mycotoxin deoxynivalenol-3-β-D-glucoside. Archives of toxicology, 90(8), 2037-2046. doi: 10.1007/s00204-015-1592-8

===Week 12/13===
====Milestone 3: Getting the data ready for analysis ====

# As a group Downloaded and examined the microarray dataset, compared it to the samples and experiment described in the journal club article.
#* [https://sgd-prod-upload.s3.amazonaws.com/S000204415/Kitagawa_2002_PMID_12269742.zip Kitagawa et al. (2002)]
#* downloaded and unzipped
#* file was downloaded but was PLC format
#* Mike figured out how to drag and drop it one to excel to open the file
# Along with the QA's, make a "sample-data relationship table" that lists all of the samples (microarray chips), noting the treatment, time point, replicate number, and other information pertaining to each sample.
#* This "Metadata" sheet was created in Excel and is present on the excel work under the week 12/13 data and files.
#* In collaboration with other groups, the Metadata sheet was filled out so that nomenclature is consistent.
# The class collectively came up with consistent column headers that summarized the information
#* As decided by all groups, the format for column headers was yeastStrain_treatmentOrMutation_concentrationAndUnits_dataType_timeAndUnits-replicateNumber.
# Organized the data in a worksheet in an Excel workbook so that:
#* MasterIndex was in the first column, ID was in the second column
#* Data columns were to the right, in increasing chronological order, using the column header pattern that was created.
#* Replicates were grouped together
# Data analysts (DA) [[User:Knguye66|Kaitlyn]] set-up the ANOVA worksheet via referencing [[Week 8]]
#* The steps for the ANOVA: Part I, Benjamini, Bonferroni, and p-value correction, as well as, a quick sanity check were followed.
# DAs [[User:Eyoung20|Eyoung20]] begin setting up for STEM analysis to complete the first stage of milestones and deliverables
# All the calculations were checked by the QA [[User:Icrespin|Iliana]].

*Each team member should reflect on the team's progress '''(Note that you will be directed to add specific information to your team's pages in the individual portion of the assignment for this and future weeks)''':
**What worked? What didn't work? What will I do next to fix what didn't work?
*** Michael Armas: What worked this week was the communication between my guild and me, and my group and me. Everyone was able to help each other out and make sure the project is coming along smoothly. What didn't work this week for me was understanding exactly what I had to do to set up spreadsheets for data analysis. However, thanks to Mihir, I was able to understand how to create a metadata sheet and reach the milestone for this week. Before I leave class from now on, I will reassure myself that I understand the information by asking Dr. Dahlquist the best way to reach the week's milestone.
*** Kaitlyn Nguyen: This week, the pattern and organization to which each group member worked flowed smoothly as every member of the group knew exactly what each person was accomplishing. Having extra time in class and staying after class helped us jump-start on our tasks together and find out what assignments work best for each team member. What didn't work this week was that each milestone and part of this project works chronologically, whereby other members have to wait for the first person to finish his/her task before beginning theirs. As the days and weeks move on, it will be good to continue this method, but switch off on who starts the tasks first for the assignment. [[User:Knguye66|Knguye66]] ([[User talk:Knguye66|talk]]) 18:44, 20 November 2019 (PST)
*** Emma Young: For this week I worked closely with [[User:Knguye66|Kaitlyn]] to start the data analysis for the rest of the project. We worked with the whole team to analyze the data from the journal article and format for the rest of the data analysis. [[User:Marmas|Mike]] worked with the other programers to formulate the metadata sheet and the format for the ANOVA sheet. More details on this can be found in his personal electronic notebook [[Marmas Week 12/13]] Then [[User:Knguye66|Kaitlyn]] worked on the ANOVA analysis of the data. [[User:Icrespin|Iliana]] double checked the the results of the analysis the details can be found in [[Icrespin Journal Week 12/13]]. After the checks were completed and any errors were found, I ran a sanity check on the ANOVA data and then formatted the STEM worksheet for future analysis. The details about what [[User:Knguye66|Kaitlyn] and [[user:eyoung20|I]] did can be found in our shared journal [[Knguye66 Eyoung20 Week 12/13]]. As can be seen in this summary this week your group was really good at communicating and working together to work on this project. We worked really well together this week. One thing that did not work as well was trying to work on the excel spreadsheet online when others were working on it, there was a large lag on the sheet. I think for the next steps I might do the work on a saved downloaded version of the excel sheet and then copy my work to the shared excel. [[User:Eyoung20|Eyoung20]] ([[User talk:Eyoung20|talk]]) 16:36, 25 November 2019 (PST)
*** Iliana Crespin: For this week, it was a better organization on completing the assignment. There is more of a pattern of what should be done throughout each day to prepare for the deadline. What didn't work out for me is still trying to see how a QA can incorporate any work, since my teammates are great. For the next few weeks, I will try to continue double checking the work and contribute more. This contribution can include working with the data analysts and seeing how I can help out a bit more. In addition, texting teammates a bit more to remind any little things that must be due before the deadline. [[User:Icrespin|Icrespin]] ([[User talk:Icrespin|talk]]) 14:48, 21 November 2019 (PST)

===Week 15===
'''Milestone 4'''

== Data and Files ==
=== Week 11 ===
* Presentation file: [[Media: Marmas_FunGals_Presentation.pptx|Group Presentation]]
=== Week 12/13 ===
*[[media: Thiuram_yeast_experiment.xlsx|Excel Workbook]]
*[[meda: FunGals_genelist.zip|Genelist from STEM]]
*[[media: FunGals_GOlist.zip|GOlist from STEM]]
===Week 15===
*[[Media:Marmas_finalProject_Expression-and-Degradation-rate-database_120319.zip|FunGals Expression Database]]

== Milestones ==
{| class="wikitable"
|-
! Tasks to be completed
! Due Date
|-
| Write down Methods and Results for Week 12/13
*Coder/designer: find out the column names and edit them, sample to data relationship table
*Data Analysis: ANOVA analysis and set-up, STEM set-up (will run STEM on Thursday)
*QA: make sure all data in original file actually made it into the database, let coder and analysts know if there are issues
| Thursday, 12:00am, 11/19/19
|-
| Team Journal Assignment, continue writing down Methods and Results for Week 12/13
*Data Analysis: finish editing missing information for ANOVA and (STRAIN) worksheet, run STEM
*Coder and QA: add standard names to genes, make sure all data in original file actually made it into the database, let coder and analysts know if there are issues
| Tuesday, 12:00am, 11/26/19
|-
| Creating the database and running queries, working with all guilds to assure project is in line to be completed
*Data Analysts: Run YEASTRACT and modify GO Terms.
*Coder: Create individual database for the team.
*QA:Design Expression Tables used to create the final individual database.
| Thursday, 12:00am, 11/28/19
|-
|Begin wrapping up with running analysis on the created database using GRNmap
*Data Analysts: Create GRNmap using individual database from MS Access.
*Coder: Communicate with the QA to ensure the database is correct and if any changes need to be made
*QA: Review the database and communicate to the Coder if any changes need to be made.
| Tuesday, 12:00am, 12/03/19
|-
| Wrap up data analysis and individual milestones and begin to gather deliverables for turn-in
*Data Analysts: Provide feedback on the database and its ease-of-use. Work with QA to gather deliverables.
*Coder: Work with the entire guild to properly combine all databases for the entire class to use.
*QA: Work with the coder to finalize the [https://www.quackit.com/microsoft_access/microsoft_access_2016/howto/how_to_create_a_database_diagram_in_access_2016.cfm database schema diagram]
| Thursday, 12:00am, 12/05/19
|-
| Final Presentation
| Tuesday, 12:00am, 12/10/19
|-
| Report submitted
| Friday, 4:00 pm, 12/13/19
|-
|}

==Acknowledgements==
This section is in acknowledgement to partner [[User:Marmas|Michael Armas]], [[User:Icrespin|Iliana Crespin]], [[User:eyoung20|Emma Young]], and [[User:knguye66|Kaitlyn Nguyen]]. I would also like to acknowledge [[User:Kdahlquist|Dr. Dahlquist]] for introducing and teaching the topic and direction of this assignment.

"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
 
[[User:Marmas|Marmas]] ([[User talk:Marmas|talk]]) 23:40, 13 November 2019 (PST)
[[User:Icrespin|Icrespin]] ([[User talk:Icrespin|talk]]) 23:46, 13 November 2019 (PST)

"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
[[User:Eyoung20|Eyoung20]] ([[User talk:Eyoung20|talk]]) 23:57, 13 November 2019 (PST) [[User:Knguye66|Knguye66]] ([[User talk:Knguye66|talk]]) 18:45, 20 November 2019 (PST)

{{FunGals}}

==References==
===Week 11===
*Kitagawa, E., Takahashi, J., Momose, Y., & Iwahashi, H. (2002). Effects of the pesticide thiuram: genome-wide screening of indicator genes by yeast DNA microarray. Environmental science & technology, 36(18), 3908-3915. DOI: 10.1021/es015705v
*Dahlquist, K. (2019, November 7). Week 11. In Wikipedia, Biological Databases. https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_1https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_11
===Week 12/13===
*Dahlquist, K. (2019, November 19). Data Analysis. In Wikipedia, Biological Databases. Retrieved 6:25, November 20, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Data_Analysis
*Dahlquist, K. (2019, November 20). Final Project Deliverables. In Wikipedia, Biological Databases. Retrieved 6:25, November 20, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Final_Project_Deliverables
*Dahlquist, K. (2019, November 19). Week 12/13. In Wikipedia, Biological Databases. Retrieved 6:25, November 20, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13
*Dahlquist, K. (2019, October 17). Week 8. In Wikipedia, Biological Databases. Retrieved 6:30, October 21, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_8
===Week 15===

Icrespin Journal Week 15

2019-12-05T23:07:10Z

Icrespin: /* Milestones */ changed format

==Electronic Lab Notebook==
{{template:Icrespin}}

==Purpose==

==Methods/Results==

==Milestones==
{| class="wikitable"
|-
! Milestones
! Due Date
! Complete/Incomplete
|-
| Annotated Bibliography
*Work on creating a bibliography with other team members
| Tuesday, 12:00am, 11/12/19
| '''COMPLETE'''
|-
| Journal Club Presentation
*Review article and ask any questions that seemed unclear
*Add important slides to powerpoint
*Practice what will be presented to audience
| Thursday, 12:00am, 11/14/19
| '''COMPLETE'''
|-
| Working with Data Analysts to Understand Microarray Dataset
*Review and double check work done by data analysts
*Complete sanity checks to make sure it matches with work
*Add any information needed to make sure everything is fine
| Tuesday, 12:00am, 11/26/19
| '''COMPLETE'''
|-
| Making Sure Expression Data has Both Sytematic Name and Standard Name ID's
*Review information to make sure this is complete
| Tuesday, 12:00am, 11/26/19
| '''COMPLETE'''
|-
| Work with Coder/Designers to Design a Database to Store Time-course Microarray Data from Four Sources
*Add database to Box folder
*Work with Coder to create MS Access database to store yeast time-course microarray
*Review information and determine headings for database
| Tuesday, 12:00am, 12/03/19
| '''COMPLETE'''
|-
| Validation and Quality Assurance on Database
*Review information to make sure it is correct
*Communicate with Coder if something is wrong/missing
| Thursday, 12:00am, 12/06/19
| '''COMPLETE'''
|-
| Final Documentation
*Review database schema diagram with Coder
| Thursday, 12:00am, 12/06/19
| '''INCOMPLETE'''
|-
| Final Presentation
| Tuesday, 12:00am, 12/10/19
| '''INCOMPLETE'''
|-
| Report submitted
| Friday, 4:00 pm, 12/13/19
| '''INCOMPLETE'''
|-
|}

==Data/Files==

==Acknowledgments==

==References==

FunGals Deliverables

2019-12-03T23:23:14Z

Icrespin: /* Checklist */ fixed list

{{template:FunGals}}

==Checklist==
{| class="wikitable"
|-
! Tasks to be completed
! Complete/Incomplete
|-
| Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents)
| Complete
|-
| Group Report (''.doc'', ''.docx'' or ''.pdf'' file)
| Incomplete
|-
| Individual statements of work, assessments, reflections (wiki page, ''.doc'', ''.docx'', ''.pdf'', or e-mailed to Dr. Dahlquist)
| Incomplete
|-
| Group PowerPoint presentation (given on Tuesday, December 10, ''.ppt'', ''.pptx'' or ''.pdf'' file)
| Incomplete
|-
| Sample-data relationship table in Excel (''.xlsx'')
| Complete
|-
| Excel spreadsheet with ANOVA results/stem formatting (''.xlsx'')
| Complete
|-
| PowerPoint of ANOVA table, screenshots of stem results (''.pptx''), screenshot of black and white GRNsight input network and colored GRNsight output networks
| Incomplete
|-
| Gene List and GO List files from each significant profile (''.txt'' compressed together in a ''.zip'' file)
| Incomplete
|-
| YEASTRACT "rank by TF" results (''.xlsx'')
| Incomplete
|-
| GRNmap input workbook (with network adjacency matrix, ''.xlsx'')
| Incomplete
|-
| GRNmap output workbook (''.xlsx'') and output plots (''.jpg'') zipped together
| Incomplete
|-
| MS Access database, unified by the three teams with expression tables and metadata table(s) created (''.accdb'')
| Incomplete
|-
| ReadMe for the database that describes the design of the database, references the sources of the data, and has a [https://www.quackit.com/microsoft_access/microsoft_access_2016/howto/how_to_create_a_database_diagram_in_access_2016.cfm database schema diagram] (''.doc'', ''.docx'', ''.pdf'')
| Incomplete
|-
| Query design for populating a GRNmap input workbook from the database (screenshot of MS Access, or SQL code, ''.txt'')
| Incomplete
|-
| Electronic notebook corresponding to these the microarray results files ([[Week 12/13]] and [[Week 15]]) to 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.
| Incomplete
|-
|}

==Group Report==

===Title===

===Introduction===

===Methods/Results/Discussion===

====Data Analysts====

====Coder====

====Quality Assurance====

===Conclusion===

==Powerpoint Presentation==

==Individual Assessment and Reflection==

===Michael Armas===

==== 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 Final 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?

===Kaitlyn Nguyen===

==== 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 Final 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?

===Emma Young===

==== 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 Final 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?

===Iliana Crespin===

==== 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 Final 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?

==Acknowledgments==

==References==

[[Category: Group Projects]]

Icrespin Journal Week 15

2019-12-03T23:10:58Z

Icrespin: added new titles

==Electronic Lab Notebook==
{{template:Icrespin}}

==Purpose==

==Methods/Results==

==Milestones==
{| class="wikitable"
|-
! Milestones
! Due Date
! Complete/Incomplete
|-
| Annotated Bibliography
*Work on creating a bibliography with other team members
| Tuesday, 12:00am, 11/12/19
| '''COMPLETE'''
|-
| Journal Club Presentation
*Review article and ask any questions that seemed unclear
*Add important slides to powerpoint
*Practice what will be presented to audience
| Thursday, 12:00am, 11/14/19
| '''COMPLETE'''
|-
| Working with Data Analysts to Understand Microarray Dataset
*Review and double check work done by data analysts
*Complete sanity checks to make sure it matches with work
*Add any information needed to make sure everything is fine
| Tuesday, 12:00am, 11/26/19
| '''COMPLETE'''
|-
| Making Sure Expression Data has Both Sytematic Name and Standard Name ID's
*Review information to make sure this is complete
| Tuesday, 12:00am, 11/26/19
| '''COMPLETE'''
|-
| Work with Coder/Designers to Design a Database to Store Time-course Microarray Data from Four Sources
*Add database to Box folder
*Work with Coder to create MS Access database to store yeast time-course microarray
*Review information and determine headings for database
| Tuesday, 12:00am, 12/03/19
| '''COMPLETE'''
|-
| Validation and Quality Assurance on Database
*Review information to make sure it is correct
*Communicate with Coder if something is wrong/missing
| Thursday, 12:00am, 12/06/19
| '''INCOMPLETE'''
|-
| Final Documentation
*Review database schema diagram with Coder
| Thursday, 12:00am, 12/06/19
| '''INCOMPLETE'''
|-
| Final Presentation
| Tuesday, 12:00am, 12/10/19
| '''INCOMPLETE'''
|-
| Report submitted
| Friday, 4:00 pm, 12/13/19
| '''INCOMPLETE'''
|-
|}

==Data/Files==

==Acknowledgments==

==References==

FunGals

2019-12-03T23:03:40Z

Icrespin: /* References */ fixed format and added new week

==Effects of the Pesticide Thiuram: Genome-wide Screening of Indicator Genes by Yeast DNA Microarray==

'''Team Information'''
Project Manager: [[User:Marmas|Michael Armas]]
Quality Assurance: [[User:Icrespin| Iliana Crespin]]
Data Analysis: [[User:eyoung20|Emma Young]], [[User:knguye66|Kaitlyn Nguyen]]
Coder: [[User:Marmas|Michael Armas]]

== Methods and Results ==
=== Week 11 ===
====Setting up the Project====
*Selected [[User:Marmas|Michael Armas]] as team's Project Manager.
*Added the name of of selected project manager to the Project Manager guild page and Overview pages.
*Named the team FunGals and created [[FunGals]] home page on the wiki.
*The name of the team home page was the selected team name.

*Created a link to team's page on the course Main page.
*Created a template for FunGal with useful information and links that you will invoke on all pages that you will create for the project.
*Created a category using team name and included it the FunGal template so that it is used on all pages created for the project. Also included the category "Group Projects" in the template. 
*Each person needs to write a short executive summary of that person's progress on the project for the week, with links to the relevant individual journal pages (which will have more detailed information).
*Each team member should reflect on the team's progress '''(Note that you will be directed to add specific information to your team's pages in the individual portion of the assignment for this and future weeks)''':
**What worked? What didn't work? What will I do next to fix what didn't work?
*** Michael Armas: Working with this team is a great pleasure! Everyone on the team is pulling their weight and providing information that contributes to the group work. Next time, as the project manager, I want to be more organized and come up with interim deadlines to make sure we are not cramming right before the actual deadline. In fact, I would have something small due every day than procrastinate until the end. However, with this team, we are making it work and doing exceptional work!
*** Kaitlyn Nguyen: What worked this week is starting the presentation formatting early, thus allocating the rest of the time to "filling in the missing parts" of the powerpoint. What also worked this week was team communication via group-chats. What didn't work this week was starting the individual assignment later, leaving less time to practicing and fully understanding the material from the journal article for the presentation in class. To fix what didn't work, I will start my individual assignment much earlier, to leave the rest of the time to focus on collaborative teamwork and group assignments. [[User:Knguye66|Knguye66]] ([[User talk:Knguye66|talk]]) 23:37, 13 November 2019 (PST)
*** Emma Young: The team seems to work really well together. I think in upcoming weeks we will really thrive in working together. A foundation for communication has already been established and we have already started reviewing each others work and providing constructive criticism and help where it is needed. The main issue this week was a matter of timing. With the amount of work we had to do in the time frame given we were not able to meet up due to busy and conflicting prior engagements. This meant that we did not reach our full potential of working together effectively as a group this week. Next week, we hopefully will be able to set better deadlines and be able to have the ability to plan out time to work on this in a less rushed manner.
*** Iliana Crespin: Overall, this group has been great. Everyone has worked together and understands what must be done. In addition, each member is understanding of the special circumstances before the deadline of this assignment. The only thing that didn't work out was how scattered each of us were because of all the assignments that had to be completed from other classes. In addition, mandated plans (school- or work-related) popped up which made it difficult to contribute equally. For the future, I will make sure to manage my time better, because I have work and school. Therefore, by doing a fair share of certain things before classes/work, I will be able to contribute more.[[User:Icrespin|Icrespin]] ([[User talk:Icrespin|talk]]) 23:46, 13 November 2019 (PST)

====Annotated Bibliography====

#Braconi, D., Bernardini, G., & Santucci, A. (2016). Saccharomyces cerevisiae as a model in ecotoxicological studies: A post-genomics perspective. Journal of Proteomics, 137, 19-34. DOI: 10.1016/j.jprot.2015.09.001
#Hinkle, K. L., & Olsen, D. (2018). Exposure to the lampricide TFM elicits an environmental stress response in yeast. FEMS yeast research, 19(1), foy121. doi: 10.1093/femsyr/foy121
#Iwahashi, Y., Hosoda, H., Park, J. H., Lee, J. H., Suzuki, Y., Kitagawa, E., ... & Iwahashi, H. (2006). Mechanisms of patulin toxicity under conditions that inhibit yeast growth. Journal of agricultural and food chemistry, 54(5), 1936-1942. doi: 10.1021/jf052264g.
#Iwahashi, H., Ishidou, E., Kitagawa, E., & Momose, Y. (2007). Combined Cadmium and Thiuram Show Synergistic Toxicity and Induce Mitochondrial Petite Mutants. Environmental Science & Technology, 41(22), 7941–7946. doi: 10.1021/es071313y
#Iwahashi, H., Ishidou, E., Kitagawa, E., & Momose, Y. (2007). Combined Cadmium and Thiuram Show Synergistic Toxicity and Induce Mitochondrial Petite Mutants. Environmental Science & Technology, 41(22), 7941–7946. doi: 10.1021/es071313y
#Kitagawa, E., Momose, Y., & Iwahashi, H. (2003). Correlation of the Structures of Agricultural Fungicides to Gene Expression in Saccharomyces cerevisiaeupon Exposure to Toxic Doses. Environmental Science & Technology, 37(12), 2788–2793. doi: 10.1021/es026156b
#Lu Yu, Na Guo, Rizeng Meng, Bin Liu, Xudong Tang, Jing Jin, Yumei Cui, Xuming Deng. Allicin-induced global gene expression profile of Saccharomyces cerevisiae. Applied Microbiology and Biotechnology 2010, 88 (1) , 219-229. DOI: 10.1007/s00253-010-2709-x.
#Pierron, A., Mimoun, S., Murate, L. S., Loiseau, N., Lippi, Y., Bracarense, A. P. F., ... & Oswald, I. P. (2016). Intestinal toxicity of the masked mycotoxin deoxynivalenol-3-β-D-glucoside. Archives of toxicology, 90(8), 2037-2046. doi: 10.1007/s00204-015-1592-8

===Week 12/13===
====Milestone 3: Getting the data ready for analysis ====

# As a group Downloaded and examined the microarray dataset, compared it to the samples and experiment described in the journal club article.
#* [https://sgd-prod-upload.s3.amazonaws.com/S000204415/Kitagawa_2002_PMID_12269742.zip Kitagawa et al. (2002)]
#* downloaded and unzipped
#* file was downloaded but was PLC format
#* Mike figured out how to drag and drop it one to excel to open the file
# Along with the QA's, make a "sample-data relationship table" that lists all of the samples (microarray chips), noting the treatment, time point, replicate number, and other information pertaining to each sample.
#* This "Metadata" sheet was created in Excel and is present on the excel work under the week 12/13 data and files.
#* In collaboration with other groups, the Metadata sheet was filled out so that nomenclature is consistent.
# The class collectively came up with consistent column headers that summarized the information
#* As decided by all groups, the format for column headers was yeastStrain_treatmentOrMutation_concentrationAndUnits_dataType_timeAndUnits-replicateNumber.
# Organized the data in a worksheet in an Excel workbook so that:
#* MasterIndex was in the first column, ID was in the second column
#* Data columns were to the right, in increasing chronological order, using the column header pattern that was created.
#* Replicates were grouped together
# Data analysts (DA) [[User:Knguye66|Kaitlyn]] set-up the ANOVA worksheet via referencing [[Week 8]]
#* The steps for the ANOVA: Part I, Benjamini, Bonferroni, and p-value correction, as well as, a quick sanity check were followed.
# DAs [[User:Eyoung20|Eyoung20]] begin setting up for STEM analysis to complete the first stage of milestones and deliverables
# All the calculations were checked by the QA [[User:Icrespin|Iliana]].

*Each team member should reflect on the team's progress '''(Note that you will be directed to add specific information to your team's pages in the individual portion of the assignment for this and future weeks)''':
**What worked? What didn't work? What will I do next to fix what didn't work?
*** Michael Armas: What worked this week was the communication between my guild and me, and my group and me. Everyone was able to help each other out and make sure the project is coming along smoothly. What didn't work this week for me was understanding exactly what I had to do to set up spreadsheets for data analysis. However, thanks to Mihir, I was able to understand how to create a metadata sheet and reach the milestone for this week. Before I leave class from now on, I will reassure myself that I understand the information by asking Dr. Dahlquist the best way to reach the week's milestone.
*** Kaitlyn Nguyen: This week, the pattern and organization to which each group member worked flowed smoothly as every member of the group knew exactly what each person was accomplishing. Having extra time in class and staying after class helped us jump-start on our tasks together and find out what assignments work best for each team member. What didn't work this week was that each milestone and part of this project works chronologically, whereby other members have to wait for the first person to finish his/her task before beginning theirs. As the days and weeks move on, it will be good to continue this method, but switch off on who starts the tasks first for the assignment. [[User:Knguye66|Knguye66]] ([[User talk:Knguye66|talk]]) 18:44, 20 November 2019 (PST)
*** Emma Young: For this week I worked closely with [[User:Knguye66|Kaitlyn]] to start the data analysis for the rest of the project. We worked with the whole team to analyze the data from the journal article and format for the rest of the data analysis. [[User:Marmas|Mike]] worked with the other programers to formulate the metadata sheet and the format for the ANOVA sheet. More details on this can be found in his personal electronic notebook [[Marmas Week 12/13]] Then [[User:Knguye66|Kaitlyn]] worked on the ANOVA analysis of the data. [[User:Icrespin|Iliana]] double checked the the results of the analysis the details can be found in [[Icrespin Journal Week 12/13]]. After the checks were completed and any errors were found, I ran a sanity check on the ANOVA data and then formatted the STEM worksheet for future analysis. The details about what [[User:Knguye66|Kaitlyn] and [[user:eyoung20|I]] did can be found in our shared journal [[Knguye66 Eyoung20 Week 12/13]]. As can be seen in this summary this week your group was really good at communicating and working together to work on this project. We worked really well together this week. One thing that did not work as well was trying to work on the excel spreadsheet online when others were working on it, there was a large lag on the sheet. I think for the next steps I might do the work on a saved downloaded version of the excel sheet and then copy my work to the shared excel. [[User:Eyoung20|Eyoung20]] ([[User talk:Eyoung20|talk]]) 16:36, 25 November 2019 (PST)
*** Iliana Crespin: For this week, it was a better organization on completing the assignment. There is more of a pattern of what should be done throughout each day to prepare for the deadline. What didn't work out for me is still trying to see how a QA can incorporate any work, since my teammates are great. For the next few weeks, I will try to continue double checking the work and contribute more. This contribution can include working with the data analysts and seeing how I can help out a bit more. In addition, texting teammates a bit more to remind any little things that must be due before the deadline. [[User:Icrespin|Icrespin]] ([[User talk:Icrespin|talk]]) 14:48, 21 November 2019 (PST)

===Week 15===

== Data and Files ==
=== Week 11 ===
* Presentation file: [[Media: Marmas_FunGals_Presentation.pptx|Group Presentation]]
=== Week 12/13 ===
*[[media: Thiuram_yeast_experiment.xlsx|Excel Workbook]]
*[[meda: FunGals_genelist.zip|Genelist from STEM]]
*[[media: FunGals_GOlist.zip|GOlist from STEM]]
===Week 15===

== Milestones ==
{| class="wikitable"
|-
! Tasks to be completed
! Due Date
|-
| Write down Methods and Results for Week 12/13
*Coder/designer: find out the column names and edit them, sample to data relationship table
*Data Analysis: ANOVA analysis and set-up, STEM set-up (will run STEM on Thursday)
*QA: make sure all data in original file actually made it into the database, let coder and analysts know if there are issues
| Thursday, 12:00am, 11/19/19
|-
| Team Journal Assignment, continue writing down Methods and Results for Week 12/13
*Data Analysis: finish editing missing information for ANOVA and (STRAIN) worksheet, run STEM
*Coder and QA: add standard names to genes, make sure all data in original file actually made it into the database, let coder and analysts know if there are issues
| Tuesday, 12:00am, 11/26/19
|-
| Creating the database and running queries, working with all guilds to assure project is in line to be completed
*Data Analysts: Run YEASTRACT and modify GO Terms.
*Coder: Create individual database for the team.
*QA:Design Expression Tables used to create the final individual database.
| Thursday, 12:00am, 11/28/19
|-
|Begin wrapping up with running analysis on the created database using GRNmap
*Data Analysts: Create GRNmap using individual database from MS Access.
*Coder: Communicate with the QA to ensure the database is correct and if any changes need to be made
*QA: Review the database and communicate to the Coder if any changes need to be made.
| Tuesday, 12:00am, 12/03/19
|-
| Wrap up data analysis and individual milestones and begin to gather deliverables for turn-in
*Data Analysts: Provide feedback on the database and its ease-of-use. Work with QA to gather deliverables.
*Coder: Work with the entire guild to properly combine all databases for the entire class to use.
*QA: Work with the coder to finalize the [https://www.quackit.com/microsoft_access/microsoft_access_2016/howto/how_to_create_a_database_diagram_in_access_2016.cfm database schema diagram]
| Thursday, 12:00am, 12/05/19
|-
| Final Presentation
| Tuesday, 12:00am, 12/10/19
|-
| Report submitted
| Friday, 4:00 pm, 12/13/19
|-
|}

==Acknowledgements==
This section is in acknowledgement to partner [[User:Marmas|Michael Armas]], [[User:Icrespin|Iliana Crespin]], [[User:eyoung20|Emma Young]], and [[User:knguye66|Kaitlyn Nguyen]]. I would also like to acknowledge [[User:Kdahlquist|Dr. Dahlquist]] for introducing and teaching the topic and direction of this assignment.

"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
 
[[User:Marmas|Marmas]] ([[User talk:Marmas|talk]]) 23:40, 13 November 2019 (PST)
[[User:Icrespin|Icrespin]] ([[User talk:Icrespin|talk]]) 23:46, 13 November 2019 (PST)

"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
[[User:Eyoung20|Eyoung20]] ([[User talk:Eyoung20|talk]]) 23:57, 13 November 2019 (PST) [[User:Knguye66|Knguye66]] ([[User talk:Knguye66|talk]]) 18:45, 20 November 2019 (PST)

{{FunGals}}

==References==
===Week 11===
*Kitagawa, E., Takahashi, J., Momose, Y., & Iwahashi, H. (2002). Effects of the pesticide thiuram: genome-wide screening of indicator genes by yeast DNA microarray. Environmental science & technology, 36(18), 3908-3915. DOI: 10.1021/es015705v
*Dahlquist, K. (2019, November 7). Week 11. In Wikipedia, Biological Databases. https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_1https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_11
===Week 12/13===
*Dahlquist, K. (2019, November 19). Data Analysis. In Wikipedia, Biological Databases. Retrieved 6:25, November 20, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Data_Analysis
*Dahlquist, K. (2019, November 20). Final Project Deliverables. In Wikipedia, Biological Databases. Retrieved 6:25, November 20, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Final_Project_Deliverables
*Dahlquist, K. (2019, November 19). Week 12/13. In Wikipedia, Biological Databases. Retrieved 6:25, November 20, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13
*Dahlquist, K. (2019, October 17). Week 8. In Wikipedia, Biological Databases. Retrieved 6:30, October 21, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_8
===Week 15===

FunGals

2019-12-03T23:02:52Z

Icrespin: /* Methods and Results */ added new week

==Effects of the Pesticide Thiuram: Genome-wide Screening of Indicator Genes by Yeast DNA Microarray==

'''Team Information'''
Project Manager: [[User:Marmas|Michael Armas]]
Quality Assurance: [[User:Icrespin| Iliana Crespin]]
Data Analysis: [[User:eyoung20|Emma Young]], [[User:knguye66|Kaitlyn Nguyen]]
Coder: [[User:Marmas|Michael Armas]]

== Methods and Results ==
=== Week 11 ===
====Setting up the Project====
*Selected [[User:Marmas|Michael Armas]] as team's Project Manager.
*Added the name of of selected project manager to the Project Manager guild page and Overview pages.
*Named the team FunGals and created [[FunGals]] home page on the wiki.
*The name of the team home page was the selected team name.

*Created a link to team's page on the course Main page.
*Created a template for FunGal with useful information and links that you will invoke on all pages that you will create for the project.
*Created a category using team name and included it the FunGal template so that it is used on all pages created for the project. Also included the category "Group Projects" in the template. 
*Each person needs to write a short executive summary of that person's progress on the project for the week, with links to the relevant individual journal pages (which will have more detailed information).
*Each team member should reflect on the team's progress '''(Note that you will be directed to add specific information to your team's pages in the individual portion of the assignment for this and future weeks)''':
**What worked? What didn't work? What will I do next to fix what didn't work?
*** Michael Armas: Working with this team is a great pleasure! Everyone on the team is pulling their weight and providing information that contributes to the group work. Next time, as the project manager, I want to be more organized and come up with interim deadlines to make sure we are not cramming right before the actual deadline. In fact, I would have something small due every day than procrastinate until the end. However, with this team, we are making it work and doing exceptional work!
*** Kaitlyn Nguyen: What worked this week is starting the presentation formatting early, thus allocating the rest of the time to "filling in the missing parts" of the powerpoint. What also worked this week was team communication via group-chats. What didn't work this week was starting the individual assignment later, leaving less time to practicing and fully understanding the material from the journal article for the presentation in class. To fix what didn't work, I will start my individual assignment much earlier, to leave the rest of the time to focus on collaborative teamwork and group assignments. [[User:Knguye66|Knguye66]] ([[User talk:Knguye66|talk]]) 23:37, 13 November 2019 (PST)
*** Emma Young: The team seems to work really well together. I think in upcoming weeks we will really thrive in working together. A foundation for communication has already been established and we have already started reviewing each others work and providing constructive criticism and help where it is needed. The main issue this week was a matter of timing. With the amount of work we had to do in the time frame given we were not able to meet up due to busy and conflicting prior engagements. This meant that we did not reach our full potential of working together effectively as a group this week. Next week, we hopefully will be able to set better deadlines and be able to have the ability to plan out time to work on this in a less rushed manner.
*** Iliana Crespin: Overall, this group has been great. Everyone has worked together and understands what must be done. In addition, each member is understanding of the special circumstances before the deadline of this assignment. The only thing that didn't work out was how scattered each of us were because of all the assignments that had to be completed from other classes. In addition, mandated plans (school- or work-related) popped up which made it difficult to contribute equally. For the future, I will make sure to manage my time better, because I have work and school. Therefore, by doing a fair share of certain things before classes/work, I will be able to contribute more.[[User:Icrespin|Icrespin]] ([[User talk:Icrespin|talk]]) 23:46, 13 November 2019 (PST)

====Annotated Bibliography====

#Braconi, D., Bernardini, G., & Santucci, A. (2016). Saccharomyces cerevisiae as a model in ecotoxicological studies: A post-genomics perspective. Journal of Proteomics, 137, 19-34. DOI: 10.1016/j.jprot.2015.09.001
#Hinkle, K. L., & Olsen, D. (2018). Exposure to the lampricide TFM elicits an environmental stress response in yeast. FEMS yeast research, 19(1), foy121. doi: 10.1093/femsyr/foy121
#Iwahashi, Y., Hosoda, H., Park, J. H., Lee, J. H., Suzuki, Y., Kitagawa, E., ... & Iwahashi, H. (2006). Mechanisms of patulin toxicity under conditions that inhibit yeast growth. Journal of agricultural and food chemistry, 54(5), 1936-1942. doi: 10.1021/jf052264g.
#Iwahashi, H., Ishidou, E., Kitagawa, E., & Momose, Y. (2007). Combined Cadmium and Thiuram Show Synergistic Toxicity and Induce Mitochondrial Petite Mutants. Environmental Science & Technology, 41(22), 7941–7946. doi: 10.1021/es071313y
#Iwahashi, H., Ishidou, E., Kitagawa, E., & Momose, Y. (2007). Combined Cadmium and Thiuram Show Synergistic Toxicity and Induce Mitochondrial Petite Mutants. Environmental Science & Technology, 41(22), 7941–7946. doi: 10.1021/es071313y
#Kitagawa, E., Momose, Y., & Iwahashi, H. (2003). Correlation of the Structures of Agricultural Fungicides to Gene Expression in Saccharomyces cerevisiaeupon Exposure to Toxic Doses. Environmental Science & Technology, 37(12), 2788–2793. doi: 10.1021/es026156b
#Lu Yu, Na Guo, Rizeng Meng, Bin Liu, Xudong Tang, Jing Jin, Yumei Cui, Xuming Deng. Allicin-induced global gene expression profile of Saccharomyces cerevisiae. Applied Microbiology and Biotechnology 2010, 88 (1) , 219-229. DOI: 10.1007/s00253-010-2709-x.
#Pierron, A., Mimoun, S., Murate, L. S., Loiseau, N., Lippi, Y., Bracarense, A. P. F., ... & Oswald, I. P. (2016). Intestinal toxicity of the masked mycotoxin deoxynivalenol-3-β-D-glucoside. Archives of toxicology, 90(8), 2037-2046. doi: 10.1007/s00204-015-1592-8

===Week 12/13===
====Milestone 3: Getting the data ready for analysis ====

# As a group Downloaded and examined the microarray dataset, compared it to the samples and experiment described in the journal club article.
#* [https://sgd-prod-upload.s3.amazonaws.com/S000204415/Kitagawa_2002_PMID_12269742.zip Kitagawa et al. (2002)]
#* downloaded and unzipped
#* file was downloaded but was PLC format
#* Mike figured out how to drag and drop it one to excel to open the file
# Along with the QA's, make a "sample-data relationship table" that lists all of the samples (microarray chips), noting the treatment, time point, replicate number, and other information pertaining to each sample.
#* This "Metadata" sheet was created in Excel and is present on the excel work under the week 12/13 data and files.
#* In collaboration with other groups, the Metadata sheet was filled out so that nomenclature is consistent.
# The class collectively came up with consistent column headers that summarized the information
#* As decided by all groups, the format for column headers was yeastStrain_treatmentOrMutation_concentrationAndUnits_dataType_timeAndUnits-replicateNumber.
# Organized the data in a worksheet in an Excel workbook so that:
#* MasterIndex was in the first column, ID was in the second column
#* Data columns were to the right, in increasing chronological order, using the column header pattern that was created.
#* Replicates were grouped together
# Data analysts (DA) [[User:Knguye66|Kaitlyn]] set-up the ANOVA worksheet via referencing [[Week 8]]
#* The steps for the ANOVA: Part I, Benjamini, Bonferroni, and p-value correction, as well as, a quick sanity check were followed.
# DAs [[User:Eyoung20|Eyoung20]] begin setting up for STEM analysis to complete the first stage of milestones and deliverables
# All the calculations were checked by the QA [[User:Icrespin|Iliana]].

*Each team member should reflect on the team's progress '''(Note that you will be directed to add specific information to your team's pages in the individual portion of the assignment for this and future weeks)''':
**What worked? What didn't work? What will I do next to fix what didn't work?
*** Michael Armas: What worked this week was the communication between my guild and me, and my group and me. Everyone was able to help each other out and make sure the project is coming along smoothly. What didn't work this week for me was understanding exactly what I had to do to set up spreadsheets for data analysis. However, thanks to Mihir, I was able to understand how to create a metadata sheet and reach the milestone for this week. Before I leave class from now on, I will reassure myself that I understand the information by asking Dr. Dahlquist the best way to reach the week's milestone.
*** Kaitlyn Nguyen: This week, the pattern and organization to which each group member worked flowed smoothly as every member of the group knew exactly what each person was accomplishing. Having extra time in class and staying after class helped us jump-start on our tasks together and find out what assignments work best for each team member. What didn't work this week was that each milestone and part of this project works chronologically, whereby other members have to wait for the first person to finish his/her task before beginning theirs. As the days and weeks move on, it will be good to continue this method, but switch off on who starts the tasks first for the assignment. [[User:Knguye66|Knguye66]] ([[User talk:Knguye66|talk]]) 18:44, 20 November 2019 (PST)
*** Emma Young: For this week I worked closely with [[User:Knguye66|Kaitlyn]] to start the data analysis for the rest of the project. We worked with the whole team to analyze the data from the journal article and format for the rest of the data analysis. [[User:Marmas|Mike]] worked with the other programers to formulate the metadata sheet and the format for the ANOVA sheet. More details on this can be found in his personal electronic notebook [[Marmas Week 12/13]] Then [[User:Knguye66|Kaitlyn]] worked on the ANOVA analysis of the data. [[User:Icrespin|Iliana]] double checked the the results of the analysis the details can be found in [[Icrespin Journal Week 12/13]]. After the checks were completed and any errors were found, I ran a sanity check on the ANOVA data and then formatted the STEM worksheet for future analysis. The details about what [[User:Knguye66|Kaitlyn] and [[user:eyoung20|I]] did can be found in our shared journal [[Knguye66 Eyoung20 Week 12/13]]. As can be seen in this summary this week your group was really good at communicating and working together to work on this project. We worked really well together this week. One thing that did not work as well was trying to work on the excel spreadsheet online when others were working on it, there was a large lag on the sheet. I think for the next steps I might do the work on a saved downloaded version of the excel sheet and then copy my work to the shared excel. [[User:Eyoung20|Eyoung20]] ([[User talk:Eyoung20|talk]]) 16:36, 25 November 2019 (PST)
*** Iliana Crespin: For this week, it was a better organization on completing the assignment. There is more of a pattern of what should be done throughout each day to prepare for the deadline. What didn't work out for me is still trying to see how a QA can incorporate any work, since my teammates are great. For the next few weeks, I will try to continue double checking the work and contribute more. This contribution can include working with the data analysts and seeing how I can help out a bit more. In addition, texting teammates a bit more to remind any little things that must be due before the deadline. [[User:Icrespin|Icrespin]] ([[User talk:Icrespin|talk]]) 14:48, 21 November 2019 (PST)

===Week 15===

== Data and Files ==
=== Week 11 ===
* Presentation file: [[Media: Marmas_FunGals_Presentation.pptx|Group Presentation]]
=== Week 12/13 ===
*[[media: Thiuram_yeast_experiment.xlsx|Excel Workbook]]
*[[meda: FunGals_genelist.zip|Genelist from STEM]]
*[[media: FunGals_GOlist.zip|GOlist from STEM]]
===Week 15===

== Milestones ==
{| class="wikitable"
|-
! Tasks to be completed
! Due Date
|-
| Write down Methods and Results for Week 12/13
*Coder/designer: find out the column names and edit them, sample to data relationship table
*Data Analysis: ANOVA analysis and set-up, STEM set-up (will run STEM on Thursday)
*QA: make sure all data in original file actually made it into the database, let coder and analysts know if there are issues
| Thursday, 12:00am, 11/19/19
|-
| Team Journal Assignment, continue writing down Methods and Results for Week 12/13
*Data Analysis: finish editing missing information for ANOVA and (STRAIN) worksheet, run STEM
*Coder and QA: add standard names to genes, make sure all data in original file actually made it into the database, let coder and analysts know if there are issues
| Tuesday, 12:00am, 11/26/19
|-
| Creating the database and running queries, working with all guilds to assure project is in line to be completed
*Data Analysts: Run YEASTRACT and modify GO Terms.
*Coder: Create individual database for the team.
*QA:Design Expression Tables used to create the final individual database.
| Thursday, 12:00am, 11/28/19
|-
|Begin wrapping up with running analysis on the created database using GRNmap
*Data Analysts: Create GRNmap using individual database from MS Access.
*Coder: Communicate with the QA to ensure the database is correct and if any changes need to be made
*QA: Review the database and communicate to the Coder if any changes need to be made.
| Tuesday, 12:00am, 12/03/19
|-
| Wrap up data analysis and individual milestones and begin to gather deliverables for turn-in
*Data Analysts: Provide feedback on the database and its ease-of-use. Work with QA to gather deliverables.
*Coder: Work with the entire guild to properly combine all databases for the entire class to use.
*QA: Work with the coder to finalize the [https://www.quackit.com/microsoft_access/microsoft_access_2016/howto/how_to_create_a_database_diagram_in_access_2016.cfm database schema diagram]
| Thursday, 12:00am, 12/05/19
|-
| Final Presentation
| Tuesday, 12:00am, 12/10/19
|-
| Report submitted
| Friday, 4:00 pm, 12/13/19
|-
|}

==Acknowledgements==
This section is in acknowledgement to partner [[User:Marmas|Michael Armas]], [[User:Icrespin|Iliana Crespin]], [[User:eyoung20|Emma Young]], and [[User:knguye66|Kaitlyn Nguyen]]. I would also like to acknowledge [[User:Kdahlquist|Dr. Dahlquist]] for introducing and teaching the topic and direction of this assignment.

"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
 
[[User:Marmas|Marmas]] ([[User talk:Marmas|talk]]) 23:40, 13 November 2019 (PST)
[[User:Icrespin|Icrespin]] ([[User talk:Icrespin|talk]]) 23:46, 13 November 2019 (PST)

"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
[[User:Eyoung20|Eyoung20]] ([[User talk:Eyoung20|talk]]) 23:57, 13 November 2019 (PST) [[User:Knguye66|Knguye66]] ([[User talk:Knguye66|talk]]) 18:45, 20 November 2019 (PST)

{{FunGals}}

==References==
-Week 11-
*Kitagawa, E., Takahashi, J., Momose, Y., & Iwahashi, H. (2002). Effects of the pesticide thiuram: genome-wide screening of indicator genes by yeast DNA microarray. Environmental science & technology, 36(18), 3908-3915. DOI: 10.1021/es015705v
*Dahlquist, K. (2019, November 7). Week 11. In Wikipedia, Biological Databases. https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_1https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_11
-Week 12/13-
*Dahlquist, K. (2019, November 19). Data Analysis. In Wikipedia, Biological Databases. Retrieved 6:25, November 20, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Data_Analysis
*Dahlquist, K. (2019, November 20). Final Project Deliverables. In Wikipedia, Biological Databases. Retrieved 6:25, November 20, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Final_Project_Deliverables
*Dahlquist, K. (2019, November 19). Week 12/13. In Wikipedia, Biological Databases. Retrieved 6:25, November 20, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13
*Dahlquist, K. (2019, October 17). Week 8. In Wikipedia, Biological Databases. Retrieved 6:30, October 21, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_8

FunGals

2019-12-03T23:02:14Z

Icrespin: /* Data and Files */ added new week

==Effects of the Pesticide Thiuram: Genome-wide Screening of Indicator Genes by Yeast DNA Microarray==

'''Team Information'''
Project Manager: [[User:Marmas|Michael Armas]]
Quality Assurance: [[User:Icrespin| Iliana Crespin]]
Data Analysis: [[User:eyoung20|Emma Young]], [[User:knguye66|Kaitlyn Nguyen]]
Coder: [[User:Marmas|Michael Armas]]

== Methods and Results ==
=== Week 11 ===
====Setting up the Project====
*Selected [[User:Marmas|Michael Armas]] as team's Project Manager.
*Added the name of of selected project manager to the Project Manager guild page and Overview pages.
*Named the team FunGals and created [[FunGals]] home page on the wiki.
*The name of the team home page was the selected team name.

*Created a link to team's page on the course Main page.
*Created a template for FunGal with useful information and links that you will invoke on all pages that you will create for the project.
*Created a category using team name and included it the FunGal template so that it is used on all pages created for the project. Also included the category "Group Projects" in the template. 
*Each person needs to write a short executive summary of that person's progress on the project for the week, with links to the relevant individual journal pages (which will have more detailed information).
*Each team member should reflect on the team's progress '''(Note that you will be directed to add specific information to your team's pages in the individual portion of the assignment for this and future weeks)''':
**What worked? What didn't work? What will I do next to fix what didn't work?
*** Michael Armas: Working with this team is a great pleasure! Everyone on the team is pulling their weight and providing information that contributes to the group work. Next time, as the project manager, I want to be more organized and come up with interim deadlines to make sure we are not cramming right before the actual deadline. In fact, I would have something small due every day than procrastinate until the end. However, with this team, we are making it work and doing exceptional work!
*** Kaitlyn Nguyen: What worked this week is starting the presentation formatting early, thus allocating the rest of the time to "filling in the missing parts" of the powerpoint. What also worked this week was team communication via group-chats. What didn't work this week was starting the individual assignment later, leaving less time to practicing and fully understanding the material from the journal article for the presentation in class. To fix what didn't work, I will start my individual assignment much earlier, to leave the rest of the time to focus on collaborative teamwork and group assignments. [[User:Knguye66|Knguye66]] ([[User talk:Knguye66|talk]]) 23:37, 13 November 2019 (PST)
*** Emma Young: The team seems to work really well together. I think in upcoming weeks we will really thrive in working together. A foundation for communication has already been established and we have already started reviewing each others work and providing constructive criticism and help where it is needed. The main issue this week was a matter of timing. With the amount of work we had to do in the time frame given we were not able to meet up due to busy and conflicting prior engagements. This meant that we did not reach our full potential of working together effectively as a group this week. Next week, we hopefully will be able to set better deadlines and be able to have the ability to plan out time to work on this in a less rushed manner.
*** Iliana Crespin: Overall, this group has been great. Everyone has worked together and understands what must be done. In addition, each member is understanding of the special circumstances before the deadline of this assignment. The only thing that didn't work out was how scattered each of us were because of all the assignments that had to be completed from other classes. In addition, mandated plans (school- or work-related) popped up which made it difficult to contribute equally. For the future, I will make sure to manage my time better, because I have work and school. Therefore, by doing a fair share of certain things before classes/work, I will be able to contribute more.[[User:Icrespin|Icrespin]] ([[User talk:Icrespin|talk]]) 23:46, 13 November 2019 (PST)

====Annotated Bibliography====

#Braconi, D., Bernardini, G., & Santucci, A. (2016). Saccharomyces cerevisiae as a model in ecotoxicological studies: A post-genomics perspective. Journal of Proteomics, 137, 19-34. DOI: 10.1016/j.jprot.2015.09.001
#Hinkle, K. L., & Olsen, D. (2018). Exposure to the lampricide TFM elicits an environmental stress response in yeast. FEMS yeast research, 19(1), foy121. doi: 10.1093/femsyr/foy121
#Iwahashi, Y., Hosoda, H., Park, J. H., Lee, J. H., Suzuki, Y., Kitagawa, E., ... & Iwahashi, H. (2006). Mechanisms of patulin toxicity under conditions that inhibit yeast growth. Journal of agricultural and food chemistry, 54(5), 1936-1942. doi: 10.1021/jf052264g.
#Iwahashi, H., Ishidou, E., Kitagawa, E., & Momose, Y. (2007). Combined Cadmium and Thiuram Show Synergistic Toxicity and Induce Mitochondrial Petite Mutants. Environmental Science & Technology, 41(22), 7941–7946. doi: 10.1021/es071313y
#Iwahashi, H., Ishidou, E., Kitagawa, E., & Momose, Y. (2007). Combined Cadmium and Thiuram Show Synergistic Toxicity and Induce Mitochondrial Petite Mutants. Environmental Science & Technology, 41(22), 7941–7946. doi: 10.1021/es071313y
#Kitagawa, E., Momose, Y., & Iwahashi, H. (2003). Correlation of the Structures of Agricultural Fungicides to Gene Expression in Saccharomyces cerevisiaeupon Exposure to Toxic Doses. Environmental Science & Technology, 37(12), 2788–2793. doi: 10.1021/es026156b
#Lu Yu, Na Guo, Rizeng Meng, Bin Liu, Xudong Tang, Jing Jin, Yumei Cui, Xuming Deng. Allicin-induced global gene expression profile of Saccharomyces cerevisiae. Applied Microbiology and Biotechnology 2010, 88 (1) , 219-229. DOI: 10.1007/s00253-010-2709-x.
#Pierron, A., Mimoun, S., Murate, L. S., Loiseau, N., Lippi, Y., Bracarense, A. P. F., ... & Oswald, I. P. (2016). Intestinal toxicity of the masked mycotoxin deoxynivalenol-3-β-D-glucoside. Archives of toxicology, 90(8), 2037-2046. doi: 10.1007/s00204-015-1592-8

===Week 12/13===
====Milestone 3: Getting the data ready for analysis ====

# As a group Downloaded and examined the microarray dataset, compared it to the samples and experiment described in the journal club article.
#* [https://sgd-prod-upload.s3.amazonaws.com/S000204415/Kitagawa_2002_PMID_12269742.zip Kitagawa et al. (2002)]
#* downloaded and unzipped
#* file was downloaded but was PLC format
#* Mike figured out how to drag and drop it one to excel to open the file
# Along with the QA's, make a "sample-data relationship table" that lists all of the samples (microarray chips), noting the treatment, time point, replicate number, and other information pertaining to each sample.
#* This "Metadata" sheet was created in Excel and is present on the excel work under the week 12/13 data and files.
#* In collaboration with other groups, the Metadata sheet was filled out so that nomenclature is consistent.
# The class collectively came up with consistent column headers that summarized the information
#* As decided by all groups, the format for column headers was yeastStrain_treatmentOrMutation_concentrationAndUnits_dataType_timeAndUnits-replicateNumber.
# Organized the data in a worksheet in an Excel workbook so that:
#* MasterIndex was in the first column, ID was in the second column
#* Data columns were to the right, in increasing chronological order, using the column header pattern that was created.
#* Replicates were grouped together
# Data analysts (DA) [[User:Knguye66|Kaitlyn]] set-up the ANOVA worksheet via referencing [[Week 8]]
#* The steps for the ANOVA: Part I, Benjamini, Bonferroni, and p-value correction, as well as, a quick sanity check were followed.
# DAs [[User:Eyoung20|Eyoung20]] begin setting up for STEM analysis to complete the first stage of milestones and deliverables
# All the calculations were checked by the QA [[User:Icrespin|Iliana]].

*Each team member should reflect on the team's progress '''(Note that you will be directed to add specific information to your team's pages in the individual portion of the assignment for this and future weeks)''':
**What worked? What didn't work? What will I do next to fix what didn't work?
*** Michael Armas: What worked this week was the communication between my guild and me, and my group and me. Everyone was able to help each other out and make sure the project is coming along smoothly. What didn't work this week for me was understanding exactly what I had to do to set up spreadsheets for data analysis. However, thanks to Mihir, I was able to understand how to create a metadata sheet and reach the milestone for this week. Before I leave class from now on, I will reassure myself that I understand the information by asking Dr. Dahlquist the best way to reach the week's milestone.
*** Kaitlyn Nguyen: This week, the pattern and organization to which each group member worked flowed smoothly as every member of the group knew exactly what each person was accomplishing. Having extra time in class and staying after class helped us jump-start on our tasks together and find out what assignments work best for each team member. What didn't work this week was that each milestone and part of this project works chronologically, whereby other members have to wait for the first person to finish his/her task before beginning theirs. As the days and weeks move on, it will be good to continue this method, but switch off on who starts the tasks first for the assignment. [[User:Knguye66|Knguye66]] ([[User talk:Knguye66|talk]]) 18:44, 20 November 2019 (PST)
*** Emma Young: For this week I worked closely with [[User:Knguye66|Kaitlyn]] to start the data analysis for the rest of the project. We worked with the whole team to analyze the data from the journal article and format for the rest of the data analysis. [[User:Marmas|Mike]] worked with the other programers to formulate the metadata sheet and the format for the ANOVA sheet. More details on this can be found in his personal electronic notebook [[Marmas Week 12/13]] Then [[User:Knguye66|Kaitlyn]] worked on the ANOVA analysis of the data. [[User:Icrespin|Iliana]] double checked the the results of the analysis the details can be found in [[Icrespin Journal Week 12/13]]. After the checks were completed and any errors were found, I ran a sanity check on the ANOVA data and then formatted the STEM worksheet for future analysis. The details about what [[User:Knguye66|Kaitlyn] and [[user:eyoung20|I]] did can be found in our shared journal [[Knguye66 Eyoung20 Week 12/13]]. As can be seen in this summary this week your group was really good at communicating and working together to work on this project. We worked really well together this week. One thing that did not work as well was trying to work on the excel spreadsheet online when others were working on it, there was a large lag on the sheet. I think for the next steps I might do the work on a saved downloaded version of the excel sheet and then copy my work to the shared excel. [[User:Eyoung20|Eyoung20]] ([[User talk:Eyoung20|talk]]) 16:36, 25 November 2019 (PST)
*** Iliana Crespin: For this week, it was a better organization on completing the assignment. There is more of a pattern of what should be done throughout each day to prepare for the deadline. What didn't work out for me is still trying to see how a QA can incorporate any work, since my teammates are great. For the next few weeks, I will try to continue double checking the work and contribute more. This contribution can include working with the data analysts and seeing how I can help out a bit more. In addition, texting teammates a bit more to remind any little things that must be due before the deadline. [[User:Icrespin|Icrespin]] ([[User talk:Icrespin|talk]]) 14:48, 21 November 2019 (PST)

== Data and Files ==
=== Week 11 ===
* Presentation file: [[Media: Marmas_FunGals_Presentation.pptx|Group Presentation]]
=== Week 12/13 ===
*[[media: Thiuram_yeast_experiment.xlsx|Excel Workbook]]
*[[meda: FunGals_genelist.zip|Genelist from STEM]]
*[[media: FunGals_GOlist.zip|GOlist from STEM]]
===Week 15===

== Milestones ==
{| class="wikitable"
|-
! Tasks to be completed
! Due Date
|-
| Write down Methods and Results for Week 12/13
*Coder/designer: find out the column names and edit them, sample to data relationship table
*Data Analysis: ANOVA analysis and set-up, STEM set-up (will run STEM on Thursday)
*QA: make sure all data in original file actually made it into the database, let coder and analysts know if there are issues
| Thursday, 12:00am, 11/19/19
|-
| Team Journal Assignment, continue writing down Methods and Results for Week 12/13
*Data Analysis: finish editing missing information for ANOVA and (STRAIN) worksheet, run STEM
*Coder and QA: add standard names to genes, make sure all data in original file actually made it into the database, let coder and analysts know if there are issues
| Tuesday, 12:00am, 11/26/19
|-
| Creating the database and running queries, working with all guilds to assure project is in line to be completed
*Data Analysts: Run YEASTRACT and modify GO Terms.
*Coder: Create individual database for the team.
*QA:Design Expression Tables used to create the final individual database.
| Thursday, 12:00am, 11/28/19
|-
|Begin wrapping up with running analysis on the created database using GRNmap
*Data Analysts: Create GRNmap using individual database from MS Access.
*Coder: Communicate with the QA to ensure the database is correct and if any changes need to be made
*QA: Review the database and communicate to the Coder if any changes need to be made.
| Tuesday, 12:00am, 12/03/19
|-
| Wrap up data analysis and individual milestones and begin to gather deliverables for turn-in
*Data Analysts: Provide feedback on the database and its ease-of-use. Work with QA to gather deliverables.
*Coder: Work with the entire guild to properly combine all databases for the entire class to use.
*QA: Work with the coder to finalize the [https://www.quackit.com/microsoft_access/microsoft_access_2016/howto/how_to_create_a_database_diagram_in_access_2016.cfm database schema diagram]
| Thursday, 12:00am, 12/05/19
|-
| Final Presentation
| Tuesday, 12:00am, 12/10/19
|-
| Report submitted
| Friday, 4:00 pm, 12/13/19
|-
|}

==Acknowledgements==
This section is in acknowledgement to partner [[User:Marmas|Michael Armas]], [[User:Icrespin|Iliana Crespin]], [[User:eyoung20|Emma Young]], and [[User:knguye66|Kaitlyn Nguyen]]. I would also like to acknowledge [[User:Kdahlquist|Dr. Dahlquist]] for introducing and teaching the topic and direction of this assignment.

"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
 
[[User:Marmas|Marmas]] ([[User talk:Marmas|talk]]) 23:40, 13 November 2019 (PST)
[[User:Icrespin|Icrespin]] ([[User talk:Icrespin|talk]]) 23:46, 13 November 2019 (PST)

"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
[[User:Eyoung20|Eyoung20]] ([[User talk:Eyoung20|talk]]) 23:57, 13 November 2019 (PST) [[User:Knguye66|Knguye66]] ([[User talk:Knguye66|talk]]) 18:45, 20 November 2019 (PST)

{{FunGals}}

==References==
-Week 11-
*Kitagawa, E., Takahashi, J., Momose, Y., & Iwahashi, H. (2002). Effects of the pesticide thiuram: genome-wide screening of indicator genes by yeast DNA microarray. Environmental science & technology, 36(18), 3908-3915. DOI: 10.1021/es015705v
*Dahlquist, K. (2019, November 7). Week 11. In Wikipedia, Biological Databases. https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_1https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_11
-Week 12/13-
*Dahlquist, K. (2019, November 19). Data Analysis. In Wikipedia, Biological Databases. Retrieved 6:25, November 20, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Data_Analysis
*Dahlquist, K. (2019, November 20). Final Project Deliverables. In Wikipedia, Biological Databases. Retrieved 6:25, November 20, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Final_Project_Deliverables
*Dahlquist, K. (2019, November 19). Week 12/13. In Wikipedia, Biological Databases. Retrieved 6:25, November 20, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13
*Dahlquist, K. (2019, October 17). Week 8. In Wikipedia, Biological Databases. Retrieved 6:30, October 21, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_8

FunGals Deliverables

2019-12-03T23:00:41Z

Icrespin: /* Checklist */ created a table

{{template:FunGals}}

==Checklist==
{| class="wikitable"
|-
! Tasks to be completed
! Complete/Incomplete
|-
| Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents)
| Incomplete
|-
| Group Report (''.doc'', ''.docx'' or ''.pdf'' file)
| Incomplete
|-
| Individual statements of work, assessments, reflections (wiki page, ''.doc'', ''.docx'', ''.pdf'', or e-mailed to Dr. Dahlquist)
| Incomplete
|-
| Group PowerPoint presentation (given on Tuesday, December 10, ''.ppt'', ''.pptx'' or ''.pdf'' file)
| Incomplete
|-
| Sample-data relationship table in Excel (''.xlsx'')
| Incomplete
|-
| Excel spreadsheet with ANOVA results/stem formatting (''.xlsx'')
| Incomplete
|-
| PowerPoint of ANOVA table, screenshots of stem results (''.pptx''), screenshot of black and white GRNsight input network and colored GRNsight output networks
| Incomplete
|-
| Gene List and GO List files from each significant profile (''.txt'' compressed together in a ''.zip'' file)
| Incomplete
|-
| YEASTRACT "rank by TF" results (''.xlsx'')
| Incomplete
|-
| GRNmap input workbook (with network adjacency matrix, ''.xlsx'')
| Incomplete
|-
| GRNmap output workbook (''.xlsx'') and output plots (''.jpg'') zipped together
| Incomplete
|-
| MS Access database, unified by the three teams with expression tables and metadata table(s) created (''.accdb'')
| Incomplete
|-
| ReadMe for the database that describes the design of the database, references the sources of the data, and has a [https://www.quackit.com/microsoft_access/microsoft_access_2016/howto/how_to_create_a_database_diagram_in_access_2016.cfm database schema diagram] (''.doc'', ''.docx'', ''.pdf'')
| Incomplete
|-
| Query design for populating a GRNmap input workbook from the database (screenshot of MS Access, or SQL code, ''.txt'')
| Incomplete
|-
| Electronic notebook corresponding to these the microarray results files ([[Week 12/13]] and [[Week 15]]) to 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.
| Incomplete
|-
|}

==Group Report==

===Title===

===Introduction===

===Methods/Results/Discussion===

====Data Analysts====

====Coder====

====Quality Assurance====

===Conclusion===

==Powerpoint Presentation==

==Individual Assessment and Reflection==

===Michael Armas===

==== 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 Final 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?

===Kaitlyn Nguyen===

==== 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 Final 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?

===Emma Young===

==== 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 Final 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?

===Iliana Crespin===

==== 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 Final 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?

==Acknowledgments==

==References==

[[Category: Group Projects]]

Icrespin Journal Week 12/13

2019-11-26T03:47:01Z

Icrespin: /* Acknowledgments */ added sign

== Electronic Lab Notebook ==
{{template:Icrespin}}

==Purpose==
The purpose of this week's assignment is to discuss the progress that has been done. Roles for each team member would be explained a bit more and the goals of completing certain tasks would be completed for this week. These tasks include finalizing the data analysis portion. As a QA, the major task is making sure the data analysts are doing okay and to help out as much as possible.

==Methods/Results: In Progress==
=== November 21, 2019 ===
*For this week, our group decided to complete some of our milestones and deliverables by Thursday's date.
*Reviewed the work that the data analysts did to make sure there weren't any errors that were made.
**Thanks to a great team, data analysts caught some things as well that were wrong.
*Made sure the metadata was up to date and asked to have few things clarified.
*Reminded to write summaries down for group's assignment.

=== November 26, 2019 ===
*Double checked the work of the data analysts again to see if things look okay.
*Added more things to the template
**Created more links that follow deliverables' requirements
**Copied and pasted questions that will be answered in the future from Dahlquist's weekly assignments
**Checked to see group's page is up to date.

== Milestones ==
{| class="wikitable"
|-
! Milestones
! Due Date
! Complete/Incomplete
|-
| Annotated Bibliography
*Work on creating a bibliography with other team members
| Tuesday, 12:00am, 11/12/19
| '''COMPLETE'''
|-
| Journal Club Presentation
*Review article and ask any questions that seemed unclear
*Add important slides to powerpoint
*Practice what will be presented to audience
| Thursday, 12:00am, 11/14/19
| '''COMPLETE'''
|-
| Working with Data Analysts to Understand Microarray Dataset
*Review and double check work done by data analysts
*Complete sanity checks to make sure it matches with work
*Add any information needed to make sure everything is fine
| Tuesday, 12:00am, 11/26/19
| '''COMPLETE'''
|-
| Making Sure Expression Data has Both Sytematic Name and Standard Name ID's
*Review information to make sure this is complete
| Tuesday, 12:00am, 11/26/19
| '''COMPLETE'''
|-
| Work with Coder/Designers to Design a Database to Store Time-course Microarray Data from Four Sources
*Add database to Box folder
*Work with Coder to create MS Access database to store yeast time-course microarray
*Review information and determine headings for database
| Tuesday, 12:00am, 12/03/19
| '''INCOMPLETE'''
|-
| Validation and Quality Assurance on Database
*Review information to make sure it is correct
*Communicate with Coder if something is wrong/missing
| Thursday, 12:00am, 12/06/19
| '''INCOMPLETE'''
|-
| Final Documentation
*Review database schema diagram with Coder
| Thursday, 12:00am, 12/06/19
| '''INCOMPLETE'''
|-
| Final Presentation
| Tuesday, 12:00am, 12/10/19
| '''INCOMPLETE'''
|-
| Report submitted
| Friday, 4:00 pm, 12/13/19
| '''INCOMPLETE'''
|-
|}

==Data and Files==
[[Media:Marmas_Metadata_Sheet.xlsx | Metadata Sheet]]

[[Media:Thiuram_yeast_experiment.xlsx|Thiuram Excel Workbook]]

==Conclusion==
Overall, it has been a bit difficult to contribute to the group because there isn't much a QA can do in the first few stages of this project. However, in the background, there have been reviewing and making sure things are being submitted on time. More messages will be sent out to group members to make sure things are being submitted on time so everyone can get the points they deserve. For the next week, the plan is to continue hitting the milestones and completing the checklist for the group's deliverables.

==Acknowledgments==
*Thank you to [[User:Knguye66|Kaitlyn Nguyen]], [[User:Eyoung20|Emma Young]], and [[User:marmas|Michael Armas]] for being great team members. The Excel workbook was copied and pasted from our shared link, whereas the metadata was copied and pasted from Michael's page.
*Thanks to Dr. Dahlquist for checking our work making sure it is being done properly.
*Thanks to other team/guild members for having the metadata formatted and prepared.
*"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."[[User:Icrespin|Icrespin]] ([[User talk:Icrespin|talk]]) 19:47, 25 November 2019 (PST)

==References==
Final Project. (2019). Deliverables. Retrieved November 25, 2019 from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Final_Project_Deliverables

LMU BioDB 2019. (2019). Week 12/13. Retrieved November 21, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13

Michael Armas. (2019). User's Week 12/13. Retrieved November 25, 2019 from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Marmas_Week_12/13

Quality Assurance. (2019). Quality Assurance Main Page. Retrieved November 21, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Quality_Assurance

[[Category: Journal Entry]]
[[Category: Group Projects]]
[[Category: FunGals]]

Category:FunGals

2019-11-26T03:44:44Z

Icrespin: /* Pages in this Category */ removed

Category:FunGals

2019-11-26T03:44:26Z

Icrespin: created page

== Pages in this Category ==
The following are pages in this category.

Icrespin Journal Week 12/13

2019-11-26T03:42:21Z

Icrespin: added categories

== Electronic Lab Notebook ==
{{template:Icrespin}}

==Purpose==
The purpose of this week's assignment is to discuss the progress that has been done. Roles for each team member would be explained a bit more and the goals of completing certain tasks would be completed for this week. These tasks include finalizing the data analysis portion. As a QA, the major task is making sure the data analysts are doing okay and to help out as much as possible.

==Methods/Results: In Progress==
=== November 21, 2019 ===
*For this week, our group decided to complete some of our milestones and deliverables by Thursday's date.
*Reviewed the work that the data analysts did to make sure there weren't any errors that were made.
**Thanks to a great team, data analysts caught some things as well that were wrong.
*Made sure the metadata was up to date and asked to have few things clarified.
*Reminded to write summaries down for group's assignment.

=== November 26, 2019 ===
*Double checked the work of the data analysts again to see if things look okay.
*Added more things to the template
**Created more links that follow deliverables' requirements
**Copied and pasted questions that will be answered in the future from Dahlquist's weekly assignments
**Checked to see group's page is up to date.

== Milestones ==
{| class="wikitable"
|-
! Milestones
! Due Date
! Complete/Incomplete
|-
| Annotated Bibliography
*Work on creating a bibliography with other team members
| Tuesday, 12:00am, 11/12/19
| '''COMPLETE'''
|-
| Journal Club Presentation
*Review article and ask any questions that seemed unclear
*Add important slides to powerpoint
*Practice what will be presented to audience
| Thursday, 12:00am, 11/14/19
| '''COMPLETE'''
|-
| Working with Data Analysts to Understand Microarray Dataset
*Review and double check work done by data analysts
*Complete sanity checks to make sure it matches with work
*Add any information needed to make sure everything is fine
| Tuesday, 12:00am, 11/26/19
| '''COMPLETE'''
|-
| Making Sure Expression Data has Both Sytematic Name and Standard Name ID's
*Review information to make sure this is complete
| Tuesday, 12:00am, 11/26/19
| '''COMPLETE'''
|-
| Work with Coder/Designers to Design a Database to Store Time-course Microarray Data from Four Sources
*Add database to Box folder
*Work with Coder to create MS Access database to store yeast time-course microarray
*Review information and determine headings for database
| Tuesday, 12:00am, 12/03/19
| '''INCOMPLETE'''
|-
| Validation and Quality Assurance on Database
*Review information to make sure it is correct
*Communicate with Coder if something is wrong/missing
| Thursday, 12:00am, 12/06/19
| '''INCOMPLETE'''
|-
| Final Documentation
*Review database schema diagram with Coder
| Thursday, 12:00am, 12/06/19
| '''INCOMPLETE'''
|-
| Final Presentation
| Tuesday, 12:00am, 12/10/19
| '''INCOMPLETE'''
|-
| Report submitted
| Friday, 4:00 pm, 12/13/19
| '''INCOMPLETE'''
|-
|}

==Data and Files==
[[Media:Marmas_Metadata_Sheet.xlsx | Metadata Sheet]]

[[Media:Thiuram_yeast_experiment.xlsx|Thiuram Excel Workbook]]

==Conclusion==
Overall, it has been a bit difficult to contribute to the group because there isn't much a QA can do in the first few stages of this project. However, in the background, there have been reviewing and making sure things are being submitted on time. More messages will be sent out to group members to make sure things are being submitted on time so everyone can get the points they deserve. For the next week, the plan is to continue hitting the milestones and completing the checklist for the group's deliverables.

==Acknowledgments==
*Thank you to [[User:Knguye66|Kaitlyn Nguyen]], [[User:Eyoung20|Emma Young]], and [[User:marmas|Michael Armas]] for being great team members. The Excel workbook was copied and pasted from our shared link, whereas the metadata was copied and pasted from Michael's page.
*Thanks to Dr. Dahlquist for checking our work making sure it is being done properly.
*Thanks to other team/guild members for having the metadata formatted and prepared.

==References==
Final Project. (2019). Deliverables. Retrieved November 25, 2019 from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Final_Project_Deliverables

LMU BioDB 2019. (2019). Week 12/13. Retrieved November 21, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13

Michael Armas. (2019). User's Week 12/13. Retrieved November 25, 2019 from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Marmas_Week_12/13

Quality Assurance. (2019). Quality Assurance Main Page. Retrieved November 21, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Quality_Assurance

[[Category: Journal Entry]]
[[Category: Group Projects]]
[[Category: FunGals]]

Template:FunGals

2019-11-26T03:39:44Z

Icrespin: /* Individual Template Pages */ removed this

=== Information and Links ===
{| class="wikitable" style="width: 100%; text-align: center"
! colspan="10"|FunGals Links
|-
! rowspan="2"|[[Main Page|BIOL Databases Main Page]]
! rowspan="2"|[[FunGals|FunGals: Project Overview Page]]
! rowspan="2"|[[Final Project Deliverables| Final Project Deliverables Requirements]]
! rowspan="2"|[[FunGals Deliverables|FunGals: Final Project Deliverables]]
|-
! Assignment Pages
| [[Week 11]]
| [[Week 12/13]]
| [[Week 15]]
|}

[[Category: Group Projects]]

* [https://pubs.acs.org/doi/10.1021/es015705v| Thiuram Article]

=== User Page ===
[[User:knguye66]]
[[User:marmas]]
[[User:Icrespin]]
[[User:eyoung20]]

=== Template Page ===

[[Template:FunGals]]

[[Category: Group Projects]]

Icrespin Journal Week 12/13

2019-11-26T03:37:14Z

Icrespin: /* References */ added references

== Electronic Lab Notebook ==
{{template:Icrespin}}

==Purpose==
The purpose of this week's assignment is to discuss the progress that has been done. Roles for each team member would be explained a bit more and the goals of completing certain tasks would be completed for this week. These tasks include finalizing the data analysis portion. As a QA, the major task is making sure the data analysts are doing okay and to help out as much as possible.

==Methods/Results: In Progress==
=== November 21, 2019 ===
*For this week, our group decided to complete some of our milestones and deliverables by Thursday's date.
*Reviewed the work that the data analysts did to make sure there weren't any errors that were made.
**Thanks to a great team, data analysts caught some things as well that were wrong.
*Made sure the metadata was up to date and asked to have few things clarified.
*Reminded to write summaries down for group's assignment.

=== November 26, 2019 ===
*Double checked the work of the data analysts again to see if things look okay.
*Added more things to the template
**Created more links that follow deliverables' requirements
**Copied and pasted questions that will be answered in the future from Dahlquist's weekly assignments
**Checked to see group's page is up to date.

== Milestones ==
{| class="wikitable"
|-
! Milestones
! Due Date
! Complete/Incomplete
|-
| Annotated Bibliography
*Work on creating a bibliography with other team members
| Tuesday, 12:00am, 11/12/19
| '''COMPLETE'''
|-
| Journal Club Presentation
*Review article and ask any questions that seemed unclear
*Add important slides to powerpoint
*Practice what will be presented to audience
| Thursday, 12:00am, 11/14/19
| '''COMPLETE'''
|-
| Working with Data Analysts to Understand Microarray Dataset
*Review and double check work done by data analysts
*Complete sanity checks to make sure it matches with work
*Add any information needed to make sure everything is fine
| Tuesday, 12:00am, 11/26/19
| '''COMPLETE'''
|-
| Making Sure Expression Data has Both Sytematic Name and Standard Name ID's
*Review information to make sure this is complete
| Tuesday, 12:00am, 11/26/19
| '''COMPLETE'''
|-
| Work with Coder/Designers to Design a Database to Store Time-course Microarray Data from Four Sources
*Add database to Box folder
*Work with Coder to create MS Access database to store yeast time-course microarray
*Review information and determine headings for database
| Tuesday, 12:00am, 12/03/19
| '''INCOMPLETE'''
|-
| Validation and Quality Assurance on Database
*Review information to make sure it is correct
*Communicate with Coder if something is wrong/missing
| Thursday, 12:00am, 12/06/19
| '''INCOMPLETE'''
|-
| Final Documentation
*Review database schema diagram with Coder
| Thursday, 12:00am, 12/06/19
| '''INCOMPLETE'''
|-
| Final Presentation
| Tuesday, 12:00am, 12/10/19
| '''INCOMPLETE'''
|-
| Report submitted
| Friday, 4:00 pm, 12/13/19
| '''INCOMPLETE'''
|-
|}

==Data and Files==
[[Media:Marmas_Metadata_Sheet.xlsx | Metadata Sheet]]

[[Media:Thiuram_yeast_experiment.xlsx|Thiuram Excel Workbook]]

==Conclusion==
Overall, it has been a bit difficult to contribute to the group because there isn't much a QA can do in the first few stages of this project. However, in the background, there have been reviewing and making sure things are being submitted on time. More messages will be sent out to group members to make sure things are being submitted on time so everyone can get the points they deserve. For the next week, the plan is to continue hitting the milestones and completing the checklist for the group's deliverables.

==Acknowledgments==
*Thank you to [[User:Knguye66|Kaitlyn Nguyen]], [[User:Eyoung20|Emma Young]], and [[User:marmas|Michael Armas]] for being great team members. The Excel workbook was copied and pasted from our shared link, whereas the metadata was copied and pasted from Michael's page.
*Thanks to Dr. Dahlquist for checking our work making sure it is being done properly.
*Thanks to other team/guild members for having the metadata formatted and prepared.

==References==
Final Project. (2019). Deliverables. Retrieved November 25, 2019 from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Final_Project_Deliverables

LMU BioDB 2019. (2019). Week 12/13. Retrieved November 21, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13

Michael Armas. (2019). User's Week 12/13. Retrieved November 25, 2019 from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Marmas_Week_12/13

Quality Assurance. (2019). Quality Assurance Main Page. Retrieved November 21, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Quality_Assurance

[[Category: Journal Entry]]

Template:FunGals

2019-11-26T03:27:38Z

Icrespin: /* Template Page */ added new title

Icrespin Journal Week 12/13

2019-11-26T03:23:52Z

Icrespin: added more categories

== Electronic Lab Notebook ==
{{template:Icrespin}}

==Purpose==
The purpose of this week's assignment is to discuss the progress that has been done. Roles for each team member would be explained a bit more and the goals of completing certain tasks would be completed for this week. These tasks include finalizing the data analysis portion. As a QA, the major task is making sure the data analysts are doing okay and to help out as much as possible.

==Methods/Results: In Progress==
=== November 21, 2019 ===
*For this week, our group decided to complete some of our milestones and deliverables by Thursday's date.
*Reviewed the work that the data analysts did to make sure there weren't any errors that were made.
**Thanks to a great team, data analysts caught some things as well that were wrong.
*Made sure the metadata was up to date and asked to have few things clarified.
*Reminded to write summaries down for group's assignment.

=== November 26, 2019 ===
*Double checked the work of the data analysts again to see if things look okay.
*Added more things to the template
**Created more links that follow deliverables' requirements
**Copied and pasted questions that will be answered in the future from Dahlquist's weekly assignments
**Checked to see group's page is up to date.

== Milestones ==
{| class="wikitable"
|-
! Milestones
! Due Date
! Complete/Incomplete
|-
| Annotated Bibliography
*Work on creating a bibliography with other team members
| Tuesday, 12:00am, 11/12/19
| '''COMPLETE'''
|-
| Journal Club Presentation
*Review article and ask any questions that seemed unclear
*Add important slides to powerpoint
*Practice what will be presented to audience
| Thursday, 12:00am, 11/14/19
| '''COMPLETE'''
|-
| Working with Data Analysts to Understand Microarray Dataset
*Review and double check work done by data analysts
*Complete sanity checks to make sure it matches with work
*Add any information needed to make sure everything is fine
| Tuesday, 12:00am, 11/26/19
| '''COMPLETE'''
|-
| Making Sure Expression Data has Both Sytematic Name and Standard Name ID's
*Review information to make sure this is complete
| Tuesday, 12:00am, 11/26/19
| '''COMPLETE'''
|-
| Work with Coder/Designers to Design a Database to Store Time-course Microarray Data from Four Sources
*Add database to Box folder
*Work with Coder to create MS Access database to store yeast time-course microarray
*Review information and determine headings for database
| Tuesday, 12:00am, 12/03/19
| '''INCOMPLETE'''
|-
| Validation and Quality Assurance on Database
*Review information to make sure it is correct
*Communicate with Coder if something is wrong/missing
| Thursday, 12:00am, 12/06/19
| '''INCOMPLETE'''
|-
| Final Documentation
*Review database schema diagram with Coder
| Thursday, 12:00am, 12/06/19
| '''INCOMPLETE'''
|-
| Final Presentation
| Tuesday, 12:00am, 12/10/19
| '''INCOMPLETE'''
|-
| Report submitted
| Friday, 4:00 pm, 12/13/19
| '''INCOMPLETE'''
|-
|}

==Data and Files==
[[Media:Marmas_Metadata_Sheet.xlsx | Metadata Sheet]]

[[Media:Thiuram_yeast_experiment.xlsx|Thiuram Excel Workbook]]

==Conclusion==
Overall, it has been a bit difficult to contribute to the group because there isn't much a QA can do in the first few stages of this project. However, in the background, there have been reviewing and making sure things are being submitted on time. More messages will be sent out to group members to make sure things are being submitted on time so everyone can get the points they deserve. For the next week, the plan is to continue hitting the milestones and completing the checklist for the group's deliverables.

==Acknowledgments==
*Thank you to [[User:Knguye66|Kaitlyn Nguyen]], [[User:Eyoung20|Emma Young]], and [[User:marmas|Michael Armas]] for being great team members. The Excel workbook was copied and pasted from our shared link, whereas the metadata was copied and pasted from Michael's page.
*Thanks to Dr. Dahlquist for checking our work making sure it is being done properly.
*Thanks to other team/guild members for having the metadata formatted and prepared.

==References==

[[Category: Journal Entry|Group Projects]]

Icrespin Journal Week 12/13

2019-11-26T03:22:52Z

Icrespin: /* Acknowledgments */ changed user

Icrespin Journal Week 12/13

2019-11-26T03:22:35Z

Icrespin: /* Acknowledgments */ changed name

== Electronic Lab Notebook ==
{{template:Icrespin}}

==Purpose==
The purpose of this week's assignment is to discuss the progress that has been done. Roles for each team member would be explained a bit more and the goals of completing certain tasks would be completed for this week. These tasks include finalizing the data analysis portion. As a QA, the major task is making sure the data analysts are doing okay and to help out as much as possible.

==Methods/Results: In Progress==
=== November 21, 2019 ===
*For this week, our group decided to complete some of our milestones and deliverables by Thursday's date.
*Reviewed the work that the data analysts did to make sure there weren't any errors that were made.
**Thanks to a great team, data analysts caught some things as well that were wrong.
*Made sure the metadata was up to date and asked to have few things clarified.
*Reminded to write summaries down for group's assignment.

=== November 26, 2019 ===
*Double checked the work of the data analysts again to see if things look okay.
*Added more things to the template
**Created more links that follow deliverables' requirements
**Copied and pasted questions that will be answered in the future from Dahlquist's weekly assignments
**Checked to see group's page is up to date.

== Milestones ==
{| class="wikitable"
|-
! Milestones
! Due Date
! Complete/Incomplete
|-
| Annotated Bibliography
*Work on creating a bibliography with other team members
| Tuesday, 12:00am, 11/12/19
| '''COMPLETE'''
|-
| Journal Club Presentation
*Review article and ask any questions that seemed unclear
*Add important slides to powerpoint
*Practice what will be presented to audience
| Thursday, 12:00am, 11/14/19
| '''COMPLETE'''
|-
| Working with Data Analysts to Understand Microarray Dataset
*Review and double check work done by data analysts
*Complete sanity checks to make sure it matches with work
*Add any information needed to make sure everything is fine
| Tuesday, 12:00am, 11/26/19
| '''COMPLETE'''
|-
| Making Sure Expression Data has Both Sytematic Name and Standard Name ID's
*Review information to make sure this is complete
| Tuesday, 12:00am, 11/26/19
| '''COMPLETE'''
|-
| Work with Coder/Designers to Design a Database to Store Time-course Microarray Data from Four Sources
*Add database to Box folder
*Work with Coder to create MS Access database to store yeast time-course microarray
*Review information and determine headings for database
| Tuesday, 12:00am, 12/03/19
| '''INCOMPLETE'''
|-
| Validation and Quality Assurance on Database
*Review information to make sure it is correct
*Communicate with Coder if something is wrong/missing
| Thursday, 12:00am, 12/06/19
| '''INCOMPLETE'''
|-
| Final Documentation
*Review database schema diagram with Coder
| Thursday, 12:00am, 12/06/19
| '''INCOMPLETE'''
|-
| Final Presentation
| Tuesday, 12:00am, 12/10/19
| '''INCOMPLETE'''
|-
| Report submitted
| Friday, 4:00 pm, 12/13/19
| '''INCOMPLETE'''
|-
|}

==Data and Files==
[[Media:Marmas_Metadata_Sheet.xlsx | Metadata Sheet]]

[[Media:Thiuram_yeast_experiment.xlsx|Thiuram Excel Workbook]]

==Conclusion==
Overall, it has been a bit difficult to contribute to the group because there isn't much a QA can do in the first few stages of this project. However, in the background, there have been reviewing and making sure things are being submitted on time. More messages will be sent out to group members to make sure things are being submitted on time so everyone can get the points they deserve. For the next week, the plan is to continue hitting the milestones and completing the checklist for the group's deliverables.

==Acknowledgments==
*Thank you to [[User:Knugye66|Kaitlyn Nguyen]], [[User:Eyoung20|Emma Young]], and [[User:marmas|Michael Armas]] for being great team members. The Excel workbook was copied and pasted from our shared link, whereas the metadata was copied and pasted from Michael's page.
*Thanks to Dr. Dahlquist for checking our work making sure it is being done properly.
*Thanks to other team/guild members for having the metadata formatted and prepared.

==References==

[[Category: Journal Entry]]

Icrespin Journal Week 12/13

2019-11-26T03:22:17Z

Icrespin: /* Acknowledgments */ added info

== Electronic Lab Notebook ==
{{template:Icrespin}}

==Purpose==
The purpose of this week's assignment is to discuss the progress that has been done. Roles for each team member would be explained a bit more and the goals of completing certain tasks would be completed for this week. These tasks include finalizing the data analysis portion. As a QA, the major task is making sure the data analysts are doing okay and to help out as much as possible.

==Methods/Results: In Progress==
=== November 21, 2019 ===
*For this week, our group decided to complete some of our milestones and deliverables by Thursday's date.
*Reviewed the work that the data analysts did to make sure there weren't any errors that were made.
**Thanks to a great team, data analysts caught some things as well that were wrong.
*Made sure the metadata was up to date and asked to have few things clarified.
*Reminded to write summaries down for group's assignment.

=== November 26, 2019 ===
*Double checked the work of the data analysts again to see if things look okay.
*Added more things to the template
**Created more links that follow deliverables' requirements
**Copied and pasted questions that will be answered in the future from Dahlquist's weekly assignments
**Checked to see group's page is up to date.

== Milestones ==
{| class="wikitable"
|-
! Milestones
! Due Date
! Complete/Incomplete
|-
| Annotated Bibliography
*Work on creating a bibliography with other team members
| Tuesday, 12:00am, 11/12/19
| '''COMPLETE'''
|-
| Journal Club Presentation
*Review article and ask any questions that seemed unclear
*Add important slides to powerpoint
*Practice what will be presented to audience
| Thursday, 12:00am, 11/14/19
| '''COMPLETE'''
|-
| Working with Data Analysts to Understand Microarray Dataset
*Review and double check work done by data analysts
*Complete sanity checks to make sure it matches with work
*Add any information needed to make sure everything is fine
| Tuesday, 12:00am, 11/26/19
| '''COMPLETE'''
|-
| Making Sure Expression Data has Both Sytematic Name and Standard Name ID's
*Review information to make sure this is complete
| Tuesday, 12:00am, 11/26/19
| '''COMPLETE'''
|-
| Work with Coder/Designers to Design a Database to Store Time-course Microarray Data from Four Sources
*Add database to Box folder
*Work with Coder to create MS Access database to store yeast time-course microarray
*Review information and determine headings for database
| Tuesday, 12:00am, 12/03/19
| '''INCOMPLETE'''
|-
| Validation and Quality Assurance on Database
*Review information to make sure it is correct
*Communicate with Coder if something is wrong/missing
| Thursday, 12:00am, 12/06/19
| '''INCOMPLETE'''
|-
| Final Documentation
*Review database schema diagram with Coder
| Thursday, 12:00am, 12/06/19
| '''INCOMPLETE'''
|-
| Final Presentation
| Tuesday, 12:00am, 12/10/19
| '''INCOMPLETE'''
|-
| Report submitted
| Friday, 4:00 pm, 12/13/19
| '''INCOMPLETE'''
|-
|}

==Data and Files==
[[Media:Marmas_Metadata_Sheet.xlsx | Metadata Sheet]]

[[Media:Thiuram_yeast_experiment.xlsx|Thiuram Excel Workbook]]

==Conclusion==
Overall, it has been a bit difficult to contribute to the group because there isn't much a QA can do in the first few stages of this project. However, in the background, there have been reviewing and making sure things are being submitted on time. More messages will be sent out to group members to make sure things are being submitted on time so everyone can get the points they deserve. For the next week, the plan is to continue hitting the milestones and completing the checklist for the group's deliverables.

==Acknowledgments==
*Thank you to [[User:Knugyen66|Kaitlyn Nguyen]], [[User:Eyoung20|Emma Young]], and [[User:marmas|Michael Armas]] for being great team members. The Excel workbook was copied and pasted from our shared link, whereas the metadata was copied and pasted from Michael's page.
*Thanks to Dr. Dahlquist for checking our work making sure it is being done properly.
*Thanks to other team/guild members for having the metadata formatted and prepared.

==References==

[[Category: Journal Entry]]

Icrespin Journal Week 12/13

2019-11-26T03:19:11Z

Icrespin: /* Milestones */ changed formatting

Icrespin Journal Week 12/13

2019-11-26T03:18:42Z

Icrespin: /* Methods/Results: In Progress */ added milestones

== Electronic Lab Notebook ==
{{template:Icrespin}}

==Purpose==
The purpose of this week's assignment is to discuss the progress that has been done. Roles for each team member would be explained a bit more and the goals of completing certain tasks would be completed for this week. These tasks include finalizing the data analysis portion. As a QA, the major task is making sure the data analysts are doing okay and to help out as much as possible.

==Methods/Results: In Progress==
=== November 21, 2019 ===
*For this week, our group decided to complete some of our milestones and deliverables by Thursday's date.
*Reviewed the work that the data analysts did to make sure there weren't any errors that were made.
**Thanks to a great team, data analysts caught some things as well that were wrong.
*Made sure the metadata was up to date and asked to have few things clarified.
*Reminded to write summaries down for group's assignment.

=== November 26, 2019 ===
*Double checked the work of the data analysts again to see if things look okay.
*Added more things to the template
**Created more links that follow deliverables' requirements
**Copied and pasted questions that will be answered in the future from Dahlquist's weekly assignments
**Checked to see group's page is up to date.

== Milestones ==
{| class="wikitable"
|-
! Milestones
! Due Date
! Complete/Incomplete
|-
| Annotated Bibliography
*Work on creating a bibliography with other team members
| Tuesday, 12:00am, 11/12/19
| '''COMPLETE'''
|-
| Journal Club Presentation
*Review article and ask any questions that seemed unclear
*Add important slides to powerpoint
*Practice what will be presented to audience
| Thursday, 12:00am, 11/14/19
| '''COMPLETE'''
|-
| Working with Data Analysts to Understand Microarray Dataset
*Review and double check work done by data analysts
*Complete sanity checks to make sure it matches with work
*Add any information needed to make sure everything is fine
| Tuesday, 12:00am, 11/26/19
| '''COMPLETE'''
|-
| Making Sure Expression Data has Both Sytematic Name and Standard Name ID's
*Review information to make sure this is complete
| Tuesday, 12:00am, 11/26/19
| '''COMPLETE'''
|-
| Work with Coder/Designers to Design a Database to Store Time-course Microarray Data from Four Sources
*Add database to Box folder
*Work with Coder to create MS Access database to store yeast time-course microarray
*Review information and determine headings for database
| Tuesday, 12:00am, 12/03/19
| '''INCOMPLETE'''
|-
| Validation and Quality Assurance on Database
*Review information to make sure it is correct
*Communicate with Coder if something is wrong/missing
| Thursday, 12:00am, 12/06/19
| '''INCOMPLETE'''
|-
| Final Documentation
*Review database schema diagram with Coder
| Thursday, 12:00am, 12/06/19
| ''INCOMPLETE''
|-
| Final Presentation
| Tuesday, 12:00am, 12/10/19
| '''INCOMPLETE'''
|-
| Report submitted
| Friday, 4:00 pm, 12/13/19
| '''INCOMPLETE'''
|-
|}

==Data and Files==
[[Media:Marmas_Metadata_Sheet.xlsx | Metadata Sheet]]

[[Media:Thiuram_yeast_experiment.xlsx|Thiuram Excel Workbook]]

==Conclusion==
Overall, it has been a bit difficult to contribute to the group because there isn't much a QA can do in the first few stages of this project. However, in the background, there have been reviewing and making sure things are being submitted on time. More messages will be sent out to group members to make sure things are being submitted on time so everyone can get the points they deserve. For the next week, the plan is to continue hitting the milestones and completing the checklist for the group's deliverables.

==Acknowledgments==

==References==

[[Category: Journal Entry]]

Template:FunGals

2019-11-26T03:04:54Z

Icrespin: changed order

Template:FunGals

2019-11-26T03:04:13Z

Icrespin: /* Group Page */ removed this title

=== User Page ===
[[User:knguye66]]
[[User:marmas]]
[[User:Icrespin]]
[[User:eyoung20]]

=== Template Page ===

[[Template:FunGals]]

[[Category: Group Projects]]

=== Information and Links ===
{| class="wikitable" style="width: 100%; text-align: center"
! colspan="10"|FunGals Links
|-
! rowspan="2"|[[Main Page|BIOL Databases Main Page]]
! rowspan="2"|[[FunGals|FunGals: Project Overview Page]]
! rowspan="2"|[[Final Project Deliverables| Final Project Deliverables Requirements]]
! rowspan="2"|[[FunGals Deliverables|FunGals: Final Project Deliverables]]
|-
! Assignment Pages
| [[Week 11]]
| [[Week 12/13]]
| [[Week 15]]
|}

[[Category: Group Projects]]

* [https://pubs.acs.org/doi/10.1021/es015705v| Thiuram Article]

Template:FunGals

2019-11-26T03:03:22Z

Icrespin: /* Information and Links */ changed name

=== Group Page ===
[https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/FunGals FunGals]

=== User Page ===
[[User:knguye66]]
[[User:marmas]]
[[User:Icrespin]]
[[User:eyoung20]]

=== Template Page ===

[[Template:FunGals]]

[[Category: Group Projects]]

=== Information and Links ===
{| class="wikitable" style="width: 100%; text-align: center"
! colspan="10"|FunGals Links
|-
! rowspan="2"|[[Main Page|BIOL Databases Main Page]]
! rowspan="2"|[[FunGals|FunGals: Project Overview Page]]
! rowspan="2"|[[Final Project Deliverables| Final Project Deliverables Requirements]]
! rowspan="2"|[[FunGals Deliverables|FunGals: Final Project Deliverables]]
|-
! Assignment Pages
| [[Week 11]]
| [[Week 12/13]]
| [[Week 15]]
|}

[[Category: Group Projects]]

* [https://pubs.acs.org/doi/10.1021/es015705v| Thiuram Article]

Icrespin Journal Week 12/13

2019-11-26T02:57:53Z

Icrespin: /* Conclusion */ added info

Icrespin Journal Week 12/13

2019-11-26T02:53:03Z

Icrespin: /* Data and Files */ copied and pasted from team members' pages since info was shared between each other

Icrespin Journal Week 12/13

2019-11-26T02:51:34Z

Icrespin: /* Methods/Results: In Progress */ added info

FunGals Deliverables

2019-11-26T02:39:30Z

Icrespin: added template

{{template:FunGals}}

==Checklist==
# Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents)
# Group Report (''.doc'', ''.docx'' or ''.pdf'' file)
# Individual statements of work, assessments, reflections (wiki page, ''.doc'', ''.docx'', ''.pdf'', or e-mailed to Dr. Dahlquist)
# Group PowerPoint presentation (given on Tuesday, December 10, ''.ppt'', ''.pptx'' or ''.pdf'' file)
# Sample-data relationship table in Excel (''.xlsx'')
# Excel spreadsheet with ANOVA results/stem formatting (''.xlsx'')
# PowerPoint of ANOVA table, screenshots of stem results (''.pptx''), screenshot of black and white GRNsight input network and colored GRNsight output networks
# 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'') and output plots (''.jpg'') zipped together
# MS Access database, unified by the three teams with expression tables and metadata table(s) created (''.accdb'')
# ReadMe for the database that describes the design of the database, references the sources of the data, and has a [https://www.quackit.com/microsoft_access/microsoft_access_2016/howto/how_to_create_a_database_diagram_in_access_2016.cfm database schema diagram] (''.doc'', ''.docx'', ''.pdf'')
# Query design for populating a GRNmap input workbook from the database (screenshot of MS Access, or SQL code, ''.txt'')
# Electronic notebook corresponding to these the microarray results files ([[Week 12/13]] and [[Week 15]]) to 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.

==Group Report==

===Title===

===Introduction===

===Methods/Results/Discussion===

====Data Analysts====

====Coder====

====Quality Assurance====

===Conclusion===

==Powerpoint Presentation==

==Individual Assessment and Reflection==

===Michael Armas===

==== 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 Final 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?

===Kaitlyn Nguyen===

==== 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 Final 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?

===Emma Young===

==== 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 Final 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?

===Iliana Crespin===

==== 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 Final 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?

==Acknowledgments==

==References==

[[Category: Group Projects]]

FunGals Deliverables

2019-11-26T02:22:11Z

Icrespin: added reflection

==Checklist==
# Organized Team deliverables wiki page (or other media (CD or flash drive) with table of contents)
# Group Report (''.doc'', ''.docx'' or ''.pdf'' file)
# Individual statements of work, assessments, reflections (wiki page, ''.doc'', ''.docx'', ''.pdf'', or e-mailed to Dr. Dahlquist)
# Group PowerPoint presentation (given on Tuesday, December 10, ''.ppt'', ''.pptx'' or ''.pdf'' file)
# Sample-data relationship table in Excel (''.xlsx'')
# Excel spreadsheet with ANOVA results/stem formatting (''.xlsx'')
# PowerPoint of ANOVA table, screenshots of stem results (''.pptx''), screenshot of black and white GRNsight input network and colored GRNsight output networks
# 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'') and output plots (''.jpg'') zipped together
# MS Access database, unified by the three teams with expression tables and metadata table(s) created (''.accdb'')
# ReadMe for the database that describes the design of the database, references the sources of the data, and has a [https://www.quackit.com/microsoft_access/microsoft_access_2016/howto/how_to_create_a_database_diagram_in_access_2016.cfm database schema diagram] (''.doc'', ''.docx'', ''.pdf'')
# Query design for populating a GRNmap input workbook from the database (screenshot of MS Access, or SQL code, ''.txt'')
# Electronic notebook corresponding to these the microarray results files ([[Week 12/13]] and [[Week 15]]) to 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.

==Group Report==

===Title===

===Introduction===

===Methods/Results/Discussion===

====Data Analysts====

====Coder====

====Quality Assurance====

===Conclusion===

==Powerpoint Presentation==

==Individual Assessment and Reflection==

===Michael Armas===

==== 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 Final 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?

===Kaitlyn Nguyen===

==== 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 Final 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?

===Emma Young===

==== 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 Final 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?

===Iliana Crespin===

==== 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 Final 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?

==Acknowledgments==

==References==

[[Category: Group Projects]]

Template:FunGals

2019-11-26T02:20:32Z

Icrespin: /* Information and Links */ removed names

=== Group Page ===
[https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/FunGals FunGals]

=== User Page ===
[[User:knguye66]]
[[User:marmas]]
[[User:Icrespin]]
[[User:eyoung20]]

=== Template Page ===

[[Template:FunGals]]

[[Category: Group Projects]]

=== Information and Links ===
{| class="wikitable" style="width: 100%; text-align: center"
! colspan="10"|FunGals Links
|-
! rowspan="2"|[[Main Page|BIOL Databases Main Page]]
! rowspan="2"|[[Fungals|FunGals: Project Overview Page]]
! rowspan="2"|[[Final Project Deliverables| Final Project Deliverables Requirements]]
! rowspan="2"|[[FunGals Deliverables|FunGals: Final Project Deliverables]]
|-
! Assignment Pages
| [[Week 11]]
| [[Week 12/13]]
| [[Week 15]]
|}

[[Category: Group Projects]]

* [https://pubs.acs.org/doi/10.1021/es015705v| Thiuram Article]

FunGals Deliverables

2019-11-26T02:14:25Z

Icrespin: added titles

FunGals Deliverables

2019-11-26T02:08:21Z

Icrespin: added new info