GENialOMICS

Weekly Group Assignments	Shared Group Journals	Project Links	Team Members
Week 10 Week 11 Week 12 Week 14 Week 15	GÉNialOMICS Week 10 GÉNialOMICS Week 11 GÉNialOMICS Week 12 GÉNialOMICS Week 14 GÉNialOMICS Week 15	GENialOMICS Home Page GENialOMICS Deliverables Gene Database Project Overview Instructions for Project Deliverables Project Manager Guild Page GenMAPP User Guild Page Quality Assurance Guild Page Coder Guild Page	Project Manager/Coder: Anu Varshneya Quality Assurance: Brandon Litvak GenMAPP User: Veronica Pacheco GenMAPP User: Kevin Wyllie

Week 10

• On November 3, 2015, GÉNialOMICS chose to create database for Burkholderia cenocepacia.
• On November 5, 2015, a journal detailing the complete genome of Burkholderia cenocepacia (strain J2315) titled The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients was found.

Week 11

Individual Goals and Progress

Weekly Goals and Progress
	Anu Varshneya	Brandon Litvak	Veronica Pacheco	Kevin Wyllie
Goals	Complete journal club individual assignment Create and practice journal club presentation with Brandon Find a MOD Create project timeline with soft deadlines for each person/milestone Complete milestone 0: Working Environment Setup Complete milestone 1: Version Control Setup Begin milestone 2: “Developer Rig” Setup and Initial As-Is Build Reformat Home Page with Dr. Dahlquists recommendations	Perform an initial import/export cycle (with Anu) Figure out a file management system (with Anu) Characterize regular expression patterns for ID detection Further explore the found MOD and review it Complete Journal Club presentation on the genome paper	Work with Kevin Wyllie Understand experimental design Understand sample-data relationship raw.zip and .sdrf Construct sample-data diagram Develop compiled raw data file	Work with Veronica Pacheco Understand experimental design Understand sample-data relationship raw.zip and .sdrf Construct sample-data diagram Develop compiled raw data file
Progress	Found a possible model organism database (with Brandon Litvak) The journal club presentation and outline was prepared; MOD was examined and reviewed Completed journal club individual assignment Created and practice journal club presentation with Brandon Found a MOD Created project timeline with soft deadlines for each person/milestone Completed milestone 0: Working Environment Setup Reformatted Home Page with Dr. Dahlquists recommendations Journal Club Presentation File: Genome Presentation	Found a possible model organism database. The more recent version of the MOD was found The regular expression patterns for J2315 were determined Preparation was done for the Genome Paper Presentation Completed outline of the genome paper File management system was determined	we understood the experimental design made chart for microarray experiment finished powerpoint on microarray paper Vpachec3 Week 11	Created methods diagram (media:KWVPMethoddiagram.jpg). File:B. Cenopacia.pptx we understood the experimental design made chart for microarray experiment finished powerpoint on microarray paper
Individual Journal Pages	Anuvarsh Week 11	Blitvak Week 11	Vpachec3 Week 11	Kevin Wyllie Week 11

File Management System

• Files utilized in weekly projects will renamed as follows: XXXX_GEN_(Initials)(Week#)_yyyymmdd, where "XXXX" is the original filename. If multiple versions of the same file (with identical filenames) are used on the same day then a (positive integer) (starting from 1) will be added to any additional versions (e.g. XXXX_GEN_BL11_yyyymmdd, XXXX_GEN_BL11_yyyymmdd(1), XXXX_GEN_BL11_yyyymmdd(2), for three different versions of the same file uploaded by Brandon Litvak during Week 11)
• Files will be uploaded to the weekly progress table under a file row with a clear label (under the respective group member that created them/used them)
• All original unmodified files will be saved and will also be uploaded, together, as a compressed zip with the filename: ORIG_GEN_(Initials)(Week#); the compressed zip containing all original files will be the last entry in the row designated for the files, with the label "ORIGINAL FILES"

Other Progress

• A journal using the B. cenocepacia genome in a microarray experiment titled Biofilm-Grown Burkholderia cepacia Complex Cells Survive Antibiotic Treatment by Avoiding Production of Reactive Oxygen Species was approved for analysis.

Journal Club Presentations

Genome Paper Presentation Week 11
Microarray Paper Presentation Week 12

Week 12

Individual Goals and Progress

Weekly Goals and Progress
	Anu Varshneya	Brandon Litvak	Veronica Pacheco	Kevin Wyllie
Goals	Complete milestone 0: Working Environment Setup Set up the development machine (my laptop) with all required software for coding. Complete milestone 1: Version Control Setup Set up a branch specific to our project and clone necessary code from GitHub onto the development machine. Complete milestone 2: “Developer Rig” Setup and Initial As-Is Build Confirm that all core software for developing, building, and testing prototype version of GenMAPP Builder are on the development machine. Set up Eclipse and java project workspace. Run initial build.	Complete Milestone 1: Initial Database Export Create a Gene Database testing report for the initial export Further explore the various ID systems; verify previous findings Create expressions for Match/PGSQL that will assist in evaluating the quality of any exported databases	Work with Kevin Wyllie Read the microarray paper to understand the experiment. Create a table or list that shows the correspondence between the samples in the experiment and the files you have downloaded. Determine how many biological or technical replicates, and which samples were labeled with Cy3 or Cy5. Create a Master Raw Data file that contains the IDs and columns of data required for further analysis. Consult with Dr. Dahlquist on how to process the data (normalization, statistics).	Work with Veronica Pacheco Read the microarray paper to understand the experiment. Create a table or list that shows the correspondence between the samples in the experiment and the files you have downloaded. Determine how many biological or technical replicates, and which samples were labeled with Cy3 or Cy5. Create a Master Raw Data file that contains the IDs and columns of data required for further analysis. Consult with Dr. Dahlquist on how to process the data (normalization, statistics).
Progress	Completed milestone 0: Working Environment Setup Completed milestone 1: Version Control Setup Completed milestone 2: “Developer Rig” Setup and Initial As-Is Build Began milestone 3: Species Profile Creation Need to consult with Brandon and/or Dr. Dionisio before continuing.	Completed Milestone 1: Initial Database Export Completed Milestone 2: ID Pattern Definition and Verification (will be revisited for future work with modified forms of GenMAPP builder) Should talk to Anu about further steps involving TallyEngine/GenMAPP builder (organize more exports)	Compiled data into one Excel spreadsheet. Centered data and began statistical analysis (stopped at T statistic).	Compiled data into one Excel spreadsheet. Centered data and began statistical analysis (stopped at T statistic).
Individual Journal Pages	Anuvarsh Week 12	Blitvak Week 12	Vpachec3 Week 12	Kevin Wyllie Week 12
Files Used/Created		Week 12 Files Starting Files	Media:Raw_compiled_data_KW20151119.xlsx	Media:Raw_compiled_data_KW20151119.xlsx

Week 14

Individual Goals and Progress

Weekly Goals and Progress
	Anu Varshneya	Brandon Litvak	Veronica Pacheco	Kevin Wyllie
Goals	Finish second build. Analyze results from previous build with Brandon Litvak and determine modifications that need to be made to code. Begin modifying code to collect gene names from "ORF" instead of "OrderedLocusTags" Start writing README and scientific paper (parts of deliverables).	Perform database export on the second build and other builds of the customized genMAPP builder Determine, with Anu, what modifications must be done to GenMAPP builder/Tallyengine Find out why most of the data/gene-names were not captured in the "OrderedLocusNames" table of the PSQL database for Export 1 Create testing reports on any builds created for the week.	Work with Kevin Wyllie Perform the statistical analysis in Excel. Format the gene expression data for import into GenMAPP. Import data into GenMAPP, create ColorSets, and run MAPPFinder. Document and take notes on test runs with GenMAPP. Use the EX.txt file to help the Coder/Quality Assurance team members to validate the .gdb. Do a journal club outline of the paper so that you can use it in the Discussion section of your group report and your final presentation. Create a .mapp file showing one pathway that is changed in your data.	Work with Veronica Pacheco Perform the statistical analysis in Excel. Format the gene expression data for import into GenMAPP. Import data into GenMAPP, create ColorSets, and run MAPPFinder. Document and take notes on test runs with GenMAPP. Use the EX.txt file to help the Coder/Quality Assurance team members to validate the .gdb. Do a journal club outline of the paper so that you can use it in the Discussion section of your group report and your final presentation. Create a .mapp file showing one pathway that is changed in your data.
Progress	Finished second build. Analyzed results from previous build with Brandon Litvak and determine modifications that need to be made to code. Began modifying code to collect gene names from "ORF" instead of "OrderedLocusTags" Finished third build. Customized Tally Engine to collect counts for ORF ID's. Finished fourth build.	It was found that the gene names of interest existed under the label of "ORF" in the XML file (explained why they weren't captured by GenMAPP builder) Created a streamlined general expression that can capture all of the IDs of interest; shared with Anu, assisted in the creation of Build 3/4 of the modified genmapp builder Found that XMLPipeDB Match gave 6 extra counts using the general expression for the IDs; excel MATCH command analysis was conducted and the discrepant IDs were found Completed gene database test reports for builds 2, 3, and 4	Work with Kevin Wyllie Performed the statistical analysis in Excel. Formatted the gene expression data for import into GenMAPP. Imported data into GenMAPP, created ColorSets, and ran MAPPFinder. Documented and took screenshots on test runs with GenMAPP. Sent the EX.txt file to Brandon and also uploaded on wiki	Work with Veronica Pacheco Performed the statistical analysis in Excel. Formatted the gene expression data for import into GenMAPP. Imported data into GenMAPP, created ColorSets, and ran MAPPFinder. Documented and took screenshots on test runs with GenMAPP. Sent the EX.txt file to Brandon and also uploaded on wiki
Individual Journal Pages	Anuvarsh Week 14	Blitvak Week 14 Build 2 Export Testing Report Build 3 Export Testing Report Build 4 Export Testing Report	Vpachec3 Week 14	Kevin Wyllie Week 14
Files Used/Created	Build 2 - with customized species profile: gmbuilder-genialomics-12012015-build-2.zip Anuvarsh (talk) 15:22, 1 December 2015 (PST) Build 3 - picking up gene names from ORF instead of ordered locus gmbuilder-genialomics-12032015-build-3.zip Anuvarsh (talk) 14:58, 3 December 2015 (PST) Build 4 - customized TallyEngine gmbuilder-genialomics-12032015-build-4.zip Anuvarsh (talk) 15:18, 3 December 2015 (PST)	Files from work done on 12/01/15 Files from work done on 12/03/15 Files from work done on 12/04/15 Files from work done on 12/07/15 Compressed gdb from Build 4	see Kevin's section -->	Final processed/formatted microarray data spreadsheet txt form of the forGenMAPP sheet Exceptions file from first export.

Reflections

Anu Varshneya

• What worked?
  • In general, I think our group worked very well together! I think we are all motivated to get this project done well, and are communicating well with each other regarding our progress.
• What didn't work?
  • I think for the most part we did a great job. I think the only ideas I have moving forward is a little bit more planning in regards to how we plan to attack the writing and presentation portion of the project. I am not concerned about us getting it done on time and with good quality, just that we create a plan of attack soon so that everyone is on the same page. :)
• What will I do next to fix what didn't work?
  • Though nothing has not worked, I think we will just talk tomorrow about how we want to approach the writing and the presentation and set up some group work times.

Kevin Wyllie

1. What worked?
   • Our initial GenMAPP import worked! 284 errors, which, out of 7251, does sound so bad to me!
2. What didn't work?
   • Maybe this isn't actually an example of something not working, but our calculated fold changes were quite different (much lower in magnitude) from those reported in Van Acker et al's paper. However, they had the same directions and generally saw the same relative trends (ie the relatively higher fold changes in the paper were among the higher in our data). Also, very few of the genes they considered significant (with their super-lenient criteria that results in 30% of the genes seeing significant changes) were significant by our criteria.
3. What will I do next to fix what didn't work?
   • We just need to triple/quadruple check that our data processing protocol is legitimate. Other than that, there's not much we can do in terms of fold changes. And for statistical significance, we potentially should reconsider heightening our BH P-value threshold above 0.05, as currently we're only considering about 8% of the genes to see a significant change. But maybe this is not too low of a number.

Veronica Pacheco

1. What worked?
   • Right off the bat, our first run through GenMAPP worked. As expected, there were exceptions and it generated an EX.txt file. There were 284 errors. We then handed over the file to Brandon so we shall see if the number of errors can decrease.
2. What didn't work?
   • What we initially thought didn't work or didn't seem correct was that fact that our values for fold changes were much smaller than the values reported in Van Acker et al's paper. The direction, for the majority, aligned with what was reported however the concrete values had large differences.
3. What will I do next to fix what didn't work?
   • Initially, we went to make sure our methods were correct. We traced back our steps and made sure the calculations were done correctly.After we double checked, we then sought help from Dr. Dahlquist and Dr. Dionisio. From their response, it seems we should go over it one more time and if there is no source of error on our part, we continue the project with our fold changes.

Brandon Litvak

1. What worked?
   • I think a lot of things worked this week. Team work and communication was a great help in getting the bulk of this week's work done. The initial exported database was not working as planned and, as a team, we discovered that the reason had to do with the fact that GenMAPP builder was utilizing the wrong type of gene name; this knowledge allowed us to create builds this week that happened to work fairly well. These new builds covered the gene names of interest and led to a relatively small amount errors in GenMAPP. I think that, above all, the thing that worked best this week was my team. We were able to communicate and collaborate very well.
2. What didn't work?
   • At the present moment, I can't really think of things that really did not work. With respect to the gene database project for J2315, everything appears to be on track; I would say that the major problems that were encountered in Week 14 were resolved. I feel that all of the major work for the project is complete; all that remains, is to synthesize the work done in a paper and presentation. As a group, we did get little work done on the final deliverables (which should be the focus, for this week) but we did get a lot of valuable work done for the project. We haven't managed to plan much regarding the final deliverables, either (but this is a minor issue).
3. What will I do next to fix what didn't work?
   • We will need to meet as a group and discuss the state of the project. I personally feel really good about the work so far and it would be helpful to hear, with the bulk of the work done, how everyone else feels. Additionally, I think that we will need to plan out our approach for the final project as soon as possible. Once we have discussed the project and made a plan, I think that we should set aside some time to work on the group project, as a team. I will check in with the group members on Tuesday, share my major findings for the week, and discuss future courses of action (regarding the last bits of the project).

Week 15

Individual Goals and Progress

Weekly Goals and Progress
	Anu Varshneya	Brandon Litvak	Veronica Pacheco	Kevin Wyllie
Goals	Fix any problems with the build Finish presentation Start paper	Work with Anu to fix any issues with the final gene database Finish presentation Prepare for presentation Work on final paper Conduct final checks on last export (check testing report, make any adjustments)	Work with Kevin Wyllie Finish example MAPPs (one for increase and decrease). Create sanity check table (with P-values). Upload deliverables. Begin PowerPoint. Begin report.	Work with Veronica Pacheco Finish example MAPPs (one for increase and decrease). Create sanity check table (with P-values). Upload deliverables. Begin PowerPoint. Begin report.
Progress	Created a new build to fix problem in TallyEngine. Contributed to final presentation and practiced speaking. Began drafting final report of findings from this project. Created ReadMe file. Modified Gene Database Schema for B. cenocepacia.	Checked final export: everything appears in order Checked new build of GenMAPP builder Realized why the UniProt count of 6994 is so different from the one reported by our database (difference between protein entry/gene name) Finalized readme Helped in finalizing the slides Practiced presentation	Finished example MAPP (decided do chose one pathway, oxidative phosphorylation). Created sanity check table (with P-values) Uploaded deliverables Began and finished PowerPoint. Began report.	Finished example MAPP (decided do chose one pathway, oxidative phosphorylation). Created sanity check table (with P-values) Uploaded deliverables Began and finished PowerPoint. Began report.
Individual Journal Pages	Anuvarsh Week 15	Blitvak Week 15	Vpachec3 Week 15	Kevin Wyllie Week 15
Files Used/Created	readMe_Bc-Std_GEN_Build4_20151204.doc.zip gmbuilder-genialomics-20151210-build-5.zip Genialomics-DatabaseSchema-20151211.pdf Final Presentation Slides (.pdf)	Final Readme Final Testing Report, as PDF Final Presentation Slides (.pdf)	Final Presentation Slides (.pdf) MAPP	Generated sanity check table. Upload deliverables. Final Presentation Slides (.pdf) MAPP

Other Progress

• On December 14, 2015, GENialOMICS completed a presentation summarizing their methods and findings.
  • GENialOMICS Final Presentation

Deliverables

• See GENialOMICS Deliverables

Burkholderia cenocepacia Genome Paper

Holden, M. T. G., Seth-Smith, H. M. B., Crossman, L. C., Sebaihia, M., Bentley, S. D., Cerdeño-Tárraga, A. M., … Parkhill, J. (2009). The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients . Journal of Bacteriology, 191(1), 261–277. http://doi.org/10.1128/JB.01230-08

• The link to the abstract from PubMed. [1]
• The link to the full text of the article in PubMedCentral. [2]
• The link to the full text of the article (HTML format) from the publisher web site. [3]
• The link to the full PDF version of the article from the publisher web site. [4]
• Who owns the rights to the article? American Society for Microbiology
  • Does the journal own the copyright? Yes
  • Do the authors own the copyright? No
  • Do the authors own the rights under a Creative Commons license? No
  • Is the article available “Open Access”? Yes
• What organization is the publisher of the article? What type of organization is it? (commercial, for-profit publisher, scientific society, respected open access organization like Public Library of Science or BioMedCentral, or predatory open access organization, see the list of) (Open Access Scholarly Publishers Association Members) here. American Society for Microbiology which is a scientific society
• Is this article available in print or online only? It is both available in print and online.
• Has LMU paid a subscription or other fee for your access to this article? Well I first looked at this article through web of science which LMU does pay for but looking at the article through PubMed, PubMed central and the publisher website was free.
• How many articles does this article cite? It has 150 cited references.
• How many articles cite this article? It is cited 128 times.
• Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced? A lot of the papers revolved around antibiotic resistance and therapeutic strategies.

Microarray Paper

Van Acker, H., Sass, A., Bazzini, S., De Roy, K., Udine, C., Messiaen, T., ... & Coenye, T. (2013). Biofilm-grown Burkholderia cepacia complex cells survive antibiotic treatment by avoiding production of reactive oxygen species. PLoS One, 8(3), e58943.

• This article is suitable for your project. — Kdahlquist (talk) 10:17, 10 November 2015 (PST)
• The link to the abstract from PubMed: http://www.ncbi.nlm.nih.gov/pubmed/?term=Biofilm-Grown+Burkholderia+cepacia+Complex+Cells+Survive+Antibiotic+Treatment+by+Avoiding+Production+of+Reactive+Oxygen+Species
• The link to the full text of the article in PubMedCentral: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596321/
• The link to the full text of the article (HTML format) from the publisher web site: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0058943
  • Cannot find HTML format on publisher web site.
• The link to the full PDF version of the article from the publisher web site: http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0058943&representation=PDF
• Who owns the rights to the article? Authors of the article: Heleen Van Acker, Andrea Sass, Silvia Bazzini, Karen De Roy, Claudia Udine, Thomas Messiaen, Giovanna Riccardi, Nico Boon, Hans J. Nelis, Eshwar Mahenthiralingam, Tom Coenye
• Does the journal own the copyright? Yes.
• Do the authors own the copyright? No.
• Do the authors own the rights under a Creative Commons license? Yes.
• Is the article available “Open Access”? Yes.
• What organization is the publisher of the article? What type of organization is it? Public Library of Science, Professional OA Publisher, Member of Open Access Scholarly Publishers Association
• Is this article available in print or online only? Available in print and online.
• Has LMU paid a subscription or other fee for your access to this article? No.
• Where does MicroArray Data reside? https://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3532/?keywords=&organism=Burkholderia+cenocepacia&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array=
• What experiment was performed? What was the "treatment" and what was the "control" in the experiment? The experiment hoped to test whether persister cells are present in Burkholderia cepacia complex (Bcc) biofilms, what the molecular basis of antimicrobial tolerance in Bcc persisters is, and how persisters can be eradicated from Bcc biofilms. Burkholderia cenocepacia biofilms were treated with 1024 µg/ml of tobramycin in the treatment group. The control group did not receive any tobramycin.
• Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each? 2 technical replicates were made across 5 biological replicates for the control, and 2 technical replicates of 3 biological replicates of the treatments.
• How many articles does this article cite? This article has 34 cited references.
• How many articles cite this article? This article is cited 17 times in All Databases, and 17 time in Web of Science Core Collection.
• Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced? Most of the articles are related to antimicrobial therapy, tolerance, and resistance.