LMU BioDB 2015 - User contributions [en]

Template:Kzebrows

2015-12-18T09:56:15Z

Kzebrows: /* Assignments */ add link to final reflection

==Assignments==

===Individual Journal Assignment Pages===

:[[Week 1 | Week 1]]
:[[Week 2 | Week 2]]
:[[Week 3 | Week 3]]
:[[Week 4 | Week 4]]
:[[Week 5 | Week 5]]
:[[Week 6 | Week 6]]
:[[Week 7 | Week 7]]
:[[Week 8 | Week 8]]
:[[Week 9 | Week 9]]
:[[Week 10 | Week 10]]
:[[Week 11 | Week 11]]
:[[Week 12 | Week 12]]
:[[Week 14 | Week 14]]
:[[Week 15 | Week 15]]

===Individual Journal Assignments=== 
:[https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/User:Kzebrows Kzebrows Week 1]
:[[Kzebrows Week 2]]
:[[Kzebrows Week 3]]
:[[Kzebrows Week 4]]
:[[Kzebrows Week 5]]
:[[Kzebrows Week 6]]
:[[Kzebrows Week 7]]
:[[Kzebrows Week 8]]
:[[Kzebrows Week 9]]
:[[Kzebrows Week 10]]
:[[Kzebrows Week 11]]
:[[Kzebrows Week 12]]
:[[Kzebrows Week 14]]
:[[Kzebrows Week 15]]
:[[Kzebrows Individual Reflection | Final Individual Reflection]]

===Shared Journal Assignments===

:[[Class Journal Week 1 | Class Journal Week 1]]
:[[Class Journal Week 2 | Class Journal Week 2]]
:[[Class Journal Week 3 | Class Journal Week 3]]
:[[Class Journal Week 4 | Class Journal Week 4]]
:[[Class Journal Week 5 | Class Journal Week 5]]
:[[Class Journal Week 6 | Class Journal Week 6]]
:[[Class Journal Week 7 | Class Journal Week 7]]
:[[Class Journal Week 8 | Class Journal Week 8]]
:[[Class Journal Week 9 | Class Journal Week 9]]
:[[Oregon Trail Survivors | Oregon Trail Survivors Week 10]]
:[[Oregon Trail Survivors | Oregon Trail Survivors Week 11]]
:[[Oregon Trail Survivors | Oregon Trail Survivors Week 12]]
:[[Oregon Trail Survivors | Oregon Trail Survivors Week 14]]

[[Category:Journal Entry]]

==Additional Links==
:'''User Page''': [[User:Kzebrows | Kristin Zebrowski]]
:'''Class Page''': [[Main Page | BIOL/CMSI 367-01]]
:'''Team Page''': [[Oregon Trail Survivors | Oregon Trail Survivors]]

OTS Deliverables

2015-12-18T09:55:19Z

Kzebrows: /* Individual Reflections */ edit name

{{Template:Oregon Trail Survivors}}
==OTS Group Files and Datasets==

[[Media:GenMAPP Builder 12 14 2015 Number 2.zip | Gene Database .gdb]]

[[Media:ReadMe Sf-Std External 20151214.pdf | ReadMe]]

[[Media:ShigellaGeneDatabaseSchema.pdf | Gene Database Schema]]

Gene Database Testing Report (.pdf)

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.xlsx | Compiled Raw Microarray Dataset (.xlsx)]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.txt | Data Used for Import into GenMAPP (.txt)]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210 (1).gex | GenMAPP Expression Dataset File (.gex)]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.EX.txt | Exceptions file (.EX.txt)]]

[[Media:Criterion.GOfiles.zip | Raw MAPPFinder results files (-GO.txt)]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.gmf | .gmf file]]

[[Media:Filtered MAPPFinder Results.xlsx | Filtered MAPPFinder Results .xlsx]]

[[Media:MAPPFinderResults.zip | Filtered MAPPFinder Results (common GO terms highlighted) .png]]

Sample MAPP (.mapp)

Group Report (.doc or .pdf)

[[Media:FinalOTSPresentation.pptx | Final PowerPoint Presentation]]

==Individual Reflections==

[[Kzebrows Individual Reflection | Kristin Zebrowski]]

OTS Deliverables

2015-12-18T09:54:54Z

Kzebrows: edit name

{{Template:Oregon Trail Survivors}}
==OTS Group Files and Datasets==

[[Media:GenMAPP Builder 12 14 2015 Number 2.zip | Gene Database .gdb]]

[[Media:ReadMe Sf-Std External 20151214.pdf | ReadMe]]

[[Media:ShigellaGeneDatabaseSchema.pdf | Gene Database Schema]]

Gene Database Testing Report (.pdf)

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.xlsx | Compiled Raw Microarray Dataset (.xlsx)]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.txt | Data Used for Import into GenMAPP (.txt)]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210 (1).gex | GenMAPP Expression Dataset File (.gex)]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.EX.txt | Exceptions file (.EX.txt)]]

[[Media:Criterion.GOfiles.zip | Raw MAPPFinder results files (-GO.txt)]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.gmf | .gmf file]]

[[Media:Filtered MAPPFinder Results.xlsx | Filtered MAPPFinder Results .xlsx]]

[[Media:MAPPFinderResults.zip | Filtered MAPPFinder Results (common GO terms highlighted) .png]]

Sample MAPP (.mapp)

Group Report (.doc or .pdf)

[[Media:FinalOTSPresentation.pptx | Final PowerPoint Presentation]]

==Individual Reflections==

[[Kzebrows Individual Reflection | Kzebrows]]

Kzebrows Individual Reflection

2015-12-18T09:53:30Z

Kzebrows: /* Statement of Work */ minor spacing edit

=== Statement of Work ===

In this project I acted as a GenMAPP User and as the Project Manager for the Oregon Trail Survivors. With the group, I helped to locate an appropriate genome and microarray paper for the project and presented on the microarray paper with Erich. I downloaded and created a compiled raw data file with Erich (I did RX samples and he did RP) and normalized log ratios and performed statistical analysis for my half of the data set. I communicated any errors or bugs with the QA and Coder as well as Dr. Dahlquist. I also performed a sanity check on my data and prepared the file for GenMAPP, which I then combined with Erich’s RP data file to create a master file. I created 12 color sets (one for each treatment) and ran the data through MAPPFinder, creating Criterion-Go.txt files that I then filtered and analyzed with Erich in order to compare with the MAPPs he created. I also helped write the final paper and presentation regarding my contributions to the project.

As Project Manager, I made sure that each team member completed their weekly status updates and checked in with them regularly regarding what they were working on. I also cleaned up the team Wiki and Deliverables pages and met with Dr. Dahlquist and Dr. Dionisio as part of the Project Managers guild to give team updates.

Files I contributed to:
*[[Media:Shigellamicroarray.pptx | Microarray Journal Club Power Point]]
*[[Media:CompiledRaw data RPRX IDLR EYKZ20152211.xlsx | Microarray Compiled Raw Data RP/RX IDLR]]
*[[Media:SamplesFilesCorrespondanceTable SF301a EYKZ201522111.xls | Microarray Corresponding Files Table]]
*[[Media:FINAL CompiledRawData RXRP EYKZ20151210.xlsx | Compiled Raw Microarray Dataset (.xlsx)]]
*[[Media:FINAL CompiledRawData RXRP EYKZ20151210.txt | Data Used for Import into GenMAPP (.txt)]]
*[[Media:FINAL CompiledRawData RXRP EYKZ20151210 (1).gex | GenMAPP Expression Dataset File (.gex)]]
*[[Media:FINAL CompiledRawData RXRP EYKZ20151210.EX.txt | Exceptions file (.EX.txt)]]
*[[Media:Criterion.GOfiles.zip | Raw MAPPFinder results files (-GO.txt)]]
*[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.gmf | .gmf file]]
*[[Media:FinalOTSPresentation.pptx | Final PowerPoint Presentation]]
*[[Media:CompiledRaw data RPRX IDLR EYKZ2015121.xlsx | ScalingCentering file 12/1 .xlsx]]

Files I created:
*[[Media:Filtered MAPPFinder Results.xlsx | Filtered MAPPFinder Results .xlsx]]
*[[Media:MAPPFinderResults.zip | Filtered MAPPFinder Results (common GO terms highlighted) .png]]
*[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.xlsx | RX Compiled Raw Data 12/6]]
*[[Media:CompiledRaw data statistics BonferroniPvalue RP IDLR EYKZ2015126.txt | RX .txt format GenMAPP ready 12/6]]
*[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.xlsx | RX Compiled Raw Data as of 12/6]]
*[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.txt | RX .txt format updated as of 12/6]]
*[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.EX.txt | RX Exceptions file]]
*[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.gex | RX .gex file]]
*[[Media:CompiledRaw data RX IDLR KZ2015126.EX.xlsx | RX Exceptions file in Excel format (filtered)]]

=== Assessment of Project ===

Our team was generally very good at communicating. We had a group text that everyone was good about responding to. We also frequently met as a group in person—we had Google docs for things like the Power Point presentations and report but mostly worked on them together instead of separately at home, allowing us to collaborate and keep tabs on what each group member was doing. We almost always met on Monday afternoons in the Bio Databases lab to check in and complete the week’s goals as a team.

Unfortunately, because we were all only simultaneously free from work/classes/other obligations on Mondays, sometimes things were left until shortly before the Tuesday deadline at midnight. While we never turned something in late, the quality of our work may have been affected slightly by this rush; however, I see this more as the nature of having a group project than in a flaw with our team itself.

If I could do it all over again I would have our group practice our presentations more. Even if we all understand our place in the team and what we are working on to a tee things like transitions are almost impossible to really get if the presentation hasn’t been practiced more than once or twice. It may have been helpful in retrospect even to practice just the transitions between slides and topics.

Evaluation:
#Content: The quality of the work is good in terms of our deliverables, although some more time could have been used to finalize the report. All of the necessary information is present and (to my knowledge) all bullet points on the Deliverables page are answered in the report.
#Organization: Our group’s Wiki page and Deliverables page are both very organized and clean, with links clearly displayed at the top. The Deliverables page has all of the additional versions and builds commented out from previous weeks’ assignments with just the final, official deliverables displayed. What has been asked to be displayed is displayed with the most recent addition at the top but it is not overly cluttered.
#Completeness: Our team did finish all of the objectives of the project, although the paper proved more difficult to complete. We were able to do so because we communicated frequently and worked together, particularly with our counterpart (QA and coder and both GenMAPP users). It would have been beneficial in retrospect to have begun this project a little earlier and maybe have had an additional week with the paper due before the presentation (instead, we tried to make our presentation and use that as a template for the paper) or have parts of the paper due along the way as part of the assignment, particularly because were working out bugs and making changes up until right before the presentation.

=== Reflection on the Process ===

What did you learn?
*With my head: I learned a lot about Shigella flexneri and about microarrays as well as how to analyze them. I've always known that bacterial resistance to antibiotics is an important area of research because of the complications it poses but it was very interesting to learn how specifically a species is circumventing the drug. It really reinforced for me how important research like what we saw in the microarray paper is and how it can be applied.
*With my heart: I learned that even if something is challenging I shouldn't be frustrated just because it's something I am unfamiliar with. If I keep at it I can make a lot of progress. This is especially apparent to me looking back at the first week and creating our Wiki pages--that seems like such a small task now. I also learned that teamwork is most effective when the team members have different strengths, as was true in the Oregon Trail Survivors. If one person didn't understand something someone else undoubtedly did and could explain it or offer a new perspective, which really helped the team to grow as a whole and proceed.
*With my hands: I learned more about Excel than I ever thought I would and now I feel like I can do so much more with Excel, which is something I can definitely take with me into my future career. I also never thought I would learn how to code and how to format a dataset to import into a program or understand how these things worked.

What lesson will you take away from this project that you will still use a year from now?
*This class and this project have taught me a great deal despite being one of the more challenging courses I have taken at LMU. First of all, I learned that no research is perfect and there is always room for improvement. In a more technical aspect it taught me to take everything with a grain of salt and always make sure data is reproducible--this was apparent after seeing some of the groups find very different things in their analysis than in their microarray papers. I also learned how "analysis" can mean so many different things and how crunching the numbers and formatting the data is only half the battle--the real challenge is what you do with the data you get and how you interpret it. I also learned that "getting answers" in a research project will always lead to more questions, which is great because it shows that there is no end to what interdisciplinary work can accomplish.

Kzebrows Individual Reflection

2015-12-18T09:52:32Z

Kzebrows: /* Reflection on the Process */ reflection

Kzebrows Individual Reflection

2015-12-18T09:34:55Z

Kzebrows: /* Assessment of Project */ assessment of project

=== Statement of Work ===

In this project I acted as a GenMAPP User and as the Project Manager for the Oregon Trail Survivors. With the group, I helped to locate an appropriate genome and microarray paper for the project and presented on the microarray paper with Erich. I downloaded and created a compiled raw data file with Erich (I did RX samples and he did RP) and normalized log ratios and performed statistical analysis for my half of the data set. I communicated any errors or bugs with the QA and Coder as well as Dr. Dahlquist. I also performed a sanity check on my data and prepared the file for GenMAPP, which I then combined with Erich’s RP data file to create a master file. I created 12 color sets (one for each treatment) and ran the data through MAPPFinder, creating Criterion-Go.txt files that I then filtered and analyzed with Erich in order to compare with the MAPPs he created. I also helped write the final paper and presentation regarding my contributions to the project.

As Project Manager, I made sure that each team member completed their weekly status updates and checked in with them regularly regarding what they were working on. I also cleaned up the team Wiki and Deliverables pages and met with Dr. Dahlquist and Dr. Dionisio as part of the Project Managers guild to give team updates.

Files I contributed to:
*[[Media:Shigellamicroarray.pptx | Microarray Journal Club Power Point]]
*[[Media:CompiledRaw data RPRX IDLR EYKZ20152211.xlsx | Microarray Compiled Raw Data RP/RX IDLR]]
*[[Media:SamplesFilesCorrespondanceTable SF301a EYKZ201522111.xls | Microarray Corresponding Files Table]]
*[[Media:FINAL CompiledRawData RXRP EYKZ20151210.xlsx | Compiled Raw Microarray Dataset (.xlsx)]]
*[[Media:FINAL CompiledRawData RXRP EYKZ20151210.txt | Data Used for Import into GenMAPP (.txt)]]
*[[Media:FINAL CompiledRawData RXRP EYKZ20151210 (1).gex | GenMAPP Expression Dataset File (.gex)]]
*[[Media:FINAL CompiledRawData RXRP EYKZ20151210.EX.txt | Exceptions file (.EX.txt)]]
*[[Media:Criterion.GOfiles.zip | Raw MAPPFinder results files (-GO.txt)]]
*[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.gmf | .gmf file]]
*[[Media:FinalOTSPresentation.pptx | Final PowerPoint Presentation]]
*[[Media:CompiledRaw data RPRX IDLR EYKZ2015121.xlsx | ScalingCentering file 12/1 .xlsx]]

Files I created:
*[[Media:Filtered MAPPFinder Results.xlsx | Filtered MAPPFinder Results .xlsx]]
*[[Media:MAPPFinderResults.zip | Filtered MAPPFinder Results (common GO terms highlighted) .png]]
*[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.xlsx | RX Compiled Raw Data 12/6]]
*[[Media:CompiledRaw data statistics BonferroniPvalue RP IDLR EYKZ2015126.txt | RX .txt format GenMAPP ready 12/6]]
*[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.xlsx | RX Compiled Raw Data as of 12/6]]
*[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.txt | RX .txt format updated as of 12/6]]
*[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.EX.txt | RX Exceptions file]]
*[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.gex | RX .gex file]]
*[[Media:CompiledRaw data RX IDLR KZ2015126.EX.xlsx | RX Exceptions file in Excel format (filtered)]]

=== Assessment of Project ===

Our team was generally very good at communicating. We had a group text that everyone was good about responding to. We also frequently met as a group in person—we had Google docs for things like the Power Point presentations and report but mostly worked on them together instead of separately at home, allowing us to collaborate and keep tabs on what each group member was doing. We almost always met on Monday afternoons in the Bio Databases lab to check in and complete the week’s goals as a team.

Unfortunately, because we were all only simultaneously free from work/classes/other obligations on Mondays, sometimes things were left until shortly before the Tuesday deadline at midnight. While we never turned something in late, the quality of our work may have been affected slightly by this rush; however, I see this more as the nature of having a group project than in a flaw with our team itself.

If I could do it all over again I would have our group practice our presentations more. Even if we all understand our place in the team and what we are working on to a tee things like transitions are almost impossible to really get if the presentation hasn’t been practiced more than once or twice. It may have been helpful in retrospect even to practice just the transitions between slides and topics.

Evaluation:
#Content: The quality of the work is good in terms of our deliverables, although some more time could have been used to finalize the report. All of the necessary information is present and (to my knowledge) all bullet points on the Deliverables page are answered in the report.
#Organization: Our group’s Wiki page and Deliverables page are both very organized and clean, with links clearly displayed at the top. The Deliverables page has all of the additional versions and builds commented out from previous weeks’ assignments with just the final, official deliverables displayed. What has been asked to be displayed is displayed with the most recent addition at the top but it is not overly cluttered.
#Completeness: Our team did finish all of the objectives of the project, although the paper proved more difficult to complete. We were able to do so because we communicated frequently and worked together, particularly with our counterpart (QA and coder and both GenMAPP users). It would have been beneficial in retrospect to have begun this project a little earlier and maybe have had an additional week with the paper due before the presentation (instead, we tried to make our presentation and use that as a template for the paper) or have parts of the paper due along the way as part of the assignment, particularly because were working out bugs and making changes up until right before the presentation.

=== 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?

Kzebrows Individual Reflection

2015-12-18T09:31:58Z

Kzebrows: statement of work

Kzebrows Individual Reflection

2015-12-18T09:18:44Z

Kzebrows: create page

OTS Deliverables

2015-12-18T09:18:24Z

Kzebrows: add individual reflection section

{{Template:Oregon Trail Survivors}}
==OTS Group Files and Datasets==

[[Media:GenMAPP Builder 12 14 2015 Number 2.zip | Gene Database .gdb]]

[[Media:ReadMe Sf-Std External 20151214.pdf | ReadMe]]

[[Media:ShigellaGeneDatabaseSchema.pdf | Gene Database Schema]]

Gene Database Testing Report (.pdf)

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.xlsx | Compiled Raw Microarray Dataset (.xlsx)]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.txt | Data Used for Import into GenMAPP (.txt)]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210 (1).gex | GenMAPP Expression Dataset File (.gex)]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.EX.txt | Exceptions file (.EX.txt)]]

[[Media:Criterion.GOfiles.zip | Raw MAPPFinder results files (-GO.txt)]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.gmf | .gmf file]]

[[Media:Filtered MAPPFinder Results.xlsx | Filtered MAPPFinder Results .xlsx]]

[[Media:MAPPFinderResults.zip | Filtered MAPPFinder Results (common GO terms highlighted) .png]]

Sample MAPP (.mapp)

Group Report (.doc or .pdf)

[[Media:FinalOTSPresentation.pptx | Final PowerPoint Presentation]]

==Individual Reflections==

[[Kzebrows Individual Reflection | Kzebrows Individual Reflection]]

Oregon Trail Survivors

2015-12-18T09:10:20Z

Kzebrows: delete file link

<div style="text-align: center; font-size: 250%; line-height: 1.25em">'''Oregon Trail Survivors'''</div>

<div class="center">
[[Image:Oregon-trail-dysentery 5 biodb.jpg | thumb | right | 350px | The third leading cause of death in the Oregon Trail.]]
</div>

== Group Members ==
*Coder: [[User:Jwoodlee | Jake Woodlee]]
*Quality Assurance: [[User:Troque | Trixie Roque]]
*GenMAPP Users: [[User:Eyanosch | Erich Yanoschik]] & [[User:Kzebrows | Kristin Zebrowski]]
* Project Manager: [[User:Kzebrows | Kristin Zebrowski]]

{{Template:Oregon Trail Survivors}}

===Group Meeting Times===
*Thursday, November 5th at 8:00 pm
*Met most Sundays and Monday evenings in the Biol DB lab to check in with one another.

== Goals ==
Over the upcoming weeks our group will be investigating ''Shigella flexneri''.

===Week 10===

# Find genome sequence paper
# Find 4-8 microarray data and paper that goes with the genome paper
# Compile team page to and create a ranked annotated bibliography

===Week 11===

#Prepare for journal club presentations in Weeks 12 and 13
#Begin initial tasks on research project

Click on username links for more information regarding each team member's contributions for Week 11.

[[Jwoodlee Week 11 | Jake]]: Read through the genome paper and tried to get through the accessible things I had the ability to understand. Made an outline for the genome paper. Worked on the presentation with Trixie and found a database. And of course I answered the assigned questions.

[[Troque Week 11 | Trixie]]: Mainly focused on the Genome paper presentation with Jake. This includes searching for a viable database that we will be using for the rest of the group assignment and actually creating the presentation we will be doing for October 17th, 2015. I've also updated our group page to reflect what Dr. Dahlquist suggested would improve our team page.

[[Eyanosch Week 11 | Erich]]: Analyzed the microarray paper in order to describe the experimental design of the microarray data, treatments, number of replicates, and dye swaps. Worked with Kristin to produce the power point for the GennMAP users presentation at Journal Club. Worked on the individual journal entry and created an outline of the microarray paper.

[[Kzebrows Week 11 | Kristin]]: Using the team's selected microarray paper I developed an outline including background information, experimental outline/methods and how samples corresponded to the data, a brief description of the results, and a discussion including the implications of the research and its results in comparison to previous studies. Using this outline, I created a flow chart corresponding to the research. I also worked with Erich in order to create a PowerPoint for the Journal Club presentation on Nov. 24.

=== Week 12 ===
#QA will be doing an initial database export.
#Coder will be setting up version control.
#GenMAPP users will compile the raw data from the micorarray file to prepare for normalization and statistic analysis (will begin if time permits after consultation with Dr. Dahlquist). Additionally, the GenMAPP users will be determining the number of biological or technical replicates and how samples were labeled.
#Coder and QA will present on genome paper in class Tuesday, Nov. 24.

Click on username links for more information regarding each team member's contributions for Week 12.
* [[Jwoodlee Week 12 | Jake]]:Setup my environment in eclipse, created the s-flexneri branch, created my own copy of GenMAPP that I can modify for later use and I cloned the repository with the Git commands.
* [[Troque Week 12 | Trixie]]: Finished the preliminary export of the XML and GOA files and the corresponding Gene Testing Report. Also started identifying the gene id's for the specie. Decided on file management system with Jake.
* [[Eyanosch Week 12 | Erich]]: Worked with Kristin in determining the total number of biological and technical replicates. Compiled the raw data for RP samples, specifically the ID and Log ratio columns. Incorporated the RP and RX data into one spreadsheet with Kristins data. We created a table of the sample data and file each corresponds with, also figured out there were no dye swaps in the experiment(The control was the Cy3 dye and the treatment the Cy5 dye).
* [[Kzebrows Week 12 | Kristin]]: Determined that there were 3 biological replicates per treatment for 6 treatments total. Compiled raw data for RX samples by re-naming columns for ID and Log Ratio and putting into same worksheet, which was later combined with Erich's worksheet for RP samples. Erich and I met and worked together to create a table of which samples correspond to which file.

===Week 14===
#QA will be documenting the IDs using MATCH, Postgres, Microsoft Access, and Excel and get a head start of Milestone 3, which is customizing the TallyEngine.
#Coder will determine and document any modified export behavior that the GenMAPP Builder will have and resolve bugs. Coder will also work with QA by uploading GM Builder for additional export.
#GenMAPP Users will perform statistical analysis on Excel (normalization, tests) and format for import into GenMAPP. Users will also import data into GenMAPP and run MAPPFinder, and then document these test runs.

Click on username links for more information regarding each team member's contributions for Week 14.
* [[Jwoodlee Week 14 | Jake]]: Finished custom GenMAPP builder, committed to GitHub, and ran the export with the custom software. This created a custom .gdb which was opened in Microsoft Access and GenMAPP to check for accuracy.
* [[Troque Week 14 | Trixie]]: Trixie has finished identifying the gene IDs using MATCH, Postgres, Microsoft Access, and Excel. It was discovered that some IDs are in "dbReference/property&type&gene ID", and so another export was done on 12/7/15 to add the newly discovered gene IDs.
* [[Eyanosch Week 14 | Erich]]: Kristin and I completed the corrections provided via Dr. Dhalquist on Kristins talk page. We split the work into two halves and I worked on the RP data. We completed the statistics, Bonferroni p value correction, and the sanity check. I downloaded the database and formatted/exported the file for GenMAPP, and tried to create a GO tree for one of the trail points with RX.
* [[Kzebrows Week 14 | Kristin]]: This week Erich and I made corrections from the talk page and normalized log ratios for the slides in the experiment. I completed the statistical analysis for RX samples and calculated the Bonferroni p value correction. I also performed a sanity check for the RX samples and, going off of that, I calculated the Benjamini & Hochberg p value correction for RX-1-30, which had the most statistically significant changes in gene expression. I also formatted and exported the file for GenMAPP, downloaded the database, and attempted to create color sets to run the data set through MappFINDER.

==== Reflection ====

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?

''Kristin'':
#What worked?
#*In terms of communication is having a group text. We also meet at least once a week outside of class in order to work together on the assignments and make sure we are all on the same page. So far, this has allowed us to troubleshoot and address bugs together as a team quickly. It also worked for Erich and I to divide up the samples so that I did all RX and Erich did all RP. Then, we could work at the same time and double-check procedures with each other but we were still getting the work done twice as quickly.
#What didn't work?
#*After creating the initial compiled raw data file, I had to make several corrections before the file could be run through GenMAPP. First of all, I had to get rid of the ".", and I also had to change all #DIV/0! with a space character for the file to be read at all. Also, although we were unable to find all of the b#### and CP#### gene ID's in UniProt or ShiBASE. Also, after creating my color set and trying to run MAPPFinder, I tried three computers and all of them crashed with the "not responding" message.
#What will I do next to fix what didn't work?
#*I will communicate with the QA and Coder in order to create a database with a minimal number of "Gene ID not found's" and then communicate with Erich when we try to run our dataset through MappFinder. Once the gene database is re-customized and the export is complete I can try and re-run my dataset to see if that makes a difference.

'' Trixie '':
# What worked?
#* What worked in identifying the gene IDs is to look export .gdb file into Excel and compare with what the OrderedLocusNames table had (from Microsoft Access). From doing this, it was easier to find which genes were not found in the .gdb file and made it easier to look through them in the UniProt XML file. With the Excel file comparing the lists of gene IDs and using the CTRL+F shortcut, I was also able to discern which tags to include into the new builds for the databases. Because of this, I was able to confirm that some genes indeed do not exist in the XML file, while only a couple exist within the "dbReference" tag. In terms of group work, what worked is posting all our files into a single page as we progress through the assignment. Night meetings were also helpful in order to better communicate with the rest of my group.
# What didn't work?
#* What didn't work is using Match multiple times without thinking. Even when I was trying to match the number of gene IDs with what Tally Engine gives me, Match didn't really help me in identifying where to find the genes in the XML file. Waiting for the database to finish didn't help much at all since our builds would take more than 4 hours to finish.
# What will I do next to fix what didn't work?
#* What I would do next to fix what didn't work is to actually use Match in conjunction to the XML file, or just use the Excel method completely since that was actually more helpful in finding the necessary tags than the Match method. I would probably have to time myself to check the lab after about 4.5 hours since one of our builds lasted that long.

''Jake'':
#What worked?
#*Almost every procedural action I took from Dondi worked. The only hiccup I had was in regard to Eclipse and navigating the directories.
#What didn't work?
#*In Eclipse, my edits to the GenMAPP builder source code were causing red error marks, but after selecting "Organize Imports" from the source menu the errors were fixed easily and the proper classes were imported. Also I had difficulty navigating to the dist file in my Temp drive, however I traced this back within Eclipse and was able to make a zip that I could hand off to Trixie for export.
#What will I do next week to fix what didn't work?
#*It seems to me that there wasn't a whole lot that went wrong with my procedure. What wasn't working I already fixed. Currently Trixie and I are running an export that will take 4 hours with the new additions in the property files, so there may be some new hiccups when that export is finished but we will have to wait and see.

''Erich'':
# What worked?
#*Having a GenMAPP user meeting with Dr. Dhalquist helped focus on what goals we wanted to achieve by the time of our next meeting. A group text helped organize meeting times of both the coders and GenMAPP users helped keep us on schedule.
# What didn't work?
#*The GenMapp Gene Ontology Tree was unable to pull files for each GO selection. We need to work on and make sure the GO files can be found. We also had to remove and edit our compiled raw data files so that they are able to be read by GenMAPP.
# What will I do next to fix what didn't work?
#*A new .gex was created, so this might help with the problems experienced in the MappBuilder. Also communicating with the QA and coder to make sure we finish up the GO tree smoothly in order to assess the results of the Publication we chose for Shigella Flexneri.

===Week 15===
#Coder: Work with QA to fix bugs.
#QA: Work with coder to fix bugs in the .gdb.
#GenMAPP Users: Finish Milestone 3. Run tests with GenMAPP. Do a journal club outline of the paper to use in the Discussion section of group report and presentation. Create a .mapp file showing one changed pathway from the data.
#All team members will be working together to put together deliverables including the final report and presentation for next Tuesday.

[[Media:OTS ShigellaFinalPresentation.pptx | '''Final PowerPoint Presentation''']]

Click on username links for more information regarding each team member's contributions for Week 14.
* [[Jwoodlee Week 15 | Jake]]: Pulled Dondi's changes, and then created a new clean distribution. I then uploaded that distribution to our OTS Files page. Edited properties file for TallyEngine.
* [[Troque Week 15 | Trixie]]: Had to re-import to PostgreSQL due to having imported twice -- this resulted in the number of counts being twice as much as what was in the XML file. Also worked with Dr. Dionisio in order to find ~92 new IDs from the XML file that were not caught before and collaborated with Jake in order to make 2 more builds that should, ideally, produce the intended 92 genes.
* [[Eyanosch Week 15 | Erich]]: Used Kristin's color sets criterion GO files to fill out my gene expression MAPP. Made MAPPS for pathways that were significantly affected such as Metabolic procceses (glycolysis, TCA cycle), Flagellar Assembly, and Ribosome. Incorporated the data into slides for the power point and analyzed the data obtained with that produced from the microarray paper.
* [[Kzebrows Week 15 | Kristin]]: I created color sets with Increased/Decreased criteria for all of the 12 treatment/time point combos. Then, based on the criterion.go files, I created tables by filtering the results comparing the most commonly induced or repressed genes for the 1 x MIC at 60 minutes and 0.5 x MIC at 10 minutes between RX and RP. Strikingly, we found that between RX and RP the effects were very similar. I then compared them with the .mapp files that Erich created and put my portion of the project (compiled sanity check, color set, comparison tables) in the power point.

==Overview of Genome Paper==
*Used the genome sequencing article to perform a prospective search in the [https://apps.webofknowledge.com/UA_GeneralSearch_input.do?product=UA&search_mode=GeneralSearch&SID=1FRKcNxUgxiGX6spITI&preferencesSaved= Web of Science] database.
*Overview of the search:
**How many articles does this article cite? 37
**How many articles cite this article? 303
**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?
***Now that the genome has been sequenced, a majority of research has been done on discovering which genes are responsible for virulence and pathogenesis as well as potential antibiotics. Genomic research is also focused on how ''S. flexneri'' has been able to develop resistance to multiple drugs. Furthermore, ''Shigella'' is suspected to have evolved from ''Escherichia coli'' so a lot of research has been done in how and when pathogenic ''Shigella'' split from ''E. coli'' on the evolutionary tree.

==Annotated Bibliography==
=== Genome Paper ===
Jin, Q., Yuan, Z., Xu, J., Wang, Y., Shen, Y., Lu, W., … Yu, J. (2002). Genome sequence of ''Shigella flexneri'' 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157. Nucleic Acids Research, 30(20), 4432–4441.
* PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/?term=Genome+sequence+of+Shigella+flexneri+2a%3A+insights+into+pathogenicity+through+comparison+with+genomes+of+Escherichia+coli+K12+and+O157
* PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC137130/
* Publisher Full Text (HTML): http://nar.oxfordjournals.org/content/30/20/4432.full
* Publisher Full Text (PDF): http://nar.oxfordjournals.org/content/30/20/4432.full.pdf+html
* Copyright: 2002 Oxford University Press
* Publisher: Oxford University Press
* Availability: in print and online
* Did LMU pay a fee for this article: no

===Microarray Paper===





Fu H, Liu L, Zhang X, Zhu Y, Zhao L, Peng J, et al. (2012) Common Changes in Global Gene Expression Induced by RNA Polymerase Inhibitors in ''shigella flexneri''. PLoS ONE 7(3): e33240. doi:10.1371/journal.pone.0033240

*The link to the [http://www.ncbi.nlm.nih.gov/pubmed/22428000 abstract]
*The link to the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3299763/ full text of the article] in PubMed Central
*The link to the [http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0033240 full text of the article] (HTML format) from the publisher web site.
*The link to the [http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0033240&representation=PDF full PDF version] of the article from the publisher web site.
*Copyright: © 2012 Fu et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
*Does the journal own the copyright? NO
*Do the authors own the copyright? Yes
*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? PLoS One is the publisher/Journal. It hosts open access research articles. (Public Library of Science)
*Is this article available in print or online only? Online only
*Has LMU paid a subscription or other fee for your access to this article? No LMU has not paid a subscription or other fee because it is open access on the Public Library of Science.
*Use the genome sequencing article you found to perform a prospective search in the ISI Web of Science/Knowledge database.
**How many articles does this article cite? 25 cited references
**How many articles cite this article? 0 articles cite this article
**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?
*Well given that there are no papers that cite this paper there hasn't been anything done to build on this specific topic. In regards to the genome I think this paper has built on the work of the people who sequenced the first genome of Shigella flexneri as well as the other micro array papers.
*State which database you used to find the data and article: ArrayExpress
*State what you used as search terms and what type of search terms they were: "shigella flexneri" filtered by organism, experiment type: "rna assay", experiment type: "array assay"
*Give an overview of the results of the search.
**How many results did you get? 7 results returned with 6 viable options due to the number assays.
**Give an assessment of how relevant the results were: Very relevant, 6/7 results were viable.
*Link to [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-32978/?keywords=shigella+flexneri&organism=Shigella+flexneri&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array= microarray data]
*What experiment was performed? What was the "treatment" and what was the "control" in the experiment?
**Antibiotics (RNA Polymerase Inhibitors) were added to ''Shigella flexneri'' in order to see if bacteria became less active. The control was a group of bacteria with no drugs added to them, and the treatment was a group of bacteria with drugs added to them.
*Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each?
**There are two drugs RX and RP with 6 samples per drug. The experiment was run 3 times which yielded 36 assays. I believe that means 3 biological replicates and 12 technical replicates within each experiment, but I am not 100 percent sure.

OTS Deliverables

2015-12-16T21:03:56Z

Kzebrows: add link to raw MAPPFinder results file

{{Template:Oregon Trail Survivors}}
==OTS Group Files and Datasets==

[[Media:GenMAPP Builder 12 14 2015 Number 2.zip | Gene Database .gdb]]

[[Media:ReadMe Sf-Std External 20151214.pdf | ReadMe]]

Gene Database Schema

Gene Database Testing Report (.pdf)

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.xlsx | Compiled Raw Microarray Dataset (.xlsx)]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.txt | Data Used for Import into GenMAPP (.txt)]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210 (1).gex | GenMAPP Expression Dataset File (.gex)]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.EX.txt | Exceptions file (.EX.txt)]]

[[Media:Criterion.GOfiles.zip | Raw MAPPFinder results files (-GO.txt)]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.gmf | .gmf file]]

[[Media:Filtered MAPPFinder Results.xlsx | Filtered MAPPFinder Results .xlsx]]

[[Media:MAPPFinderResults.zip | Filtered MAPPFinder Results (common GO terms highlighted) .png]]

Sample MAPP (.mapp)

Group Report (.doc or .pdf)

[[Media:FinalOTSPresentation.pptx | Final PowerPoint Presentation]]

File:Criterion.GOfiles.zip

2015-12-16T21:00:27Z

Kzebrows: zipped .txt criterion-GO files for OTS

zipped .txt criterion-GO files for OTS

Template:Oregon Trail Survivors

2015-12-16T20:53:29Z

Kzebrows: /* Helpful Links */ delete link

== Helpful Links ==

{| class="wikitable" style="width: 100%; text-align: center"
! colspan="6"| Team Links
|-
! Files
! Team Members
! [[Week 11 | Week 11 Assignment]]
! [[Week 12 | Week 12 Assignment]]
! [[Week 14 | Week 14 Assignment]]
! [[Week 15 | Week 15 Assignment]]
|-
| rowspan="2" | [[OTS Deliverables | OTS Deliverables]]
| [[User:Troque | Trixie]]
| [[Troque_Week_11 | Week 11]]
| [[Troque_Week_12 | Week 12]]
| [[Troque_Week_14 | Week 14]]
| [[Troque_Week_15 | Week 15]]
|-
| [[User:Jwoodlee | Jake]]
| [[Jwoodlee_Week_11|Week 11]]
| [[Jwoodlee_Week_12|Week 12]]
| [[Jwoodlee_Week_14|Week 14]]
| [[Jwoodlee_Week_15|Week 15]]
|-
| rowspan="2" | [[Gene_Database_Testing_Report_-_Oregon_Trail_Survivors | Gene Database Testing Report]]
| [[User:Eyanosch | Erich]]
| [[Eyanosch Week 11|Week 11]]
| [[Eyanosch Week 12|Week 12]]
| [[Eyanosch Week 14|Week 14]]
| [[Eyanosch Week 15|Week 15]]
|-
| [[User:Kzebrows | Kristin]]
| [[Kzebrows Week 11| Week 11]]
| [[Kzebrows Week 12| Week 12]]
| [[Kzebrows Week 14| Week 14]]
| [[Kzebrows Week 15| Week 15]]
|-
|}

[[Category:Group Projects]]
[[Category:Oregon Trail Survivors]]

{{Gene Database Project Links}}

OTS Deliverables

2015-12-16T20:51:22Z

Kzebrows: comment out old links, add concise dataset list

{{Template:Oregon Trail Survivors}}
==OTS Group Files and Datasets==

[[Media:GenMAPP Builder 12 14 2015 Number 2.zip | Gene Database .gdb]]

[[Media:ReadMe Sf-Std External 20151214.pdf | ReadMe]]

Gene Database Schema

Gene Database Testing Report (.pdf)

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.xlsx | Compiled Raw Microarray Dataset (.xlsx)]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.txt | Data Used for Import into GenMAPP (.txt)]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210 (1).gex | GenMAPP Expression Dataset File (.gex)]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.EX.txt | Exceptions file (.EX.txt)]]

Raw MAPPFinder results files

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.gmf | .gmf file]]

[[Media:Filtered MAPPFinder Results.xlsx | Filtered MAPPFinder Results .xlsx]]

[[Media:MAPPFinderResults.zip | Filtered MAPPFinder Results (common GO terms highlighted) .png]]

Sample MAPP (.mapp)

Group Report (.doc or .pdf)

[[Media:FinalOTSPresentation.pptx | Final PowerPoint Presentation]]

File:FINAL CompiledRawData RXRP EYKZ20151210.EX.txt

2015-12-16T20:42:06Z

Kzebrows: final compiled raw data exceptions file OTS

final compiled raw data exceptions file OTS

OTS Deliverables

2015-12-16T20:40:57Z

Kzebrows: /* OTS Group Files and Datasets */ edit name

==OTS Group Files and Datasets==

[[Media:GenMAPP Builder 12 14 2015 Number 2.zip | Gene Database .gdb]]

ReadMe

Gene Database Schema

Gene Database Testing Report (.pdf)

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.xlsx | Final Compiled Raw Data .xlsx]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.txt | Final Compiled Raw Data .txt]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210 (1).gex | Final Compiled Raw Data .gex]]

==OTS Files==

[[Media:Micro Array Shigella Flexneri 20151011.pdf | Shigella Flexneri Microarray Paper (PDF)]]

[[Media:Shigellamicroarray.pptx | Microarray Journal Club Power Point]]

[[Media:CompiledRaw data RPRX IDLR EYKZ20152211.xlsx | Microarray Compiled Raw Data RP/RX IDLR]]

[[Media:SamplesFilesCorrespondanceTable SF301a EYKZ201522111.xls | Microarray Corresponding Files Table]]

[[Media: GMBuilder Shigella flexneri.zip]]

[[Media: QA Files.zip | Download QA files]]

[[Media:GMBuilder December7 2015 build 2.zip]]

[[Media:GenMAPP Builder 12 14 2015.zip]]

[[Media:FinalOTSPresentation.pptx | '''Final PowerPoint Presentation''']]

==GenMAPP User Files==
[[Media:CompiledRaw data RPRX IDLR EYKZ2015121.xlsx | ScalingCentering file 12/1 .xlsx]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.gmf | Compiled Raw Data 12/8 .gmf]]

[[Media:Filtered MAPPFinder Results.xlsx | Filtered MAPPFinder Results .xlsx]]

[[Media:MAPPFinderResults.zip | Filtered MAPPFinder Results (common GO terms highlighted) .png]]

[[Media:Flagellum Ribosomal Mapp 1 60min 20151012.jpg | RP vs RX 1 MIC @ 60 minutes MAPP 12/12 .jpg]]

[[Media:Flagellum Ribosomal Mapp 0pt5 10min 20151012.jpg | RP vs RX 0.5 MIC @ 10 minutes MAPP 12/12 .jpg]]

====RP (Erich)====
[[Media:CompiledRaw data GenMAPP Final RP IDLR EYKZ2015126.xlsx | RP Compiled Raw Data Final 12/10]]

[[Media:CompiledRaw data GenMAPP ready RP IDLR EYKZ2015126.txt | RP .txt format GenMAPP ready 12/6]]

[[Media:CompiledRaw data Errors RP EYKZ2015126.EX.xlsx | RP Exceptions file in Excel format (filtered)]]

[[Media:CompiledRaw data Errors RP EYKZ2015126.EX.txt | RP Exceptions (txt)]]

[[Media:CompiledRaw data GenMAPP ready RP IDLR EYKZ2015126.gex | RP .gex file]]

====RX (Kristin)====
[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.xlsx | RX Compiled Raw Data 12/6]]

[[Media:CompiledRaw data statistics BonferroniPvalue RP IDLR EYKZ2015126.txt | RX .txt format GenMAPP ready 12/6]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.xlsx | RX Compiled Raw Data as of 12/6]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.txt | RX .txt format updated as of 12/6]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.EX.txt | RX Exceptions file]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.gex | RX .gex file]]

[[Media:CompiledRaw data RX IDLR KZ2015126.EX.xlsx | RX Exceptions file in Excel format (filtered)]]

{{Template:Oregon Trail Survivors}}

OTS Deliverables

2015-12-16T20:40:38Z

Kzebrows: /* OTS Group Files and Datasets */ edit link name

==OTS Group Files and Datasets==

[[Media:GenMAPP Builder 12 14 2015 Number 2.zip | Gene Database]]

ReadMe

Gene Database Schema

Gene Database Testing Report (.pdf)

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.xlsx | Final Compiled Raw Data .xlsx]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.txt | Final Compiled Raw Data .txt]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210 (1).gex | Final Compiled Raw Data .gex]]

==OTS Files==

[[Media:Micro Array Shigella Flexneri 20151011.pdf | Shigella Flexneri Microarray Paper (PDF)]]

[[Media:Shigellamicroarray.pptx | Microarray Journal Club Power Point]]

[[Media:CompiledRaw data RPRX IDLR EYKZ20152211.xlsx | Microarray Compiled Raw Data RP/RX IDLR]]

[[Media:SamplesFilesCorrespondanceTable SF301a EYKZ201522111.xls | Microarray Corresponding Files Table]]

[[Media: GMBuilder Shigella flexneri.zip]]

[[Media: QA Files.zip | Download QA files]]

[[Media:GMBuilder December7 2015 build 2.zip]]

[[Media:GenMAPP Builder 12 14 2015.zip]]

[[Media:FinalOTSPresentation.pptx | '''Final PowerPoint Presentation''']]

==GenMAPP User Files==
[[Media:CompiledRaw data RPRX IDLR EYKZ2015121.xlsx | ScalingCentering file 12/1 .xlsx]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.gmf | Compiled Raw Data 12/8 .gmf]]

[[Media:Filtered MAPPFinder Results.xlsx | Filtered MAPPFinder Results .xlsx]]

[[Media:MAPPFinderResults.zip | Filtered MAPPFinder Results (common GO terms highlighted) .png]]

[[Media:Flagellum Ribosomal Mapp 1 60min 20151012.jpg | RP vs RX 1 MIC @ 60 minutes MAPP 12/12 .jpg]]

[[Media:Flagellum Ribosomal Mapp 0pt5 10min 20151012.jpg | RP vs RX 0.5 MIC @ 10 minutes MAPP 12/12 .jpg]]

====RP (Erich)====
[[Media:CompiledRaw data GenMAPP Final RP IDLR EYKZ2015126.xlsx | RP Compiled Raw Data Final 12/10]]

[[Media:CompiledRaw data GenMAPP ready RP IDLR EYKZ2015126.txt | RP .txt format GenMAPP ready 12/6]]

[[Media:CompiledRaw data Errors RP EYKZ2015126.EX.xlsx | RP Exceptions file in Excel format (filtered)]]

[[Media:CompiledRaw data Errors RP EYKZ2015126.EX.txt | RP Exceptions (txt)]]

[[Media:CompiledRaw data GenMAPP ready RP IDLR EYKZ2015126.gex | RP .gex file]]

====RX (Kristin)====
[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.xlsx | RX Compiled Raw Data 12/6]]

[[Media:CompiledRaw data statistics BonferroniPvalue RP IDLR EYKZ2015126.txt | RX .txt format GenMAPP ready 12/6]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.xlsx | RX Compiled Raw Data as of 12/6]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.txt | RX .txt format updated as of 12/6]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.EX.txt | RX Exceptions file]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.gex | RX .gex file]]

[[Media:CompiledRaw data RX IDLR KZ2015126.EX.xlsx | RX Exceptions file in Excel format (filtered)]]

{{Template:Oregon Trail Survivors}}

OTS Deliverables

2015-12-16T20:40:02Z

Kzebrows: /* OTS Group Files and Datasets */ edit link names

==OTS Group Files and Datasets==

[[Media:GenMAPP Builder 12 14 2015 Number 2.zip]]

ReadMe

Gene Database Schema

Gene Database Testing Report (.pdf)

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.xlsx | Final Compiled Raw Data .xlsx]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.txt | Final Compiled Raw Data .txt]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210 (1).gex | Final Compiled Raw Data .gex]]

==OTS Files==

[[Media:Micro Array Shigella Flexneri 20151011.pdf | Shigella Flexneri Microarray Paper (PDF)]]

[[Media:Shigellamicroarray.pptx | Microarray Journal Club Power Point]]

[[Media:CompiledRaw data RPRX IDLR EYKZ20152211.xlsx | Microarray Compiled Raw Data RP/RX IDLR]]

[[Media:SamplesFilesCorrespondanceTable SF301a EYKZ201522111.xls | Microarray Corresponding Files Table]]

[[Media: GMBuilder Shigella flexneri.zip]]

[[Media: QA Files.zip | Download QA files]]

[[Media:GMBuilder December7 2015 build 2.zip]]

[[Media:GenMAPP Builder 12 14 2015.zip]]

[[Media:FinalOTSPresentation.pptx | '''Final PowerPoint Presentation''']]

==GenMAPP User Files==
[[Media:CompiledRaw data RPRX IDLR EYKZ2015121.xlsx | ScalingCentering file 12/1 .xlsx]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.gmf | Compiled Raw Data 12/8 .gmf]]

[[Media:Filtered MAPPFinder Results.xlsx | Filtered MAPPFinder Results .xlsx]]

[[Media:MAPPFinderResults.zip | Filtered MAPPFinder Results (common GO terms highlighted) .png]]

[[Media:Flagellum Ribosomal Mapp 1 60min 20151012.jpg | RP vs RX 1 MIC @ 60 minutes MAPP 12/12 .jpg]]

[[Media:Flagellum Ribosomal Mapp 0pt5 10min 20151012.jpg | RP vs RX 0.5 MIC @ 10 minutes MAPP 12/12 .jpg]]

====RP (Erich)====
[[Media:CompiledRaw data GenMAPP Final RP IDLR EYKZ2015126.xlsx | RP Compiled Raw Data Final 12/10]]

[[Media:CompiledRaw data GenMAPP ready RP IDLR EYKZ2015126.txt | RP .txt format GenMAPP ready 12/6]]

[[Media:CompiledRaw data Errors RP EYKZ2015126.EX.xlsx | RP Exceptions file in Excel format (filtered)]]

[[Media:CompiledRaw data Errors RP EYKZ2015126.EX.txt | RP Exceptions (txt)]]

[[Media:CompiledRaw data GenMAPP ready RP IDLR EYKZ2015126.gex | RP .gex file]]

====RX (Kristin)====
[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.xlsx | RX Compiled Raw Data 12/6]]

[[Media:CompiledRaw data statistics BonferroniPvalue RP IDLR EYKZ2015126.txt | RX .txt format GenMAPP ready 12/6]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.xlsx | RX Compiled Raw Data as of 12/6]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.txt | RX .txt format updated as of 12/6]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.EX.txt | RX Exceptions file]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.gex | RX .gex file]]

[[Media:CompiledRaw data RX IDLR KZ2015126.EX.xlsx | RX Exceptions file in Excel format (filtered)]]

{{Template:Oregon Trail Survivors}}

OTS Deliverables

2015-12-16T20:39:40Z

Kzebrows: edit links

==OTS Group Files and Datasets==

[[Media:GenMAPP Builder 12 14 2015 Number 2.zip]]

ReadMe

Gene Database Schema

Gene Database Testing Report (.pdf)

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.xlsx | Final Compiled Raw Data 12/10 .xlsx]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.txt | Final Compiled Raw Data 12/10 .txt]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210 (1).gex | Final Compiled Raw Data 12/12 .gex]]

==OTS Files==

[[Media:Micro Array Shigella Flexneri 20151011.pdf | Shigella Flexneri Microarray Paper (PDF)]]

[[Media:Shigellamicroarray.pptx | Microarray Journal Club Power Point]]

[[Media:CompiledRaw data RPRX IDLR EYKZ20152211.xlsx | Microarray Compiled Raw Data RP/RX IDLR]]

[[Media:SamplesFilesCorrespondanceTable SF301a EYKZ201522111.xls | Microarray Corresponding Files Table]]

[[Media: GMBuilder Shigella flexneri.zip]]

[[Media: QA Files.zip | Download QA files]]

[[Media:GMBuilder December7 2015 build 2.zip]]

[[Media:GenMAPP Builder 12 14 2015.zip]]

[[Media:FinalOTSPresentation.pptx | '''Final PowerPoint Presentation''']]

==GenMAPP User Files==
[[Media:CompiledRaw data RPRX IDLR EYKZ2015121.xlsx | ScalingCentering file 12/1 .xlsx]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.gmf | Compiled Raw Data 12/8 .gmf]]

[[Media:Filtered MAPPFinder Results.xlsx | Filtered MAPPFinder Results .xlsx]]

[[Media:MAPPFinderResults.zip | Filtered MAPPFinder Results (common GO terms highlighted) .png]]

[[Media:Flagellum Ribosomal Mapp 1 60min 20151012.jpg | RP vs RX 1 MIC @ 60 minutes MAPP 12/12 .jpg]]

[[Media:Flagellum Ribosomal Mapp 0pt5 10min 20151012.jpg | RP vs RX 0.5 MIC @ 10 minutes MAPP 12/12 .jpg]]

====RP (Erich)====
[[Media:CompiledRaw data GenMAPP Final RP IDLR EYKZ2015126.xlsx | RP Compiled Raw Data Final 12/10]]

[[Media:CompiledRaw data GenMAPP ready RP IDLR EYKZ2015126.txt | RP .txt format GenMAPP ready 12/6]]

[[Media:CompiledRaw data Errors RP EYKZ2015126.EX.xlsx | RP Exceptions file in Excel format (filtered)]]

[[Media:CompiledRaw data Errors RP EYKZ2015126.EX.txt | RP Exceptions (txt)]]

[[Media:CompiledRaw data GenMAPP ready RP IDLR EYKZ2015126.gex | RP .gex file]]

====RX (Kristin)====
[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.xlsx | RX Compiled Raw Data 12/6]]

[[Media:CompiledRaw data statistics BonferroniPvalue RP IDLR EYKZ2015126.txt | RX .txt format GenMAPP ready 12/6]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.xlsx | RX Compiled Raw Data as of 12/6]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.txt | RX .txt format updated as of 12/6]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.EX.txt | RX Exceptions file]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.gex | RX .gex file]]

[[Media:CompiledRaw data RX IDLR KZ2015126.EX.xlsx | RX Exceptions file in Excel format (filtered)]]

{{Template:Oregon Trail Survivors}}

Template:Oregon Trail Survivors

2015-12-16T20:34:47Z

Kzebrows: /* Helpful Links */ edit name

== Helpful Links ==

[[OTS Deliverables | Deliverables]]
{| class="wikitable" style="width: 100%; text-align: center"
! colspan="6"| Team Links
|-
! Files
! Team Members
! [[Week 11 | Week 11 Assignment]]
! [[Week 12 | Week 12 Assignment]]
! [[Week 14 | Week 14 Assignment]]
! [[Week 15 | Week 15 Assignment]]
|-
| rowspan="2" | [[OTS Deliverables | OTS Deliverables]]
| [[User:Troque | Trixie]]
| [[Troque_Week_11 | Week 11]]
| [[Troque_Week_12 | Week 12]]
| [[Troque_Week_14 | Week 14]]
| [[Troque_Week_15 | Week 15]]
|-
| [[User:Jwoodlee | Jake]]
| [[Jwoodlee_Week_11|Week 11]]
| [[Jwoodlee_Week_12|Week 12]]
| [[Jwoodlee_Week_14|Week 14]]
| [[Jwoodlee_Week_15|Week 15]]
|-
| rowspan="2" | [[Gene_Database_Testing_Report_-_Oregon_Trail_Survivors | Gene Database Testing Report]]
| [[User:Eyanosch | Erich]]
| [[Eyanosch Week 11|Week 11]]
| [[Eyanosch Week 12|Week 12]]
| [[Eyanosch Week 14|Week 14]]
| [[Eyanosch Week 15|Week 15]]
|-
| [[User:Kzebrows | Kristin]]
| [[Kzebrows Week 11| Week 11]]
| [[Kzebrows Week 12| Week 12]]
| [[Kzebrows Week 14| Week 14]]
| [[Kzebrows Week 15| Week 15]]
|-
|}

[[Category:Group Projects]]
[[Category:Oregon Trail Survivors]]

{{Gene Database Project Links}}

OTS Deliverables

2015-12-16T20:33:56Z

Kzebrows: Kzebrows moved page OTS Files to OTS Deliverables

==OTS Files==

[[Media:Micro Array Shigella Flexneri 20151011.pdf | Shigella Flexneri Microarray Paper (PDF)]]

[[Media:Shigellamicroarray.pptx | Microarray Journal Club Power Point]]

[[Media:CompiledRaw data RPRX IDLR EYKZ20152211.xlsx | Microarray Compiled Raw Data RP/RX IDLR]]

[[Media:SamplesFilesCorrespondanceTable SF301a EYKZ201522111.xls | Microarray Corresponding Files Table]]

[[Media: GMBuilder Shigella flexneri.zip]]

[[Media: QA Files.zip | Download QA files]]

[[Media:GMBuilder December7 2015 build 2.zip]]

[[Media:GenMAPP Builder 12 14 2015.zip]]

[[Media:GenMAPP Builder 12 14 2015 Number 2.zip]]

[[Media:FinalOTSPresentation.pptx | '''Final PowerPoint Presentation''']]

==GenMAPP User Files==
[[Media:CompiledRaw data RPRX IDLR EYKZ2015121.xlsx | ScalingCentering file 12/1 .xlsx]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.gmf | Compiled Raw Data 12/8 .gmf]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.xlsx | Final Compiled Raw Data 12/10 .xlsx]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.txt | Final Compiled Raw Data 12/10 .xlsx]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210 (1).gex | Final Compiled Raw Data 12/12 .gex]]

[[Media:Filtered MAPPFinder Results.xlsx | Filtered MAPPFinder Results .xlsx]]

[[Media:MAPPFinderResults.zip | Filtered MAPPFinder Results (common GO terms highlighted) .png]]

[[Media:Flagellum Ribosomal Mapp 1 60min 20151012.jpg | RP vs RX 1 MIC @ 60 minutes MAPP 12/12 .jpg]]

[[Media:Flagellum Ribosomal Mapp 0pt5 10min 20151012.jpg | RP vs RX 0.5 MIC @ 10 minutes MAPP 12/12 .jpg]]

====RP (Erich)====
[[Media:CompiledRaw data GenMAPP Final RP IDLR EYKZ2015126.xlsx | RP Compiled Raw Data Final 12/10]]

[[Media:CompiledRaw data GenMAPP ready RP IDLR EYKZ2015126.txt | RP .txt format GenMAPP ready 12/6]]

[[Media:CompiledRaw data Errors RP EYKZ2015126.EX.xlsx | RP Exceptions file in Excel format (filtered)]]

[[Media:CompiledRaw data Errors RP EYKZ2015126.EX.txt | RP Exceptions (txt)]]

[[Media:CompiledRaw data GenMAPP ready RP IDLR EYKZ2015126.gex | RP .gex file]]

====RX (Kristin)====
[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.xlsx | RX Compiled Raw Data 12/6]]

[[Media:CompiledRaw data statistics BonferroniPvalue RP IDLR EYKZ2015126.txt | RX .txt format GenMAPP ready 12/6]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.xlsx | RX Compiled Raw Data as of 12/6]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.txt | RX .txt format updated as of 12/6]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.EX.txt | RX Exceptions file]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.gex | RX .gex file]]

[[Media:CompiledRaw data RX IDLR KZ2015126.EX.xlsx | RX Exceptions file in Excel format (filtered)]]

{{Template:Oregon Trail Survivors}}

OTS Files

2015-12-16T20:33:56Z

Kzebrows: Kzebrows moved page OTS Files to OTS Deliverables

#REDIRECT [[OTS Deliverables]]

OTS Deliverables

2015-12-16T19:44:48Z

Kzebrows: /* GenMAPP User Files */ edit names

OTS Deliverables

2015-12-16T19:44:15Z

Kzebrows: /* GenMAPP User Files */ edit link names

==OTS Files==

[[Media:Micro Array Shigella Flexneri 20151011.pdf | Shigella Flexneri Microarray Paper (PDF)]]

[[Media:Shigellamicroarray.pptx | Microarray Journal Club Power Point]]

[[Media:CompiledRaw data RPRX IDLR EYKZ20152211.xlsx | Microarray Compiled Raw Data RP/RX IDLR]]

[[Media:SamplesFilesCorrespondanceTable SF301a EYKZ201522111.xls | Microarray Corresponding Files Table]]

[[Media: GMBuilder Shigella flexneri.zip]]

[[Media: QA Files.zip | Download QA files]]

[[Media:GMBuilder December7 2015 build 2.zip]]

[[Media:GenMAPP Builder 12 14 2015.zip]]

[[Media:GenMAPP Builder 12 14 2015 Number 2.zip]]

[[Media:FinalOTSPresentation.pptx | '''Final PowerPoint Presentation''']]

==GenMAPP User Files==
[[Media:CompiledRaw data RPRX IDLR EYKZ2015121.xlsx | ScalingCentering file from 12/1]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.gmf | Compiled Raw Data .gmf 12/8]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.xlsx | Final Compiled Raw Data 12/10 Excel format]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.txt | Final Compiled Raw Data 12/10 .txt format]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210 (1).gex | Final Compiled Raw Data 12/12 .gex]]

[[Media:Filtered MAPPFinder Results.xlsx | Filtered MAPPFinder Results .xlsx]]

[[Media:MAPPFinderResults.zip | Filtered MAPPFinder Results (common GO terms highlighted) .png]]

[[Media:Flagellum Ribosomal Mapp 1 60min 20151012.jpg | RP vs RX 1 MIC @ 60 minutes MAPP 12/12 .jpg]]

[[Media:Flagellum Ribosomal Mapp 0pt5 10min 20151012.jpg | RP vs RX 0.5 MIC @ 10 minutes MAPP 12/12 .jpg]]

====RP (Erich)====
[[Media:CompiledRaw data GenMAPP Final RP IDLR EYKZ2015126.xlsx | RP Compiled Raw Data Final 12/10]]

[[Media:CompiledRaw data GenMAPP ready RP IDLR EYKZ2015126.txt | RP .txt format GenMAPP ready 12/6]]

[[Media:CompiledRaw data Errors RP EYKZ2015126.EX.xlsx | RP Exceptions file in Excel format (filtered)]]

[[Media:CompiledRaw data Errors RP EYKZ2015126.EX.txt | RP Exceptions (txt)]]

[[Media:CompiledRaw data GenMAPP ready RP IDLR EYKZ2015126.gex | RP .gex file]]

====RX (Kristin)====
[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.xlsx | RX Compiled Raw Data 12/6]]

[[Media:CompiledRaw data statistics BonferroniPvalue RP IDLR EYKZ2015126.txt | RX .txt format GenMAPP ready 12/6]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.xlsx | RX Compiled Raw Data as of 12/6]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.txt | RX .txt format updated as of 12/6]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.EX.txt | RX Exceptions file]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.gex | RX .gex file]]

[[Media:CompiledRaw data RX IDLR KZ2015126.EX.xlsx | RX Exceptions file in Excel format (filtered)]]

{{Template:Oregon Trail Survivors}}

OTS Deliverables

2015-12-16T19:43:20Z

Kzebrows: /* GenMAPP User Files */ add link to filtered and highlighted results

==OTS Files==

[[Media:Micro Array Shigella Flexneri 20151011.pdf | Shigella Flexneri Microarray Paper (PDF)]]

[[Media:Shigellamicroarray.pptx | Microarray Journal Club Power Point]]

[[Media:CompiledRaw data RPRX IDLR EYKZ20152211.xlsx | Microarray Compiled Raw Data RP/RX IDLR]]

[[Media:SamplesFilesCorrespondanceTable SF301a EYKZ201522111.xls | Microarray Corresponding Files Table]]

[[Media: GMBuilder Shigella flexneri.zip]]

[[Media: QA Files.zip | Download QA files]]

[[Media:GMBuilder December7 2015 build 2.zip]]

[[Media:GenMAPP Builder 12 14 2015.zip]]

[[Media:GenMAPP Builder 12 14 2015 Number 2.zip]]

[[Media:FinalOTSPresentation.pptx | '''Final PowerPoint Presentation''']]

==GenMAPP User Files==
[[Media:CompiledRaw data RPRX IDLR EYKZ2015121.xlsx | ScalingCentering file from 12/1]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.gmf | Compiled Raw Data .gmf 12/8]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.xlsx | Final Compiled Raw Data 12/10 Excel format]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.txt | Final Compiled Raw Data 12/10 .txt format]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210 (1).gex | Final Compiled Raw Data 12/12 .gex]]

[[Media:Filtered MAPPFinder Results.xlsx | Filtered MAPPFinder Results]]

[[Media:MAPPFinderResults.zip | Filtered MAPPFinder results with common GO terms highlighted]]

[[Media:Flagellum Ribosomal Mapp 1 60min 20151012.jpg | RP vs RX 1 MIC @ 60 minutes MAPP 12/12 .jpg]]

[[Media:Flagellum Ribosomal Mapp 0pt5 10min 20151012.jpg | RP vs RX 0.5 MIC @ 10 minutes MAPP 12/12 .jpg]]

====RP (Erich)====
[[Media:CompiledRaw data GenMAPP Final RP IDLR EYKZ2015126.xlsx | RP Compiled Raw Data Final 12/10]]

[[Media:CompiledRaw data GenMAPP ready RP IDLR EYKZ2015126.txt | RP .txt format GenMAPP ready 12/6]]

[[Media:CompiledRaw data Errors RP EYKZ2015126.EX.xlsx | RP Exceptions file in Excel format (filtered)]]

[[Media:CompiledRaw data Errors RP EYKZ2015126.EX.txt | RP Exceptions (txt)]]

[[Media:CompiledRaw data GenMAPP ready RP IDLR EYKZ2015126.gex | RP .gex file]]

====RX (Kristin)====
[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.xlsx | RX Compiled Raw Data 12/6]]

[[Media:CompiledRaw data statistics BonferroniPvalue RP IDLR EYKZ2015126.txt | RX .txt format GenMAPP ready 12/6]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.xlsx | RX Compiled Raw Data as of 12/6]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.txt | RX .txt format updated as of 12/6]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.EX.txt | RX Exceptions file]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.gex | RX .gex file]]

[[Media:CompiledRaw data RX IDLR KZ2015126.EX.xlsx | RX Exceptions file in Excel format (filtered)]]

{{Template:Oregon Trail Survivors}}

OTS Deliverables

2015-12-16T19:42:28Z

Kzebrows: /* OTS Files */ edit name

==OTS Files==

[[Media:Micro Array Shigella Flexneri 20151011.pdf | Shigella Flexneri Microarray Paper (PDF)]]

[[Media:Shigellamicroarray.pptx | Microarray Journal Club Power Point]]

[[Media:CompiledRaw data RPRX IDLR EYKZ20152211.xlsx | Microarray Compiled Raw Data RP/RX IDLR]]

[[Media:SamplesFilesCorrespondanceTable SF301a EYKZ201522111.xls | Microarray Corresponding Files Table]]

[[Media: GMBuilder Shigella flexneri.zip]]

[[Media: QA Files.zip | Download QA files]]

[[Media:GMBuilder December7 2015 build 2.zip]]

[[Media:GenMAPP Builder 12 14 2015.zip]]

[[Media:GenMAPP Builder 12 14 2015 Number 2.zip]]

[[Media:FinalOTSPresentation.pptx | '''Final PowerPoint Presentation''']]

==GenMAPP User Files==
[[Media:CompiledRaw data RPRX IDLR EYKZ2015121.xlsx | ScalingCentering file from 12/1]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.gmf | Compiled Raw Data .gmf 12/8]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.xlsx | Final Compiled Raw Data 12/10 Excel format]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.txt | Final Compiled Raw Data 12/10 .txt format]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210 (1).gex | Final Compiled Raw Data 12/12 .gex]]

[[Media:Filtered MAPPFinder Results.xlsx | Filtered MAPPFinder Results]]

[[Media:Flagellum Ribosomal Mapp 1 60min 20151012.jpg | RP vs RX 1 MIC @ 60 minutes MAPP 12/12 .jpg]]

[[Media:Flagellum Ribosomal Mapp 0pt5 10min 20151012.jpg | RP vs RX 0.5 MIC @ 10 minutes MAPP 12/12 .jpg]]

====RP (Erich)====
[[Media:CompiledRaw data GenMAPP Final RP IDLR EYKZ2015126.xlsx | RP Compiled Raw Data Final 12/10]]

[[Media:CompiledRaw data GenMAPP ready RP IDLR EYKZ2015126.txt | RP .txt format GenMAPP ready 12/6]]

[[Media:CompiledRaw data Errors RP EYKZ2015126.EX.xlsx | RP Exceptions file in Excel format (filtered)]]

[[Media:CompiledRaw data Errors RP EYKZ2015126.EX.txt | RP Exceptions (txt)]]

[[Media:CompiledRaw data GenMAPP ready RP IDLR EYKZ2015126.gex | RP .gex file]]

====RX (Kristin)====
[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.xlsx | RX Compiled Raw Data 12/6]]

[[Media:CompiledRaw data statistics BonferroniPvalue RP IDLR EYKZ2015126.txt | RX .txt format GenMAPP ready 12/6]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.xlsx | RX Compiled Raw Data as of 12/6]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.txt | RX .txt format updated as of 12/6]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.EX.txt | RX Exceptions file]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.gex | RX .gex file]]

[[Media:CompiledRaw data RX IDLR KZ2015126.EX.xlsx | RX Exceptions file in Excel format (filtered)]]

{{Template:Oregon Trail Survivors}}

File:MAPPFinderResults.zip

2015-12-16T19:41:38Z

Kzebrows: MAPPFinder Results for OTS with common GO terms highlighted.

MAPPFinder Results for OTS with common GO terms highlighted.

OTS Deliverables

2015-12-16T19:23:54Z

Kzebrows: /* GenMAPP User Files */ add link to .gmf

==OTS Files==

[[Media:Micro Array Shigella Flexneri 20151011.pdf | Shigella Flexneri Microarray Paper (PDF)]]

[[Media:Shigellamicroarray.pptx | Microarray Journal Club Power Point]]

[[Media:CompiledRaw data RPRX IDLR EYKZ20152211.xlsx | Microarray Compiled Raw Data RP/RX IDLR]]

[[Media:SamplesFilesCorrespondanceTable SF301a EYKZ201522111.xls | Microarray Corresponding Files Table]]

[[Media: GMBuilder Shigella flexneri.zip]]

[[Media: QA Files.zip | Download QA files]]

[[File:GMBuilder December7 2015 build 2.zip]]

[[File:GenMAPP Builder 12 14 2015.zip]]

[[File:GenMAPP Builder 12 14 2015 Number 2.zip]]

[[Media:FinalOTSPresentation.pptx | '''Final PowerPoint Presentation''']]

==GenMAPP User Files==
[[Media:CompiledRaw data RPRX IDLR EYKZ2015121.xlsx | ScalingCentering file from 12/1]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.gmf | Compiled Raw Data .gmf 12/8]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.xlsx | Final Compiled Raw Data 12/10 Excel format]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.txt | Final Compiled Raw Data 12/10 .txt format]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210 (1).gex | Final Compiled Raw Data 12/12 .gex]]

[[Media:Filtered MAPPFinder Results.xlsx | Filtered MAPPFinder Results]]

[[Media:Flagellum Ribosomal Mapp 1 60min 20151012.jpg | RP vs RX 1 MIC @ 60 minutes MAPP 12/12 .jpg]]

[[Media:Flagellum Ribosomal Mapp 0pt5 10min 20151012.jpg | RP vs RX 0.5 MIC @ 10 minutes MAPP 12/12 .jpg]]

====RP (Erich)====
[[Media:CompiledRaw data GenMAPP Final RP IDLR EYKZ2015126.xlsx | RP Compiled Raw Data Final 12/10]]

[[Media:CompiledRaw data GenMAPP ready RP IDLR EYKZ2015126.txt | RP .txt format GenMAPP ready 12/6]]

[[Media:CompiledRaw data Errors RP EYKZ2015126.EX.xlsx | RP Exceptions file in Excel format (filtered)]]

[[Media:CompiledRaw data Errors RP EYKZ2015126.EX.txt | RP Exceptions (txt)]]

[[Media:CompiledRaw data GenMAPP ready RP IDLR EYKZ2015126.gex | RP .gex file]]

====RX (Kristin)====
[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.xlsx | RX Compiled Raw Data 12/6]]

[[Media:CompiledRaw data statistics BonferroniPvalue RP IDLR EYKZ2015126.txt | RX .txt format GenMAPP ready 12/6]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.xlsx | RX Compiled Raw Data as of 12/6]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.txt | RX .txt format updated as of 12/6]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.EX.txt | RX Exceptions file]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.gex | RX .gex file]]

[[Media:CompiledRaw data RX IDLR KZ2015126.EX.xlsx | RX Exceptions file in Excel format (filtered)]]

{{Template:Oregon Trail Survivors}}

File:CompiledRaw data RPRX IDLR EYKZ2015126.gmf

2015-12-16T19:22:08Z

Kzebrows: Compiled Raw Data .gmf file for OTS

Compiled Raw Data .gmf file for OTS

Kzebrows Week 15

2015-12-16T00:06:38Z

Kzebrows: /* Electronic Lab Notebook */ update powerpoint link

==Electronic Lab Notebook==

Given the "Run Time 53" error when I tried to run my color set through MAPPFinder, I tried something else with the help of Dr. Dahlquist.
*Opened Criterion-GO.txt file in Excel
*Filtered Excel file:
**Number Changed by between 4 and 100
**Z score by greater than 2
**PermuteP by less than 0.05
**Adjusted P by less than 0.1

We decided to look at the criterion files for RX and RP -0pt5-10 and RX and RP -1-60. These were the samples at the smallest and largest time points at both concentrations, and by looking at the files and filtering them by the above criteria we were able to find some similarities:
*RX and RP 0pt5-10 gene expression significantly increased: metabolic processes
*RX and RP 0pt5-10 gene expression significantly decreased: ribosome
*RX and RP 1-60 gene expression significantly increased: flagellar production
*RX and RP 1-60 gene expression significantly decreased: metabolic processes

Next, with the help of Dr. Dahlquist, Erich and I decided that Erich would work on creating the gene mapp and I would work on creating color sets for each sample/time period. I created a final compiled raw data file by copying/pasting Erich's RP sample data into my RX sample data file. This file can be found on the [[OTS Files | OTS Files]] page under GenMAPP User Files.

Next I made sure the correct database build was being used in the GenMAPP program. I selected Data > Expression Dataset Manager and under Color Sets > Name I typed RX-0pt5-10. For Gene Value I typed Avg_LogFC RX-0pt5-10. I then added a New color set with the label "Increased", color red, and criterion "[Avg_LogFC RX-0pt5-10] > 0.25 AND [PValue_LogFC RX-0pt5-10] < 0.05." I added a second color set with the label "Decreased", color green, and criterion "[Avg_LogFC RX-0pt5-10] <-0.25 AND [Pvalue_LogFC RX-0pt5-10] < 0.05." I then saved this color set so it would appear on the mapp. I added 12 color sets, one for each sample/time period combo, starting with all RX-0.5 x MICs and then the corresponding 0.5 x MIC for RP. I then did the same for 1 x MIC. When I got to 1 x MIC at 30 minutes I encountered a GenMAPP error where the file could not be read. At that point I spoke to Dr. Dahlquist, who was able to fix it on my .gex file and upload that file, which I could then edit and use in order to proceed.

I then opened all of the Criterion files with Excel and made a compiled filtered file with the criteria above, the completed version of which is found [[Media:Filtered MAPPFinder Results.xlsx | here]]. I color coded each file (RP is blue, RX is pink) to highlight the top 10 GO terms for the different drugs at 1 x MIC at 60 minutes and 0.5 x MIC at 10 minutes (chosen because of their significance in the sanity check and out of our personal preferences with what we had already worked with) and put images of these tables in the team Power Point. I deleted all columns except for GO ID, name of GO term, number changed/present and percentage, number present/number in GO and percentage, regular p value, and adjusted p value.

[[Media:FinalOTSPresentation.pptx | '''Final PowerPoint Presentation''']]
{{Template:Kzebrows}} [[Category: Journal Entry]]

OTS Deliverables

2015-12-16T00:06:08Z

Kzebrows: /* OTS Files */ edit final OTS presentation link

==OTS Files==

[[Media:Micro Array Shigella Flexneri 20151011.pdf | Shigella Flexneri Microarray Paper (PDF)]]

[[Media:Shigellamicroarray.pptx | Microarray Journal Club Power Point]]

[[Media:CompiledRaw data RPRX IDLR EYKZ20152211.xlsx | Microarray Compiled Raw Data RP/RX IDLR]]

[[Media:SamplesFilesCorrespondanceTable SF301a EYKZ201522111.xls | Microarray Corresponding Files Table]]

[[Media: GMBuilder Shigella flexneri.zip]]

[[Media: QA Files.zip | Download QA files]]

[[File:GMBuilder December7 2015 build 2.zip]]

[[File:GenMAPP Builder 12 14 2015.zip]]

[[File:GenMAPP Builder 12 14 2015 Number 2.zip]]

[[Media:FinalOTSPresentation.pptx | '''Final PowerPoint Presentation''']]

==GenMAPP User Files==
[[Media:CompiledRaw data RPRX IDLR EYKZ2015121.xlsx | ScalingCentering file from 12/1]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.xlsx | Final Compiled Raw Data 12/10 Excel format]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.txt | Final Compiled Raw Data 12/10 .txt format]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210 (1).gex | Final Compiled Raw Data 12/12 .gex]]

[[Media:Filtered MAPPFinder Results.xlsx | Filtered MAPPFinder Results]]

[[Media:Flagellum Ribosomal Mapp 1 60min 20151012.jpg | RP vs RX 1 MIC @ 60 minutes MAPP 12/12 .jpg]]

[[Media:Flagellum Ribosomal Mapp 0pt5 10min 20151012.jpg | RP vs RX 0.5 MIC @ 10 minutes MAPP 12/12 .jpg]]

====RP (Erich)====
[[Media:CompiledRaw data GenMAPP Final RP IDLR EYKZ2015126.xlsx | RP Compiled Raw Data Final 12/10]]

[[Media:CompiledRaw data GenMAPP ready RP IDLR EYKZ2015126.txt | RP .txt format GenMAPP ready 12/6]]

[[Media:CompiledRaw data Errors RP EYKZ2015126.EX.xlsx | RP Exceptions file in Excel format (filtered)]]

[[Media:CompiledRaw data Errors RP EYKZ2015126.EX.txt | RP Exceptions (txt)]]

[[Media:CompiledRaw data GenMAPP ready RP IDLR EYKZ2015126.gex | RP .gex file]]

====RX (Kristin)====
[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.xlsx | RX Compiled Raw Data 12/6]]

[[Media:CompiledRaw data statistics BonferroniPvalue RP IDLR EYKZ2015126.txt | RX .txt format GenMAPP ready 12/6]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.xlsx | RX Compiled Raw Data as of 12/6]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.txt | RX .txt format updated as of 12/6]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.EX.txt | RX Exceptions file]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.gex | RX .gex file]]

[[Media:CompiledRaw data RX IDLR KZ2015126.EX.xlsx | RX Exceptions file in Excel format (filtered)]]

{{Template:Oregon Trail Survivors}}

File:FinalOTSPresentation.pptx

2015-12-16T00:04:14Z

Kzebrows: final OTS presentation

final OTS presentation

Eyanosch Week 15

2015-12-15T07:33:29Z

Kzebrows: /* Electronic Lab Notebook */ link to final Power Point

==Erich Yanoschik==
[[User:Eyanosch | Erich Yanoschik]]

==Electronic lab notebook==
*Ran GenMAPP and produced Criterion0-GO.txt files for increased and decreased of both RP drug times. with the data from the GO map. Analyzed this data in excel
*Opened the Criterion0-GO.txt file in excel
*Focus on the most Induced or Repressed GO terms so set the Z score Greater than 2, PermuteP less than 0.05, Adjusted P less than 0.1, and Number Changed (is greater than or equal to 4, and is less than or equal to 100)
*For RP-1-60 The major Genes Induced dealt with cell motility (Cell projection, pilus, cell adhesion, and biological adhesion)
*Something interesting to note is that Cell Projection had 35/42

I will be working on the RPs and Kristin will be working on the RXs of the same time points and compare our results. (We hypothesize that we will see similar Inductions and Reductions of Genes.

===RP-1-60 Increased and Decreased===

=====Increased=====

The genes that showed an increase in expression were mainly associated with flagellar assembly and motility. I.E. cell projection, pilus, cell adhesion, bacterial-type flagellum, etc.

=====Decreased=====

The genes that showed a decrease in expression were associated with ribosomes and protein synthesis. I.E. translation, peptide biosynthetic process, peptide metabolic process, ribosome, RNA binding, etc.

===RP-0.5-10 Increased and Decreased===

=====Increased=====

The genes that showed an increase in expression were involved in metabolic processes and cell projection. I.E. NADP metabolic process, glucose 6-phosphate metabolic process, nucleoside phosphate metabolic process, cellular metabolic compound salvage, cell projection organization, etc.

=====Decreased=====

The genes that showed a decease in expression were involved in the ribosome. I.E. Ribosome, ribonucleoprotein complex, structural constituent of ribosome, structural molecule activity, translation, etc.

=====Flagellar assembly=====
*Looked up genes for Flagellar assembly - Shigella flexneri 301 (serotype 2a) at (http://www.genome.jp/kegg-bin/show_pathway?org_name=sfl&mapno=02040&mapscale=&show_description=show)
*right click on the gene box and enter the information for Gene identification
**Gene ID
***SF1966
**Gene ID System
*** OrderedLocusNames
**Gene Label
***fliC
*If the box appears blank, just reset the desired expression data set.

=====Ribosome=====
*Searched genes related to Ribosome - Shigella flexneri 301 (serotype 2a)
*Completed same process as denoted within Flagellar assembly

=====Metabolic Process=====
*Searched genes related to the metabolic processes of Glycolysis and the TCA cycle
*Completed same process as Flagellar assembly

====Create Genes on our Map====
*searched genes based on the pathways of greatest expression
*to create genes on our map click the gene button on the left next to label, click a place on the map.
*Go to http://www.genome.jp/kegg/pathway.html (Kegg pathway Database)
*search organism Shigella Flexneri 301 (serotype 2a)
*Enter the GO keyword or pathway you are looking into (I.E. cell projection)

===PowerPoint===
*worked on slides
**Background for Shigella flexneri
**GenMAPP MAPP slides and the pathways involved
**Overall final analysis part

[[Media:OTS ShigellaFinalPresentation.pptx | '''Final PowerPoint Presentation''']]

All the current files are located under RP (Erich) of the [[OTS Files | Wiki page]]

{{Template: Pertinent Class Information}}

[[Category: Personal Journal Week 14]]

Oregon Trail Survivors

2015-12-15T07:33:01Z

Kzebrows: /* Goals */ add link to final power point

<div style="text-align: center; font-size: 250%; line-height: 1.25em">'''Oregon Trail Survivors'''</div>

<div class="center">
[[Image:Oregon-trail-dysentery 5 biodb.jpg | thumb | right | 350px | The third leading cause of death in the Oregon Trail.]]
</div>

== Group Members ==
*Coder: [[User:Jwoodlee | Jake Woodlee]]
*Quality Assurance: [[User:Troque | Trixie Roque]]
*GenMAPP Users: [[User:Eyanosch | Erich Yanoschik]] & [[User:Kzebrows | Kristin Zebrowski]]
* Project Manager: [[User:Kzebrows | Kristin Zebrowski]]

{{Template:Oregon Trail Survivors}}

=== Presentation (QA/Coder) ===
* PDF can be seen [[Media: Genome Paper Presentation BioDB.pdf | here]]

===Group Meeting Times===
*Thursday, November 5th at 8:00 pm
*Met most Sundays and Monday evenings in the Biol DB lab to check in with one another.

== Goals ==
Over the upcoming weeks our group will be investigating ''Shigella flexneri''.

===Week 10===

# Find genome sequence paper
# Find 4-8 microarray data and paper that goes with the genome paper
# Compile team page to and create a ranked annotated bibliography

===Week 11===

#Prepare for journal club presentations in Weeks 12 and 13
#Begin initial tasks on research project

Click on username links for more information regarding each team member's contributions for Week 11.

[[Jwoodlee Week 11 | Jake]]: Read through the genome paper and tried to get through the accessible things I had the ability to understand. Made an outline for the genome paper. Worked on the presentation with Trixie and found a database. And of course I answered the assigned questions.

[[Troque Week 11 | Trixie]]: Mainly focused on the Genome paper presentation with Jake. This includes searching for a viable database that we will be using for the rest of the group assignment and actually creating the presentation we will be doing for October 17th, 2015. I've also updated our group page to reflect what Dr. Dahlquist suggested would improve our team page.

[[Eyanosch Week 11 | Erich]]: Analyzed the microarray paper in order to describe the experimental design of the microarray data, treatments, number of replicates, and dye swaps. Worked with Kristin to produce the power point for the GennMAP users presentation at Journal Club. Worked on the individual journal entry and created an outline of the microarray paper.

[[Kzebrows Week 11 | Kristin]]: Using the team's selected microarray paper I developed an outline including background information, experimental outline/methods and how samples corresponded to the data, a brief description of the results, and a discussion including the implications of the research and its results in comparison to previous studies. Using this outline, I created a flow chart corresponding to the research. I also worked with Erich in order to create a PowerPoint for the Journal Club presentation on Nov. 24.

=== Week 12 ===
#QA will be doing an initial database export.
#Coder will be setting up version control.
#GenMAPP users will compile the raw data from the micorarray file to prepare for normalization and statistic analysis (will begin if time permits after consultation with Dr. Dahlquist). Additionally, the GenMAPP users will be determining the number of biological or technical replicates and how samples were labeled.
#Coder and QA will present on genome paper in class Tuesday, Nov. 24.

Click on username links for more information regarding each team member's contributions for Week 12.
* [[Jwoodlee Week 12 | Jake]]:Setup my environment in eclipse, created the s-flexneri branch, created my own copy of GenMAPP that I can modify for later use and I cloned the repository with the Git commands.
* [[Troque Week 12 | Trixie]]: Finished the preliminary export of the XML and GOA files and the corresponding Gene Testing Report. Also started identifying the gene id's for the specie. Decided on file management system with Jake.
* [[Eyanosch Week 12 | Erich]]: Worked with Kristin in determining the total number of biological and technical replicates. Compiled the raw data for RP samples, specifically the ID and Log ratio columns. Incorporated the RP and RX data into one spreadsheet with Kristins data. We created a table of the sample data and file each corresponds with, also figured out there were no dye swaps in the experiment(The control was the Cy3 dye and the treatment the Cy5 dye).
* [[Kzebrows Week 12 | Kristin]]: Determined that there were 3 biological replicates per treatment for 6 treatments total. Compiled raw data for RX samples by re-naming columns for ID and Log Ratio and putting into same worksheet, which was later combined with Erich's worksheet for RP samples. Erich and I met and worked together to create a table of which samples correspond to which file.

===Week 14===
#QA will be documenting the IDs using MATCH, Postgres, Microsoft Access, and Excel and get a head start of Milestone 3, which is customizing the TallyEngine.
#Coder will determine and document any modified export behavior that the GenMAPP Builder will have and resolve bugs. Coder will also work with QA by uploading GM Builder for additional export.
#GenMAPP Users will perform statistical analysis on Excel (normalization, tests) and format for import into GenMAPP. Users will also import data into GenMAPP and run MAPPFinder, and then document these test runs.

Click on username links for more information regarding each team member's contributions for Week 14.
* [[Jwoodlee Week 14 | Jake]]: Finished custom GenMAPP builder, committed to GitHub, and ran the export with the custom software. This created a custom .gdb which was opened in Microsoft Access and GenMAPP to check for accuracy.
* [[Troque Week 14 | Trixie]]: Trixie has finished identifying the gene IDs using MATCH, Postgres, Microsoft Access, and Excel. It was discovered that some IDs are in "dbReference/property&type&gene ID", and so another export was done on 12/7/15 to add the newly discovered gene IDs.
* [[Eyanosch Week 14 | Erich]]: Kristin and I completed the corrections provided via Dr. Dhalquist on Kristins talk page. We split the work into two halves and I worked on the RP data. We completed the statistics, Bonferroni p value correction, and the sanity check. I downloaded the database and formatted/exported the file for GenMAPP, and tried to create a GO tree for one of the trail points with RX.
* [[Kzebrows Week 14 | Kristin]]: This week Erich and I made corrections from the talk page and normalized log ratios for the slides in the experiment. I completed the statistical analysis for RX samples and calculated the Bonferroni p value correction. I also performed a sanity check for the RX samples and, going off of that, I calculated the Benjamini & Hochberg p value correction for RX-1-30, which had the most statistically significant changes in gene expression. I also formatted and exported the file for GenMAPP, downloaded the database, and attempted to create color sets to run the data set through MappFINDER.

==== Reflection ====

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?

''Kristin'':
#What worked?
#*In terms of communication is having a group text. We also meet at least once a week outside of class in order to work together on the assignments and make sure we are all on the same page. So far, this has allowed us to troubleshoot and address bugs together as a team quickly. It also worked for Erich and I to divide up the samples so that I did all RX and Erich did all RP. Then, we could work at the same time and double-check procedures with each other but we were still getting the work done twice as quickly.
#What didn't work?
#*After creating the initial compiled raw data file, I had to make several corrections before the file could be run through GenMAPP. First of all, I had to get rid of the ".", and I also had to change all #DIV/0! with a space character for the file to be read at all. Also, although we were unable to find all of the b#### and CP#### gene ID's in UniProt or ShiBASE. Also, after creating my color set and trying to run MAPPFinder, I tried three computers and all of them crashed with the "not responding" message.
#What will I do next to fix what didn't work?
#*I will communicate with the QA and Coder in order to create a database with a minimal number of "Gene ID not found's" and then communicate with Erich when we try to run our dataset through MappFinder. Once the gene database is re-customized and the export is complete I can try and re-run my dataset to see if that makes a difference.

'' Trixie '':
# What worked?
#* What worked in identifying the gene IDs is to look export .gdb file into Excel and compare with what the OrderedLocusNames table had (from Microsoft Access). From doing this, it was easier to find which genes were not found in the .gdb file and made it easier to look through them in the UniProt XML file. With the Excel file comparing the lists of gene IDs and using the CTRL+F shortcut, I was also able to discern which tags to include into the new builds for the databases. Because of this, I was able to confirm that some genes indeed do not exist in the XML file, while only a couple exist within the "dbReference" tag. In terms of group work, what worked is posting all our files into a single page as we progress through the assignment. Night meetings were also helpful in order to better communicate with the rest of my group.
# What didn't work?
#* What didn't work is using Match multiple times without thinking. Even when I was trying to match the number of gene IDs with what Tally Engine gives me, Match didn't really help me in identifying where to find the genes in the XML file. Waiting for the database to finish didn't help much at all since our builds would take more than 4 hours to finish.
# What will I do next to fix what didn't work?
#* What I would do next to fix what didn't work is to actually use Match in conjunction to the XML file, or just use the Excel method completely since that was actually more helpful in finding the necessary tags than the Match method. I would probably have to time myself to check the lab after about 4.5 hours since one of our builds lasted that long.

''Jake'':
#What worked?
#*Almost every procedural action I took from Dondi worked. The only hiccup I had was in regard to Eclipse and navigating the directories.
#What didn't work?
#*In Eclipse, my edits to the GenMAPP builder source code were causing red error marks, but after selecting "Organize Imports" from the source menu the errors were fixed easily and the proper classes were imported. Also I had difficulty navigating to the dist file in my Temp drive, however I traced this back within Eclipse and was able to make a zip that I could hand off to Trixie for export.
#What will I do next week to fix what didn't work?
#*It seems to me that there wasn't a whole lot that went wrong with my procedure. What wasn't working I already fixed. Currently Trixie and I are running an export that will take 4 hours with the new additions in the property files, so there may be some new hiccups when that export is finished but we will have to wait and see.

''Erich'':
# What worked?
#*Having a GenMAPP user meeting with Dr. Dhalquist helped focus on what goals we wanted to achieve by the time of our next meeting. A group text helped organize meeting times of both the coders and GenMAPP users helped keep us on schedule.
# What didn't work?
#*The GenMapp Gene Ontology Tree was unable to pull files for each GO selection. We need to work on and make sure the GO files can be found. We also had to remove and edit our compiled raw data files so that they are able to be read by GenMAPP.
# What will I do next to fix what didn't work?
#*A new .gex was created, so this might help with the problems experienced in the MappBuilder. Also communicating with the QA and coder to make sure we finish up the GO tree smoothly in order to assess the results of the Publication we chose for Shigella Flexneri.

===Week 15===
#Coder: Work with QA to fix bugs.
#QA: Work with coder to fix bugs in the .gdb.
#GenMAPP Users: Finish Milestone 3. Run tests with GenMAPP. Do a journal club outline of the paper to use in the Discussion section of group report and presentation. Create a .mapp file showing one changed pathway from the data.
#All team members will be working together to put together deliverables including the final report and presentation for next Tuesday.

[[Media:OTS ShigellaFinalPresentation.pptx | '''Final PowerPoint Presentation''']]

Click on username links for more information regarding each team member's contributions for Week 14.
* [[Jwoodlee Week 15 | Jake]]: Pulled Dondi's changes, and then created a new clean distribution. I then uploaded that distribution to our OTS Files page. Edited properties file for TallyEngine.
* [[Troque Week 15 | Trixie]]: Had to re-import to PostgreSQL due to having imported twice -- this resulted in the number of counts being twice as much as what was in the XML file. Also worked with Dr. Dionisio in order to find ~92 new IDs from the XML file that were not caught before and collaborated with Jake in order to make 2 more builds that should, ideally, produce the intended 92 genes.
* [[Eyanosch Week 15 | Erich]]: Used Kristin's color sets criterion GO files to fill out my gene expression MAPP. Made MAPPS for pathways that were significantly affected such as Metabolic procceses (glycolysis, TCA cycle), Flagellar Assembly, and Ribosome. Incorporated the data into slides for the power point and analyzed the data obtained with that produced from the microarray paper.
* [[Kzebrows Week 15 | Kristin]]: I created color sets with Increased/Decreased criteria for all of the 12 treatment/time point combos. Then, based on the criterion.go files, I created tables by filtering the results comparing the most commonly induced or repressed genes for the 1 x MIC at 60 minutes and 0.5 x MIC at 10 minutes between RX and RP. Strikingly, we found that between RX and RP the effects were very similar. I then compared them with the .mapp files that Erich created and put my portion of the project (compiled sanity check, color set, comparison tables) in the power point.

==Overview of Genome Paper==
*Used the genome sequencing article to perform a prospective search in the [https://apps.webofknowledge.com/UA_GeneralSearch_input.do?product=UA&search_mode=GeneralSearch&SID=1FRKcNxUgxiGX6spITI&preferencesSaved= Web of Science] database.
*Overview of the search:
**How many articles does this article cite? 37
**How many articles cite this article? 303
**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?
***Now that the genome has been sequenced, a majority of research has been done on discovering which genes are responsible for virulence and pathogenesis as well as potential antibiotics. Genomic research is also focused on how ''S. flexneri'' has been able to develop resistance to multiple drugs. Furthermore, ''Shigella'' is suspected to have evolved from ''Escherichia coli'' so a lot of research has been done in how and when pathogenic ''Shigella'' split from ''E. coli'' on the evolutionary tree.

==Annotated Bibliography==
=== Genome Paper ===
Jin, Q., Yuan, Z., Xu, J., Wang, Y., Shen, Y., Lu, W., … Yu, J. (2002). Genome sequence of ''Shigella flexneri'' 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157. Nucleic Acids Research, 30(20), 4432–4441.
* PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/?term=Genome+sequence+of+Shigella+flexneri+2a%3A+insights+into+pathogenicity+through+comparison+with+genomes+of+Escherichia+coli+K12+and+O157
* PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC137130/
* Publisher Full Text (HTML): http://nar.oxfordjournals.org/content/30/20/4432.full
* Publisher Full Text (PDF): http://nar.oxfordjournals.org/content/30/20/4432.full.pdf+html
* Copyright: 2002 Oxford University Press
* Publisher: Oxford University Press
* Availability: in print and online
* Did LMU pay a fee for this article: no

===Microarray Paper===





Fu H, Liu L, Zhang X, Zhu Y, Zhao L, Peng J, et al. (2012) Common Changes in Global Gene Expression Induced by RNA Polymerase Inhibitors in ''shigella flexneri''. PLoS ONE 7(3): e33240. doi:10.1371/journal.pone.0033240

*The link to the [http://www.ncbi.nlm.nih.gov/pubmed/22428000 abstract]
*The link to the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3299763/ full text of the article] in PubMed Central
*The link to the [http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0033240 full text of the article] (HTML format) from the publisher web site.
*The link to the [http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0033240&representation=PDF full PDF version] of the article from the publisher web site.
*Copyright: © 2012 Fu et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
*Does the journal own the copyright? NO
*Do the authors own the copyright? Yes
*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? PLoS One is the publisher/Journal. It hosts open access research articles. (Public Library of Science)
*Is this article available in print or online only? Online only
*Has LMU paid a subscription or other fee for your access to this article? No LMU has not paid a subscription or other fee because it is open access on the Public Library of Science.
*Use the genome sequencing article you found to perform a prospective search in the ISI Web of Science/Knowledge database.
**How many articles does this article cite? 25 cited references
**How many articles cite this article? 0 articles cite this article
**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?
*Well given that there are no papers that cite this paper there hasn't been anything done to build on this specific topic. In regards to the genome I think this paper has built on the work of the people who sequenced the first genome of Shigella flexneri as well as the other micro array papers.
*State which database you used to find the data and article: ArrayExpress
*State what you used as search terms and what type of search terms they were: "shigella flexneri" filtered by organism, experiment type: "rna assay", experiment type: "array assay"
*Give an overview of the results of the search.
**How many results did you get? 7 results returned with 6 viable options due to the number assays.
**Give an assessment of how relevant the results were: Very relevant, 6/7 results were viable.
*Link to [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-32978/?keywords=shigella+flexneri&organism=Shigella+flexneri&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array= microarray data]
*What experiment was performed? What was the "treatment" and what was the "control" in the experiment?
**Antibiotics (RNA Polymerase Inhibitors) were added to ''Shigella flexneri'' in order to see if bacteria became less active. The control was a group of bacteria with no drugs added to them, and the treatment was a group of bacteria with drugs added to them.
*Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each?
**There are two drugs RX and RP with 6 samples per drug. The experiment was run 3 times which yielded 36 assays. I believe that means 3 biological replicates and 12 technical replicates within each experiment, but I am not 100 percent sure.

Kzebrows Week 15

2015-12-15T07:32:16Z

Kzebrows: /* Electronic Lab Notebook */ minor edit

==Electronic Lab Notebook==

Given the "Run Time 53" error when I tried to run my color set through MAPPFinder, I tried something else with the help of Dr. Dahlquist.
*Opened Criterion-GO.txt file in Excel
*Filtered Excel file:
**Number Changed by between 4 and 100
**Z score by greater than 2
**PermuteP by less than 0.05
**Adjusted P by less than 0.1

We decided to look at the criterion files for RX and RP -0pt5-10 and RX and RP -1-60. These were the samples at the smallest and largest time points at both concentrations, and by looking at the files and filtering them by the above criteria we were able to find some similarities:
*RX and RP 0pt5-10 gene expression significantly increased: metabolic processes
*RX and RP 0pt5-10 gene expression significantly decreased: ribosome
*RX and RP 1-60 gene expression significantly increased: flagellar production
*RX and RP 1-60 gene expression significantly decreased: metabolic processes

Next, with the help of Dr. Dahlquist, Erich and I decided that Erich would work on creating the gene mapp and I would work on creating color sets for each sample/time period. I created a final compiled raw data file by copying/pasting Erich's RP sample data into my RX sample data file. This file can be found on the [[OTS Files | OTS Files]] page under GenMAPP User Files.

Next I made sure the correct database build was being used in the GenMAPP program. I selected Data > Expression Dataset Manager and under Color Sets > Name I typed RX-0pt5-10. For Gene Value I typed Avg_LogFC RX-0pt5-10. I then added a New color set with the label "Increased", color red, and criterion "[Avg_LogFC RX-0pt5-10] > 0.25 AND [PValue_LogFC RX-0pt5-10] < 0.05." I added a second color set with the label "Decreased", color green, and criterion "[Avg_LogFC RX-0pt5-10] <-0.25 AND [Pvalue_LogFC RX-0pt5-10] < 0.05." I then saved this color set so it would appear on the mapp. I added 12 color sets, one for each sample/time period combo, starting with all RX-0.5 x MICs and then the corresponding 0.5 x MIC for RP. I then did the same for 1 x MIC. When I got to 1 x MIC at 30 minutes I encountered a GenMAPP error where the file could not be read. At that point I spoke to Dr. Dahlquist, who was able to fix it on my .gex file and upload that file, which I could then edit and use in order to proceed.

I then opened all of the Criterion files with Excel and made a compiled filtered file with the criteria above, the completed version of which is found [[Media:Filtered MAPPFinder Results.xlsx | here]]. I color coded each file (RP is blue, RX is pink) to highlight the top 10 GO terms for the different drugs at 1 x MIC at 60 minutes and 0.5 x MIC at 10 minutes (chosen because of their significance in the sanity check and out of our personal preferences with what we had already worked with) and put images of these tables in the team Power Point. I deleted all columns except for GO ID, name of GO term, number changed/present and percentage, number present/number in GO and percentage, regular p value, and adjusted p value.

[[Media:OTS ShigellaFinalPresentation.pptx | '''Final PowerPoint Presentation''']]
{{Template:Kzebrows}} [[Category: Journal Entry]]

Kzebrows Week 15

2015-12-15T07:31:32Z

Kzebrows: /* Electronic Lab Notebook */ link to final Power Point

==Electronic Lab Notebook==

Given the "Run Time 53" error when I tried to run my color set through MAPPFinder, I tried something else with the help of Dr. Dahlquist.
*Opened Criterion-GO.txt file in Excel
*Filtered Excel file:
**Number Changed by between 4 and 100
**Z score by greater than 2
**PermuteP by less than 0.05
**Adjusted P by less than 0.1

We decided to look at the criterion files for RX and RP -0pt5-10 and RX and RP -1-60. These were the samples at the smallest and largest time points at both concentrations, and by looking at the files and filtering them by the above criteria we were able to find some similarities:
*RX and RP 0pt5-10 gene expression significantly increased: metabolic processes
*RX and RP 0pt5-10 gene expression significantly decreased: ribosome
*RX and RP 1-60 gene expression significantly increased: flagellar production
*RX and RP 1-60 gene expression significantly decreased: metabolic processes

Next, with the help of Dr. Dahlquist, Erich and I decided that Erich would work on creating the gene mapp and I would work on creating color sets for each sample/time period. I created a final compiled raw data file by copying/pasting Erich's RP sample data into my RX sample data file. This file can be found on the [[OTS Files | OTS Files]] page under GenMAPP User Files.

Next I made sure the correct database build was being used in the GenMAPP program. I selected Data > Expression Dataset Manager and under Color Sets > Name I typed RX-0pt5-10. For Gene Value I typed Avg_LogFC RX-0pt5-10. I then added a New color set with the label "Increased", color red, and criterion "[Avg_LogFC RX-0pt5-10] > 0.25 AND [PValue_LogFC RX-0pt5-10] < 0.05." I added a second color set with the label "Decreased", color green, and criterion "[Avg_LogFC RX-0pt5-10] <-0.25 AND [Pvalue_LogFC RX-0pt5-10] < 0.05." I then saved this color set so it would appear on the mapp. I added 12 color sets, one for each sample/time period combo, starting with all RX-0.5 x MICs and then the corresponding 0.5 x MIC for RP. I then did the same for 1 x MIC. When I got to 1 x MIC at 30 minutes I encountered a GenMAPP error where the file could not be read. At that point I spoke to Dr. Dahlquist, who was able to fix it on my .gex file and upload that file, which I could then edit and use in order to proceed.

I then opened all of the Criterion files with Excel and made a compiled filtered file with the criteria above, the completed version of which is found [[Media:Filtered MAPPFinder Results.xlsx | here]]. I color coded each file (RP is blue, RX is pink) to highlight the top 10 GO terms for the different drugs at 1 x MIC at 60 minutes and 0.5 x MIC at 10 minutes (chosen because of their significance in the sanity check and out of our personal preferences with what we had already worked with) and put images of these tables in the team Power Point. I deleted all columns except for GO ID, name of GO term, number changed/present and percentage, number present/number in GO and percentage, regular p value, and adjusted p value.

[[Media:OTS ShigellaFinalPresentation.pptx | '''Final PowerPoint Presentation''']]

{{Template:Kzebrows}} [[Category: Journal Entry]]

OTS Deliverables

2015-12-15T07:29:14Z

Kzebrows: /* OTS Files */ added link to final power point

==OTS Files==

[[Media:Micro Array Shigella Flexneri 20151011.pdf | Shigella Flexneri Microarray Paper (PDF)]]

[[Media:Shigellamicroarray.pptx | Microarray Journal Club Power Point]]

[[Media:CompiledRaw data RPRX IDLR EYKZ20152211.xlsx | Microarray Compiled Raw Data RP/RX IDLR]]

[[Media:SamplesFilesCorrespondanceTable SF301a EYKZ201522111.xls | Microarray Corresponding Files Table]]

[[Media: GMBuilder Shigella flexneri.zip]]

[[Media: QA Files.zip | Download QA files]]

[[File:GMBuilder December7 2015 build 2.zip]]

[[File:GenMAPP Builder 12 14 2015.zip]]

[[File:GenMAPP Builder 12 14 2015 Number 2.zip]]

[[Media:OTS ShigellaFinalPresentation.pptx | '''Final PowerPoint Presentation''']]

==GenMAPP User Files==
[[Media:CompiledRaw data RPRX IDLR EYKZ2015121.xlsx | ScalingCentering file from 12/1]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.xlsx | Final Compiled Raw Data 12/10 Excel format]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.txt | Final Compiled Raw Data 12/10 .txt format]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210 (1).gex | Final Compiled Raw Data 12/12 .gex]]

[[Media:Filtered MAPPFinder Results.xlsx | Filtered MAPPFinder Results]]

[[Media:Flagellum Ribosomal Mapp 1 60min 20151012.jpg | RP vs RX 1 MIC @ 60 minutes MAPP 12/12 .jpg]]

[[Media:Flagellum Ribosomal Mapp 0pt5 10min 20151012.jpg | RP vs RX 0.5 MIC @ 10 minutes MAPP 12/12 .jpg]]

====RP (Erich)====
[[Media:CompiledRaw data GenMAPP Final RP IDLR EYKZ2015126.xlsx | RP Compiled Raw Data Final 12/10]]

[[Media:CompiledRaw data GenMAPP ready RP IDLR EYKZ2015126.txt | RP .txt format GenMAPP ready 12/6]]

[[Media:CompiledRaw data Errors RP EYKZ2015126.EX.xlsx | RP Exceptions file in Excel format (filtered)]]

[[Media:CompiledRaw data Errors RP EYKZ2015126.EX.txt | RP Exceptions (txt)]]

[[Media:CompiledRaw data GenMAPP ready RP IDLR EYKZ2015126.gex | RP .gex file]]

====RX (Kristin)====
[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.xlsx | RX Compiled Raw Data 12/6]]

[[Media:CompiledRaw data statistics BonferroniPvalue RP IDLR EYKZ2015126.txt | RX .txt format GenMAPP ready 12/6]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.xlsx | RX Compiled Raw Data as of 12/6]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.txt | RX .txt format updated as of 12/6]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.EX.txt | RX Exceptions file]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.gex | RX .gex file]]

[[Media:CompiledRaw data RX IDLR KZ2015126.EX.xlsx | RX Exceptions file in Excel format (filtered)]]

{{Template:Oregon Trail Survivors}}

File:OTS ShigellaFinalPresentation.pptx

2015-12-15T07:26:30Z

Kzebrows: OTS Shigella final presentation

OTS Shigella final presentation

Kzebrows Week 15

2015-12-15T03:50:21Z

Kzebrows: /* Electronic Lab Notebook */ edit of electronic lab notebook

Kzebrows Week 15

2015-12-15T03:43:39Z

Kzebrows: /* Electronic Lab Notebook */ edit link

==Electronic Lab Notebook==

Given the "Run Time 53" error when I tried to run my color set through MAPPFinder, I tried something else with the help of Dr. Dahlquist.
*Opened Criterion-GO.txt file in Excel
*Filtered Excel file:
**Number Changed by between 4 and 100
**Z score by greater than 2
**PermuteP by less than 0.05
**Adjusted P by less than 0.1

We decided to look at the criterion files for RX and RP -0pt5-10 and RX and RP -1-60. These were the samples at the smallest and largest time points at both concentrations, and by looking at the files and filtering them by the above criteria we were able to find some similarities:
*RX and RP 0pt5-10 gene expression significantly increased: metabolic processes
*RX and RP 0pt5-10 gene expression significantly decreased: ribosome
*RX and RP 1-60 gene expression significantly increased: flagellar production
*RX and RP 1-60 gene expression significantly decreased: metabolic processes

Next, with the help of Dr. Dahlquist, Erich and I decided that Erich would work on creating the gene mapp and I would work on creating color sets for each sample/time period. I created a final compiled raw data file by copying/pasting Erich's RP sample data into my RX sample data file. This file can be found on the [[OTS Files | OTS Files]] page under GenMAPP User Files.

Next I made sure the correct database build was being used in the GenMAPP program. I selected Data > Expression Dataset Manager and under Color Sets > Name I typed RX-0pt5-10. For Gene Value I typed Avg_LogFC RX-0pt5-10. I then added a New color set with the label "Increased", color red, and criterion "[Avg_LogFC RX-0pt5-10] > 0.25 AND [PValue_LogFC RX-0pt5-10] < 0.05." I added a second color set with the label "Decreased", color green, and criterion "[Avg_LogFC RX-0pt5-10] <-0.25 AND [Pvalue_LogFC RX-0pt5-10] < 0.05." I then saved this color set so it would appear on the mapp. I added 12 color sets, one for each sample/time period combo, starting with all RX-0.5 x MICs and then the corresponding 0.5 x MIC for RP. I then did the same for 1 x MIC. When I got to 1 x MIC at 30 minutes I encountered a GenMAPP error where the file could not be read. At that point I spoke to Dr. Dahlquist, who was able to fix it on my .gex file and upload that file, which I could then edit and use in order to proceed.

I then opened all of the Criterion files with Excel and made a compiled filtered file with the criteria above, the completed version of which is found [[Media:Filtered MAPPFinder Results.xlsx | here]]. I color coded each file (RP is blue, RX is pink) to highlight the top 10 GO terms for the different drugs at 1 x MIC at 60 minutes and 0.5 x MIC at 10 minutes (chosen because of their significance in the sanity check and out of our personal preferences with what we had already worked with) and put images of these tables in the team Power Point.

{{Template:Kzebrows}} [[Category: Journal Entry]]

Kzebrows Week 15

2015-12-15T03:43:00Z

Kzebrows: /* Electronic Lab Notebook */ criterion files tables

==Electronic Lab Notebook==

Given the "Run Time 53" error when I tried to run my color set through MAPPFinder, I tried something else with the help of Dr. Dahlquist.
*Opened Criterion-GO.txt file in Excel
*Filtered Excel file:
**Number Changed by between 4 and 100
**Z score by greater than 2
**PermuteP by less than 0.05
**Adjusted P by less than 0.1

We decided to look at the criterion files for RX and RP -0pt5-10 and RX and RP -1-60. These were the samples at the smallest and largest time points at both concentrations, and by looking at the files and filtering them by the above criteria we were able to find some similarities:
*RX and RP 0pt5-10 gene expression significantly increased: metabolic processes
*RX and RP 0pt5-10 gene expression significantly decreased: ribosome
*RX and RP 1-60 gene expression significantly increased: flagellar production
*RX and RP 1-60 gene expression significantly decreased: metabolic processes

Next, with the help of Dr. Dahlquist, Erich and I decided that Erich would work on creating the gene mapp and I would work on creating color sets for each sample/time period. I created a final compiled raw data file by copying/pasting Erich's RP sample data into my RX sample data file. This file can be found on the [[OTS Files | OTS Files]] page under GenMAPP User Files.

Next I made sure the correct database build was being used in the GenMAPP program. I selected Data > Expression Dataset Manager and under Color Sets > Name I typed RX-0pt5-10. For Gene Value I typed Avg_LogFC RX-0pt5-10. I then added a New color set with the label "Increased", color red, and criterion "[Avg_LogFC RX-0pt5-10] > 0.25 AND [PValue_LogFC RX-0pt5-10] < 0.05." I added a second color set with the label "Decreased", color green, and criterion "[Avg_LogFC RX-0pt5-10] <-0.25 AND [Pvalue_LogFC RX-0pt5-10] < 0.05." I then saved this color set so it would appear on the mapp. I added 12 color sets, one for each sample/time period combo, starting with all RX-0.5 x MICs and then the corresponding 0.5 x MIC for RP. I then did the same for 1 x MIC. When I got to 1 x MIC at 30 minutes I encountered a GenMAPP error where the file could not be read. At that point I spoke to Dr. Dahlquist, who was able to fix it on my .gex file and upload that file, which I could then edit and use in order to proceed.

I then opened all of the Criterion files with Excel and made a compiled filtered file with the criteria above, the completed version of which is found [[[Media:Filtered MAPPFinder Results.xlsx | here]]. I color coded each file (RP is blue, RX is pink) to highlight the top 10 GO terms for the different drugs at 1 x MIC at 60 minutes and 0.5 x MIC at 10 minutes (chosen because of their significance in the sanity check and out of our personal preferences with what we had already worked with) and put images of these tables in the team Power Point.

{{Template:Kzebrows}} [[Category: Journal Entry]]

Oregon Trail Survivors

2015-12-15T03:24:52Z

Kzebrows: /* Week 15 */ status report

<div style="text-align: center; font-size: 250%; line-height: 1.25em">'''Oregon Trail Survivors'''</div>

<div class="center">
[[Image:Oregon-trail-dysentery 5 biodb.jpg | thumb | right | 350px | The third leading cause of death in the Oregon Trail.]]
</div>

== Group Members ==
*Coder: [[User:Jwoodlee | Jake Woodlee]]
*Quality Assurance: [[User:Troque | Trixie Roque]]
*GenMAPP Users: [[User:Eyanosch | Erich Yanoschik]] & [[User:Kzebrows | Kristin Zebrowski]]
* Project Manager: [[User:Kzebrows | Kristin Zebrowski]]

{{Template:Oregon Trail Survivors}}

=== Presentation (QA/Coder) ===
* PDF can be seen [[Media: Genome Paper Presentation BioDB.pdf | here]]

===Group Meeting Times===
*Thursday, November 5th at 8:00 pm
*Met most Sundays and Monday evenings in the Biol DB lab to check in with one another.

== Goals ==
Over the upcoming weeks our group will be investigating ''Shigella flexneri''.

===Week 10===

# Find genome sequence paper
# Find 4-8 microarray data and paper that goes with the genome paper
# Compile team page to and create a ranked annotated bibliography

===Week 11===

#Prepare for journal club presentations in Weeks 12 and 13
#Begin initial tasks on research project

Click on username links for more information regarding each team member's contributions for Week 11.

[[Jwoodlee Week 11 | Jake]]: Read through the genome paper and tried to get through the accessible things I had the ability to understand. Made an outline for the genome paper. Worked on the presentation with Trixie and found a database. And of course I answered the assigned questions.

[[Troque Week 11 | Trixie]]: Mainly focused on the Genome paper presentation with Jake. This includes searching for a viable database that we will be using for the rest of the group assignment and actually creating the presentation we will be doing for October 17th, 2015. I've also updated our group page to reflect what Dr. Dahlquist suggested would improve our team page.

[[Eyanosch Week 11 | Erich]]: Analyzed the microarray paper in order to describe the experimental design of the microarray data, treatments, number of replicates, and dye swaps. Worked with Kristin to produce the power point for the GennMAP users presentation at Journal Club. Worked on the individual journal entry and created an outline of the microarray paper.

[[Kzebrows Week 11 | Kristin]]: Using the team's selected microarray paper I developed an outline including background information, experimental outline/methods and how samples corresponded to the data, a brief description of the results, and a discussion including the implications of the research and its results in comparison to previous studies. Using this outline, I created a flow chart corresponding to the research. I also worked with Erich in order to create a PowerPoint for the Journal Club presentation on Nov. 24.

=== Week 12 ===
#QA will be doing an initial database export.
#Coder will be setting up version control.
#GenMAPP users will compile the raw data from the micorarray file to prepare for normalization and statistic analysis (will begin if time permits after consultation with Dr. Dahlquist). Additionally, the GenMAPP users will be determining the number of biological or technical replicates and how samples were labeled.
#Coder and QA will present on genome paper in class Tuesday, Nov. 24.

Click on username links for more information regarding each team member's contributions for Week 12.
* [[Jwoodlee Week 12 | Jake]]:Setup my environment in eclipse, created the s-flexneri branch, created my own copy of GenMAPP that I can modify for later use and I cloned the repository with the Git commands.
* [[Troque Week 12 | Trixie]]: Finished the preliminary export of the XML and GOA files and the corresponding Gene Testing Report. Also started identifying the gene id's for the specie. Decided on file management system with Jake.
* [[Eyanosch Week 12 | Erich]]: Worked with Kristin in determining the total number of biological and technical replicates. Compiled the raw data for RP samples, specifically the ID and Log ratio columns. Incorporated the RP and RX data into one spreadsheet with Kristins data. We created a table of the sample data and file each corresponds with, also figured out there were no dye swaps in the experiment(The control was the Cy3 dye and the treatment the Cy5 dye).
* [[Kzebrows Week 12 | Kristin]]: Determined that there were 3 biological replicates per treatment for 6 treatments total. Compiled raw data for RX samples by re-naming columns for ID and Log Ratio and putting into same worksheet, which was later combined with Erich's worksheet for RP samples. Erich and I met and worked together to create a table of which samples correspond to which file.

===Week 14===
#QA will be documenting the IDs using MATCH, Postgres, Microsoft Access, and Excel and get a head start of Milestone 3, which is customizing the TallyEngine.
#Coder will determine and document any modified export behavior that the GenMAPP Builder will have and resolve bugs. Coder will also work with QA by uploading GM Builder for additional export.
#GenMAPP Users will perform statistical analysis on Excel (normalization, tests) and format for import into GenMAPP. Users will also import data into GenMAPP and run MAPPFinder, and then document these test runs.

Click on username links for more information regarding each team member's contributions for Week 14.
* [[Jwoodlee Week 14 | Jake]]: Finished custom GenMAPP builder, committed to GitHub, and ran the export with the custom software. This created a custom .gdb which was opened in Microsoft Access and GenMAPP to check for accuracy.
* [[Troque Week 14 | Trixie]]: Trixie has finished identifying the gene IDs using MATCH, Postgres, Microsoft Access, and Excel. It was discovered that some IDs are in "dbReference/property&type&gene ID", and so another export was done on 12/7/15 to add the newly discovered gene IDs.
* [[Eyanosch Week 14 | Erich]]: Kristin and I completed the corrections provided via Dr. Dhalquist on Kristins talk page. We split the work into two halves and I worked on the RP data. We completed the statistics, Bonferroni p value correction, and the sanity check. I downloaded the database and formatted/exported the file for GenMAPP, and tried to create a GO tree for one of the trail points with RX.
* [[Kzebrows Week 14 | Kristin]]: This week Erich and I made corrections from the talk page and normalized log ratios for the slides in the experiment. I completed the statistical analysis for RX samples and calculated the Bonferroni p value correction. I also performed a sanity check for the RX samples and, going off of that, I calculated the Benjamini & Hochberg p value correction for RX-1-30, which had the most statistically significant changes in gene expression. I also formatted and exported the file for GenMAPP, downloaded the database, and attempted to create color sets to run the data set through MappFINDER.

==== Reflection ====

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?

''Kristin'':
#What worked?
#*In terms of communication is having a group text. We also meet at least once a week outside of class in order to work together on the assignments and make sure we are all on the same page. So far, this has allowed us to troubleshoot and address bugs together as a team quickly. It also worked for Erich and I to divide up the samples so that I did all RX and Erich did all RP. Then, we could work at the same time and double-check procedures with each other but we were still getting the work done twice as quickly.
#What didn't work?
#*After creating the initial compiled raw data file, I had to make several corrections before the file could be run through GenMAPP. First of all, I had to get rid of the ".", and I also had to change all #DIV/0! with a space character for the file to be read at all. Also, although we were unable to find all of the b#### and CP#### gene ID's in UniProt or ShiBASE. Also, after creating my color set and trying to run MAPPFinder, I tried three computers and all of them crashed with the "not responding" message.
#What will I do next to fix what didn't work?
#*I will communicate with the QA and Coder in order to create a database with a minimal number of "Gene ID not found's" and then communicate with Erich when we try to run our dataset through MappFinder. Once the gene database is re-customized and the export is complete I can try and re-run my dataset to see if that makes a difference.

'' Trixie '':
# What worked?
#* What worked in identifying the gene IDs is to look export .gdb file into Excel and compare with what the OrderedLocusNames table had (from Microsoft Access). From doing this, it was easier to find which genes were not found in the .gdb file and made it easier to look through them in the UniProt XML file. With the Excel file comparing the lists of gene IDs and using the CTRL+F shortcut, I was also able to discern which tags to include into the new builds for the databases. Because of this, I was able to confirm that some genes indeed do not exist in the XML file, while only a couple exist within the "dbReference" tag. In terms of group work, what worked is posting all our files into a single page as we progress through the assignment. Night meetings were also helpful in order to better communicate with the rest of my group.
# What didn't work?
#* What didn't work is using Match multiple times without thinking. Even when I was trying to match the number of gene IDs with what Tally Engine gives me, Match didn't really help me in identifying where to find the genes in the XML file. Waiting for the database to finish didn't help much at all since our builds would take more than 4 hours to finish.
# What will I do next to fix what didn't work?
#* What I would do next to fix what didn't work is to actually use Match in conjunction to the XML file, or just use the Excel method completely since that was actually more helpful in finding the necessary tags than the Match method. I would probably have to time myself to check the lab after about 4.5 hours since one of our builds lasted that long.

''Jake'':
#What worked?
#*Almost every procedural action I took from Dondi worked. The only hiccup I had was in regard to Eclipse and navigating the directories.
#What didn't work?
#*In Eclipse, my edits to the GenMAPP builder source code were causing red error marks, but after selecting "Organize Imports" from the source menu the errors were fixed easily and the proper classes were imported. Also I had difficulty navigating to the dist file in my Temp drive, however I traced this back within Eclipse and was able to make a zip that I could hand off to Trixie for export.
#What will I do next week to fix what didn't work?
#*It seems to me that there wasn't a whole lot that went wrong with my procedure. What wasn't working I already fixed. Currently Trixie and I are running an export that will take 4 hours with the new additions in the property files, so there may be some new hiccups when that export is finished but we will have to wait and see.

''Erich'':
# What worked?
#*Having a GenMAPP user meeting with Dr. Dhalquist helped focus on what goals we wanted to achieve by the time of our next meeting. A group text helped organize meeting times of both the coders and GenMAPP users helped keep us on schedule.
# What didn't work?
#*The GenMapp Gene Ontology Tree was unable to pull files for each GO selection. We need to work on and make sure the GO files can be found. We also had to remove and edit our compiled raw data files so that they are able to be read by GenMAPP.
# What will I do next to fix what didn't work?
#*A new .gex was created, so this might help with the problems experienced in the MappBuilder. Also communicating with the QA and coder to make sure we finish up the GO tree smoothly in order to assess the results of the Publication we chose for Shigella Flexneri.

===Week 15===
#Coder: Work with QA to fix bugs.
#QA: Work with coder to fix bugs in the .gdb.
#GenMAPP Users: Finish Milestone 3. Run tests with GenMAPP. Do a journal club outline of the paper to use in the Discussion section of group report and presentation. Create a .mapp file showing one changed pathway from the data.
#All team members will be working together to put together deliverables including the final report and presentation for next Tuesday.

Click on username links for more information regarding each team member's contributions for Week 14.
* [[Jwoodlee Week 15 | Jake]]:
* [[Troque Week 15 | Trixie]]:
* [[Eyanosch Week 15 | Erich]]:
* [[Kzebrows Week 15 | Kristin]]: I created color sets with Increased/Decreased criteria for all of the 12 treatment/time point combos. Then, based on the criterion.go files, I created tables by filtering the results comparing the most commonly induced or repressed genes for the 1 x MIC at 60 minutes and 0.5 x MIC at 10 minutes between RX and RP. Strikingly, we found that between RX and RP the effects were very similar. I then compared them with the .mapp files that Erich created and put my portion of the project (compiled sanity check, color set, comparison tables) in the power point.

==Overview of Genome Paper==
*Used the genome sequencing article to perform a prospective search in the [https://apps.webofknowledge.com/UA_GeneralSearch_input.do?product=UA&search_mode=GeneralSearch&SID=1FRKcNxUgxiGX6spITI&preferencesSaved= Web of Science] database.
*Overview of the search:
**How many articles does this article cite? 37
**How many articles cite this article? 303
**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?
***Now that the genome has been sequenced, a majority of research has been done on discovering which genes are responsible for virulence and pathogenesis as well as potential antibiotics. Genomic research is also focused on how ''S. flexneri'' has been able to develop resistance to multiple drugs. Furthermore, ''Shigella'' is suspected to have evolved from ''Escherichia coli'' so a lot of research has been done in how and when pathogenic ''Shigella'' split from ''E. coli'' on the evolutionary tree.

==Annotated Bibliography==
=== Genome Paper ===
Jin, Q., Yuan, Z., Xu, J., Wang, Y., Shen, Y., Lu, W., … Yu, J. (2002). Genome sequence of ''Shigella flexneri'' 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157. Nucleic Acids Research, 30(20), 4432–4441.
* PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/?term=Genome+sequence+of+Shigella+flexneri+2a%3A+insights+into+pathogenicity+through+comparison+with+genomes+of+Escherichia+coli+K12+and+O157
* PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC137130/
* Publisher Full Text (HTML): http://nar.oxfordjournals.org/content/30/20/4432.full
* Publisher Full Text (PDF): http://nar.oxfordjournals.org/content/30/20/4432.full.pdf+html
* Copyright: 2002 Oxford University Press
* Publisher: Oxford University Press
* Availability: in print and online
* Did LMU pay a fee for this article: no

===Microarray Paper===





Fu H, Liu L, Zhang X, Zhu Y, Zhao L, Peng J, et al. (2012) Common Changes in Global Gene Expression Induced by RNA Polymerase Inhibitors in ''shigella flexneri''. PLoS ONE 7(3): e33240. doi:10.1371/journal.pone.0033240

*The link to the [http://www.ncbi.nlm.nih.gov/pubmed/22428000 abstract]
*The link to the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3299763/ full text of the article] in PubMed Central
*The link to the [http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0033240 full text of the article] (HTML format) from the publisher web site.
*The link to the [http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0033240&representation=PDF full PDF version] of the article from the publisher web site.
*Copyright: © 2012 Fu et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
*Does the journal own the copyright? NO
*Do the authors own the copyright? Yes
*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? PLoS One is the publisher/Journal. It hosts open access research articles. (Public Library of Science)
*Is this article available in print or online only? Online only
*Has LMU paid a subscription or other fee for your access to this article? No LMU has not paid a subscription or other fee because it is open access on the Public Library of Science.
*Use the genome sequencing article you found to perform a prospective search in the ISI Web of Science/Knowledge database.
**How many articles does this article cite? 25 cited references
**How many articles cite this article? 0 articles cite this article
**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?
*Well given that there are no papers that cite this paper there hasn't been anything done to build on this specific topic. In regards to the genome I think this paper has built on the work of the people who sequenced the first genome of Shigella flexneri as well as the other micro array papers.
*State which database you used to find the data and article: ArrayExpress
*State what you used as search terms and what type of search terms they were: "shigella flexneri" filtered by organism, experiment type: "rna assay", experiment type: "array assay"
*Give an overview of the results of the search.
**How many results did you get? 7 results returned with 6 viable options due to the number assays.
**Give an assessment of how relevant the results were: Very relevant, 6/7 results were viable.
*Link to [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-32978/?keywords=shigella+flexneri&organism=Shigella+flexneri&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array= microarray data]
*What experiment was performed? What was the "treatment" and what was the "control" in the experiment?
**Antibiotics (RNA Polymerase Inhibitors) were added to ''Shigella flexneri'' in order to see if bacteria became less active. The control was a group of bacteria with no drugs added to them, and the treatment was a group of bacteria with drugs added to them.
*Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each?
**There are two drugs RX and RP with 6 samples per drug. The experiment was run 3 times which yielded 36 assays. I believe that means 3 biological replicates and 12 technical replicates within each experiment, but I am not 100 percent sure.

Kzebrows Week 15

2015-12-15T02:36:41Z

Kzebrows: /* Electronic Lab Notebook */ lab notebook edit

Oregon Trail Survivors

2015-12-15T02:33:16Z

Kzebrows: /* Week 15 */ status report

<div style="text-align: center; font-size: 250%; line-height: 1.25em">'''Oregon Trail Survivors'''</div>

<div class="center">
[[Image:Oregon-trail-dysentery 5 biodb.jpg | thumb | right | 350px | The third leading cause of death in the Oregon Trail.]]
</div>

== Group Members ==
*Coder: [[User:Jwoodlee | Jake Woodlee]]
*Quality Assurance: [[User:Troque | Trixie Roque]]
*GenMAPP Users: [[User:Eyanosch | Erich Yanoschik]] & [[User:Kzebrows | Kristin Zebrowski]]
* Project Manager: [[User:Kzebrows | Kristin Zebrowski]]

{{Template:Oregon Trail Survivors}}

=== Presentation (QA/Coder) ===
* PDF can be seen [[Media: Genome Paper Presentation BioDB.pdf | here]]

===Group Meeting Times===
*Thursday, November 5th at 8:00 pm
*Met most Sundays and Monday evenings in the Biol DB lab to check in with one another.

== Goals ==
Over the upcoming weeks our group will be investigating ''Shigella flexneri''.

===Week 10===

# Find genome sequence paper
# Find 4-8 microarray data and paper that goes with the genome paper
# Compile team page to and create a ranked annotated bibliography

===Week 11===

#Prepare for journal club presentations in Weeks 12 and 13
#Begin initial tasks on research project

Click on username links for more information regarding each team member's contributions for Week 11.

[[Jwoodlee Week 11 | Jake]]: Read through the genome paper and tried to get through the accessible things I had the ability to understand. Made an outline for the genome paper. Worked on the presentation with Trixie and found a database. And of course I answered the assigned questions.

[[Troque Week 11 | Trixie]]: Mainly focused on the Genome paper presentation with Jake. This includes searching for a viable database that we will be using for the rest of the group assignment and actually creating the presentation we will be doing for October 17th, 2015. I've also updated our group page to reflect what Dr. Dahlquist suggested would improve our team page.

[[Eyanosch Week 11 | Erich]]: Analyzed the microarray paper in order to describe the experimental design of the microarray data, treatments, number of replicates, and dye swaps. Worked with Kristin to produce the power point for the GennMAP users presentation at Journal Club. Worked on the individual journal entry and created an outline of the microarray paper.

[[Kzebrows Week 11 | Kristin]]: Using the team's selected microarray paper I developed an outline including background information, experimental outline/methods and how samples corresponded to the data, a brief description of the results, and a discussion including the implications of the research and its results in comparison to previous studies. Using this outline, I created a flow chart corresponding to the research. I also worked with Erich in order to create a PowerPoint for the Journal Club presentation on Nov. 24.

=== Week 12 ===
#QA will be doing an initial database export.
#Coder will be setting up version control.
#GenMAPP users will compile the raw data from the micorarray file to prepare for normalization and statistic analysis (will begin if time permits after consultation with Dr. Dahlquist). Additionally, the GenMAPP users will be determining the number of biological or technical replicates and how samples were labeled.
#Coder and QA will present on genome paper in class Tuesday, Nov. 24.

Click on username links for more information regarding each team member's contributions for Week 12.
* [[Jwoodlee Week 12 | Jake]]:Setup my environment in eclipse, created the s-flexneri branch, created my own copy of GenMAPP that I can modify for later use and I cloned the repository with the Git commands.
* [[Troque Week 12 | Trixie]]: Finished the preliminary export of the XML and GOA files and the corresponding Gene Testing Report. Also started identifying the gene id's for the specie. Decided on file management system with Jake.
* [[Eyanosch Week 12 | Erich]]: Worked with Kristin in determining the total number of biological and technical replicates. Compiled the raw data for RP samples, specifically the ID and Log ratio columns. Incorporated the RP and RX data into one spreadsheet with Kristins data. We created a table of the sample data and file each corresponds with, also figured out there were no dye swaps in the experiment(The control was the Cy3 dye and the treatment the Cy5 dye).
* [[Kzebrows Week 12 | Kristin]]: Determined that there were 3 biological replicates per treatment for 6 treatments total. Compiled raw data for RX samples by re-naming columns for ID and Log Ratio and putting into same worksheet, which was later combined with Erich's worksheet for RP samples. Erich and I met and worked together to create a table of which samples correspond to which file.

===Week 14===
#QA will be documenting the IDs using MATCH, Postgres, Microsoft Access, and Excel and get a head start of Milestone 3, which is customizing the TallyEngine.
#Coder will determine and document any modified export behavior that the GenMAPP Builder will have and resolve bugs. Coder will also work with QA by uploading GM Builder for additional export.
#GenMAPP Users will perform statistical analysis on Excel (normalization, tests) and format for import into GenMAPP. Users will also import data into GenMAPP and run MAPPFinder, and then document these test runs.

Click on username links for more information regarding each team member's contributions for Week 14.
* [[Jwoodlee Week 14 | Jake]]: Finished custom GenMAPP builder, committed to GitHub, and ran the export with the custom software. This created a custom .gdb which was opened in Microsoft Access and GenMAPP to check for accuracy.
* [[Troque Week 14 | Trixie]]: Trixie has finished identifying the gene IDs using MATCH, Postgres, Microsoft Access, and Excel. It was discovered that some IDs are in "dbReference/property&type&gene ID", and so another export was done on 12/7/15 to add the newly discovered gene IDs.
* [[Eyanosch Week 14 | Erich]]: Kristin and I completed the corrections provided via Dr. Dhalquist on Kristins talk page. We split the work into two halves and I worked on the RP data. We completed the statistics, Bonferroni p value correction, and the sanity check. I downloaded the database and formatted/exported the file for GenMAPP, and tried to create a GO tree for one of the trail points with RX.
* [[Kzebrows Week 14 | Kristin]]: This week Erich and I made corrections from the talk page and normalized log ratios for the slides in the experiment. I completed the statistical analysis for RX samples and calculated the Bonferroni p value correction. I also performed a sanity check for the RX samples and, going off of that, I calculated the Benjamini & Hochberg p value correction for RX-1-30, which had the most statistically significant changes in gene expression. I also formatted and exported the file for GenMAPP, downloaded the database, and attempted to create color sets to run the data set through MappFINDER.

==== Reflection ====

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?

''Kristin'':
#What worked?
#*In terms of communication is having a group text. We also meet at least once a week outside of class in order to work together on the assignments and make sure we are all on the same page. So far, this has allowed us to troubleshoot and address bugs together as a team quickly. It also worked for Erich and I to divide up the samples so that I did all RX and Erich did all RP. Then, we could work at the same time and double-check procedures with each other but we were still getting the work done twice as quickly.
#What didn't work?
#*After creating the initial compiled raw data file, I had to make several corrections before the file could be run through GenMAPP. First of all, I had to get rid of the ".", and I also had to change all #DIV/0! with a space character for the file to be read at all. Also, although we were unable to find all of the b#### and CP#### gene ID's in UniProt or ShiBASE. Also, after creating my color set and trying to run MAPPFinder, I tried three computers and all of them crashed with the "not responding" message.
#What will I do next to fix what didn't work?
#*I will communicate with the QA and Coder in order to create a database with a minimal number of "Gene ID not found's" and then communicate with Erich when we try to run our dataset through MappFinder. Once the gene database is re-customized and the export is complete I can try and re-run my dataset to see if that makes a difference.

'' Trixie '':
# What worked?
#* What worked in identifying the gene IDs is to look export .gdb file into Excel and compare with what the OrderedLocusNames table had (from Microsoft Access). From doing this, it was easier to find which genes were not found in the .gdb file and made it easier to look through them in the UniProt XML file. With the Excel file comparing the lists of gene IDs and using the CTRL+F shortcut, I was also able to discern which tags to include into the new builds for the databases. Because of this, I was able to confirm that some genes indeed do not exist in the XML file, while only a couple exist within the "dbReference" tag. In terms of group work, what worked is posting all our files into a single page as we progress through the assignment. Night meetings were also helpful in order to better communicate with the rest of my group.
# What didn't work?
#* What didn't work is using Match multiple times without thinking. Even when I was trying to match the number of gene IDs with what Tally Engine gives me, Match didn't really help me in identifying where to find the genes in the XML file. Waiting for the database to finish didn't help much at all since our builds would take more than 4 hours to finish.
# What will I do next to fix what didn't work?
#* What I would do next to fix what didn't work is to actually use Match in conjunction to the XML file, or just use the Excel method completely since that was actually more helpful in finding the necessary tags than the Match method. I would probably have to time myself to check the lab after about 4.5 hours since one of our builds lasted that long.

''Jake'':
#What worked?
#*Almost every procedural action I took from Dondi worked. The only hiccup I had was in regard to Eclipse and navigating the directories.
#What didn't work?
#*In Eclipse, my edits to the GenMAPP builder source code were causing red error marks, but after selecting "Organize Imports" from the source menu the errors were fixed easily and the proper classes were imported. Also I had difficulty navigating to the dist file in my Temp drive, however I traced this back within Eclipse and was able to make a zip that I could hand off to Trixie for export.
#What will I do next week to fix what didn't work?
#*It seems to me that there wasn't a whole lot that went wrong with my procedure. What wasn't working I already fixed. Currently Trixie and I are running an export that will take 4 hours with the new additions in the property files, so there may be some new hiccups when that export is finished but we will have to wait and see.

''Erich'':
# What worked?
#*Having a GenMAPP user meeting with Dr. Dhalquist helped focus on what goals we wanted to achieve by the time of our next meeting. A group text helped organize meeting times of both the coders and GenMAPP users helped keep us on schedule.
# What didn't work?
#*The GenMapp Gene Ontology Tree was unable to pull files for each GO selection. We need to work on and make sure the GO files can be found. We also had to remove and edit our compiled raw data files so that they are able to be read by GenMAPP.
# What will I do next to fix what didn't work?
#*A new .gex was created, so this might help with the problems experienced in the MappBuilder. Also communicating with the QA and coder to make sure we finish up the GO tree smoothly in order to assess the results of the Publication we chose for Shigella Flexneri.

===Week 15===
#Coder: Work with QA to fix bugs.
#QA: Work with coder to fix bugs in the .gdb.
#GenMAPP Users: Finish Milestone 3. Run tests with GenMAPP. Do a journal club outline of the paper to use in the Discussion section of group report and presentation. Create a .mapp file showing one changed pathway from the data.
#All team members will be working together to put together deliverables including the final report and presentation for next Tuesday.

Click on username links for more information regarding each team member's contributions for Week 14.
* [[Jwoodlee Week 15 | Jake]]:
* [[Troque Week 15 | Trixie]]:
* [[Eyanosch Week 15 | Erich]]:
* [[Kzebrows Week 15 | Kristin]]: I created color sets with Increased/Decreased criteria for all of the 12 treatment/time point combos.

==Overview of Genome Paper==
*Used the genome sequencing article to perform a prospective search in the [https://apps.webofknowledge.com/UA_GeneralSearch_input.do?product=UA&search_mode=GeneralSearch&SID=1FRKcNxUgxiGX6spITI&preferencesSaved= Web of Science] database.
*Overview of the search:
**How many articles does this article cite? 37
**How many articles cite this article? 303
**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?
***Now that the genome has been sequenced, a majority of research has been done on discovering which genes are responsible for virulence and pathogenesis as well as potential antibiotics. Genomic research is also focused on how ''S. flexneri'' has been able to develop resistance to multiple drugs. Furthermore, ''Shigella'' is suspected to have evolved from ''Escherichia coli'' so a lot of research has been done in how and when pathogenic ''Shigella'' split from ''E. coli'' on the evolutionary tree.

==Annotated Bibliography==
=== Genome Paper ===
Jin, Q., Yuan, Z., Xu, J., Wang, Y., Shen, Y., Lu, W., … Yu, J. (2002). Genome sequence of ''Shigella flexneri'' 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157. Nucleic Acids Research, 30(20), 4432–4441.
* PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/?term=Genome+sequence+of+Shigella+flexneri+2a%3A+insights+into+pathogenicity+through+comparison+with+genomes+of+Escherichia+coli+K12+and+O157
* PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC137130/
* Publisher Full Text (HTML): http://nar.oxfordjournals.org/content/30/20/4432.full
* Publisher Full Text (PDF): http://nar.oxfordjournals.org/content/30/20/4432.full.pdf+html
* Copyright: 2002 Oxford University Press
* Publisher: Oxford University Press
* Availability: in print and online
* Did LMU pay a fee for this article: no

===Microarray Paper===





Fu H, Liu L, Zhang X, Zhu Y, Zhao L, Peng J, et al. (2012) Common Changes in Global Gene Expression Induced by RNA Polymerase Inhibitors in ''shigella flexneri''. PLoS ONE 7(3): e33240. doi:10.1371/journal.pone.0033240

*The link to the [http://www.ncbi.nlm.nih.gov/pubmed/22428000 abstract]
*The link to the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3299763/ full text of the article] in PubMed Central
*The link to the [http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0033240 full text of the article] (HTML format) from the publisher web site.
*The link to the [http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0033240&representation=PDF full PDF version] of the article from the publisher web site.
*Copyright: © 2012 Fu et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
*Does the journal own the copyright? NO
*Do the authors own the copyright? Yes
*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? PLoS One is the publisher/Journal. It hosts open access research articles. (Public Library of Science)
*Is this article available in print or online only? Online only
*Has LMU paid a subscription or other fee for your access to this article? No LMU has not paid a subscription or other fee because it is open access on the Public Library of Science.
*Use the genome sequencing article you found to perform a prospective search in the ISI Web of Science/Knowledge database.
**How many articles does this article cite? 25 cited references
**How many articles cite this article? 0 articles cite this article
**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?
*Well given that there are no papers that cite this paper there hasn't been anything done to build on this specific topic. In regards to the genome I think this paper has built on the work of the people who sequenced the first genome of Shigella flexneri as well as the other micro array papers.
*State which database you used to find the data and article: ArrayExpress
*State what you used as search terms and what type of search terms they were: "shigella flexneri" filtered by organism, experiment type: "rna assay", experiment type: "array assay"
*Give an overview of the results of the search.
**How many results did you get? 7 results returned with 6 viable options due to the number assays.
**Give an assessment of how relevant the results were: Very relevant, 6/7 results were viable.
*Link to [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-32978/?keywords=shigella+flexneri&organism=Shigella+flexneri&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array= microarray data]
*What experiment was performed? What was the "treatment" and what was the "control" in the experiment?
**Antibiotics (RNA Polymerase Inhibitors) were added to ''Shigella flexneri'' in order to see if bacteria became less active. The control was a group of bacteria with no drugs added to them, and the treatment was a group of bacteria with drugs added to them.
*Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each?
**There are two drugs RX and RP with 6 samples per drug. The experiment was run 3 times which yielded 36 assays. I believe that means 3 biological replicates and 12 technical replicates within each experiment, but I am not 100 percent sure.

Kzebrows Week 15

2015-12-12T23:39:51Z

Kzebrows: /* Electronic Lab Notebook */ similarities between RX and RP

OTS Deliverables

2015-12-12T22:43:01Z

Kzebrows: /* GenMAPP User Files */ filtered mappfinder results link

==OTS Files==

[[Media:Micro Array Shigella Flexneri 20151011.pdf | Shigella Flexneri Microarray Paper (PDF)]]

[[Media:Shigellamicroarray.pptx | Microarray Journal Club Power Point]]

[[Media:CompiledRaw data RPRX IDLR EYKZ20152211.xlsx | Microarray Compiled Raw Data RP/RX IDLR]]

[[Media:SamplesFilesCorrespondanceTable SF301a EYKZ201522111.xls | Microarray Corresponding Files Table]]

[[Media: GMBuilder Shigella flexneri.zip]]

[[Media: QA Files.zip | Download QA files]]

[[File:GMBuilder December7 2015 build 2.zip]]

==GenMAPP User Files==
[[Media:CompiledRaw data RPRX IDLR EYKZ2015121.xlsx | ScalingCentering file from 12/1]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.xlsx | Final Compiled Raw Data 12/10 Excel format]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.txt | Final Compiled Raw Data 12/10 .txt format]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210 (1).gex | Final Compiled Raw Data 12/12 .gex]]

[[Media:Filtered MAPPFinder Results.xlsx | Filtered MAPPFinder Results]]

====RP (Erich)====
[[Media:CompiledRaw data GenMAPP Final RP IDLR EYKZ2015126.xlsx | RP Compiled Raw Data Final 12/10]]

[[Media:CompiledRaw data GenMAPP ready RP IDLR EYKZ2015126.txt | RP .txt format GenMAPP ready 12/6]]

[[Media:CompiledRaw data Errors RP EYKZ2015126.EX.xlsx | RP Exceptions file in Excel format (filtered)]]

[[Media:CompiledRaw data Errors RP EYKZ2015126.EX.txt | RP Exceptions (txt)]]

[[Media:CompiledRaw data GenMAPP ready RP IDLR EYKZ2015126.gex | RP .gex file]]

====RX (Kristin)====
[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.xlsx | RX Compiled Raw Data 12/6]]

[[Media:CompiledRaw data statistics BonferroniPvalue RP IDLR EYKZ2015126.txt | RX .txt format GenMAPP ready 12/6]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.xlsx | RX Compiled Raw Data as of 12/6]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.txt | RX .txt format updated as of 12/6]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.EX.txt | RX Exceptions file]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.gex | RX .gex file]]

[[Media:CompiledRaw data RX IDLR KZ2015126.EX.xlsx | RX Exceptions file in Excel format (filtered)]]

{{Template:Oregon Trail Survivors}}

File:Filtered MAPPFinder Results.xlsx

2015-12-12T22:42:07Z

Kzebrows: Filtered MAPPFinder results for Oregon Trail Survivors

Filtered MAPPFinder results for Oregon Trail Survivors

OTS Deliverables

2015-12-12T21:16:26Z

Kzebrows: /* GenMAPP User Files */ edit link to final .gex

==OTS Files==

[[Media:Micro Array Shigella Flexneri 20151011.pdf | Shigella Flexneri Microarray Paper (PDF)]]

[[Media:Shigellamicroarray.pptx | Microarray Journal Club Power Point]]

[[Media:CompiledRaw data RPRX IDLR EYKZ20152211.xlsx | Microarray Compiled Raw Data RP/RX IDLR]]

[[Media:SamplesFilesCorrespondanceTable SF301a EYKZ201522111.xls | Microarray Corresponding Files Table]]

[[Media: GMBuilder Shigella flexneri.zip]]

[[Media: QA Files.zip | Download QA files]]

[[File:GMBuilder December7 2015 build 2.zip]]

==GenMAPP User Files==
[[Media:CompiledRaw data RPRX IDLR EYKZ2015121.xlsx | ScalingCentering file from 12/1]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.xlsx | Final Compiled Raw Data 12/10 Excel format]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210.txt | Final Compiled Raw Data 12/10 .txt format]]

[[Media:FINAL CompiledRawData RXRP EYKZ20151210 (1).gex | Final Compiled Raw Data 12/12 .gex]]

====RP (Erich)====
[[Media:CompiledRaw data GenMAPP Final RP IDLR EYKZ2015126.xlsx | RP Compiled Raw Data Final 12/10]]

[[Media:CompiledRaw data GenMAPP ready RP IDLR EYKZ2015126.txt | RP .txt format GenMAPP ready 12/6]]

[[Media:CompiledRaw data Errors RP EYKZ2015126.EX.xlsx | RP Exceptions file in Excel format (filtered)]]

[[Media:CompiledRaw data Errors RP EYKZ2015126.EX.txt | RP Exceptions (txt)]]

[[Media:CompiledRaw data GenMAPP ready RP IDLR EYKZ2015126.gex | RP .gex file]]

====RX (Kristin)====
[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.xlsx | RX Compiled Raw Data 12/6]]

[[Media:CompiledRaw data statistics BonferroniPvalue RP IDLR EYKZ2015126.txt | RX .txt format GenMAPP ready 12/6]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.xlsx | RX Compiled Raw Data as of 12/6]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.txt | RX .txt format updated as of 12/6]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.EX.txt | RX Exceptions file]]

[[Media:CompiledRaw data RPRX IDLR EYKZ2015126.gex | RX .gex file]]

[[Media:CompiledRaw data RX IDLR KZ2015126.EX.xlsx | RX Exceptions file in Excel format (filtered)]]

{{Template:Oregon Trail Survivors}}

File:FINAL CompiledRawData RXRP EYKZ20151210 (1).gex

2015-12-12T21:15:28Z

Kzebrows: final .gex file for color sets, RX and RP for OTS

final .gex file for color sets, RX and RP for OTS

Kzebrows Week 15

2015-12-12T20:14:20Z

Kzebrows: looking at criterion files