LMU BioDB 2019 - User contributions [en]

FunGals

2019-12-13T21:59:38Z

Marmas: /* Week 15 */ added my 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
#***I believe that the best thing we as a group did for the progress of this project was meeting up in person. Our in-person meetings in the lab we’re very productive; communicating over text or calling was always less fluid. What didn’t really work for me was being last minute on certain milestones or assignments. The desire to procrastinate is natural, but avoiding it should be a top priority to decrease stress towards the end of the project. However, I was always confident of actually getting the work done. In the future, I want to put getting things done early at the top of the priority list, making deadlines much less stressed and rushed. 
[[User:Marmas|Marmas]] ([[User talk:Marmas|talk]]) 13:59, 13 December 2019 (PST)
#**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]]
*[[media: 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]]
*[[media:Queries_Run_for_the_Red_Profile_in_Acess_Database.pptx|Query Designs Red Profile]]

== 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

2019-12-13T18:55:49Z

Marmas: /* Acknowledgments */ trying to fix holding

{{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
| '''Complete'''
|-
| 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==
*Group Report
*Group PowerPoint presentation
**[[Media:FunGals_Final_Presentation.pptx | Final Presentation]]
*Metadata Workbook
**[[Media:Metadata_Sheet_(1).xlsx | Sample-Data Relationship Table (Metadata Sheet)]]
*ANOVA results/STEM formatting
**[[media: Thiuram_yeast_experiment.xlsx| ANOVA Results/STEM formatting (.xlsx)]]
*Figure Slides
**[[Media:FunGals_Figures_Slides.pptx| Figures Slides]]
*Gene List and GO List
**[[media: FunGals_genelist.zip|Genelist from STEM]]
**[[media: FunGals_GOlist.zip|GOlist from STEM]]
*YEASTRACT "rank by TF" results
**[[media:Genelist_combined_profiles_FunGals.xlsx| YEASTRACT Rank by TF - Green and Red Profiles (.xlsx)]]
*GRNmap Input Workbooks
**[[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)]]
*GRNmap Output Workbooks
**[[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)]]
*MS Access Database
**[[media:FunGals_BioDB_CombinedDatabase_final.accdb.zip|Combined Database]]
*ReadMe
**[[media:FunGals_ReadMe.docx | ReadMe with Relationship Report]]
*Query Design Screenshot
**

==Individual Assessment and Reflection==

===Michael Armas===

==== Statement of Work ====

* Describe exactly what you did on the project.
** As a coder is was my responsibility to do the database work. I created the database in MS Access, the metadata sheets, and the read me. This included working with the database to organize and universalize the data with the other groups. For the final report, I wrote the Introduction for the paper as well as added methods concerning the creation of the database and a few concluding points about the facilitation of results through the database. The presentation was mostly formatted by some of the other group members, but I was able to help a lot with the explanation of data during the presentation. The whole group worked hard to help each other with what was to be said during the presentation as well! As the project manager, I organized meeting times and made sure the entire group was on top of milestones and deliverables. I feel as if my contribution, alongside the help of my fellow group members, helped the outcome of the final project.
* Provide references or links to artifacts of your work, such as:
** Wiki pages
***[[Marmas Week 11|Individual Journal Week 11]]
***[[Marmas Week 12/13|Individual Journal Week 12/13]]
***[[Marmas Week 15|Individual Journal Week 15]]
** Other files or documents
***Significant Files I produced or helped produce:
****[[Media:Metadata_Sheet_(1).xlsx | Sample-Data Relationship Table (Metadata Sheet)]]
****[[media:FunGals_BioDB_CombinedDatabase_final.accdb.zip|Combined Database]]
****[[media:FunGals_ReadMe.docx | ReadMe with Relationship Report]]
** Code or scripts
*** Not very applicable, but the database is outlined in the files above.

==== Assessment of Project ====

* Give an objective assessment of the success of your project workflow and teamwork.
**I felt as if my success during this project was very satisfying. Hearing from the DA's that the database worked successfully was great to hear that I was able to help out with the assessment of data. For the other components, I feel as if I held my weight very much so when writing for the paper or presenting to the class. I enjoyed being the project manager for this group and felt as if my organization of meetings and milestones helped keep the group on track!
* What worked and what didn't work?
** Meeting at certain times was great and it really helped to communicate in person rather than over text or call. This worked well with our team and I feel as if this was the most successful way to work. What I felt didn't work was sometimes leaving some assignments to the last minute. While we were able to get the work in on time always, it was stressful to be working sometimes until late into the night.
* What would you do differently if you could do it all over again?
** I would get started with things much earlier. I am a person that tries to avoid procrastination, but sometimes that doesn't go as planned. If I could encourage myself and others to get started early on this project, I would be much less stressed during finals week.
* Evaluate your team’s portion of the Final Project and Group Report in the following areas:
*# Content: What is the quality of the work?
*#* The quality of the work was great, I think we are all happy with how the project turned out and with our discoveries. Going through and organizing some pages gave the final touches to the presentation of the project to make it look clean.
*# Organization: Comment on the organization of the project and of your group's wiki pages.
*#* The pages are organized and easy to follow. Headers are established and a table of contents allowed for things to be found easily. Most importantly, our deliverables are all organized into a page that has different sections to find files that will be graded.
*# Completeness: Did your team achieve all of the project objectives? Why or why not?
*#* Yes, we did achieve all of the project objectives. As I type this, we are just finishing the final touches on the final report, and will be ready to turn in the assignment before 4:00pm on Friday.

==== Reflection on the Process ====

* What did you learn?
** With your head (biological or computer science principles)
***I learned a lot about bioinformatics, a field of study which I really knew nothing about. This field allows for the ability to do something that humans could never do. The efficiency of bioinformatics blows me away with how fast data can be analyzed.
** With your heart (personal qualities and teamwork qualities that make things work or not work)?
***I continue to develop interpersonal skills with people when doing group projects. Working with a group always comes with its set of challenges, but working through problems is what being human is all about! I really did enjoy working with this group!
** With your hands (technical skills)?
***Being able to work with MS Access and virtual machines is a skill I never thought I would need. However, I understand how the familiarity with MS Access and all of the bioinformatics software is valuable to employers in that field. These skills will absolutely be going on my CV!
* What lesson will you take away from this project that you will still use a year from now?
**I hope that my interpersonal skills with group members continues to develop. Working with groups will be something I absolutely do in the future. Additionally, maybe in the next year I will be working for a company that will need me to work with databases or bioinformatics.

===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)
[[User:Marmas|Marmas]] ([[User talk:Marmas|talk]]) 10:52, 13 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

2019-12-13T18:55:03Z

Marmas: /* Acknowledgments */ holding

{{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
| '''Complete'''
|-
| 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==
*Group Report
*Group PowerPoint presentation
**[[Media:FunGals_Final_Presentation.pptx | Final Presentation]]
*Metadata Workbook
**[[Media:Metadata_Sheet_(1).xlsx | Sample-Data Relationship Table (Metadata Sheet)]]
*ANOVA results/STEM formatting
**[[media: Thiuram_yeast_experiment.xlsx| ANOVA Results/STEM formatting (.xlsx)]]
*Figure Slides
**[[Media:FunGals_Figures_Slides.pptx| Figures Slides]]
*Gene List and GO List
**[[media: FunGals_genelist.zip|Genelist from STEM]]
**[[media: FunGals_GOlist.zip|GOlist from STEM]]
*YEASTRACT "rank by TF" results
**[[media:Genelist_combined_profiles_FunGals.xlsx| YEASTRACT Rank by TF - Green and Red Profiles (.xlsx)]]
*GRNmap Input Workbooks
**[[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)]]
*GRNmap Output Workbooks
**[[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)]]
*MS Access Database
**[[media:FunGals_BioDB_CombinedDatabase_final.accdb.zip|Combined Database]]
*ReadMe
**[[media:FunGals_ReadMe.docx | ReadMe with Relationship Report]]
*Query Design Screenshot
**

==Individual Assessment and Reflection==

===Michael Armas===

==== Statement of Work ====

* Describe exactly what you did on the project.
** As a coder is was my responsibility to do the database work. I created the database in MS Access, the metadata sheets, and the read me. This included working with the database to organize and universalize the data with the other groups. For the final report, I wrote the Introduction for the paper as well as added methods concerning the creation of the database and a few concluding points about the facilitation of results through the database. The presentation was mostly formatted by some of the other group members, but I was able to help a lot with the explanation of data during the presentation. The whole group worked hard to help each other with what was to be said during the presentation as well! As the project manager, I organized meeting times and made sure the entire group was on top of milestones and deliverables. I feel as if my contribution, alongside the help of my fellow group members, helped the outcome of the final project.
* Provide references or links to artifacts of your work, such as:
** Wiki pages
***[[Marmas Week 11|Individual Journal Week 11]]
***[[Marmas Week 12/13|Individual Journal Week 12/13]]
***[[Marmas Week 15|Individual Journal Week 15]]
** Other files or documents
***Significant Files I produced or helped produce:
****[[Media:Metadata_Sheet_(1).xlsx | Sample-Data Relationship Table (Metadata Sheet)]]
****[[media:FunGals_BioDB_CombinedDatabase_final.accdb.zip|Combined Database]]
****[[media:FunGals_ReadMe.docx | ReadMe with Relationship Report]]
** Code or scripts
*** Not very applicable, but the database is outlined in the files above.

==== Assessment of Project ====

* Give an objective assessment of the success of your project workflow and teamwork.
**I felt as if my success during this project was very satisfying. Hearing from the DA's that the database worked successfully was great to hear that I was able to help out with the assessment of data. For the other components, I feel as if I held my weight very much so when writing for the paper or presenting to the class. I enjoyed being the project manager for this group and felt as if my organization of meetings and milestones helped keep the group on track!
* What worked and what didn't work?
** Meeting at certain times was great and it really helped to communicate in person rather than over text or call. This worked well with our team and I feel as if this was the most successful way to work. What I felt didn't work was sometimes leaving some assignments to the last minute. While we were able to get the work in on time always, it was stressful to be working sometimes until late into the night.
* What would you do differently if you could do it all over again?
** I would get started with things much earlier. I am a person that tries to avoid procrastination, but sometimes that doesn't go as planned. If I could encourage myself and others to get started early on this project, I would be much less stressed during finals week.
* Evaluate your team’s portion of the Final Project and Group Report in the following areas:
*# Content: What is the quality of the work?
*#* The quality of the work was great, I think we are all happy with how the project turned out and with our discoveries. Going through and organizing some pages gave the final touches to the presentation of the project to make it look clean.
*# Organization: Comment on the organization of the project and of your group's wiki pages.
*#* The pages are organized and easy to follow. Headers are established and a table of contents allowed for things to be found easily. Most importantly, our deliverables are all organized into a page that has different sections to find files that will be graded.
*# Completeness: Did your team achieve all of the project objectives? Why or why not?
*#* Yes, we did achieve all of the project objectives. As I type this, we are just finishing the final touches on the final report, and will be ready to turn in the assignment before 4:00pm on Friday.

==== Reflection on the Process ====

* What did you learn?
** With your head (biological or computer science principles)
***I learned a lot about bioinformatics, a field of study which I really knew nothing about. This field allows for the ability to do something that humans could never do. The efficiency of bioinformatics blows me away with how fast data can be analyzed.
** With your heart (personal qualities and teamwork qualities that make things work or not work)?
***I continue to develop interpersonal skills with people when doing group projects. Working with a group always comes with its set of challenges, but working through problems is what being human is all about! I really did enjoy working with this group!
** With your hands (technical skills)?
***Being able to work with MS Access and virtual machines is a skill I never thought I would need. However, I understand how the familiarity with MS Access and all of the bioinformatics software is valuable to employers in that field. These skills will absolutely be going on my CV!
* What lesson will you take away from this project that you will still use a year from now?
**I hope that my interpersonal skills with group members continues to develop. Working with groups will be something I absolutely do in the future. Additionally, maybe in the next year I will be working for a company that will need me to work with databases or bioinformatics.

===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)
[[User:Marmas|Marmas]] ([[User talk:Marmas|talk]]) 10:52, 13 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

2019-12-13T18:52:46Z

Marmas: /* Acknowledgments */ Added sig

{{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
| '''Complete'''
|-
| 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==
*Group Report
*Group PowerPoint presentation
**[[Media:FunGals_Final_Presentation.pptx | Final Presentation]]
*Metadata Workbook
**[[Media:Metadata_Sheet_(1).xlsx | Sample-Data Relationship Table (Metadata Sheet)]]
*ANOVA results/STEM formatting
**[[media: Thiuram_yeast_experiment.xlsx| ANOVA Results/STEM formatting (.xlsx)]]
*Figure Slides
**[[Media:FunGals_Figures_Slides.pptx| Figures Slides]]
*Gene List and GO List
**[[media: FunGals_genelist.zip|Genelist from STEM]]
**[[media: FunGals_GOlist.zip|GOlist from STEM]]
*YEASTRACT "rank by TF" results
**[[media:Genelist_combined_profiles_FunGals.xlsx| YEASTRACT Rank by TF - Green and Red Profiles (.xlsx)]]
*GRNmap Input Workbooks
**[[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)]]
*GRNmap Output Workbooks
**[[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)]]
*MS Access Database
**[[media:FunGals_BioDB_CombinedDatabase_final.accdb.zip|Combined Database]]
*ReadMe
**[[media:FunGals_ReadMe.docx | ReadMe with Relationship Report]]
*Query Design Screenshot
**

==Individual Assessment and Reflection==

===Michael Armas===

==== Statement of Work ====

* Describe exactly what you did on the project.
** As a coder is was my responsibility to do the database work. I created the database in MS Access, the metadata sheets, and the read me. This included working with the database to organize and universalize the data with the other groups. For the final report, I wrote the Introduction for the paper as well as added methods concerning the creation of the database and a few concluding points about the facilitation of results through the database. The presentation was mostly formatted by some of the other group members, but I was able to help a lot with the explanation of data during the presentation. The whole group worked hard to help each other with what was to be said during the presentation as well! As the project manager, I organized meeting times and made sure the entire group was on top of milestones and deliverables. I feel as if my contribution, alongside the help of my fellow group members, helped the outcome of the final project.
* Provide references or links to artifacts of your work, such as:
** Wiki pages
***[[Marmas Week 11|Individual Journal Week 11]]
***[[Marmas Week 12/13|Individual Journal Week 12/13]]
***[[Marmas Week 15|Individual Journal Week 15]]
** Other files or documents
***Significant Files I produced or helped produce:
****[[Media:Metadata_Sheet_(1).xlsx | Sample-Data Relationship Table (Metadata Sheet)]]
****[[media:FunGals_BioDB_CombinedDatabase_final.accdb.zip|Combined Database]]
****[[media:FunGals_ReadMe.docx | ReadMe with Relationship Report]]
** Code or scripts
*** Not very applicable, but the database is outlined in the files above.

==== Assessment of Project ====

* Give an objective assessment of the success of your project workflow and teamwork.
**I felt as if my success during this project was very satisfying. Hearing from the DA's that the database worked successfully was great to hear that I was able to help out with the assessment of data. For the other components, I feel as if I held my weight very much so when writing for the paper or presenting to the class. I enjoyed being the project manager for this group and felt as if my organization of meetings and milestones helped keep the group on track!
* What worked and what didn't work?
** Meeting at certain times was great and it really helped to communicate in person rather than over text or call. This worked well with our team and I feel as if this was the most successful way to work. What I felt didn't work was sometimes leaving some assignments to the last minute. While we were able to get the work in on time always, it was stressful to be working sometimes until late into the night.
* What would you do differently if you could do it all over again?
** I would get started with things much earlier. I am a person that tries to avoid procrastination, but sometimes that doesn't go as planned. If I could encourage myself and others to get started early on this project, I would be much less stressed during finals week.
* Evaluate your team’s portion of the Final Project and Group Report in the following areas:
*# Content: What is the quality of the work?
*#* The quality of the work was great, I think we are all happy with how the project turned out and with our discoveries. Going through and organizing some pages gave the final touches to the presentation of the project to make it look clean.
*# Organization: Comment on the organization of the project and of your group's wiki pages.
*#* The pages are organized and easy to follow. Headers are established and a table of contents allowed for things to be found easily. Most importantly, our deliverables are all organized into a page that has different sections to find files that will be graded.
*# Completeness: Did your team achieve all of the project objectives? Why or why not?
*#* Yes, we did achieve all of the project objectives. As I type this, we are just finishing the final touches on the final report, and will be ready to turn in the assignment before 4:00pm on Friday.

==== Reflection on the Process ====

* What did you learn?
** With your head (biological or computer science principles)
***I learned a lot about bioinformatics, a field of study which I really knew nothing about. This field allows for the ability to do something that humans could never do. The efficiency of bioinformatics blows me away with how fast data can be analyzed.
** With your heart (personal qualities and teamwork qualities that make things work or not work)?
***I continue to develop interpersonal skills with people when doing group projects. Working with a group always comes with its set of challenges, but working through problems is what being human is all about! I really did enjoy working with this group!
** With your hands (technical skills)?
***Being able to work with MS Access and virtual machines is a skill I never thought I would need. However, I understand how the familiarity with MS Access and all of the bioinformatics software is valuable to employers in that field. These skills will absolutely be going on my CV!
* What lesson will you take away from this project that you will still use a year from now?
**I hope that my interpersonal skills with group members continues to develop. Working with groups will be something I absolutely do in the future. Additionally, maybe in the next year I will be working for a company that will need me to work with databases or bioinformatics.

===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)
[[User:Marmas|Marmas]] ([[User talk:Marmas|talk]]) 10:52, 13 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

2019-12-13T18:50:42Z

Marmas: /* Data and Files */ fixed typo

==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]]
*[[media: 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

2019-12-13T08:28:23Z

Marmas: /* Michael Armas */ added reflection

{{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
| '''Complete'''
|-
| 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==
*Group Report
*Group PowerPoint presentation
**[[Media:FunGals_Final_Presentation.pptx | Final Presentation]]
*Metadata Workbook
**[[Media:Metadata_Sheet_(1).xlsx | Sample-Data Relationship Table (Metadata Sheet)]]
*ANOVA results/STEM formatting
**[[media: Thiuram_yeast_experiment.xlsx| ANOVA Results/STEM formatting (.xlsx)]]
*Figure Slides
**[[Media:FunGals_Figures_Slides.pptx| Figures Slides]]
*Gene List and GO List
**[[media: FunGals_genelist.zip|Genelist from STEM]]
**[[media: FunGals_GOlist.zip|GOlist from STEM]]
*YEASTRACT "rank by TF" results
**[[media:Genelist_combined_profiles_FunGals.xlsx| YEASTRACT Rank by TF - Green and Red Profiles (.xlsx)]]
*GRNmap Input Workbooks
**[[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)]]
*GRNmap Output Workbooks
**[[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)]]
*MS Access Database
**[[media:FunGals_BioDB_CombinedDatabase_final.accdb.zip|Combined Database]]
*ReadMe
**[[media:FunGals_ReadMe.docx | ReadMe with Relationship Report]]
*Query Design Screenshot
**

==Individual Assessment and Reflection==

===Michael Armas===

==== Statement of Work ====

* Describe exactly what you did on the project.
** As a coder is was my responsibility to do the database work. I created the database in MS Access, the metadata sheets, and the read me. This included working with the database to organize and universalize the data with the other groups. For the final report, I wrote the Introduction for the paper as well as added methods concerning the creation of the database and a few concluding points about the facilitation of results through the database. The presentation was mostly formatted by some of the other group members, but I was able to help a lot with the explanation of data during the presentation. The whole group worked hard to help each other with what was to be said during the presentation as well! As the project manager, I organized meeting times and made sure the entire group was on top of milestones and deliverables. I feel as if my contribution, alongside the help of my fellow group members, helped the outcome of the final project.
* Provide references or links to artifacts of your work, such as:
** Wiki pages
***[[Marmas Week 11|Individual Journal Week 11]]
***[[Marmas Week 12/13|Individual Journal Week 12/13]]
***[[Marmas Week 15|Individual Journal Week 15]]
** Other files or documents
***Significant Files I produced or helped produce:
****[[Media:Metadata_Sheet_(1).xlsx | Sample-Data Relationship Table (Metadata Sheet)]]
****[[media:FunGals_BioDB_CombinedDatabase_final.accdb.zip|Combined Database]]
****[[media:FunGals_ReadMe.docx | ReadMe with Relationship Report]]
** Code or scripts
*** Not very applicable, but the database is outlined in the files above.

==== Assessment of Project ====

* Give an objective assessment of the success of your project workflow and teamwork.
**I felt as if my success during this project was very satisfying. Hearing from the DA's that the database worked successfully was great to hear that I was able to help out with the assessment of data. For the other components, I feel as if I held my weight very much so when writing for the paper or presenting to the class. I enjoyed being the project manager for this group and felt as if my organization of meetings and milestones helped keep the group on track!
* What worked and what didn't work?
** Meeting at certain times was great and it really helped to communicate in person rather than over text or call. This worked well with our team and I feel as if this was the most successful way to work. What I felt didn't work was sometimes leaving some assignments to the last minute. While we were able to get the work in on time always, it was stressful to be working sometimes until late into the night.
* What would you do differently if you could do it all over again?
** I would get started with things much earlier. I am a person that tries to avoid procrastination, but sometimes that doesn't go as planned. If I could encourage myself and others to get started early on this project, I would be much less stressed during finals week.
* Evaluate your team’s portion of the Final Project and Group Report in the following areas:
*# Content: What is the quality of the work?
*#* The quality of the work was great, I think we are all happy with how the project turned out and with our discoveries. Going through and organizing some pages gave the final touches to the presentation of the project to make it look clean.
*# Organization: Comment on the organization of the project and of your group's wiki pages.
*#* The pages are organized and easy to follow. Headers are established and a table of contents allowed for things to be found easily. Most importantly, our deliverables are all organized into a page that has different sections to find files that will be graded.
*# Completeness: Did your team achieve all of the project objectives? Why or why not?
*#* Yes, we did achieve all of the project objectives. As I type this, we are just finishing the final touches on the final report, and will be ready to turn in the assignment before 4:00pm on Friday.

==== Reflection on the Process ====

* What did you learn?
** With your head (biological or computer science principles)
***I learned a lot about bioinformatics, a field of study which I really knew nothing about. This field allows for the ability to do something that humans could never do. The efficiency of bioinformatics blows me away with how fast data can be analyzed.
** With your heart (personal qualities and teamwork qualities that make things work or not work)?
***I continue to develop interpersonal skills with people when doing group projects. Working with a group always comes with its set of challenges, but working through problems is what being human is all about! I really did enjoy working with this group!
** With your hands (technical skills)?
***Being able to work with MS Access and virtual machines is a skill I never thought I would need. However, I understand how the familiarity with MS Access and all of the bioinformatics software is valuable to employers in that field. These skills will absolutely be going on my CV!
* What lesson will you take away from this project that you will still use a year from now?
**I hope that my interpersonal skills with group members continues to develop. Working with groups will be something I absolutely do in the future. Additionally, maybe in the next year I will be working for a company that will need me to work with databases or bioinformatics.

===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

2019-12-13T07:50:49Z

Marmas: /* Checklist */ checked off a deliverabe

Marmas Week 15

2019-12-13T07:49:48Z

Marmas: /* Acknowledgments */ added a reference

{{marmas}}
==Purpose==
The main directives for this week involves the finalization of the project. Deliverables will be organzied into the deliverables page and remaining steps will be completed. The database will be made and a relationship report will be formed to show the the relationships between the tables in the database. The final presentation will be made to presnet the findings of this group. Finally, a final report will be written as documentation of our findings.

==Account of Activity==
===Week 11===
*A Metadata sheet was made with assistance from [[User:Msamdars|Mihir Samdarshi]] and [[User:Dmadere| DeLisa Madere]]. This sheet is used to show ana analyze the relationship between the samples and the corresponding data. Categories remain universal between all groups.
**Categories chosen for the metadata sheet were article title, PubMed ID, authors, yeast strain, treatment, concentration value, concentration units, time value, and time units.
**The Metadata sheet can be found in the Data and Files section of this page.
*To categorize columns, a nomenclature was chosen amongst the three coders/designers to reflect ample information of each sample. The nomenclature for the samples is yeastStrain_treatmentOrMutation_concentrationWithUnits_LogFC_t+timeWithUnits-replicate.
**For example, to title the column for the log fold change of first replicate of a sample treated with 75uM Thiuram for 15 minutes would be S288C_thiuram_75uM_LogFC_t15m-1.
===Week 12/13===
*Worked with Data Analysts to add in column headers according to the nomenclature decided on last week.
*A new sheet was created called "Citations". This sheet listed the papers and the data of article including PubMed ID and Authors. This was made separate from the sample to data sheet.
*The metadata sheet was updated to accommodate PubMed ID of each article to be the link between sheets.
*Little was done on the actual "coding" side of the data analysis. This is due to the proactive and helpful data analysts [[User:knguye66|Kaitlyn]] and [[User:eyoung20|Emma]] who were more ahead than expected. This has put the project ahead of schedule
**Thus, we are waiting for STEM analysis to be performed on 11/26 in the computer lab. All worksheets have been checked and are ready to be analyzed on STEM.
*Additionally, thanks to [[User:msamdars|Mihir Samdarshi]], a private server using Microsoft Azure was set up so that MS Access can be used away from the computer lab.
*Tomorrow (11/26) a database will be started in class to further progress the project
===Week12/13 (cont.)===
*Database started on MS Access.
*Metadata sheet was separated into references and samples to data.
**New sheets now account for PubMed ID as primary connection between sample to data sheet and references sheet.
*From the MS Access file on the wiki (including Dr. Dahlquist's data and production and degradation rates), names for each sheet were changed to include the author and the year.
** The FunGals' expression sheet title changed to include the author of the paper and the publication year. Other members in the Coder/Designer Guild have done the same.
*Relationship Schema is started but not finished, connections need to be made between expression data and the two metadata sheets.
===Week 15===
*The MS database is complete.
** Databases was merged between the FunGals data and the data of the other in-class groups.
** The Dahlquist Lab data was also included, including all of their expression tables
** production and degradation rates tables were also included.
** To relate these tables, the systematic gene names were used as the linkage between all tables.
*The relationship report was made using the relationship tools in MS Access.
**The relationship report included all of the expression tables, the production rates and degradation rates tables, and the two metadata tables.
** The expression data tables, the production rates table, and the degradation rates table were shown to be linked by the systematic gene names.
***For the expression data tables, the systematic gene names were in the column titled "ID"
**For the production rates and degradation rates tables, the systematic gene names were in the column titled "systematic name."
**The two metadata tables are linked by the "PubMed ID" column, which contains consistent values between both tables.
** The whole relationship report is a separated graph. The metadata sheets show no connection to the expression data tables, the production rates table, and the degradation rates table.
***This is due to the difficulty in finding an easy correlation that intertwines the tables. However, a ReadMe is written to explain the correlation between the metadata tables and data tables.
*A ReadMe was written to understand the the database as a whole, including its connections.
** The ReadMe includes an image of the relationship report and an explanation of the universal column header format, which is considered to link the metadata tables to the data tables.
*Final Presenation was started, and will be presented next week.

==Data and Files==
*[[Media:Metadata_Sheet_(1).xlsx | Sample-Data Relationship Table (Metadata Sheet)]]
*[[Media:FunGals_Final_Presentation.pptx | Final Presentation]]
*[[media:FunGals_BioDB_CombinedDatabase_final.accdb.zip|Combined Database]]
*[[media:FunGals_ReadMe.docx | ReadMe with Relationship Report]]
*[[Media:FunGals_Final_Presentation.pptx | Final Presentation]]

==Conclusion==
The project is just beginning to wrap up. The database was completed in MS Access and linked together to find inputs for a GRNmap Input workbook. This part of the pipeline will give the resulting weighted adjacency matrix and gene regulatory network. A relationship report was created to show how the database is linked. This was performed using the relationship tools found in MS Access. These tools allowed for the linkage between data tables, and between the metadata sheets. A ReadMe document was created to explain these relationships formed in the database. Additionally, it explains how the metadata tables are linked to the rest of the data tables. Finally, a the final presentation and report are being started for turn-in next week.

==Acknowledgments==
*I would like to acknowledge Dr. Dahlquist for her help with the formation of the database and understanding the expression data.
*I would like to acknowledge my group, the [[FunGals]], who are helping with reaching deadlines and understanding the material.
*I would like to acknowledge Mihir Samdarshi and Delisa for helping with the creation of the database.
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]]) 21:37, 20 November 2019 (PST)
==References==
*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.

Marmas Week 12/13

2019-12-13T07:49:26Z

Marmas: /* Acknowledgments */ added a reference

{{marmas}}
==Purpose==
The purpose of the project is to analyze the mircroarray data of a previously performed experiment titled "Effects of the Pesticide Thiuram: Genome-wide Screening of Indicator Genes by Yeast DNA Microarray" (Kitagawa et al., 2002). The group will begin data analysis and organization of deliverables. Milestones are established to keep up with the workload due by the end of the semester. Milestones are can be found on the [[FunGals|Fungals Team Page]]. For the week of November 18th, the Coder/Designer guild will establish a meta data sheet and universalize column header nomenclature.

==Account of Activity==
===Week 11===
*A Metadata sheet was made with assistance from [[User:Msamdars|Mihir Samdarshi]] and [[User:Dmadere| DeLisa Madere]]. This sheet is used to show ana analyze the relationship between the samples and the corresponding data. Categories remain universal between all groups.
**Categories chosen for the metadata sheet were article title, PubMed ID, authors, yeast strain, treatment, concentration value, concentration units, time value, and time units.
**The Metadata sheet can be found in the Data and Files section of this page.
*To categorize columns, a nomenclature was chosen amongst the three coders/designers to reflect ample information of each sample. The nomenclature for the samples is yeastStrain_treatmentOrMutation_concentrationWithUnits_LogFC_t+timeWithUnits-replicate.
**For example, to title the column for the log fold change of first replicate of a sample treated with 75uM Thiuram for 15 minutes would be S288C_thiuram_75uM_LogFC_t15m-1.
===Week 12/13===
*Worked with Data Analysts to add in column headers according to the nomenclature decided on last week.
*A new sheet was created called "Citations". This sheet listed the papers and the data of article including PubMed ID and Authors. This was made separate from the sample to data sheet.
*The metadata sheet was updated to accommodate PubMed ID of each article to be the link between sheets.
*Little was done on the actual "coding" side of the data analysis. This is due to the proactive and helpful data analysts [[User:knguye66|Kaitlyn]] and [[User:eyoung20|Emma]] who were more ahead than expected. This has put the project ahead of schedule
**Thus, we are waiting for STEM analysis to be performed on 11/26 in the computer lab. All worksheets have been checked and are ready to be analyzed on STEM.
*Additionally, thanks to [[User:msamdars|Mihir Samdarshi]], a private server using Microsoft Azure was set up so that MS Access can be used away from the computer lab.
*Tomorrow (11/26) a database will be started in class to further progress the project
===Week12/13 (cont.)===
*Database started on MS Access.
*Metadata sheet was separated into references and samples to data.
**New sheets now account for PubMed ID as primary connection between sample to data sheet and references sheet.
*From the MS Access file on the wiki (including Dr. Dahlquist's data and production and degradation rates), names for each sheet were changed to include the author and the year.
** The FunGals' expression sheet title changed to include the author of the paper and the publication year. Other members in the Coder/Designer Guild have done the same.
*Relationship Schema is started but not finished, connections need to be made between expression data and the two metadata sheets.

==Data and Files==
[[Media:Metadata_Sheet_(1).xlsx | Metadata Sheet]]
*Note: This data sheet is current as of 11:00pm on Nov 25, 2019. Other groups will add information at another time.

==Conclusion==
The metadata sheet was made alongside [[User:Msamdars|Mihir Samdarshi]] and [[User:Dmadere| DeLisa Madere]]. In conjunction with these two members of the Code/Designer guild to decide on the column headers that would be used for the expression data sheets. Two metadata sheets were made, one consisting of the metadata for each of the examined articles, and one consisting of the sample information. Finally, the database was started in MS Access, but many problems arose, so this will be performed next week.
==Acknowledgments==
*I would like to acknowledge Dr. Dahlquist for her continous help with this project.
*I would like to acknowledge my group, the [[FunGals]], who are helping with reaching deadlines and understanding the material.
*I would like to acknowledge Mihir Samdarshi for explaining Metadata to me and how to create one.
'''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]]) 21:37, 20 November 2019 (PST)
==References==
*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.

Marmas Week 11

2019-12-13T07:49:03Z

Marmas: /* References */ fixed type

{{marmas}}
==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]]

==Purpose==
The purpose of this assignment is to begin in-depth analysis of the paper assigned for the final project and presentation of BIOL 367-01. The article assigned to this group, FunGals, is titled "Effects of the Pesticide Thiuram: Genome-wide Screening of Indicator Genes by Yeast DNA Microarray." This week, ten unknown terms from the paper will be defined for clarification, and an outline of the article will be posted to summarize the reading.

==Ten Terms==
#'''Thiuram''': "The counting and/or measuring of cells in a fluid suspension" (Oxford Dictionary of Biochemistry and Molecular Biology, 2008).
#'''Mutagen''': "Any physical or chemical agent that is capable of increasing the frequency of mutation above the spontaneous, background level"(Oxford Dictionary of Biochemistry and Molecular Biology, 2008).
#'''Disulfiram''': "Trivial name for tetraethylthiuram disulfide; bis(diethylthiocarbamoyl) disulfide; a drug used to deter alcohol abuse in the treatment of alcoholism. Alcohol ingestion after disulfiram causes vasomotor disturbances, nausea, vomiting, and even unconsciousness and death. It acts by inhibiting the enzyme acetaldehyde dehydrogenase and hence slows the removal of acetaldehyde. It occurs naturally in the otherwise edible fruit body of the agaric mushroom Coprinus atramentarius. One proprietary name is Antabuse" (Oxford Dictionary of Biochemistry and Molecular Biology, 2008).
#'''Erythrocyte''': "A mature red blood cell; in mammals it is non‐nucleated and lacks mitochondria. Erythrocytes contain, but are no longer capable of synthesizing, hemoglobin and they function in the transport of oxygen. Mammalian erythrocytes obtain energy from anaerobic glycolysis and also metabolize glucose via the phosphogluconate pathway"(Oxford Dictionary of Biochemistry and Molecular Biology, 2008).
#'''Cytometry''': "The counting and/or measuring of cells in a fluid suspension"(Oxford Dictionary of Biochemistry and Molecular Biology, 2008).
#'''Glutathione''': "A tripeptide that is widely distributed in most if not all cells. It acts as a coenzyme for some enzymes and as an antioxidant in the protection of sulfhydryl groups in enzymes and other proteins; it has a specific role in the reduction of hydrogen peroxide and oxidized ascorbate, and it participates in the γ ‐glutamyl cycle. Oxidation links two molecules by a disulfide bond (represented as GSSG). For clarity, glutathione is sometimes termed reduced glutathione (or the reduced form of glutathione). It is involved in the synthesis of certain leukotrienes"(Oxford Dictionary of Biochemistry and Molecular Biology, 2008).
#'''Glutathione Dehydrogenase''': "An enzyme that catalyses the reduction by two molecules of glutathione of dehydroascorbate to form oxidized glutathione and ascorbate"(Oxford Dictionary of Biochemistry and Molecular Biology, 2008).
#'''Base Excision Repair''': "One of the intracellular mechanisms for the repair of DNA lesions (single‐strand breaks, damaged bases, etc.). It occurs in the following stages: (1) recognition of the damaged region; (2) removal of the damaged oligonucleotide by two enzymic nucleolytic reactions (excision); (3) synthesis by DNA polymerase of the excised oligonucleotide using the second (intact) DNA strand as template; and (4) covalent joining by DNA ligase of the newly synthesized segment to the existing ends of the originally damaged DNA strand. The process is light‐independent"(Oxford Dictionary of Biochemistry and Molecular Biology, 2008).
#'''Transformant''': "A bacterial cell that has undergone transformation, i.e. one that contains integrated donor genes that can be detected by plating on media selective for some or all of the donor genes"(Oxford Dictionary of Biochemistry and Molecular Biology, 2008).
#'''Oxidative Stress''': "A state of metabolic imbalance within cells that favours pro‐oxidant substances (e.g. superoxide, hydrogen peroxide, hypochlorous acid, nitric oxide, peroxynitrite) rather than antioxidants (e.g. glutathione, ascorbic acid) and antioxidant enzyme systems (e.g. superoxide dismutases, catalase). This leads to oxidative damage to all classes of the major biomolecules. Depending on the degree of imbalance, a cell may die or it might survive in a changed state. Such stress can be important in causing a wide variety of degenerative states, including atherosclerosis, ischemia/reperfusion injury in heart and brain, mutagenesis, and chronic inflammatory disease"(Oxford Dictionary of Biochemistry and Molecular Biology, 2008).

==Article Outline==
# What is the main result presented in this paper?
#* This paper showed that the DNA microarray data is used to understand toxicity of chemicals in the environment. Specifically, YKL071W, YCR102C, YLR303W, YLL057C were selected for in the resulting microarray data and used for the promoted activity assay. The thiuram treatment directly affected the promoted of these genes. These results mean that this technique can be used for the selection of biomarkers.
# What is the importance or significance of this work?
#* With the discoveries from the microarray data, these techniques can be used to find biomarkers for thiuram. By characterizing the toxicity in yeast cells treated with thiuram, yeast will serve as a biomarker as its levels of toxicity can be observed to see the presence of thiuram in an environment.
# What were the limitations in previous studies that led them to perform this work?
#*Previous studies have shown that the thiuram pesticide is a potentially toxic chemical. Other studies have shown the effects of thiuram on yeast, but its toxic effects have not been observed using a DNA microarray experiment.
# How did they treat the yeast cells (what experiment were they doing?)
#* ''Saccharomyces cerevisiae'' S288C was the strain used for analysis of this experiment. Yeast cultures (OD_660 = 1.0) were treated with 300µL of 50mM thiuram. Samples were prepared that differed by the amount of time allowed to grow in the mixture. These times varied from 15 minutes to 2 hours, after which, the cells were harvested using centrifugation. RNA was extracted by hot-phenol method and purified using a Oligotex-dT30 mRNA purification kit.
# What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
#* The researchers used ''Saccaromyces cerevisiae'' S288C as the experimental strain. According to Engel et al., S288C is a haploid yeast strain.
# What media did they grow them in? What temperature? What type of incubator? For how long?
#* The yeast cells were grown in a YPD media at 25˚C overnight. For incubation, a Biomek 2000 Laboratory Automation Workstation from Beckman Counter, Inc. was used at 25˚C.
# What controls did they use?
#* The control used for this experiment was simply not treated with the thiuram pesticide. Additionally, the control was labeled with a Cy3 fluorescent label, while the thiuram-treated samples were labeled with a Cy5 fluorescent label.
# How many replicates did they perform per treatment or timepoint?
#* The replicates differed in the time treated with thiuram before cell harvesting. The samples were treated for timepoints between 15 minutes and 2 hours in increments of 15 minutes. However, the most discussed results come from the control group (0 minutes), the 30 minute group, and the 120 minute group.
# What method did they use to prepare the RNA, label it and hybridize it to the microarray?
#* RNA was extracted by using a hot-phenol method, and poly(A)+ RNA was purified from about 400µg of RNA using a Oligotex dT30 mRNA purification kit. At least 4µg of mRNa and a 0.4µM oligo dT primer were denatured at 70˚C for 5 minutes. This produced the labeled cDNA. Hybridiation onto the DNA microarray was carried out at 65˚C for 24 to 48 hours, after which, the microarray slides were washed with wash buffer twice and rincsed with SCC, centrifuged, and dried.
# What mathematical/statistical method did they use to analyze the data?
#* Mathematical and statistical methods were not used to analyze the data. However, much of the analysis was performed using Munich Information Center for Protein Sequences (MIPS), a yeast database.
# Are the data publicly available for download? From which web site?
#* The data for this article was not found
#Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.
#* What do the X and Y axes represent?
#** Figure 1A: OD_650 versus Time(hours)
#** Figure 1B: Relative growth for 2 hours (%) versus Concentration of thiuram (µM)
#** Figure 2: Intensity of Cy5 versus Intensity of Cy3
#** Figure 3B: MIPS Classifications versus number of induced genes
#** Figure 4B: MIPS Classifications versus number of repressed genes
#* How were the measurements made?
#** Figure 1A: Yeast growth was measured by comparing OD_650 at different thiuram treatment levels over time.
#** Figure 1B: Yeast growth was measured comparatively by percentage by concentration of thiuram at OD = 1.
#** Figure 2: All three graphs measure the fluorescence of each label compared to the control Cy3 tag. this was measured by the intensities represented by the DNA microarray experiments.
#** Figure 3A: The overlapping of genes induced by each treatment. Acquired using databases analysis.
#** Figure 3B: Using MIPS, classifications are determined for the function of each gene. This is then compared to the levels of induction.
#** Figure 4A: The overlapping of genes repressed by each treatment. Acquired using databases analysis.
#** Figure 4B:Using MIPS, classifications are determined for the function of each gene. This is then compared to the levels of repression.
#* What trends are shown by the plots and what conclusions can you draw from the data?
#** Figure 1A: Samples treated with little thiuram increased in ocular density, while those treated with more thiuram struggled to increase in ocular density.
#** Figure 1B: Relative growth decreases as concentration of thiuram increases.
#** Figure 2: In all three graphs, the intensity of Cy5 increases as the intensity of Cy3 increases.
#** Figure 3A: As more time elapses, the more genes are induced. While some induced genes overlap with different time increments, some genes are not induced as time progresses.
#** Figure 3B: The MIPS Classifications individually increase as time progresses. This graph only shows time increments at 30 minutes and 120 minutes.
#** Figure 4A: As more time elapses, the more genes are repressed. While some repressed genes overlap with different time increments, some genes are not repressed as time progresses.
#** Figure 4B: The MIPS Classifications individually increase as time progresses. This graph only shows time increments at 30 minutes and 120 minutes.
# How does this work compare with previous studies?
#* Previous studies have looked at the toxicity of thiuram, but none have observed the toxicity on the classification of gene function via DNA microarray analysis. From this, the effects of thiuram on yeast can be used as a biomarker to detect an environment polluted with thiuram.
# What are the important implications of this work?
#* When testing to see if an environment is polluted with thiuram, the gene regulation of the biomass in the surrounding area can be observed using DNA microarray analysis.
# What future directions should the authors take?
#* This experiment has identified a biomarker for thiuram pollution in an environment. The researchers should continue the research in other pesticides. It is important to realize that pesticide pollution does not only stem from one type of pesticide. The applications of DNA microanalysis are vast and can be used to further pollution identification.
# Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?
#* I believe that this paper was, for the most part, very straight forward and understandable. There were very few words that I was unable to understand, which is great when readers are not completely on board with the field of study. Some of the figures and graphs are poorly labeled, which made their analysis somewhat difficult. While the methods section was extensive, I felt lost at times when trying to reference this section with the figures and tables in the results section.
==Annotated Bibliography==
#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
#*PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/?term=Exposure+to+the+lampricide+TFM+elicits+an+environemental+stress+response+in+yeast
#*PubMed Central: N/A
#*Publisher Full Text (HTML): https://academic.oup.com/femsyr/article/19/1/foy121/5184468
#*Publisher Full Text (PDF): https://academic.oup.com/femsyr/article-pdf/19/1/foy121/27073366/foy121.pdf
#*Copyright: 2019 Federation of European Microbiological Societies
#*Article is not open access, LMU pays for a substriction to this publisher and allows access to students and faculty.
#*Availablity: in print and online
#*Publisher: Oxford Academic, non-profit, not a member of the OAPA.
#*Journal started in April of 2001
#*Peer Reviewed Articles: Yes
#*Editorial Board: https://academic.oup.com/femsyr/pages/Editorial_Board
#*Impact Factor: 2.458
#*Primary research article
#*Data available at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE101178

#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
#*PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/26404761
#*PubMed Central: N/A
#*Publisher Full Text (HTML): https://link.springer.com/article/10.1007/s00204-015-1592-8
#*Publisher Full Text (PDF): https://link.springer.com/content/pdf/10.1007%2Fs00204-015-1592-8.pdf
#*Copyright: Springer-Verlag Berlin Heidelberg 2015
#*This Article is not available to the public. LMU has paid for access to Springer Link for the article.
#*Availability: In print and online
#*Publisher: Springer Nature, for-profit, not a member of the OAPA
#*Journal Started in 1930
#*Peer Reveiwed Articles: Yes
#*Editorial board: https://www.springer.com/journal/204/editors
#*Impact Factor: 5.741
#*Primary Research Article
#*Data available at: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?token=olixoosedvmdnqr&acc=GSE66918
*Database Search with Database Tools
**PubMed
*** I used keywords "microarray data" and "toxicity."
*** When using these keywords, I found that there were many articles that came up. I had to do some searching to find articles I wanted to use. 1130 results came up.
**Google Scholar
***I used keywords "microarray data" and "toxicity," but this time I added "yeast."
*** After trying to use the same keywords that I used on PubMed, I added the keyword "yeast" to narrow down the search. Google is much more vast in data that PubMed, and it gave me about 59,000 results.
**Web of Science
***I once again used keywords "microarray data," "toxicity," and "yeast."
***These keywords were the same as the ones I chose to use on Google Scholar as I wanted to use these keywords on a smaller database. Web of Science pulled up 23 results.
*Advanced search functions
**PubMed
***I found the "title" category to the most useful. It allowed me to put in words I wanted to find in a title and brought them accurately.
**Google Scholar
*** While I really liked Google Scholar's normal search function and its interface as a whole, I was not too fond of it's advanced search function. I found it too specific on search parameters I didn't want to use, and lacking in those I did want to use, such as the ability to specifically search the title or abstract.
**Web of Science
***The different options for the advanced search on Web of Science were vast and specific. It even gave the option to search in different languages. Additionally, they have different tabs for author and cited reference searches.

*Reflect
**Keywords have always been my preffered way to search for an article. I can keep refining my search of keywords until I find something that I want. Using long phrases often makes the search complicated and inefficient. Choosing the right keywords that are broad enough to find articles is key to finding what you are looking for.
**Google Scholar's interface and data is unrivaled. It perfectly meshes with university credentials and is very easy to use. However, it's advanced search function was average at best. Web of Science lacks the amount of data that Google Scholar has, but its advanced search functions are unparalleled. I have yet to see a data base or search engine with the same specificity as Web of Science. In my opinion, PubMed was average all around. I really didn't use it too much and stuck mostly with Google Scholar. Since I am not a big advocate for using advanced search fields, I did not use Web of Science's advanced search since Google Scholar's regular search sufficed.

==Conclusion==
The assigned article was analyze to understand the purpose and significance of the article. The exercise of examining the article for unknown words made understanding the article much easier. Additionally, other supporting papers were found to further understand the current research being done in microarray analysis involving toxicity and stress. This article is now more understood and the purpose for our bioinformatics study can progress with confidence.

==Acknowledgments==
* I would like to acknowledge Dr. Dahlquist for the assistance with organization and the lecture about this group project.
* I would like to acknowledge my group, the [[FunGals]], for their continued support. Team members other than myself are Kaitlyn Nguyen, Emma Young, and Iliana Crespin.
'''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]]) 23:39, 13 November 2019 (PST)

==References==
*Engel, S. R., Dietrich, F. S., Fisk, D. G., Binkley, G., Balakrishnan, R., Costanzo, M. C., ... & Weng, S. (2014). The reference genome sequence of Saccharomyces cerevisiae: then and now. G3: Genes, Genomes, Genetics, 4(3), 389-398. doi: 10.1534/g3.113.008995.

*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.

*LMU BioDB 2019. (2019). Week 11. Retrieved November 12, 2019 from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_11.

*Smith, A. (2008). Oxford Dictionary of Biochemistry and Molecular Biology: 2nd Edition. Oxford University Press.

Marmas Week 15

2019-12-13T07:48:13Z

Marmas: /* Conclusion */ fixed a typo

Marmas Week 15

2019-12-13T07:48:02Z

Marmas: /* Conclusion */ added conclusion

{{marmas}}
==Purpose==
The main directives for this week involves the finalization of the project. Deliverables will be organzied into the deliverables page and remaining steps will be completed. The database will be made and a relationship report will be formed to show the the relationships between the tables in the database. The final presentation will be made to presnet the findings of this group. Finally, a final report will be written as documentation of our findings.

==Account of Activity==
===Week 11===
*A Metadata sheet was made with assistance from [[User:Msamdars|Mihir Samdarshi]] and [[User:Dmadere| DeLisa Madere]]. This sheet is used to show ana analyze the relationship between the samples and the corresponding data. Categories remain universal between all groups.
**Categories chosen for the metadata sheet were article title, PubMed ID, authors, yeast strain, treatment, concentration value, concentration units, time value, and time units.
**The Metadata sheet can be found in the Data and Files section of this page.
*To categorize columns, a nomenclature was chosen amongst the three coders/designers to reflect ample information of each sample. The nomenclature for the samples is yeastStrain_treatmentOrMutation_concentrationWithUnits_LogFC_t+timeWithUnits-replicate.
**For example, to title the column for the log fold change of first replicate of a sample treated with 75uM Thiuram for 15 minutes would be S288C_thiuram_75uM_LogFC_t15m-1.
===Week 12/13===
*Worked with Data Analysts to add in column headers according to the nomenclature decided on last week.
*A new sheet was created called "Citations". This sheet listed the papers and the data of article including PubMed ID and Authors. This was made separate from the sample to data sheet.
*The metadata sheet was updated to accommodate PubMed ID of each article to be the link between sheets.
*Little was done on the actual "coding" side of the data analysis. This is due to the proactive and helpful data analysts [[User:knguye66|Kaitlyn]] and [[User:eyoung20|Emma]] who were more ahead than expected. This has put the project ahead of schedule
**Thus, we are waiting for STEM analysis to be performed on 11/26 in the computer lab. All worksheets have been checked and are ready to be analyzed on STEM.
*Additionally, thanks to [[User:msamdars|Mihir Samdarshi]], a private server using Microsoft Azure was set up so that MS Access can be used away from the computer lab.
*Tomorrow (11/26) a database will be started in class to further progress the project
===Week12/13 (cont.)===
*Database started on MS Access.
*Metadata sheet was separated into references and samples to data.
**New sheets now account for PubMed ID as primary connection between sample to data sheet and references sheet.
*From the MS Access file on the wiki (including Dr. Dahlquist's data and production and degradation rates), names for each sheet were changed to include the author and the year.
** The FunGals' expression sheet title changed to include the author of the paper and the publication year. Other members in the Coder/Designer Guild have done the same.
*Relationship Schema is started but not finished, connections need to be made between expression data and the two metadata sheets.
===Week 15===
*The MS database is complete.
** Databases was merged between the FunGals data and the data of the other in-class groups.
** The Dahlquist Lab data was also included, including all of their expression tables
** production and degradation rates tables were also included.
** To relate these tables, the systematic gene names were used as the linkage between all tables.
*The relationship report was made using the relationship tools in MS Access.
**The relationship report included all of the expression tables, the production rates and degradation rates tables, and the two metadata tables.
** The expression data tables, the production rates table, and the degradation rates table were shown to be linked by the systematic gene names.
***For the expression data tables, the systematic gene names were in the column titled "ID"
**For the production rates and degradation rates tables, the systematic gene names were in the column titled "systematic name."
**The two metadata tables are linked by the "PubMed ID" column, which contains consistent values between both tables.
** The whole relationship report is a separated graph. The metadata sheets show no connection to the expression data tables, the production rates table, and the degradation rates table.
***This is due to the difficulty in finding an easy correlation that intertwines the tables. However, a ReadMe is written to explain the correlation between the metadata tables and data tables.
*A ReadMe was written to understand the the database as a whole, including its connections.
** The ReadMe includes an image of the relationship report and an explanation of the universal column header format, which is considered to link the metadata tables to the data tables.
*Final Presenation was started, and will be presented next week.

==Data and Files==
*[[Media:Metadata_Sheet_(1).xlsx | Sample-Data Relationship Table (Metadata Sheet)]]
*[[Media:FunGals_Final_Presentation.pptx | Final Presentation]]
*[[media:FunGals_BioDB_CombinedDatabase_final.accdb.zip|Combined Database]]
*[[media:FunGals_ReadMe.docx | ReadMe with Relationship Report]]
*[[Media:FunGals_Final_Presentation.pptx | Final Presentation]]

==Conclusion==
The project is just beginning to wrap up. The database was completed in MS Access and linked together to find inputs for a GRNmap Input workbook. This part of the pipeline will give the resulting weighted adjacency matrix and gene regulatory network. A relationship report was created to show how the database is linked. This was performed using the relationship tools found in MS Access. These tools allowed for the linkage between data tables, and between the metadata sheets. A ReadMe document was created to explain these relationships formed in the database. Additionally, it explains how the metadata tables are linked to the rest of the data tables. Finally, a the final presenation and report are being started for turn-in next week.

==Acknowledgments==
*I would like to acknowledge Dr. Dahlquist for her help with the formation of the database and understanding the expression data.
*I would like to acknowledge my group, the [[FunGals]], who are helping with reaching deadlines and understanding the material.
*I would like to acknowledge Mihir Samdarshi and Delisa for helping with the creation of the database.
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]]) 21:37, 20 November 2019 (PST)

Marmas Week 15

2019-12-13T07:25:38Z

Marmas: added methods for week 15

{{marmas}}
==Purpose==
The main directives for this week involves the finalization of the project. Deliverables will be organzied into the deliverables page and remaining steps will be completed. The database will be made and a relationship report will be formed to show the the relationships between the tables in the database. The final presentation will be made to presnet the findings of this group. Finally, a final report will be written as documentation of our findings.

==Account of Activity==
===Week 11===
*A Metadata sheet was made with assistance from [[User:Msamdars|Mihir Samdarshi]] and [[User:Dmadere| DeLisa Madere]]. This sheet is used to show ana analyze the relationship between the samples and the corresponding data. Categories remain universal between all groups.
**Categories chosen for the metadata sheet were article title, PubMed ID, authors, yeast strain, treatment, concentration value, concentration units, time value, and time units.
**The Metadata sheet can be found in the Data and Files section of this page.
*To categorize columns, a nomenclature was chosen amongst the three coders/designers to reflect ample information of each sample. The nomenclature for the samples is yeastStrain_treatmentOrMutation_concentrationWithUnits_LogFC_t+timeWithUnits-replicate.
**For example, to title the column for the log fold change of first replicate of a sample treated with 75uM Thiuram for 15 minutes would be S288C_thiuram_75uM_LogFC_t15m-1.
===Week 12/13===
*Worked with Data Analysts to add in column headers according to the nomenclature decided on last week.
*A new sheet was created called "Citations". This sheet listed the papers and the data of article including PubMed ID and Authors. This was made separate from the sample to data sheet.
*The metadata sheet was updated to accommodate PubMed ID of each article to be the link between sheets.
*Little was done on the actual "coding" side of the data analysis. This is due to the proactive and helpful data analysts [[User:knguye66|Kaitlyn]] and [[User:eyoung20|Emma]] who were more ahead than expected. This has put the project ahead of schedule
**Thus, we are waiting for STEM analysis to be performed on 11/26 in the computer lab. All worksheets have been checked and are ready to be analyzed on STEM.
*Additionally, thanks to [[User:msamdars|Mihir Samdarshi]], a private server using Microsoft Azure was set up so that MS Access can be used away from the computer lab.
*Tomorrow (11/26) a database will be started in class to further progress the project
===Week12/13 (cont.)===
*Database started on MS Access.
*Metadata sheet was separated into references and samples to data.
**New sheets now account for PubMed ID as primary connection between sample to data sheet and references sheet.
*From the MS Access file on the wiki (including Dr. Dahlquist's data and production and degradation rates), names for each sheet were changed to include the author and the year.
** The FunGals' expression sheet title changed to include the author of the paper and the publication year. Other members in the Coder/Designer Guild have done the same.
*Relationship Schema is started but not finished, connections need to be made between expression data and the two metadata sheets.
===Week 15===
*The MS database is complete.
** Databases was merged between the FunGals data and the data of the other in-class groups.
** The Dahlquist Lab data was also included, including all of their expression tables
** production and degradation rates tables were also included.
** To relate these tables, the systematic gene names were used as the linkage between all tables.
*The relationship report was made using the relationship tools in MS Access.
**The relationship report included all of the expression tables, the production rates and degradation rates tables, and the two metadata tables.
** The expression data tables, the production rates table, and the degradation rates table were shown to be linked by the systematic gene names.
***For the expression data tables, the systematic gene names were in the column titled "ID"
**For the production rates and degradation rates tables, the systematic gene names were in the column titled "systematic name."
**The two metadata tables are linked by the "PubMed ID" column, which contains consistent values between both tables.
** The whole relationship report is a separated graph. The metadata sheets show no connection to the expression data tables, the production rates table, and the degradation rates table.
***This is due to the difficulty in finding an easy correlation that intertwines the tables. However, a ReadMe is written to explain the correlation between the metadata tables and data tables.
*A ReadMe was written to understand the the database as a whole, including its connections.
** The ReadMe includes an image of the relationship report and an explanation of the universal column header format, which is considered to link the metadata tables to the data tables.
*Final Presenation was started, and will be presented next week.

==Data and Files==
*[[Media:Metadata_Sheet_(1).xlsx | Sample-Data Relationship Table (Metadata Sheet)]]
*[[Media:FunGals_Final_Presentation.pptx | Final Presentation]]
*[[media:FunGals_BioDB_CombinedDatabase_final.accdb.zip|Combined Database]]
*[[media:FunGals_ReadMe.docx | ReadMe with Relationship Report]]
*[[Media:FunGals_Final_Presentation.pptx | Final Presentation]]

==Conclusion==

==Acknowledgments==
*I would like to acknowledge Dr. Dahlquist for her help with the formation of the database and understanding the expression data.
*I would like to acknowledge my group, the [[FunGals]], who are helping with reaching deadlines and understanding the material.
*I would like to acknowledge Mihir Samdarshi and Delisa for helping with the creation of the database.
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]]) 21:37, 20 November 2019 (PST)

FunGals Deliverables

2019-12-13T07:00:06Z

Marmas: /* Data and Files */ removed a file

Marmas Week 15

2019-12-13T06:56:11Z

Marmas: /* Data and Files */ added files

Marmas Week 15

2019-12-13T06:55:05Z

Marmas: /* Data and Files */ added files

FunGals Deliverables

2019-12-13T06:49:10Z

Marmas: /* Data and Files */ fixed readme link

FunGals Deliverables

2019-12-13T06:48:52Z

Marmas: /* Data and Files */ added file

File:FunGals Figures Slides.pptx

2019-12-13T06:48:26Z

Marmas:

FunGals Deliverables

2019-12-13T06:46:02Z

Marmas: /* Data and Files */ added two more files

File:FunGals ReadMe.docx

2019-12-13T06:45:19Z

Marmas:

File:FunGals BioDB CombinedDatabase final.accdb.zip

2019-12-13T06:44:04Z

Marmas:

FunGals Deliverables

2019-12-13T06:43:07Z

Marmas: /* Data and Files */ organized deliverables

Marmas Week 15

2019-12-13T06:42:54Z

Marmas: /* Data and Files */ added some files

Marmas Week 15

2019-12-13T06:24:25Z

Marmas: /* Purpose */ added purpose

Marmas Week 15

2019-12-13T06:19:05Z

Marmas: copied over, edited headers, added acknoledgments

{{marmas}}
==Purpose==

==Account of Activity==
===Week 11===
*A Metadata sheet was made with assistance from [[User:Msamdars|Mihir Samdarshi]] and [[User:Dmadere| DeLisa Madere]]. This sheet is used to show ana analyze the relationship between the samples and the corresponding data. Categories remain universal between all groups.
**Categories chosen for the metadata sheet were article title, PubMed ID, authors, yeast strain, treatment, concentration value, concentration units, time value, and time units.
**The Metadata sheet can be found in the Data and Files section of this page.
*To categorize columns, a nomenclature was chosen amongst the three coders/designers to reflect ample information of each sample. The nomenclature for the samples is yeastStrain_treatmentOrMutation_concentrationWithUnits_LogFC_t+timeWithUnits-replicate.
**For example, to title the column for the log fold change of first replicate of a sample treated with 75uM Thiuram for 15 minutes would be S288C_thiuram_75uM_LogFC_t15m-1.
===Week 12/13===
*Worked with Data Analysts to add in column headers according to the nomenclature decided on last week.
*A new sheet was created called "Citations". This sheet listed the papers and the data of article including PubMed ID and Authors. This was made separate from the sample to data sheet.
*The metadata sheet was updated to accommodate PubMed ID of each article to be the link between sheets.
*Little was done on the actual "coding" side of the data analysis. This is due to the proactive and helpful data analysts [[User:knguye66|Kaitlyn]] and [[User:eyoung20|Emma]] who were more ahead than expected. This has put the project ahead of schedule
**Thus, we are waiting for STEM analysis to be performed on 11/26 in the computer lab. All worksheets have been checked and are ready to be analyzed on STEM.
*Additionally, thanks to [[User:msamdars|Mihir Samdarshi]], a private server using Microsoft Azure was set up so that MS Access can be used away from the computer lab.
*Tomorrow (11/26) a database will be started in class to further progress the project
===Week12/13 (cont.)===
*Database started on MS Access.
*Metadata sheet was separated into references and samples to data.
**New sheets now account for PubMed ID as primary connection between sample to data sheet and references sheet.
*From the MS Access file on the wiki (including Dr. Dahlquist's data and production and degradation rates), names for each sheet were changed to include the author and the year.
** The FunGals' expression sheet title changed to include the author of the paper and the publication year. Other members in the Coder/Designer Guild have done the same.
*Relationship Schema is started but not finished, connections need to be made between expression data and the two metadata sheets.
===Week 15===

==Data and Files==

==Conclusion==

==Acknowledgments==
*I would like to acknowledge Dr. Dahlquist for her help with the formation of the database and understanding the expression data.
*I would like to acknowledge my group, the [[FunGals]], who are helping with reaching deadlines and understanding the material.
*I would like to acknowledge Mihir Samdarshi and Delisa for helping with the creation of the database.
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]]) 21:37, 20 November 2019 (PST)

Marmas Week 12/13

2019-12-13T06:16:35Z

Marmas: added conclusion

Marmas Week 11

2019-12-13T06:04:19Z

Marmas: /* Conclusion */ added conclusion

{{marmas}}
==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]]

==Purpose==
The purpose of this assignment is to begin in-depth analysis of the paper assigned for the final project and presentation of BIOL 367-01. The article assigned to this group, FunGals, is titled "Effects of the Pesticide Thiuram: Genome-wide Screening of Indicator Genes by Yeast DNA Microarray." This week, ten unknown terms from the paper will be defined for clarification, and an outline of the article will be posted to summarize the reading.

==Ten Terms==
#'''Thiuram''': "The counting and/or measuring of cells in a fluid suspension" (Oxford Dictionary of Biochemistry and Molecular Biology, 2008).
#'''Mutagen''': "Any physical or chemical agent that is capable of increasing the frequency of mutation above the spontaneous, background level"(Oxford Dictionary of Biochemistry and Molecular Biology, 2008).
#'''Disulfiram''': "Trivial name for tetraethylthiuram disulfide; bis(diethylthiocarbamoyl) disulfide; a drug used to deter alcohol abuse in the treatment of alcoholism. Alcohol ingestion after disulfiram causes vasomotor disturbances, nausea, vomiting, and even unconsciousness and death. It acts by inhibiting the enzyme acetaldehyde dehydrogenase and hence slows the removal of acetaldehyde. It occurs naturally in the otherwise edible fruit body of the agaric mushroom Coprinus atramentarius. One proprietary name is Antabuse" (Oxford Dictionary of Biochemistry and Molecular Biology, 2008).
#'''Erythrocyte''': "A mature red blood cell; in mammals it is non‐nucleated and lacks mitochondria. Erythrocytes contain, but are no longer capable of synthesizing, hemoglobin and they function in the transport of oxygen. Mammalian erythrocytes obtain energy from anaerobic glycolysis and also metabolize glucose via the phosphogluconate pathway"(Oxford Dictionary of Biochemistry and Molecular Biology, 2008).
#'''Cytometry''': "The counting and/or measuring of cells in a fluid suspension"(Oxford Dictionary of Biochemistry and Molecular Biology, 2008).
#'''Glutathione''': "A tripeptide that is widely distributed in most if not all cells. It acts as a coenzyme for some enzymes and as an antioxidant in the protection of sulfhydryl groups in enzymes and other proteins; it has a specific role in the reduction of hydrogen peroxide and oxidized ascorbate, and it participates in the γ ‐glutamyl cycle. Oxidation links two molecules by a disulfide bond (represented as GSSG). For clarity, glutathione is sometimes termed reduced glutathione (or the reduced form of glutathione). It is involved in the synthesis of certain leukotrienes"(Oxford Dictionary of Biochemistry and Molecular Biology, 2008).
#'''Glutathione Dehydrogenase''': "An enzyme that catalyses the reduction by two molecules of glutathione of dehydroascorbate to form oxidized glutathione and ascorbate"(Oxford Dictionary of Biochemistry and Molecular Biology, 2008).
#'''Base Excision Repair''': "One of the intracellular mechanisms for the repair of DNA lesions (single‐strand breaks, damaged bases, etc.). It occurs in the following stages: (1) recognition of the damaged region; (2) removal of the damaged oligonucleotide by two enzymic nucleolytic reactions (excision); (3) synthesis by DNA polymerase of the excised oligonucleotide using the second (intact) DNA strand as template; and (4) covalent joining by DNA ligase of the newly synthesized segment to the existing ends of the originally damaged DNA strand. The process is light‐independent"(Oxford Dictionary of Biochemistry and Molecular Biology, 2008).
#'''Transformant''': "A bacterial cell that has undergone transformation, i.e. one that contains integrated donor genes that can be detected by plating on media selective for some or all of the donor genes"(Oxford Dictionary of Biochemistry and Molecular Biology, 2008).
#'''Oxidative Stress''': "A state of metabolic imbalance within cells that favours pro‐oxidant substances (e.g. superoxide, hydrogen peroxide, hypochlorous acid, nitric oxide, peroxynitrite) rather than antioxidants (e.g. glutathione, ascorbic acid) and antioxidant enzyme systems (e.g. superoxide dismutases, catalase). This leads to oxidative damage to all classes of the major biomolecules. Depending on the degree of imbalance, a cell may die or it might survive in a changed state. Such stress can be important in causing a wide variety of degenerative states, including atherosclerosis, ischemia/reperfusion injury in heart and brain, mutagenesis, and chronic inflammatory disease"(Oxford Dictionary of Biochemistry and Molecular Biology, 2008).

==Article Outline==
# What is the main result presented in this paper?
#* This paper showed that the DNA microarray data is used to understand toxicity of chemicals in the environment. Specifically, YKL071W, YCR102C, YLR303W, YLL057C were selected for in the resulting microarray data and used for the promoted activity assay. The thiuram treatment directly affected the promoted of these genes. These results mean that this technique can be used for the selection of biomarkers.
# What is the importance or significance of this work?
#* With the discoveries from the microarray data, these techniques can be used to find biomarkers for thiuram. By characterizing the toxicity in yeast cells treated with thiuram, yeast will serve as a biomarker as its levels of toxicity can be observed to see the presence of thiuram in an environment.
# What were the limitations in previous studies that led them to perform this work?
#*Previous studies have shown that the thiuram pesticide is a potentially toxic chemical. Other studies have shown the effects of thiuram on yeast, but its toxic effects have not been observed using a DNA microarray experiment.
# How did they treat the yeast cells (what experiment were they doing?)
#* ''Saccharomyces cerevisiae'' S288C was the strain used for analysis of this experiment. Yeast cultures (OD_660 = 1.0) were treated with 300µL of 50mM thiuram. Samples were prepared that differed by the amount of time allowed to grow in the mixture. These times varied from 15 minutes to 2 hours, after which, the cells were harvested using centrifugation. RNA was extracted by hot-phenol method and purified using a Oligotex-dT30 mRNA purification kit.
# What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
#* The researchers used ''Saccaromyces cerevisiae'' S288C as the experimental strain. According to Engel et al., S288C is a haploid yeast strain.
# What media did they grow them in? What temperature? What type of incubator? For how long?
#* The yeast cells were grown in a YPD media at 25˚C overnight. For incubation, a Biomek 2000 Laboratory Automation Workstation from Beckman Counter, Inc. was used at 25˚C.
# What controls did they use?
#* The control used for this experiment was simply not treated with the thiuram pesticide. Additionally, the control was labeled with a Cy3 fluorescent label, while the thiuram-treated samples were labeled with a Cy5 fluorescent label.
# How many replicates did they perform per treatment or timepoint?
#* The replicates differed in the time treated with thiuram before cell harvesting. The samples were treated for timepoints between 15 minutes and 2 hours in increments of 15 minutes. However, the most discussed results come from the control group (0 minutes), the 30 minute group, and the 120 minute group.
# What method did they use to prepare the RNA, label it and hybridize it to the microarray?
#* RNA was extracted by using a hot-phenol method, and poly(A)+ RNA was purified from about 400µg of RNA using a Oligotex dT30 mRNA purification kit. At least 4µg of mRNa and a 0.4µM oligo dT primer were denatured at 70˚C for 5 minutes. This produced the labeled cDNA. Hybridiation onto the DNA microarray was carried out at 65˚C for 24 to 48 hours, after which, the microarray slides were washed with wash buffer twice and rincsed with SCC, centrifuged, and dried.
# What mathematical/statistical method did they use to analyze the data?
#* Mathematical and statistical methods were not used to analyze the data. However, much of the analysis was performed using Munich Information Center for Protein Sequences (MIPS), a yeast database.
# Are the data publicly available for download? From which web site?
#* The data for this article was not found
#Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.
#* What do the X and Y axes represent?
#** Figure 1A: OD_650 versus Time(hours)
#** Figure 1B: Relative growth for 2 hours (%) versus Concentration of thiuram (µM)
#** Figure 2: Intensity of Cy5 versus Intensity of Cy3
#** Figure 3B: MIPS Classifications versus number of induced genes
#** Figure 4B: MIPS Classifications versus number of repressed genes
#* How were the measurements made?
#** Figure 1A: Yeast growth was measured by comparing OD_650 at different thiuram treatment levels over time.
#** Figure 1B: Yeast growth was measured comparatively by percentage by concentration of thiuram at OD = 1.
#** Figure 2: All three graphs measure the fluorescence of each label compared to the control Cy3 tag. this was measured by the intensities represented by the DNA microarray experiments.
#** Figure 3A: The overlapping of genes induced by each treatment. Acquired using databases analysis.
#** Figure 3B: Using MIPS, classifications are determined for the function of each gene. This is then compared to the levels of induction.
#** Figure 4A: The overlapping of genes repressed by each treatment. Acquired using databases analysis.
#** Figure 4B:Using MIPS, classifications are determined for the function of each gene. This is then compared to the levels of repression.
#* What trends are shown by the plots and what conclusions can you draw from the data?
#** Figure 1A: Samples treated with little thiuram increased in ocular density, while those treated with more thiuram struggled to increase in ocular density.
#** Figure 1B: Relative growth decreases as concentration of thiuram increases.
#** Figure 2: In all three graphs, the intensity of Cy5 increases as the intensity of Cy3 increases.
#** Figure 3A: As more time elapses, the more genes are induced. While some induced genes overlap with different time increments, some genes are not induced as time progresses.
#** Figure 3B: The MIPS Classifications individually increase as time progresses. This graph only shows time increments at 30 minutes and 120 minutes.
#** Figure 4A: As more time elapses, the more genes are repressed. While some repressed genes overlap with different time increments, some genes are not repressed as time progresses.
#** Figure 4B: The MIPS Classifications individually increase as time progresses. This graph only shows time increments at 30 minutes and 120 minutes.
# How does this work compare with previous studies?
#* Previous studies have looked at the toxicity of thiuram, but none have observed the toxicity on the classification of gene function via DNA microarray analysis. From this, the effects of thiuram on yeast can be used as a biomarker to detect an environment polluted with thiuram.
# What are the important implications of this work?
#* When testing to see if an environment is polluted with thiuram, the gene regulation of the biomass in the surrounding area can be observed using DNA microarray analysis.
# What future directions should the authors take?
#* This experiment has identified a biomarker for thiuram pollution in an environment. The researchers should continue the research in other pesticides. It is important to realize that pesticide pollution does not only stem from one type of pesticide. The applications of DNA microanalysis are vast and can be used to further pollution identification.
# Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?
#* I believe that this paper was, for the most part, very straight forward and understandable. There were very few words that I was unable to understand, which is great when readers are not completely on board with the field of study. Some of the figures and graphs are poorly labeled, which made their analysis somewhat difficult. While the methods section was extensive, I felt lost at times when trying to reference this section with the figures and tables in the results section.
==Annotated Bibliography==
#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
#*PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/?term=Exposure+to+the+lampricide+TFM+elicits+an+environemental+stress+response+in+yeast
#*PubMed Central: N/A
#*Publisher Full Text (HTML): https://academic.oup.com/femsyr/article/19/1/foy121/5184468
#*Publisher Full Text (PDF): https://academic.oup.com/femsyr/article-pdf/19/1/foy121/27073366/foy121.pdf
#*Copyright: 2019 Federation of European Microbiological Societies
#*Article is not open access, LMU pays for a substriction to this publisher and allows access to students and faculty.
#*Availablity: in print and online
#*Publisher: Oxford Academic, non-profit, not a member of the OAPA.
#*Journal started in April of 2001
#*Peer Reviewed Articles: Yes
#*Editorial Board: https://academic.oup.com/femsyr/pages/Editorial_Board
#*Impact Factor: 2.458
#*Primary research article
#*Data available at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE101178

#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
#*PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/26404761
#*PubMed Central: N/A
#*Publisher Full Text (HTML): https://link.springer.com/article/10.1007/s00204-015-1592-8
#*Publisher Full Text (PDF): https://link.springer.com/content/pdf/10.1007%2Fs00204-015-1592-8.pdf
#*Copyright: Springer-Verlag Berlin Heidelberg 2015
#*This Article is not available to the public. LMU has paid for access to Springer Link for the article.
#*Availability: In print and online
#*Publisher: Springer Nature, for-profit, not a member of the OAPA
#*Journal Started in 1930
#*Peer Reveiwed Articles: Yes
#*Editorial board: https://www.springer.com/journal/204/editors
#*Impact Factor: 5.741
#*Primary Research Article
#*Data available at: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?token=olixoosedvmdnqr&acc=GSE66918
*Database Search with Database Tools
**PubMed
*** I used keywords "microarray data" and "toxicity."
*** When using these keywords, I found that there were many articles that came up. I had to do some searching to find articles I wanted to use. 1130 results came up.
**Google Scholar
***I used keywords "microarray data" and "toxicity," but this time I added "yeast."
*** After trying to use the same keywords that I used on PubMed, I added the keyword "yeast" to narrow down the search. Google is much more vast in data that PubMed, and it gave me about 59,000 results.
**Web of Science
***I once again used keywords "microarray data," "toxicity," and "yeast."
***These keywords were the same as the ones I chose to use on Google Scholar as I wanted to use these keywords on a smaller database. Web of Science pulled up 23 results.
*Advanced search functions
**PubMed
***I found the "title" category to the most useful. It allowed me to put in words I wanted to find in a title and brought them accurately.
**Google Scholar
*** While I really liked Google Scholar's normal search function and its interface as a whole, I was not too fond of it's advanced search function. I found it too specific on search parameters I didn't want to use, and lacking in those I did want to use, such as the ability to specifically search the title or abstract.
**Web of Science
***The different options for the advanced search on Web of Science were vast and specific. It even gave the option to search in different languages. Additionally, they have different tabs for author and cited reference searches.

*Reflect
**Keywords have always been my preffered way to search for an article. I can keep refining my search of keywords until I find something that I want. Using long phrases often makes the search complicated and inefficient. Choosing the right keywords that are broad enough to find articles is key to finding what you are looking for.
**Google Scholar's interface and data is unrivaled. It perfectly meshes with university credentials and is very easy to use. However, it's advanced search function was average at best. Web of Science lacks the amount of data that Google Scholar has, but its advanced search functions are unparalleled. I have yet to see a data base or search engine with the same specificity as Web of Science. In my opinion, PubMed was average all around. I really didn't use it too much and stuck mostly with Google Scholar. Since I am not a big advocate for using advanced search fields, I did not use Web of Science's advanced search since Google Scholar's regular search sufficed.

==Conclusion==
The assigned article was analyze to understand the purpose and significance of the article. The exercise of examining the article for unknown words made understanding the article much easier. Additionally, other supporting papers were found to further understand the current research being done in microarray analysis involving toxicity and stress. This article is now more understood and the purpose for our bioinformatics study can progress with confidence.

==Acknowledgments==
* I would like to acknowledge Dr. Dahlquist for the assistance with organization and the lecture about this group project.
* I would like to acknowledge my group, the [[FunGals]], for their continued support. Team members other than myself are Kaitlyn Nguyen, Emma Young, and Iliana Crespin.
'''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]]) 23:39, 13 November 2019 (PST)

==References==
*Engel, S. R., Dietrich, F. S., Fisk, D. G., Binkley, G., Balakrishnan, R., Costanzo, M. C., ... & Weng, S. (2014). The reference genome sequence of Saccharomyces cerevisiae: then and now. G3: Genes, Genomes, Genetics, 4(3), 389-398. doi: 10.1534/g3.113.008995

*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

*LMU BioDB 2019. (2019). Week 11. Retrieved November 12, 2019 from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_11

*Smith, A. (2008). Oxford Dictionary of Biochemistry and Molecular Biology: 2nd Edition. Oxford University Press.

Template:Marmas

2019-12-13T05:45:50Z

Marmas: added link to week 15 and fixed link for 12\13

[[Category:Journal Entry]]
{| class="wikitable"
|-
! colspan = "3" |[[user:marmas| Michael Armas' User Page]]
|-
! Weekly Pages
! Individual Journals
! Shared Journals
|-
| [[Week 1| Week 1]]
| [[User:marmas|Individual Journal Week 1]]
| [[Class Journal Week 1|Class Journal Week 1]]
|-
| [[Week 2| Week 2]]
| [[marmas Week 2|Individual Journal Week 2]]
| [[Class Journal Week 2|Class Journal Week 2]]
|-
| [[Week 3| Week 3]]
| [[ASP1/YDR321W Week 3|Individual Journal Week 3]]
| [[Class Journal Week 3|Class Journal Week 3]]
|-
| [[Week 4| Week 4]]
| [[Marmas Week 4|Individual Journal Week 4]]
| [[Class Journal Week 4|Class Journal Week 4]]
|-
| [[Week 5| Week 5]]
| [[iDog Week 5|Individual Journal Week 5]]
| [[Class Journal Week 5|Class Journal Week 5]]
|-
| [[Week 6| Week 6]]
| [[Marmas Week 6|Individual Journal Week 6]]
| [[Class Journal Week 6|Class Journal Week 6]]
|-
| [[Week 7| Week 7]]
| [[Marmas Week 7|Individual Journal Week 7]]
| [[Class Journal Week 7|Class Journal Week 7]]
|-
| [[Week 8| Week 8]]
| [[Marmas Week 8|Individual Journal Week 8]]
| [[Class Journal Week 8|Class Journal Week 8]]
|-
| [[Week 9| Week 9]]
| [[Marmas Week 9|Individual Journal Week 9]]
| [[Class Journal Week 9|Class Journal Week 9]]
|-
| [[Week 10| Week 10]]
| [[Marmas Week 10|Individual Journal Week 10]]
| [[Class Journal Week 10|Class Journal Week 10]]
|-
| [[Week 11| Week 11]]
| [[Marmas Week 11|Individual Journal Week 11]]
| [[FunGals|Class Journal Week 11]]
|-
| [[Week 12/13| Week 12/13]]
| [[Marmas Week 12/13|Individual Journal Week 12/13]]
| [[FunGals|Class Journal Week 12/13]]
|-
| [[Week 15| Week 15]]
| [[Marmas Week 15|Individual Journal Week 15]]
| [[FunGals|Class Journal Week 15]]
|-
|}

FunGals Deliverables

2019-12-12T21:57:59Z

Marmas: /* Powerpoint Presentation */ deleted powerpoint presentatio

FunGals Deliverables

2019-12-12T21:57:44Z

Marmas: /* Group Report */ deleted group report

FunGals Deliverables

2019-12-12T21:57:12Z

Marmas: /* Checklist */ change some things to complete

Template:FunGals

2019-12-12T21:55:25Z

Marmas: /* User Page */ made it so just name appears

=== 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 Pages ===
[[User:knguye66|Knguye66]]
[[User:marmas|Marmas]]
[[User:Icrespin|Icrespin]]
[[User:eyoung20|Eyoung20]]

=== Template Page ===

[[Template:FunGals]]

[[Category: Group Projects]]

FunGals Deliverables

2019-12-10T19:57:37Z

Marmas: /* Data and Files */ fixed download link for ppt

FunGals Deliverables

2019-12-10T19:57:05Z

Marmas: /* Data and Files */ added final presentation

File:FunGals Final Presentation.pptx

2019-12-10T19:56:31Z

Marmas:

FunGals Deliverables

2019-12-08T22:02:20Z

Marmas: /* Checklist */ changed somethings to complete

Marmas Week 12/13

2019-12-05T06:11:42Z

Marmas: /* Account of Activity */ added to account of activity

{{marmas}}
==Purpose==
The purpose of the project is to analyze the mircroarray data of a previously performed experiment titled "Effects of the Pesticide Thiuram: Genome-wide Screening of Indicator Genes by Yeast DNA Microarray" (Kitagawa et al., 2002). The group will begin data analysis and organization of deliverables. Milestones are established to keep up with the workload due by the end of the semester. Milestones are can be found on the [[FunGals|Fungals Team Page]]. For the week of November 18th, the Coder/Designer guild will establish a meta data sheet and universalize column header nomenclature.

==Account of Activity==
===Week 11===
*A Metadata sheet was made with assistance from [[User:Msamdars|Mihir Samdarshi]] and [[User:Dmadere| DeLisa Madere]]. This sheet is used to show ana analyze the relationship between the samples and the corresponding data. Categories remain universal between all groups.
**Categories chosen for the metadata sheet were article title, PubMed ID, authors, yeast strain, treatment, concentration value, concentration units, time value, and time units.
**The Metadata sheet can be found in the Data and Files section of this page.
*To categorize columns, a nomenclature was chosen amongst the three coders/designers to reflect ample information of each sample. The nomenclature for the samples is yeastStrain_treatmentOrMutation_concentrationWithUnits_LogFC_t+timeWithUnits-replicate.
**For example, to title the column for the log fold change of first replicate of a sample treated with 75uM Thiuram for 15 minutes would be S288C_thiuram_75uM_LogFC_t15m-1.
===Week 12/13===
*Worked with Data Analysts to add in column headers according to the nomenclature decided on last week.
*A new sheet was created called "Citations". This sheet listed the papers and the data of article including PubMed ID and Authors. This was made separate from the sample to data sheet.
*The metadata sheet was updated to accommodate PubMed ID of each article to be the link between sheets.
*Little was done on the actual "coding" side of the data analysis. This is due to the proactive and helpful data analysts [[User:knguye66|Kaitlyn]] and [[User:eyoung20|Emma]] who were more ahead than expected. This has put the project ahead of schedule
**Thus, we are waiting for STEM analysis to be performed on 11/26 in the computer lab. All worksheets have been checked and are ready to be analyzed on STEM.
*Additionally, thanks to [[User:msamdars|Mihir Samdarshi]], a private server using Microsoft Azure was set up so that MS Access can be used away from the computer lab.
*Tomorrow (11/26) a database will be started in class to further progress the project
===Week12/13 (cont.)===
*Database started on MS Access.
*Metadata sheet was separated into references and samples to data.
**New sheets now account for PubMed ID as primary connection between sample to data sheet and references sheet.
*From the MS Access file on the wiki (including Dr. Dahlquist's data and production and degradation rates), names for each sheet were changed to include the author and the year.
** The FunGals' expression sheet title changed to include the author of the paper and the publication year. Other members in the Coder/Designer Guild have done the same.
*Relationship Schema is started but not finished, connections need to be made between expression data and the two metadata sheets.

==Data and Files==
[[Media:Metadata_Sheet_(1).xlsx | Metadata Sheet]]
*Note: This data sheet is current as of 11:00pm on Nov 25, 2019. Other groups will add information at another time.

==Conclusion==
==Acknowledgments==
*I would like to acknowledge Dr. Dahlquist for her continous help with this project.
*I would like to acknowledge my group, the [[FunGals]], who are helping with reaching deadlines and understanding the material.
*I would like to acknowledge Mihir Samdarshi for explaining Metadata to me and how to create one.
'''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]]) 21:37, 20 November 2019 (PST)

FunGals Deliverables

2019-12-03T23:55:29Z

Marmas: /* Checklist */ bolded things

FunGals

2019-12-03T23:44:08Z

Marmas: /* Week 15 */ added bullet point

==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===
*[[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

2019-12-03T23:43:53Z

Marmas: /* Week 15 */ added our database

==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===
[[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===

File:Marmas finalProject Expression-and-Degradation-rate-database 120319.zip

2019-12-03T23:43:15Z

Marmas:

FunGals

2019-11-26T21:11:54Z

Marmas: /* Milestones */ added the rest of milestones

==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]]

== 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

Marmas Week 12/13

2019-11-26T20:47:26Z

Marmas: /* Data and Files */ when adding the time stamp for the meta data sheet, I put nov 26th instead of nov 25th. sorry for the confusion!

Marmas Week 12/13

2019-11-26T07:19:24Z

Marmas: /* Week 12/13 */ fixed user names

Marmas Week 12/13

2019-11-26T07:18:52Z

Marmas: /* Week 12/13 */ added more to account of activity

Marmas Week 12/13

2019-11-26T07:15:17Z

Marmas: /* Data and Files */ updated time stamp for current version

Marmas Week 12/13

2019-11-26T07:14:52Z

Marmas: /* Data and Files */ added metadata sheet again, trouble updating

Marmas Week 12/13

2019-11-26T07:13:34Z

Marmas: /* Data and Files */ added new metadata sheet

File:Metadata Sheet (1).xlsx

2019-11-26T07:10:57Z

Marmas: