LMU BioDB 2015 - User contributions [en]

OTS Deliverables

2015-12-19T00:03:27Z

Eyanosch: /* OTS Group Files and Datasets */ uploaded and posted the final deliverable of the group report

{{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]]

[[Media:Gene Database Testing Report for Shigella flexneri 2a str 301.pdf | 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]]

[[Media:RPRX MAPPs.zip | .zip of .mapp s of relevant genes]]

[[Media:OTSDeliverables.docx | Final Group Report .docx]]

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

==Individual Reflections==

[[Kzebrows Individual Reflection | Kristin Zebrowski]]

[[Eyanosch Individual Reflection | Erich Yanoschik]]

[[Jwoodlee Individual Reflection | Jake Woodlee]]

[[Troque Individual Reflection | Trixie Roque]]

File:OTSDeliverables.docx

2015-12-19T00:01:56Z

Eyanosch: Deliverable paper

Deliverable paper

Eyanosch Individual Reflection

2015-12-18T16:56:45Z

Eyanosch: Finalizing the Individual reflection for the class

===Statement of work===

Researched Shigella flexneri with Oregon Trail survivors and found a microarray paper suitable for the final project review. I was one of the GenMAPP users along with Kristin, we took the LogRatios from our mircroarray paper and compiled an indepth analysis of the effects of rifamycin on Shigella flexneri. A power point was made explaining the experimental method of the microarray. A journal presentation was created by along with the other GenMAPP user to identify and explain the methods and purpose of the microarray experiment. A final presentation was given in regards to our findings using PostgreSQL, GenMAPP, and other programs to create a succinct analysis of the microarray papers data. I created Gene MAPPS for the most induced or repressed pathways within our criterionGO files of RPRX at 0.5xMIC at 10 minutes and RPRX at1xMIC at 60 minutes for both drugs.
Provide references or links to artifacts of your work, such as:

Wiki pages
[[Eyanosch Week 15]]

[[Eyanosch Week 14]]

[[Eyanosch Week 12]]

[[Eyanosch Week 11]]

[[OTS Deliverables]]

Files Created:

*[[Media:Flagellum Ribosomal Mapp 0pt5 10min 20151012.jpg | Flagellum Ribosomal Map 0pt5 10min]]
*[[Media:Flagellum Ribosomal Mapp 1 60min 20151012.jpg‎ | Flagellum Ribosomal Mapp 1 60min]]
*[[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]]

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]]

===Assessment of Project===

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

What worked and what didn't work?

The workload is divided into two basically, the biologist side and the computational computer science side. I found it difficult to help the QA and coder when it was just me and them working on the project. Although they are working on a completely different part of the project, it helps to be able to bounce questions off each other. I relied on Kristin and Dr. Dhalquist whenever an issue came up that I couldn't solve on my own. I felt like the in-class time dedicated to working on the project and asking questions helped.

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

Start the deliverables a weekend earlier and practice our presentations a few more times. Often times we found our group meeting Sunday or Monday night and trying to crank out the assignment due that midnight. Giving ourselves more time to complete these tasks may have lessened the level and stress and improved quality of work.

Evaluate the Gene Database Project and Group Report in the following areas:

Content: What is the quality of the work?

The quality of work is good, we have all of the deliverables completed. Every bullet point was taken care of and completed within a google doc that will be uploaded as the final culmination to a good semester.

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

Our group was fairly organized in terms of managing time even when we couldn't all meet together. Conversations were had about what needs to be done or what was done. Our Oregon trail survivors page is fairly easy to traverse and aesthetically pleasing.

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

Our team completed all the project objectives. We made sure to check off everything when we finished it and have someone review our work. Kristin and I reviewed each others input into the final project to make sure it met the criteria we both deemed necessary for this project. There was a constant dialogue going back and forth among our team. Oregon Trail Survivors completed all of the project objectives because we kept each other accountable and planned ahead. During Finals time people's lives become hectic and its hard to find a time everyone can meet. We had a group messaging system going to make sure each section was being taken care of or if anyone had questions those were addressed.

===Reflection on the Process===

I liked how the process of the final project was constructed. For the last assignment in class we did a mock final genMAPP assignment with the vibrio cholera data. This laid the foundation for which the GenMAPP users would essentially use. The first time using GenMAPP I was completely and utterly lost, after a few times I gradually picked up on the format and the different files needed and how the database .gbd and .gex files relate to each other. The gradual build up to the final project definately helped with preparations. I did like how we gave a power point presentation before the deliverables were due, this allowed for us to obtain feedback that we used, I know I did personally, towards the deliverables. I found the constructive criticism very helpful.

What did you learn?

With your head (biological or computer science principles)

I learned new analytical techniques regarding both biological and computer science principles. Taking the best of both worlds and formulating it into one. Before this class I wasn't familiar with many of the concepts we discussed but over time and with many hours of practice I have built a framework for these ideas to stick to. This class has challenged me to being uncomfortable and working through that in order to meet the end result which has been so rewarding.

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

I have developed a soft spot for this class. The computer science students and biology students meshed well together in this class, especially when working out of ones comfort zone and in an area not of their expertise. The camaraderie within this class is unlike any other I've taken. This class has helped improve skills regarding teamwork and setting goals towards accomplishing a group effort final task.

With your hands (technical skills)?

I have become more resourceful when it comes to collecting data from outside sources and compiling that information together. This class has provided the tools to become better adapted to work involving online databases and bioinformatics. I pick up much easier on things now that I have been exposed to programming logic. I have become better at conceptualizing the computer science and biological aspect of the class.

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

I will take away this research experience and how it brought forth teamwork, technical skill, and a greater understanding of community standards within the scientific community and if I want to be a contributing factor what is required. Research in bioinformatics and genetics is an upcoming field and will only become more relevant. I will take with me the readings from the class of those who paved the way so that we can analyze and compare massive databases with the click of a button. The importance of making reproducible work has been ingrained into my being.

OTS Deliverables

2015-12-18T15:41:25Z

Eyanosch: /* OTS Group Files and Datasets */

{{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]]

[[Media:RPRX MAPPs.zip | .zip of .mapp s of relevant genes]]

Group Report (.doc or .pdf)

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

==Individual Reflections==

[[Kzebrows Individual Reflection | Kristin Zebrowski]]

[[Eyanosch Individual Reflection | Erich Yanoschik]]

OTS Deliverables

2015-12-18T15:41:05Z

Eyanosch: /* OTS Group Files and Datasets */ added a zip file incorporating all the mapps

{{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)[[Media:RPRX MAPPs.zip | .zip of .mapp s of relevant genes]]

Group Report (.doc or .pdf)

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

==Individual Reflections==

[[Kzebrows Individual Reflection | Kristin Zebrowski]]

[[Eyanosch Individual Reflection | Erich Yanoschik]]

File:RPRX MAPPs.zip

2015-12-18T15:39:22Z

Eyanosch: zip of all the .MAPPS created for this project

zip of all the .MAPPS created for this project

Eyanosch Individual Reflection

2015-12-18T15:04:35Z

Eyanosch: edited the OTSdeliverables link, described a little more in depth of what I did. answered a few more questions

Each person on the team will complete an assessment and reflection individually. If you are comfortable with making this assessment publicly available, you may write it up as a wiki page or as a Word document uploaded to your group deliveables page. If you prefer to communicate your assessment privately, then email this to both Drs. Dahlquist and Dionisio.

Statement of Work[edit]
Describe exactly what you did on the project.

Researched Shigella flexneri with Oregon Trail survivors and found a microarray paper suitable for the final project review. I was one of the GenMAPP users along with Kristin, we took the LogRatios from our mircroarray paper and compiled an indepth analysis of the effects of rifamycin on Shigella flexneri. A power point was made explaining the experimental method of the microarray. A journal presentation was created by along with the other GenMAPP user to identify and explain the methods and purpose of the microarray experiment. A final presentation was given in regards to our findings using PostgreSQL, GenMAPP, and other programs to create a succinct analysis of the microarray papers data. I created Gene MAPPS for the most induced or repressed pathways within our criterionGO files of RPRX at 0.5xMIC at 10 minutes and RPRX at1xMIC at 60 minutes for both drugs.
Provide references or links to artifacts of your work, such as:

Wiki pages
[[Eyanosch Week 15]]

[[Eyanosch Week 14]]

[[Eyanosch Week 12]]

[[Eyanosch Week 11]]

[[OTS Deliverables]]

Files Created:

*[[Media:Flagellum Ribosomal Mapp 0pt5 10min 20151012.jpg | Flagellum Ribosomal Map 0pt5 10min]]
*[[Media:Flagellum Ribosomal Mapp 1 60min 20151012.jpg‎ | Flagellum Ribosomal Mapp 1 60min]]
*[[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]]

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]]

Code or scripts
Assessment of Project[edit]

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

What worked and what didn't work?
The workload is divided into two halves, the biologist side and the computational computer science side. I found it difficult to help the QA and coder when it was just me and them working on the project. Although they are working on a completely different part of the program it helps to be able to bounce questions off each other. I relied on Kristin and Dr. Dhalquist whenever an issue came up that I couldn't solve on my own.

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

Start the deliverables a weekend earlier and practice our presentations a few more times. Often times we found our group meeting Sunday or Monday night and trying to crank out the assignment due that midnight. Giving ourselves more time to complete these tasks may have lessened the level and stress and improved quality of work.

Evaluate the Gene Database Project and Group Report in the following areas:

Content: What is the quality of the work?

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

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

Oregon Trail Survivors completed all of the project objectives because we kept each other accountable and planned ahead. During Finals time people's lives become hectic and its hard to find a time everyone can meet. We had a group messaging system going to make sure each section was being taken care of or if anyone had questions those were addressed.

Reflection on the Process[edit]

I liked how the process of the final project was constructed. For the last assignment in class we did a mock final genMAPP assignment with the vibrio cholera data. This laid the foundation for which the GenMAPP users would essentially use. The first time using GenMAPP I was completely and utterly lost, after a few times I gradually picked up on the format and the different files needed and how the database .gbd and .gex files relate to each other. The gradual build up to the final project definately helped with preparations. I did like how we gave a power point presentation before the deliverables were due, this allowed for us to obtain feedback that we used, I know I did personally, towards the deliverables. I found the constructive criticism very helpful.

What did you learn?

With your head (biological or computer science principles)

I learned new analytical techniques regarding both biological and computer science principles. Taking the best of both worlds and formulating it into one. Before this class I wasn't familiar with many of the concepts we discussed but over time and with many hours of practice I have built a framework for these ideas to stick to. This class has challenged me to being uncomfortable and working through that in order to meet the end result which has been so rewarding.

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

I have developed a soft spot for this class. The computer science students and biology students meshed well together in this class, especially when working out of ones comfort zone and in an area not of their expertise. The camaraderie within this class is unlike any other I've taken. This class has helped improve skills regarding teamwork and setting goals towards accomplishing a group effort final task.

With your hands (technical skills)?

I have become more resourceful when it comes to collecting data from outside sources and compiling that information together. This class has provided the tools to become

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

OTS Deliverables

2015-12-18T14:51:06Z

Eyanosch: /* Individual Reflections */

{{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]]

[[Eyanosch Individual Reflection | Erich Yanoschik]]

OTS Deliverables

2015-12-18T14:50:46Z

Eyanosch: /* Individual Reflections */

{{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]]
[[Eyanosch Individual Reflection | Erich Yanoschik]]

Eyanosch Individual Reflection

2015-12-18T14:48:48Z

Eyanosch: Adding the statement of work, Individual reflection for Erich Yanoschik

Each person on the team will complete an assessment and reflection individually. If you are comfortable with making this assessment publicly available, you may write it up as a wiki page or as a Word document uploaded to your group deliveables page. If you prefer to communicate your assessment privately, then email this to both Drs. Dahlquist and Dionisio.

Statement of Work[edit]
Describe exactly what you did on the project.
Researched Shigella flexneri with Oregon Trail survivors and found a microarray paper suitable for the final project review. I was one of the GenMAPP users along with Kristin, we took the LogRatios from our mircroarray paper and compiled an indepth analysis of the effects of rifamycin on Shigella flexneri. A power point was made explaining the experimental method of the microarray.
Provide references or links to artifacts of your work, such as:

Wiki pages
[[Eyanosch Week 15]]

[[Eyanosch Week 14]]

[[Eyanosch Week 12]]

[[Eyanosch Week 11]]

[[OTS deliverables]]

Files Created:

*[[Media:Flagellum Ribosomal Mapp 0pt5 10min 20151012.jpg | Flagellum Ribosomal Map 0pt5 10min]]
*[[Media:Flagellum Ribosomal Mapp 1 60min 20151012.jpg‎ | Flagellum Ribosomal Mapp 1 60min]]
*[[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]]

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]]

Code or scripts
Assessment of Project[edit]

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

What worked and what didn't work?

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

Evaluate the Gene Database Project and Group Report in the following areas:

Content: What is the quality of the work?

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

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

Oregon Trail Survivors completed all of the project objectives because we kept each other accountable and planned ahead. During Finals time people's lives become hectic and its hard to find a time everyone can meet. We had a group messaging system going to make sure each section was being taken care of or if anyone had questions those were addressed.

Reflection on the Process[edit]

I liked how the process of the final project was constructed. For the last assignment in class we did a mock final genMAPP assignment with the vibrio cholera data. This laid the foundation for which the GenMAPP users would essentially use. The first time using GenMAPP I was completely and utterly lost, after a few times I gradually picked up on the format and the different files needed and how the database .gbd and .gex files relate to each other. The gradual build up to the final project definately helped with preparations. I did like how we gave a power point presentation before the deliverables were due, this allowed for us to obtain feedback that we used, I know I did personally, towards the deliverables. I found the constructive criticism very helpful.

What did you learn?

With your head (biological or computer science principles)

I learned new analytical techniques regarding both biological and computer science principles. Taking the best of both worlds and formulating it into one. Before this class I wasn't familiar with many of the concepts we discussed but over time and with many hours of practice I have built a framework for these ideas to stick to. This class has challenged me to being uncomfortable and working through that in order to meet the end result which has been so rewarding.

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

I have developed a soft spot for this class. The computer science students and biology students meshed well together in this class, especially when working out of ones comfort zone and in an area not of their expertise. The camaraderie within this class is unlike any other I've taken. This class has helped improve skills regarding teamwork and setting goals towards accomplishing a group effort final task.

With your hands (technical skills)?

I have become more resourceful when it comes to collecting data from outside sources and compiling that information together. This class has provided the tools to become

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

User:Eyanosch

2015-12-18T13:57:19Z

Eyanosch:

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

==Erich Yanoschik==

[[ eyanosch Individual Reflection]]

===Contacts===
* Email - eyanosch@lion.lmu.edu or yanoxc@gmail.com
* Phone - 714.393.6175 (cell)

==Education==
* Loyola Marymount University
* Fullerton College
** Biology Major
** Class of 2016
** Currently taking Field Methods Lab, Field Vertebrate Biology, Biology, Film, & Science Communication, Biological Databases, and last but certainly not least God and the Human Experience.
* California Institute of Medical Training
** CA Certified EMT (OC certified, LA certification pending)

==Career Interests & Goals==
* Emergency Medicine
* Future PA

==Work Experience==
* Wilkinson Chiropractic and Rehabilitation (August 2013 - August 2014)
** Chiropractic Assistant
*** Under the supervision of Dr. Bob Wilkinson and Andy Shore
*** Shadow and observe the techniques used in the examination and implementation of rehabilitation processes
*** Responsible for providing preliminary treatment upon patient arrival and ensuring patient rehabilitation treatment
*** Ultrasound frequency treatment, muscle stimulation, oversee the completion of various rehabilitation exercises, stretch patients
**** Maintain a clean and safe work environment
* Old Spaghetti Factory (October 2012 - July 2013)

==Hobbies & Interests==
* Running & Sports
**LMU Cross Country and Track
[[Image:CrossCountryBanquet.jpg]]
* Hiking & Camping
* Emergency Medicine

===Favorite aspect of Biology===
* The diversity among the science that allows for such a greater understanding of the natural world. There is a niche for everyone, from studying microbes to population tendencies. The possibilities for research and advancement are endless.

===Favorite aspect of Computer Science===
* The convenience provided to every day life that otherwise would not be possible.

{{Template: Pertinent Class Information}}

[[http://www.lmu.edu/ | LMU]]

[[Media:CampusMap.pdf | LMU Campus Map]]

[[Category: Erich Yanoschik]]

Oregon Trail Survivors

2015-12-15T06:01:59Z

Eyanosch: /* Week 15 */ Week 15 contributions

<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]]: 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]]:
* [[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.

Eyanosch Week 15

2015-12-15T05:57:17Z

Eyanosch:

==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

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

{{Template: Pertinent Class Information}}

[[Category: Personal Journal Week 14]]

Eyanosch Week 15

2015-12-14T21:35:39Z

Eyanosch: /* RP-0.5-10 Increased and Decreased */

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

==Electronic lab notebook==
*When GenMAPP is run it creates a Criterion0-GO.txt file with the data from the GO map. Analyze this data in excel
*Open 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

====Create Genes on our Map====
*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)
=====Flagellar assembly=====
*Looking 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.

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.

Created map for ribosomal related genes

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

{{Template: Pertinent Class Information}}

[[Category: Personal Journal Week 14]]

Eyanosch Week 15

2015-12-14T21:31:16Z

Eyanosch: /* RP-1-60 Increased and Decreased */ updated information regarding the results from analyzing the criterion GO files

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

==Electronic lab notebook==
*When GenMAPP is run it creates a Criterion0-GO.txt file with the data from the GO map. Analyze this data in excel
*Open 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

====Create Genes on our Map====
*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)
=====Flagellar assembly=====
*Looking 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.

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=====

=====Decreased=====

Created map for ribosomal related genes

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

{{Template: Pertinent Class Information}}

[[Category: Personal Journal Week 14]]

OTS Deliverables

2015-12-12T23:04:04Z

Eyanosch: /* GenMAPP User Files */ uploaded the map of RX vs RP at 10 minutes 0.5 MIC

==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]]

[[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:Flagellum Ribosomal Mapp 0pt5 10min 20151012.jpg

2015-12-12T23:02:57Z

Eyanosch: Mapp of rx vs rp @ 10 minutes

Mapp of rx vs rp @ 10 minutes

OTS Deliverables

2015-12-12T23:02:27Z

Eyanosch: /* GenMAPP User Files */ uploaded the map of RX vs RP

==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]]

[[Media:Flagellum Ribosomal Mapp 1 60min 20151012.jpg | RP vs RX 1 MIC @ 60 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:Flagellum Ribosomal Mapp 1 60min 20151012.jpg

2015-12-12T23:00:23Z

Eyanosch: Compared the RX and RP results at 60 minutes

Compared the RX and RP results at 60 minutes

Eyanosch Week 15

2015-12-12T21:36:19Z

Eyanosch: /* Decreased */

OTS Deliverables

2015-12-10T23:37:32Z

Eyanosch: /* RP (Erich) */

==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]]

====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 GenMAPP Final RP IDLR EYKZ2015126.xlsx

2015-12-10T23:36:54Z

Eyanosch: Final upload for RP

Final upload for RP

Eyanosch Week 15

2015-12-10T22:40:04Z

Eyanosch: added a subsection for flagellar assembly, going to add subsections for each pathway that was most affected by the treatment

Eyanosch Week 15

2015-12-10T22:30:02Z

Eyanosch:

Eyanosch Week 15

2015-12-09T00:59:09Z

Eyanosch: edited formatting

Eyanosch Week 15

2015-12-09T00:58:26Z

Eyanosch: Electronic lab note book, opened the files from the GO tree and adjusted them to show the top altered Genes, pulled Gene terms from Kegg db to create genes on the map, and finally will compare the results from Increased and Decreased for both trials

Eyanosch Week 15

2015-12-08T22:49:45Z

Eyanosch: formatting this weeks electronic notes

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

==Electronic lab notebook==

====GenMAPP====

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

2015-12-08T22:34:06Z

Eyanosch: /* Week 14 */ Week 14 summary of items completed this week

<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

== 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===
#
#
#

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]]:

==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.

Eyanosch Week 14

2015-12-08T07:49:29Z

Eyanosch: /* Erich Yanoschik */

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

==Electronic lab notebook==

Dividing the Statistical analysis by the two types of drugs (Kristin is doing RX and I am doing RP) Since we performed the same tasks for the two different types of drugs, I borrowed Kristin's electronic lab notebook layout and some information.

====Corrections from talk page====
*Renamed the columns by replacing LR with LogFC, Re-named Sheet 1 "MasterSheet".
*Renamed column A "ID"
*Inserted a ccolumn to the left of Column B and re-named it "MasterIndex". Typed "1" and cell B2 and 2 and Cell B3 and selected both cells. Filled in the column with numbers 1-4224
*Selected the data and sorted from A to Z on the "ID" column. Any rows that had "Empty" or "Blank#### IDs were deleted
*Sorted by the MasterIndex column to put the IDs back in order from 1 to 3926(new total # of files)
*585 cells with "Error" messages replaced with nothing (left them empty)
*copied into Sheet 2 that was named "scalingCentering'

Followed the instructions from [http://www.openwetware.org/wiki/BIOL398-01/S10:Sample_Microarray_Analysis_Vibrio_cholerae Sample Microarray Analysis Vibrio cholerae].

====Normalizing the log ratios for the set of slides in the experiment====
*Copied all the data from MasterSheet and named cell A2 "Average" and named cell A3 "StdDev".
*In cell C2 I typed =AVERAGE(C4:C3929) and in cell C3 I typed =STDEV(C4:C3929). I pressed enter and copied this equation across the rest of the columns through column AL.
*I then copied the column headings for all data columns and pasted them to the right of the last column, I renamed each column with "_Scaled_Centered" at the end
*In cell AM4 I typed =(C4-C$2)/C$3 indicating that I wanted data in cell C4 to have the average subtracted from it and then to divide it by the standard deviation.
*I then copy and pasted that equation across the entire column. I copied and pasted this equation for each column of the data.

====Perform statistical analysis on the ratios====
*Created a new sheet called "Statistics" and copied the information over
*I copied and pasted the ID column from the ScalingCentering worksheet into the first column of the new worksheet, copied all Scaled_Centered columns from the ScalingCentering worksheet, pasted the values into column B1 of the new sheet, and deleted "Average" and "StDev" columns
*Here is when we divided the work, Kristin worked on RX and I worked on RP. (I left the RX data in my excel sheet but only worked on RP)
*Inserted column to the right and typed headers Avg_LogFC RP-0.5-10, Avg_LogFC RP-0.5-30, Avg_LogFC RP-0.5-60, Avg_LogFC RP-1-10, Avg_LogFC RP-1-30, and Avg_LogFC RP-1-60 into the top cells of the next 6 columns.
*Computed the average log fold change per treatment and time period by typing the following equations: =AVERAGE(T2:V2), =AVERAGE(AB2:AD2), =AVERAGE(AJ2:AL2), =AVERAGE(AR2:AT2)), =AVERAGE(AZ2:BB2), and =AVERAGE(BH2:BJ2) below each corresponding Avg_LogFC column. Copied and pasted the equations throughout the entire column.
*I then inserted a new column to the right and named it "Avg_LogFC_all" and typed the equation =AVERAGE(T2:Y2).
*I inserted a new "Tstat" column next to Avg_LogFC. Into column AA2 I typed =AVERAGE(BE2:BG2)/(STDEV(BE2:BG2)/SQRT(6)), indicating 6 replicates. I copied this equation into the whole column. I also used this format for the Tstats of the other RP trials.
*I inserted a new column and called it "Pvalue". I entered the equation =TDIST(ABS(BI2),5,2) for BI2, the T-stat column and 5 degrees of freedom.

====Calculate Bonferroni p value correction====
*Inserted a new column to the right labeled Bonferroni_Pvalue (did this twice)
*In the first Bonferroni_Pvalue column I typed =BJ2*3928 and copied this equation for the entire column.
*In order to replace any corrected P value that was greater than 1 with the number 1, I typed the equation =IF(BK2>1,1,BK2) and pasted it through the entire second Bonferroni_Pvalue column.
*I then saved the most updated version of the file to my ThawSpace and completed the work on thursday.

====Analysis corrections====
After uploading my 12/1 file to the [[OTS Files | OTS Files]] page and consulting with Dr. Dahlquist, I realized that I needed to make several corrections. Originally, I calculated the T-stat, Pvalue, Bonferroni P value, and adjusted Bonferroni P value using a LogFC_all column, which was incorrect. Because this experiment involved multiple treatments (of which I was analyzing 6 for the RX samples) I needed to calculate those four things for all 6 treatments (RX-0.5-10, RX-0.5-30, RX-0.5-60, RX-1-10, RX-1-30, and RX-1-60). I inserted columns for all four items for all 6 treatments I was looking at, and following the same procedure as before, I calculated the T-stat, P value, Bonferroni P value, and adjusted Bonferroni P value for each treatment. Here are some sample equations for the RX-0.5-10 treatment:
*Column Z named Tstat_LogFC RX-0.5-10: =AVERAGE(B2:D2)/(STDEV(B2:D2)/SQRT(3)), denoting that I want a T statistic representative of all three RX-0.5-10 replicates.
*Column AA named Pvalue_LogFC RX-0.5-10: =TDIST(ABS(Z2),2,2), indicating that i wanted the P value calculated from the T statistic column.
*Column AB named Bonferroni_Pvalue_LogFC RX-0.5-10: =AA2*3926
*Column AC named Bonferroni_Pvalue_LogFC RX-0.5-10: =IF(AB2>1,1,AB2) in reference to the first Bonferroni P value column.

Dr Dahlquist also made a change to the file where she replaced all of the nothing boxes with a space/character/space. The amount of replacements was still the same as before but this was done to insure that the analysis was as accurate as possible. I proceeded to do a sanity check before moving on to the Benjamini-Hochberg corrections.
*This was taken from Kristens page, she talked with Dr. Dhalquist about the necessary corrections to complete our portion of the project.

====Prepare file for GenMAPP====
*I inserted a new worksheet and named it "forGenMAPP."
*I selected all from the Statistics worksheet and pasted the values on the new sheet.
*I selected all fold changes and changed them to 2 decimal places by selecting Format > Cells.
*I selected all columns with p values including the T stat column and changed them to 4 decimal places by selecting Format > Cells.
*I deleted the left-most Bonferroni p value columns (the ones without the "IF" statements) from each treatment.
*I inserted a column to the right of the ID column and named it "SystemCode". I filled the whole column with the letter N by typing N in the first cell after the heading and double-clicking on the little black cross.
*I selected File > Save As "Text (Tab-delimited) (*.txt). I clicked through the different warnings and uploaded both files to the team's [[OTS Files | Wiki page]]. (CompiledRaw_data_GenMAPP_ready)

====Sanity Check====
Next I performed a sanity check, I opened the "forGenMAPP" tab and selected "Custom Filter" from the filter options. I then performed the following procedure for all 6 RX treatments.
*Filtered P value column by less than 0.05, 0.01, and 0.001. Recorded results and percentages out of 3,926.
*Filtered Bonferroni p value column by less than 0.05 and recorded results and percentages out of 3,926. The table can be located on my updated excel file from 12/3 found on the team Wiki.
The RP tests that showed the most gene manipulations were the 1 MIC at 60 minutes and 30 minutes with 64.32% and 64.34% respectively. The next closest was RP at 0.5 MIC at the 30 minute marker with 41.14%.

====Running GenMAPP and MAPPFinder====
*upon running genmapp and producing the GO tree. A runtime error occurs ("Run-time error '53': File not found") when clicking on the GO terms.

====Instructions from Dr. Dahlquist====
*Increased LogFC>0.25 and p<0.05
*Decreased LogFC<-0.25 and p<0.05
*Do Benjamini-Hochberg correction for the treatment with the most significant genes out of all 6
*need to do this by tomorrow (the Benjamini-Hochberg correction)

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

{{Template: Pertinent Class Information}}

[[Category: Personal Journal Week 14]]

Eyanosch Week 14

2015-12-08T07:48:55Z

Eyanosch: added the category and my template

==Erich Yanoschik==

==Electronic lab notebook==

Dividing the Statistical analysis by the two types of drugs (Kristin is doing RX and I am doing RP) Since we performed the same tasks for the two different types of drugs, I borrowed Kristin's electronic lab notebook layout and some information.

====Corrections from talk page====
*Renamed the columns by replacing LR with LogFC, Re-named Sheet 1 "MasterSheet".
*Renamed column A "ID"
*Inserted a ccolumn to the left of Column B and re-named it "MasterIndex". Typed "1" and cell B2 and 2 and Cell B3 and selected both cells. Filled in the column with numbers 1-4224
*Selected the data and sorted from A to Z on the "ID" column. Any rows that had "Empty" or "Blank#### IDs were deleted
*Sorted by the MasterIndex column to put the IDs back in order from 1 to 3926(new total # of files)
*585 cells with "Error" messages replaced with nothing (left them empty)
*copied into Sheet 2 that was named "scalingCentering'

Followed the instructions from [http://www.openwetware.org/wiki/BIOL398-01/S10:Sample_Microarray_Analysis_Vibrio_cholerae Sample Microarray Analysis Vibrio cholerae].

====Normalizing the log ratios for the set of slides in the experiment====
*Copied all the data from MasterSheet and named cell A2 "Average" and named cell A3 "StdDev".
*In cell C2 I typed =AVERAGE(C4:C3929) and in cell C3 I typed =STDEV(C4:C3929). I pressed enter and copied this equation across the rest of the columns through column AL.
*I then copied the column headings for all data columns and pasted them to the right of the last column, I renamed each column with "_Scaled_Centered" at the end
*In cell AM4 I typed =(C4-C$2)/C$3 indicating that I wanted data in cell C4 to have the average subtracted from it and then to divide it by the standard deviation.
*I then copy and pasted that equation across the entire column. I copied and pasted this equation for each column of the data.

====Perform statistical analysis on the ratios====
*Created a new sheet called "Statistics" and copied the information over
*I copied and pasted the ID column from the ScalingCentering worksheet into the first column of the new worksheet, copied all Scaled_Centered columns from the ScalingCentering worksheet, pasted the values into column B1 of the new sheet, and deleted "Average" and "StDev" columns
*Here is when we divided the work, Kristin worked on RX and I worked on RP. (I left the RX data in my excel sheet but only worked on RP)
*Inserted column to the right and typed headers Avg_LogFC RP-0.5-10, Avg_LogFC RP-0.5-30, Avg_LogFC RP-0.5-60, Avg_LogFC RP-1-10, Avg_LogFC RP-1-30, and Avg_LogFC RP-1-60 into the top cells of the next 6 columns.
*Computed the average log fold change per treatment and time period by typing the following equations: =AVERAGE(T2:V2), =AVERAGE(AB2:AD2), =AVERAGE(AJ2:AL2), =AVERAGE(AR2:AT2)), =AVERAGE(AZ2:BB2), and =AVERAGE(BH2:BJ2) below each corresponding Avg_LogFC column. Copied and pasted the equations throughout the entire column.
*I then inserted a new column to the right and named it "Avg_LogFC_all" and typed the equation =AVERAGE(T2:Y2).
*I inserted a new "Tstat" column next to Avg_LogFC. Into column AA2 I typed =AVERAGE(BE2:BG2)/(STDEV(BE2:BG2)/SQRT(6)), indicating 6 replicates. I copied this equation into the whole column. I also used this format for the Tstats of the other RP trials.
*I inserted a new column and called it "Pvalue". I entered the equation =TDIST(ABS(BI2),5,2) for BI2, the T-stat column and 5 degrees of freedom.

====Calculate Bonferroni p value correction====
*Inserted a new column to the right labeled Bonferroni_Pvalue (did this twice)
*In the first Bonferroni_Pvalue column I typed =BJ2*3928 and copied this equation for the entire column.
*In order to replace any corrected P value that was greater than 1 with the number 1, I typed the equation =IF(BK2>1,1,BK2) and pasted it through the entire second Bonferroni_Pvalue column.
*I then saved the most updated version of the file to my ThawSpace and completed the work on thursday.

====Analysis corrections====
After uploading my 12/1 file to the [[OTS Files | OTS Files]] page and consulting with Dr. Dahlquist, I realized that I needed to make several corrections. Originally, I calculated the T-stat, Pvalue, Bonferroni P value, and adjusted Bonferroni P value using a LogFC_all column, which was incorrect. Because this experiment involved multiple treatments (of which I was analyzing 6 for the RX samples) I needed to calculate those four things for all 6 treatments (RX-0.5-10, RX-0.5-30, RX-0.5-60, RX-1-10, RX-1-30, and RX-1-60). I inserted columns for all four items for all 6 treatments I was looking at, and following the same procedure as before, I calculated the T-stat, P value, Bonferroni P value, and adjusted Bonferroni P value for each treatment. Here are some sample equations for the RX-0.5-10 treatment:
*Column Z named Tstat_LogFC RX-0.5-10: =AVERAGE(B2:D2)/(STDEV(B2:D2)/SQRT(3)), denoting that I want a T statistic representative of all three RX-0.5-10 replicates.
*Column AA named Pvalue_LogFC RX-0.5-10: =TDIST(ABS(Z2),2,2), indicating that i wanted the P value calculated from the T statistic column.
*Column AB named Bonferroni_Pvalue_LogFC RX-0.5-10: =AA2*3926
*Column AC named Bonferroni_Pvalue_LogFC RX-0.5-10: =IF(AB2>1,1,AB2) in reference to the first Bonferroni P value column.

Dr Dahlquist also made a change to the file where she replaced all of the nothing boxes with a space/character/space. The amount of replacements was still the same as before but this was done to insure that the analysis was as accurate as possible. I proceeded to do a sanity check before moving on to the Benjamini-Hochberg corrections.
*This was taken from Kristens page, she talked with Dr. Dhalquist about the necessary corrections to complete our portion of the project.

====Prepare file for GenMAPP====
*I inserted a new worksheet and named it "forGenMAPP."
*I selected all from the Statistics worksheet and pasted the values on the new sheet.
*I selected all fold changes and changed them to 2 decimal places by selecting Format > Cells.
*I selected all columns with p values including the T stat column and changed them to 4 decimal places by selecting Format > Cells.
*I deleted the left-most Bonferroni p value columns (the ones without the "IF" statements) from each treatment.
*I inserted a column to the right of the ID column and named it "SystemCode". I filled the whole column with the letter N by typing N in the first cell after the heading and double-clicking on the little black cross.
*I selected File > Save As "Text (Tab-delimited) (*.txt). I clicked through the different warnings and uploaded both files to the team's [[OTS Files | Wiki page]]. (CompiledRaw_data_GenMAPP_ready)

====Sanity Check====
Next I performed a sanity check, I opened the "forGenMAPP" tab and selected "Custom Filter" from the filter options. I then performed the following procedure for all 6 RX treatments.
*Filtered P value column by less than 0.05, 0.01, and 0.001. Recorded results and percentages out of 3,926.
*Filtered Bonferroni p value column by less than 0.05 and recorded results and percentages out of 3,926. The table can be located on my updated excel file from 12/3 found on the team Wiki.
The RP tests that showed the most gene manipulations were the 1 MIC at 60 minutes and 30 minutes with 64.32% and 64.34% respectively. The next closest was RP at 0.5 MIC at the 30 minute marker with 41.14%.

====Running GenMAPP and MAPPFinder====
*upon running genmapp and producing the GO tree. A runtime error occurs ("Run-time error '53': File not found") when clicking on the GO terms.

====Instructions from Dr. Dahlquist====
*Increased LogFC>0.25 and p<0.05
*Decreased LogFC<-0.25 and p<0.05
*Do Benjamini-Hochberg correction for the treatment with the most significant genes out of all 6
*need to do this by tomorrow (the Benjamini-Hochberg correction)

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

{{Template: Pertinent Class Information}}

[[Category: Personal Journal Week 14]]

Eyanosch Week 14

2015-12-08T07:48:18Z

Eyanosch:

Eyanosch Week 14

2015-12-08T07:47:33Z

Eyanosch: /* Electronic lab notebook */ added the notes for this past weeks notebook, the steps taken to where we are now.

Oregon Trail Survivors

2015-12-08T06:41:08Z

Eyanosch: /* Reflection */ Added my reflection to the group page

<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

== 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]]:
* [[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.

==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.

Eyanosch Week 14

2015-12-07T01:41:15Z

Eyanosch: set up a layout for this weeks electronic lab notebook

==Erich Yanoschik==

==Electronic lab notebook==

Dividing the Statistical analysis by the two types of drugs (Kristin is doing RX and Erich is doing RP) Since we performed the same tasks for the two different types of drugs, I borrowed Kristin's electronic lab notebook layout.

====Corrections from talk page====

====Normalizing the log ratios for the set of slides in the experiment====

====Calculate Bonferroni p value correction====

====Analysis corrections====

====Prepare file for GenMAPP====

====Sanity Check====

====Benjamini & Hochberg p value correction====

====Running GenMAPP and MAPPFinder====

====Instructions from Dr. Dahlquist====
*Increased LogFC>0.25 and p<0.05
*Decreased LogFC<-0.25 and p<0.05
*Do Benjamini-Hochberg correction for the treatment with the most significant genes out of all 6

*3,926 records left after deleting blanks and empty ID's
*585 cells with "Error" messages replaced with nothing (left them empty)

created MasterIndex Sheet and imported the data from Sheet CompiledRawData
added a MasterIndex Column with values 1-4224

*created new statistics worksheet and imported the data from the ID column and the _Scaled_Centered Columns
*Then the Standard deviation row and average are deleted

Dividing the Statistical analysis by the two types of drugs (Kristin is doing RX and Erich is doing RP)
There will be 6 averages (3 for the 1 x MIC at time points 10, 30, 60) and (3 for the 0.5 x MIC at time points 10, 30, 60)

48 replacements (replacing periods with the letters pt)

Number of errors--> 416

OTS Deliverables

2015-12-07T00:56:21Z

Eyanosch: /* GenMAPP User Files */ uploaded the RP .gex file

==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]]

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

====RP (Erich)====
[[Media:CompiledRaw data statistics BonferroniPvalue RP IDLR EYKZ2015123.xlsx | RP Compiled Raw Data 12/6]]

[[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 GenMAPP ready RP IDLR EYKZ2015126.gex

2015-12-07T00:55:49Z

Eyanosch: Gex file for RP

Gex file for RP

File:CompiledRaw data Errors RP EYKZ2015126.EX.xlsx

2015-12-07T00:54:45Z

Eyanosch: Eyanosch uploaded a new version of File:CompiledRaw data Errors RP EYKZ2015126.EX.xlsx

Exceptions file

OTS Deliverables

2015-12-07T00:54:28Z

Eyanosch: /* GenMAPP User Files */

==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]]

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

====RP (Erich)====
[[Media:CompiledRaw data statistics BonferroniPvalue RP IDLR EYKZ2015123.xlsx | RP Compiled Raw Data 12/6]]

[[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)]]

====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 Errors RP EYKZ2015126.EX.txt

2015-12-07T00:54:08Z

Eyanosch: Eyanosch uploaded a new version of File:CompiledRaw data Errors RP EYKZ2015126.EX.txt

text file of exceptions

OTS Deliverables

2015-12-07T00:49:34Z

Eyanosch: /* GenMAPP User Files */

==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]]

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

====RP (Erich)====
[[Media:CompiledRaw data statistics BonferroniPvalue RP IDLR EYKZ2015123.xlsx | RP Compiled Raw Data 12/6]]

[[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 GenMAPP ready RP IDLR EYKZ2015126.EX.txt | RP Exceptions (txt)]]

====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

2015-12-07T00:49:13Z

Eyanosch: /* GenMAPP User Files */

==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]]

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

====RP (Erich)====
[[Media:CompiledRaw data statistics BonferroniPvalue RP IDLR EYKZ2015123.xlsx | RP Compiled Raw Data 12/6]]

[[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 IDLR EYKZ2015126.EX.txt | RP Exceptions (txt)]]

====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 GenMAPP ready RP IDLR EYKZ2015126.EX.txt

2015-12-07T00:48:18Z

Eyanosch:

File:CompiledRaw data statistics BonferroniPvalue RP IDLR EYKZ2015123.xlsx

2015-12-07T00:38:44Z

Eyanosch: Eyanosch uploaded a new version of File:CompiledRaw data statistics BonferroniPvalue RP IDLR EYKZ2015123.xlsx

Compiled data with statistics and GenMapp ready information regarding SF

OTS Deliverables

2015-12-07T00:38:22Z

Eyanosch: /* GenMAPP User Files */

==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]]

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

====RP (Erich)====
[[Media:CompiledRaw data statistics BonferroniPvalue RP IDLR EYKZ2015123.xlsx | RP Compiled Raw Data 12/6]]

[[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)]]

====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

2015-12-07T00:38:05Z

Eyanosch: /* GenMAPP User Files */ edited gen mapp ready file

==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]]

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

====RP (Erich)====
[[Media:CompiledRaw data statistics BonferroniPvalue RP IDLR EYKZ2015123.xlsx | RP Compiled Raw Data 12/3]]

[[Media:CompiledRaw data GenMAPP ready RP IDLR EYKZ2015126.txt | RP .txt format GenMAPP ready 12/3]]

[[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)]]

====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 GenMAPP ready RP IDLR EYKZ2015126.txt

2015-12-07T00:37:43Z

Eyanosch: GenMAPP ready RP file

GenMAPP ready RP file

OTS Deliverables

2015-12-07T00:24:12Z

Eyanosch: /* RP (Erich) */

==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]]

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

====RP (Erich)====
[[Media:CompiledRaw data statistics BonferroniPvalue RP IDLR EYKZ2015123.xlsx | RP Compiled Raw Data 12/3]]

[[Media:CompiledRaw data statistics BonferroniPvalue RP IDLR EYKZ2015123.xlsx | RP .txt format GenMAPP ready 12/3]]

[[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)]]

====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

2015-12-07T00:23:55Z

Eyanosch: /* GenMAPP User Files */

==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]]

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

====RP (Erich)====
[[Media:CompiledRaw data statistics BonferroniPvalue RP IDLR EYKZ2015123.xlsx | RP Compiled Raw Data 12/3]]

[[Media:CompiledRaw data statistics BonferroniPvalue RP IDLR EYKZ2015123.xlsx | RP .txt format GenMAPP ready 12/3]]

[[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 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

2015-12-07T00:23:43Z

Eyanosch: /* GenMAPP User Files */ uploaded the exceptions for RP in a text file

==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]]

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

====RP (Erich)====
[[Media:CompiledRaw data statistics BonferroniPvalue RP IDLR EYKZ2015123.xlsx | RP Compiled Raw Data 12/3]]

[[Media:CompiledRaw data statistics BonferroniPvalue RP IDLR EYKZ2015123.xlsx | RP .txt format GenMAPP ready 12/3]]

[[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 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 Errors RP EYKZ2015126.EX.txt

2015-12-07T00:23:03Z

Eyanosch: text file of exceptions

text file of exceptions