LMU BioDB 2015 - User contributions [en]

Heavy Metal HaterZ Deliverables

2015-12-18T22:46:09Z

Malverso: /* Group Files and Datasets */ added title

{{Template:Heavy Metal HaterZ}}

== Individual Assessments and Reflections ==
[[Malverso Assessments & Reflections]]

[https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Emilysimso_Week_15#Statement_of_Work Emily Simso (on Week 15 Assignment Page)]

== Group Files and Datasets ==

* [[Media:So-Std_HMH_20151214.zip | GenMAPP Gene Database for assigned species]]
* ReadMe file to accompany the Gene Database (''.pdf'')
** [[Media:ReadMe So-Std 20151214.pdf | Shewanella onedensis ReadMe]]
* [[Media:Gene Database Testing Report - Heavy Metal HaterZ.pdf | Gene Database Testing Report]] for final submitted Gene Database
* Processed and analyzed DNA microarray dataset (''.xls'' or ''.xlsx'')
**[[File:UpdatedCompiledRawData WithGenMAPP 20151210 ES HMH.xlsx]]
* [[Media:CompiledRawData ForGenMAPP 20151208 HMH.txt | Data file]] used for import into GenMAPP
* [[Media:CompiledRawData ForGenMAPP 20151210 HMH.gex | GenMAPP Expression Dataset file]]
* [[Media:CompiledRawData ForGenMAPP 20151210 HMH.EX.txt | Exceptions file]] of data imported into GenMAPP
* Raw MAPPFinder results files:
** [[Media:MAPPFINDER 20151212-Criterion0-GO.txt | criterion 0]]
** [[Media:MAPPFINDER 20151212-Criterion1-GO.txt | criterion 1]]
* [[Media:CompiledRawData ForGenMAPP 20151210 HMH.zip | ''.gmf'' file]]
* Filtered MAPPFinder Results (''.xls'' or ''.xlsx'')
**[[Media:MAPPFINDER 20151212-Criterion0-GO.xlsx | criterion 0]]
**[[Media:MAPPFINDER 20151212-Criterion1-GO 20151212 HMH.xlsx | criterion 1]]
* Sample MAPP file of a relevant biological pathway for your species (''.mapp'')
**[[File:Fatty Acid Degradation Soneidensis 20151213 HMH.mapp | Fatty Acid Degradation]]
**[[File:Compiled Fatty Acid Degradation 20151216 HMH.mapp | Compiled Fatty Acid Degradation]]
**[[File:Ribosomal Soneidensis 20151213 HMH.mapp | Ribosome]]
**[[File:Compiled Ribosome 20151216 HMH.mapp | Compiled Ribosome]]
===Final Report and Presentation===
* [[File:Final_Report_20151218_2_HMH.docx | Final Group Report]]
* [[Media:Biol Data Final Presentation.pdf | PowerPoint presentation]] given on Tuesday, December 15

[[Gene Database Project Deliverables]]
[[Category:Heavy Metal HaterZ]]
[[Category:Group Projects]]

Heavy Metal HaterZ Deliverables

2015-12-18T22:45:17Z

Malverso: /* Group Files and Datasets */ uploaded group report

{{Template:Heavy Metal HaterZ}}

== Individual Assessments and Reflections ==
[[Malverso Assessments & Reflections]]

[https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Emilysimso_Week_15#Statement_of_Work Emily Simso (on Week 15 Assignment Page)]

== Group Files and Datasets ==

===Gene Database===

* [[Media:So-Std_HMH_20151214.zip | GenMAPP Gene Database for assigned species]]
* ReadMe file to accompany the Gene Database (''.pdf'')
** [[Media:ReadMe So-Std 20151214.pdf | Shewanella onedensis ReadMe]]
* [[Media:Gene Database Testing Report - Heavy Metal HaterZ.pdf | Gene Database Testing Report]] for final submitted Gene Database
* Processed and analyzed DNA microarray dataset (''.xls'' or ''.xlsx'')
**[[File:UpdatedCompiledRawData WithGenMAPP 20151210 ES HMH.xlsx]]
* [[Media:CompiledRawData ForGenMAPP 20151208 HMH.txt | Data file]] used for import into GenMAPP
* [[Media:CompiledRawData ForGenMAPP 20151210 HMH.gex | GenMAPP Expression Dataset file]]
* [[Media:CompiledRawData ForGenMAPP 20151210 HMH.EX.txt | Exceptions file]] of data imported into GenMAPP
* Raw MAPPFinder results files:
** [[Media:MAPPFINDER 20151212-Criterion0-GO.txt | criterion 0]]
** [[Media:MAPPFINDER 20151212-Criterion1-GO.txt | criterion 1]]
* [[Media:CompiledRawData ForGenMAPP 20151210 HMH.zip | ''.gmf'' file]]
* Filtered MAPPFinder Results (''.xls'' or ''.xlsx'')
**[[Media:MAPPFINDER 20151212-Criterion0-GO.xlsx | criterion 0]]
**[[Media:MAPPFINDER 20151212-Criterion1-GO 20151212 HMH.xlsx | criterion 1]]
* Sample MAPP file of a relevant biological pathway for your species (''.mapp'')
**[[File:Fatty Acid Degradation Soneidensis 20151213 HMH.mapp | Fatty Acid Degradation]]
**[[File:Compiled Fatty Acid Degradation 20151216 HMH.mapp | Compiled Fatty Acid Degradation]]
**[[File:Ribosomal Soneidensis 20151213 HMH.mapp | Ribosome]]
**[[File:Compiled Ribosome 20151216 HMH.mapp | Compiled Ribosome]]
* [[File:Final_Report_20151218_2_HMH.docx | Final Group Report]]
* [[Media:Biol Data Final Presentation.pdf | PowerPoint presentation]] given on Tuesday, December 15

[[Gene Database Project Deliverables]]
[[Category:Heavy Metal HaterZ]]
[[Category:Group Projects]]

Template:Heavy Metal HaterZ

2015-12-18T22:43:20Z

Malverso: updated paper

[[Image:HeavyMetal.jpg | 200px | right]]
==''Shewanella oneidensis''==
'''[[Gene Database Testing Report - Heavy Metal HaterZ | Our Gene Database Testing Report ]]'''

'''Group Paper''' - [[File:Final_Report_20151218_2_HMH.docx]]

==Group Members==
*Coder:[[User:Malverso | Mary Alverson]]
*GenMAPP User & Project Manager:[[User:Rlegaspi | Ron Legaspi]]
*Quality Assurance:[[User:Jkuroda | Josh Kuroda]]
*GenMAPP User:[[User:Emilysimso | Emily Simso]]
==Important Links==
====[[Heavy Metal HaterZ Files | Our Files]]====
====[[Heavy Metal HaterZ Deliverables | Our Deliverables]]====
{{Gene_Database_Project_Links}}
{{HMH Individual Journal Entries}}

[[Category:Group Projects]]
[[Category:Heavy Metal HaterZ]]

File:Final Report 20151218 2 HMH.docx

2015-12-18T22:42:42Z

Malverso:

Malverso Assessments & Reflections

2015-12-18T20:46:45Z

Malverso: added group page link

[[Heavy Metal HaterZ]]
==Statement of Work==
* Link to my code on github: https://github.com/lmu-bioinformatics/xmlpipedb/blob/s-oneidensis/gmbuilder/src/edu/lmu/xmlpipedb/gmbuilder/databasetoolkit/profiles/ShewanellaOneidensisUniProtSpeciesProfile.java
#[[Malverso Week 11]]
#*During week 11, I located the Model Organism Database and determined the regular gene ID format for Shewanella oneidensis. I also set up the [[Heavy Metal HaterZ]] page, which included creating a template and a logo.
#[[Malverso Week 12]]
#*I downloaded eclipse and git for windows on one of the Seaver 120 computers to use for the duration of this project. I also added myself as a developer on github so my code could be uploaded and merged with existing code, and I created a branch of xmlpipedb called s-oneidensis. I linked eclipse to xmlpipedb and cloned the code and I ran an initial build, which made a genMAPPBuilder that I could test. This week I also worked with Josh to prepare our [[File:Genome Paper Presentation 20151124 HMH.pptx]].
#[[Malverso Week 14]]
#*This week I created a new species profile on xmlpipedb by creating a new class called ShewanellaOneidensisUniProtSpeciesProfile. In this new file, I used Dondi's guidlines to customize code for my specific species. To do this I had to first look up the taxon ID and the MOD link for a specific gene and adapted that line to be generic. Then I ran another Ant Build and gave the dist folder (which contained [[File:ShewanellaOneidensisGMBuilder_20151201_HMH.zip]]) to josh. Next I committed my code to github.
#[[Malverso Week 15]]
#*This week I used data from Emily and Ron to create a new expression dataset on genMAPP. Every single entry resulted in an error, which Josh and I located to be a missing underscore. I adapted code from Vibrio cholerae's species profile so that the program could handle underscore-less gene ID's. The first time I did this, I accidentally added underscores instead of taking them away, so I had to fix the error and then re-create the database. This database was successful, so I committed it to github. It can be downloaded [[Media:So-Std_HMH_20151214.zip | here]]. This week I also wrote slides for our [[Media:Biol Data Final Presentation.pdf | final presentation]] and wrote portions of the paper. I wrote the section in the introduction that discussed the genome paper, and I wrote a significant amount of the results section (the schema, explaining the figures about ID counts, explaining the code changes). I also compiled the figures to correspond to these sections.

==Assessment of Project==
#What worked and what didn't work?
#*It worked to have an established way to communicate between all of the team members. We had a group text that allowed us to keep each other updated, and worked well to remind each other about completing tasks such as the status reports. It also worked well that we trusted each other to get our own work done on time (It helped that everyone did their own work in a timely manner). What didn't work as well as it could was the fact that for awhile, Josh's computer was the hub for all activity when it could have and should have been spread between a few computers so that we could work simultaneously. By the end of the project, we were utilizing more computers but I should have started to use mine for creating databases earlier so that I could preform tests separate of him and the GenMAPP users.
#What would you do differently if you could do it all over again?
#*I kind of just answered this above, but other than what was just mentioned, I probably would have enjoyed being a little more in the loop with what the results of the GenMAPP users were. Since we were all working simultaneously, I didn't know the results until we practiced our final presentation. I also made a mistake in comprehending the initial error in our database, which costed me some time. I should have understood what I was doing better before trying to fix it just because exporting the database takes so long.
#Evaluate the Gene Database Project and Group Report in the following areas:
#*Content: What is the quality of the work?
#**I think that the quality of our work is fairly high. At least from my stand point, my ability to write in a scientific manner has vastly improved. Also, it is not even an option to cut corner on the coding portion of this project because the code either works or does not. I also think that as a group our public speaking has improved through our various presentations.
#*Organization: Comment on the organization of the project and of your group's wiki pages.
#**Our wiki pages were very organized, other than the page where all of our files lived. However, our files were often both on the files page as well as linked from other pages such as electronic journals or testing reports that made it easy to find what I needed when I needed it. It was good that everyone in our group was good about uploading their files, so they were accessible for all no matter the time.
#*Completeness: Did your team achieve all of the project objectives? Why or why not?
#**We finished all of the deliverables on time which is the most important thing, provided our paper gets turned in (I am writing this after I finished my portion of the paper but before it has been uploaded). I also think that we have all grown in a variety of ways, which is also an important object of this project. I think our team could have benefited from a little bit more unity when working on the projects, but some of the reasoning behind a lot of our work being done separate from each other could be because of all of our various extracurricular activities.

==Reflection on the Process==
*What did you learn?
*#With your head (biological or computer science principles)
*#*As far as biology goes, I had little knowledge before this class. I definitely feel more comfortable with gene related terms as well as reading scientific papers and actually being able to understand what is going on. In the computer science realm, I have gotten way more comfortable using unix on the command line, I know basic principles about relational databases, and I can create various SQL commands. Adding to a pre-existing program was also a new experience for me.
*#With your heart (personal qualities and teamwork qualities that make things work or not work)?
*#*Since this was a group project, procrastination wasn't an option - others depended on me. I definitely have grown in my time management areas. I also have gotten better at following directions. This sounds a bit silly, but I skipped over things by accident in the first few journal assignments and I have gotten better at being thorough when reading directions.
*#With your hands (technical skills)?
*#*I learned new coding languages, and learned how to put together a database as well as how to use big databases online, and how to use this wiki. I also learned how to make better scientific presentations, and how to give better presentations.
*What lesson will you take away from this project that you will still use a year from now?
*#*A big lesson that I learned was how to be disciplined with my time. I needed to set aside time that I knew I could fully focus on this class and project, which is how I was able to stay on track with my tasks week after week. This is a helpful skill because by scheduling out time to work, I avoid procrastinating or forgetting about what I need to do.

Malverso Assessments & Reflections

2015-12-18T20:45:49Z

Malverso: did group eval

==Statement of Work==
* Link to my code on github: https://github.com/lmu-bioinformatics/xmlpipedb/blob/s-oneidensis/gmbuilder/src/edu/lmu/xmlpipedb/gmbuilder/databasetoolkit/profiles/ShewanellaOneidensisUniProtSpeciesProfile.java
#[[Malverso Week 11]]
#*During week 11, I located the Model Organism Database and determined the regular gene ID format for Shewanella oneidensis. I also set up the [[Heavy Metal HaterZ]] page, which included creating a template and a logo.
#[[Malverso Week 12]]
#*I downloaded eclipse and git for windows on one of the Seaver 120 computers to use for the duration of this project. I also added myself as a developer on github so my code could be uploaded and merged with existing code, and I created a branch of xmlpipedb called s-oneidensis. I linked eclipse to xmlpipedb and cloned the code and I ran an initial build, which made a genMAPPBuilder that I could test. This week I also worked with Josh to prepare our [[File:Genome Paper Presentation 20151124 HMH.pptx]].
#[[Malverso Week 14]]
#*This week I created a new species profile on xmlpipedb by creating a new class called ShewanellaOneidensisUniProtSpeciesProfile. In this new file, I used Dondi's guidlines to customize code for my specific species. To do this I had to first look up the taxon ID and the MOD link for a specific gene and adapted that line to be generic. Then I ran another Ant Build and gave the dist folder (which contained [[File:ShewanellaOneidensisGMBuilder_20151201_HMH.zip]]) to josh. Next I committed my code to github.
#[[Malverso Week 15]]
#*This week I used data from Emily and Ron to create a new expression dataset on genMAPP. Every single entry resulted in an error, which Josh and I located to be a missing underscore. I adapted code from Vibrio cholerae's species profile so that the program could handle underscore-less gene ID's. The first time I did this, I accidentally added underscores instead of taking them away, so I had to fix the error and then re-create the database. This database was successful, so I committed it to github. It can be downloaded [[Media:So-Std_HMH_20151214.zip | here]]. This week I also wrote slides for our [[Media:Biol Data Final Presentation.pdf | final presentation]] and wrote portions of the paper. I wrote the section in the introduction that discussed the genome paper, and I wrote a significant amount of the results section (the schema, explaining the figures about ID counts, explaining the code changes). I also compiled the figures to correspond to these sections.

==Assessment of Project==
#What worked and what didn't work?
#*It worked to have an established way to communicate between all of the team members. We had a group text that allowed us to keep each other updated, and worked well to remind each other about completing tasks such as the status reports. It also worked well that we trusted each other to get our own work done on time (It helped that everyone did their own work in a timely manner). What didn't work as well as it could was the fact that for awhile, Josh's computer was the hub for all activity when it could have and should have been spread between a few computers so that we could work simultaneously. By the end of the project, we were utilizing more computers but I should have started to use mine for creating databases earlier so that I could preform tests separate of him and the GenMAPP users.
#What would you do differently if you could do it all over again?
#*I kind of just answered this above, but other than what was just mentioned, I probably would have enjoyed being a little more in the loop with what the results of the GenMAPP users were. Since we were all working simultaneously, I didn't know the results until we practiced our final presentation. I also made a mistake in comprehending the initial error in our database, which costed me some time. I should have understood what I was doing better before trying to fix it just because exporting the database takes so long.
#Evaluate the Gene Database Project and Group Report in the following areas:
#*Content: What is the quality of the work?
#**I think that the quality of our work is fairly high. At least from my stand point, my ability to write in a scientific manner has vastly improved. Also, it is not even an option to cut corner on the coding portion of this project because the code either works or does not. I also think that as a group our public speaking has improved through our various presentations.
#*Organization: Comment on the organization of the project and of your group's wiki pages.
#**Our wiki pages were very organized, other than the page where all of our files lived. However, our files were often both on the files page as well as linked from other pages such as electronic journals or testing reports that made it easy to find what I needed when I needed it. It was good that everyone in our group was good about uploading their files, so they were accessible for all no matter the time.
#*Completeness: Did your team achieve all of the project objectives? Why or why not?
#**We finished all of the deliverables on time which is the most important thing, provided our paper gets turned in (I am writing this after I finished my portion of the paper but before it has been uploaded). I also think that we have all grown in a variety of ways, which is also an important object of this project. I think our team could have benefited from a little bit more unity when working on the projects, but some of the reasoning behind a lot of our work being done separate from each other could be because of all of our various extracurricular activities.

==Reflection on the Process==
*What did you learn?
*#With your head (biological or computer science principles)
*#*As far as biology goes, I had little knowledge before this class. I definitely feel more comfortable with gene related terms as well as reading scientific papers and actually being able to understand what is going on. In the computer science realm, I have gotten way more comfortable using unix on the command line, I know basic principles about relational databases, and I can create various SQL commands. Adding to a pre-existing program was also a new experience for me.
*#With your heart (personal qualities and teamwork qualities that make things work or not work)?
*#*Since this was a group project, procrastination wasn't an option - others depended on me. I definitely have grown in my time management areas. I also have gotten better at following directions. This sounds a bit silly, but I skipped over things by accident in the first few journal assignments and I have gotten better at being thorough when reading directions.
*#With your hands (technical skills)?
*#*I learned new coding languages, and learned how to put together a database as well as how to use big databases online, and how to use this wiki. I also learned how to make better scientific presentations, and how to give better presentations.
*What lesson will you take away from this project that you will still use a year from now?
*#*A big lesson that I learned was how to be disciplined with my time. I needed to set aside time that I knew I could fully focus on this class and project, which is how I was able to stay on track with my tasks week after week. This is a helpful skill because by scheduling out time to work, I avoid procrastinating or forgetting about what I need to do.

Malverso Assessments & Reflections

2015-12-17T06:33:47Z

Malverso: added reflections

==Statement of Work==
* Link to my code on github: https://github.com/lmu-bioinformatics/xmlpipedb/blob/s-oneidensis/gmbuilder/src/edu/lmu/xmlpipedb/gmbuilder/databasetoolkit/profiles/ShewanellaOneidensisUniProtSpeciesProfile.java
#[[Malverso Week 11]]
#*During week 11, I located the Model Organism Database and determined the regular gene ID format for Shewanella oneidensis. I also set up the [[Heavy Metal HaterZ]] page, which included creating a template and a logo.
#[[Malverso Week 12]]
#*I downloaded eclipse and git for windows on one of the Seaver 120 computers to use for the duration of this project. I also added myself as a developer on github so my code could be uploaded and merged with existing code, and I created a branch of xmlpipedb called s-oneidensis. I linked eclipse to xmlpipedb and cloned the code and I ran an initial build, which made a genMAPPBuilder that I could test. This week I also worked with Josh to prepare our [[File:Genome Paper Presentation 20151124 HMH.pptx]].
#[[Malverso Week 14]]
#*This week I created a new species profile on xmlpipedb by creating a new class called ShewanellaOneidensisUniProtSpeciesProfile. In this new file, I used Dondi's guidlines to customize code for my specific species. To do this I had to first look up the taxon ID and the MOD link for a specific gene and adapted that line to be generic. Then I ran another Ant Build and gave the dist folder (which contained [[File:ShewanellaOneidensisGMBuilder_20151201_HMH.zip]]) to josh. Next I committed my code to github.
#[[Malverso Week 15]]
#*This week I used data from Emily and Ron to create a new expression dataset on genMAPP. Every single entry resulted in an error, which Josh and I located to be a missing underscore. I adapted code from Vibrio cholerae's species profile so that the program could handle underscore-less gene ID's. The first time I did this, I accidentally added underscores instead of taking them away, so I had to fix the error and then re-create the database. This database was successful, so I committed it to github. It can be downloaded [[Media:So-Std_HMH_20151214.zip | here]]. This week I also wrote slides for our [[Media:Biol Data Final Presentation.pdf | final presentation]] and wrote as well as reviewed parts of our final paper. <-- LINK

==Assessment of Project==
#What worked and what didn't work?
#*It worked to have an established way to communicate between all of the team members. We had a group text that allowed us to keep each other updated, and worked well to remind each other about completing tasks such as the status reports. It also worked well that we trusted each other to get our own work done on time (It helped that everyone did their own work in a timely manner). What didn't work as well as it could was the fact that for awhile, Josh's computer was the hub for all activity when it could have and should have been spread between a few computers so that we could work simultaneously. By the end of the project, we were utilizing more computers but I should have started to use mine for creating databases earlier so that I could preform tests separate of him and the GenMAPP users.
#What would you do differently if you could do it all over again?
#*I kind of just answered this above, but other than what was just mentioned, I probably would have enjoyed being a little more in the loop with what the results of the GenMAPP users were. Since we were all working simultaneously, I didn't know the results until we practiced our final presentation. I also made a mistake in comprehending the initial error in our database, which costed me some time. I should have understood what I was doing better before trying to fix it just because exporting the database takes so long.
#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?

==Reflection on the Process==
*What did you learn?
*#With your head (biological or computer science principles)
*#*As far as biology goes, I had little knowledge before this class. I definitely feel more comfortable with gene related terms as well as reading scientific papers and actually being able to understand what is going on. In the computer science realm, I have gotten way more comfortable using unix on the command line, I know basic principles about relational databases, and I can create various SQL commands. Adding to a pre-existing program was also a new experience for me.
*#With your heart (personal qualities and teamwork qualities that make things work or not work)?
*#*Since this was a group project, procrastination wasn't an option - others depended on me. I definitely have grown in my time management areas. I also have gotten better at following directions. This sounds a bit silly, but I skipped over things by accident in the first few journal assignments and I have gotten better at being thorough when reading directions.
*#With your hands (technical skills)?
*#*I learned new coding languages, and learned how to put together a database as well as how to use big databases online, and how to use this wiki. I also learned how to make better scientific presentations, and how to give better presentations.
*What lesson will you take away from this project that you will still use a year from now?
*#*A big lesson that I learned was how to be disciplined with my time. I needed to set aside time that I knew I could fully focus on this class and project, which is how I was able to stay on track with my tasks week after week. This is a helpful skill because by scheduling out time to work, I avoid procrastinating or forgetting about what I need to do.

Malverso Assessments & Reflections

2015-12-17T05:36:16Z

Malverso: assessed the project

Malverso Assessments & Reflections

2015-12-17T05:26:01Z

Malverso: /* Statement of Work */ added link

Heavy Metal HaterZ Files

2015-12-17T05:24:12Z

Malverso: /* GenMapp Builder */ addde note

==All Files==
*All files will be listed here.
*Appropriate way to title files:
**FileName_YYYYMMDD_HMH

===Gene Database===
*[[File:So-Std_HMH_20151214.zip]]

===Initial Flow Chart===
*Initial flow chart for experimental design - [[File:Experimental Design Flow Chart 20151115 HMH.pptx]]

===Journal Club Presentation Power Points===
*Microarray Paper Presentation - [[File:SoMicroarrayPaperPresentation 20151117 HMH.pptx]]
*Genome Paper Presentation - [[File:GenomePPT_20151123_HMH.pdf]]

===Data Processing Notes from Dr. Dahlquist===
*Page 1 of Notes - [[Media:DrDDataProcessNotes1 20151119 HMH.JPG]]
*Page 2 of Notes - [[Media:DrDDataProcessNotes2 20151119 HMH.JPG]]

===GenMapp Builder===
*Note:This is now outdated.
*[[File:ShewanellaOneidensisGMBuilder_20151201_HMH.zip]]

===Statistical Analysis Excel Sheets===
*Prior to Splitting:
*#[[File:UpdatedCompiledRawData Shewanella RARL 20151201 HMH.xlsx]]
*#[[File:UpdatedCompiledRawData 20151206 HMH.xlsx]]
* After splitting, use this one:
*# [[Media:UpdatedCompiledRawData_Shewanella_RARL_20151201_HMH_forsplitting.xlsx | UpdatedCompiledRawData_Shewanella_RARL_20151201_HMH_forsplitting.xlsx]]
*Following the splitting, averages taken and ttests done to data sets:
*#[[File:StatisticalAnalysis Shewanella RARL 20151207 HMH.xlsx]]
*#[[File:UpdatedCompiledRawData Shewanella RARL 20151201 ES HMH forsplitting.xlsx]]
*#* [[Media:UpdatedCompiledRawData_Shewanella_RARL_20151201_ES_HMH_forsplitting_KD.xlsx | UpdatedCompiledRawData_Shewanella_RARL_20151201_ES_HMH_forsplitting_KD.xlsx]]
*#* I made corrections to Emily's file because there are 5408 genes, not 5408. I think that both files have the same results not and you can move on to the next step. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:22, 9 December 2015 (PST)''
*Ready for GenMAPP
**[[File:UpdatedCompiledRawData WithGenMAPP 20151210 ES HMH.xlsx]]
*.txt file for GenMAPP
**[[File:CompiledRawData ForGenMAPP 20151208 HMH.txt]]
* Ranked List from MAPPFinder: [[File:Ranked list from MAPPFinder.PNG]]

===Sanity Check Table===
*[[File:Sanity Check Chart 20151212 HMH.xlsx]]

===MAPPFinder Documents===
*gdb file - [[File:So-Std 20151201special.zip]]
*[[File:ColorSetforExpressionData F60C60 20151210 HMH.gex]]
*GenMAPP with all comparisons - [[File:FilesForComparison AllTrials WithGenMAPP 20151212 ES HMH.gex]]
*Filtered GO terms for increased - [[File:MAPPFINDER 20151212-Criterion0-GO 20151212 HMH.xlsx]]
**[[File:MAPPFINDER 20151212-Criterion0-GO 20151212 HMH.txt]]
*Filtered GO terms for decreased - [[File:MAPPFINDER 20151212-Criterion1-GO 20151212 HMH.xlsx]]
**[[File:MAPPFINDER 20151212-Criterion1-GO 20151212 HMH.txt]]
*Screenshots showing significant results - [[File:CompiledScreenShots 20151212 HMH.docx]]
*MAPP for Fatty Acid Degradation - [[File:Fatty Acid Degradation Soneidensis 20151213 HMH.mapp]]
**Screenshot of results - [[File:Fatty Acid Degradation 20151214 HMH.PNG]]
*MAPP for Ribosome - [[File:Ribosomal Soneidensis 20151213 HMH.mapp]]
**Screenshot of results - [[File:Ribosomal Pathway 20151213 HMH.PNG]]
*MAPP for Compiled Ribosome - [[File:Compiled Ribosome 20151216 HMH.mapp]]
**Screenshot of results - [[File:Compiled Ribosome Image 20151216 HMH.PNG]]
*MAPP for Compiled Fatty Acid Degradation -[[File:Compiled Fatty Acid Degradation 20151216 HMH.mapp]]
**Screenshot of results - [[File:Fatty Acid Degradation Compiled 20151216 HMH.PNG]]

===KEGG Screenshots===
*Fatty Acid Degradation [[File:Fatty Acid Pathway from KEGG 20151216 HMH.PNG]]
*Ribosome [[File:Ribosome Pathway from KEGG 20151216 HMH.PNG]]

===Tables for Paper===
*Table showing variations between Yang et al. paper for 6 chosen genes and our results - [[File:Gene Comparison 20151216 HMH.xlsx]]
*Tale showing variations between Yang et al. paper for genes involved in the ribosome pathway and our results - [[File:Ribosome Pathway Comparison 20151216 HMH.xlsx]]

[[Category:Heavy Metal HaterZ]]
[[Category:Group Projects]]

Malverso Assessments & Reflections

2015-12-17T05:22:39Z

Malverso: fixed errors

Malverso Assessments & Reflections

2015-12-17T05:21:32Z

Malverso: /* Statement of Work */ added links

Malverso Assessments & Reflections

2015-12-17T05:09:10Z

Malverso: wrote week 15

==Statement of Work==
#[[Malverso Week 11]]
#*During week 11, I located the Model Organism Database and determined the regular gene ID format for Shewanella oneidensis. I also set up the Heavy Metal HaterZ page, which included creating a template and a logo.
#[[Malverso Week 12]]
#*I downloaded eclipse and git for windows on one of the Seaver 120 computers to use for the duration of this project. I also added myself as a developer on github so my code could be uploaded and merged with existing code, and I created a branch of xmlpipedb called s-oneidensis. I linked eclipse to xmlpipedb and cloned the code and I ran an initial build, which made a genMAPPBuilder that I could test. LINK
#[[Malverso Week 14]]
#*This week I created a new species profile on xmlpipedb by creating a new class called ShewanellaOneidensisUniProtSpeciesProfile. In this new file, I used Dondi's guidlines to customize code for my specific species. To do this I had to first look up the taxon ID and the MOD link for a specific gene and adapted that line to be generic. Then I ran another Ant Build and uploaded the dist file to the wiki LINK. Next I committed my code to github.
#[[Malverso Week 15]]
#*This week I used data from Emily and Ron to create a new expression dataset on genMAPP. Every single entry resulted in an error, which Josh and I located to be a missing underscore. I adapted code from Vibrio cholerae's species profile so that the program could handle underscore-less gene ID's. The first time I did this, I accidentally added underscores instead of taking them away, so I had to fix the error and then re-create the database. This database was successful, so I committed it to github.
Describe exactly what you did on the project. This week I also wrote slides for our final presentation and wrote as well as reviewed parts of our final paper. LINK

==Assessment of Project==
Give an objective assessment of the success of your project workflow and teamwork.
What worked and what didn't work?
What would you do differently if you could do it all over again?
Evaluate 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?

==Reflection on the Process==
What did you learn?
With your head (biological or computer science principles)
With your heart (personal qualities and teamwork qualities that make things work or not work)?
With your hands (technical skills)?
What lesson will you take away from this project that you will still use a year from now?

Malverso Assessments & Reflections

2015-12-17T05:00:09Z

Malverso: did week 14

==Statement of Work==
#[[Malverso Week 11]]
#*During week 11, I located the Model Organism Database and determined the regular gene ID format for Shewanella oneidensis. I also set up the Heavy Metal HaterZ page, which included creating a template and a logo.

#[[Malverso Week 12]]
#*I downloaded eclipse and git for windows on one of the Seaver 120 computers to use for the duration of this project. I also added myself as a developer on github so my code could be uploaded and merged with existing code, and I created a branch of xmlpipedb called s-oneidensis. I linked eclipse to xmlpipedb and cloned the code and I ran an initial build, which made a genMAPPBuilder that I could test. LINK

#[[Malverso Week 14]]
#*This week I created a new species profile on xmlpipedb by creating a new class called ShewanellaOneidensisUniProtSpeciesProfile. In this new file, I used Dondi's guidlines to customize code for my specific species. To do this I had to first look up the taxon ID and the MOD link for a specific gene and adapated that line to be generic. Then I ran another Ant Build and uploaded the dist file to the wiki LINK. Next I committed my code to github.

#[[Malverso Week 15]]
Describe exactly what you did on the project.
Provide references or links to artifacts of your work, such as:
Wiki pages
Other files or documents
Code or scripts

==Assessment of Project==
Give an objective assessment of the success of your project workflow and teamwork.
What worked and what didn't work?
What would you do differently if you could do it all over again?
Evaluate 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?

==Reflection on the Process==
What did you learn?
With your head (biological or computer science principles)
With your heart (personal qualities and teamwork qualities that make things work or not work)?
With your hands (technical skills)?
What lesson will you take away from this project that you will still use a year from now?

Malverso Assessments & Reflections

2015-12-17T04:49:59Z

Malverso: wrote week 12

Malverso Assessments & Reflections

2015-12-17T04:44:05Z

Malverso: did week 11

==Statement of Work==
#[[Malverso Week 11]]
#*During week 11, I located the Model Organism Database and determined the regular gene ID format for Shewanella oneidensis. I downloaded eclipse and git for windows on one of the Seaver 120 computers to use for the duration of this project. I also set up the Heavy Metal HaterZ page, which included creating a template and a logo.
#[[Malverso Week 12]]
[[Malverso Week 14]]
[[Malverso Week 15]]
Describe exactly what you did on the project.
Provide references or links to artifacts of your work, such as:
Wiki pages
Other files or documents
Code or scripts

==Assessment of Project==
Give an objective assessment of the success of your project workflow and teamwork.
What worked and what didn't work?
What would you do differently if you could do it all over again?
Evaluate 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?

==Reflection on the Process==
What did you learn?
With your head (biological or computer science principles)
With your heart (personal qualities and teamwork qualities that make things work or not work)?
With your hands (technical skills)?
What lesson will you take away from this project that you will still use a year from now?

Malverso Assessments & Reflections

2015-12-17T04:27:44Z

Malverso: added reflection questions

==Statement of Work==
Describe exactly what you did on the project.
Provide references or links to artifacts of your work, such as:
Wiki pages
Other files or documents
Code or scripts

==Assessment of Project==
Give an objective assessment of the success of your project workflow and teamwork.
What worked and what didn't work?
What would you do differently if you could do it all over again?
Evaluate 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?

==Reflection on the Process==
What did you learn?
With your head (biological or computer science principles)
With your heart (personal qualities and teamwork qualities that make things work or not work)?
With your hands (technical skills)?
What lesson will you take away from this project that you will still use a year from now?

Heavy Metal HaterZ Deliverables

2015-12-17T04:26:33Z

Malverso: added individual reflection

{{Template:Heavy Metal HaterZ}}

== Individual Assessments and Reflections ==
[[Malverso Assessments & Reflections]]

== Group Files and Datasets ==

===Gene Database===

* [[Media:So-Std_HMH_20151214.zip | GenMAPP Gene Database for assigned species]]
* ReadMe file to accompany the Gene Database (''.pdf'')
** [[Media:ReadMe So-Std 20151214.pdf | Shewanella onedensis ReadMe]]
* [[Media:Gene Database Testing Report - Heavy Metal HaterZ.pdf | Gene Database Testing Report]] for final submitted Gene Database
* Processed and analyzed DNA microarray dataset (''.xls'' or ''.xlsx'')
* [[Media:CompiledRawData ForGenMAPP 20151208 HMH.txt | Data file]] used for import into GenMAPP
* [[Media:CompiledRawData ForGenMAPP 20151210 HMH.gex | GenMAPP Expression Dataset file]]
* [[Media:CompiledRawData ForGenMAPP 20151210 HMH.EX.txt | Exceptions file]] of data imported into GenMAPP
* Raw MAPPFinder results files:
** [[Media:MAPPFINDER 20151212-Criterion0-GO.txt | criterion 0]]
** [[Media:MAPPFINDER 20151212-Criterion1-GO.txt | criterion 1]]
* [[Media:CompiledRawData ForGenMAPP 20151210 HMH.zip | ''.gmf'' file]]
* Filtered MAPPFinder Results (''.xls'' or ''.xlsx'')
**[[Media:MAPPFINDER 20151212-Criterion0-GO.xlsx | criterion 0]]
**[[Media:MAPPFINDER 20151212-Criterion1-GO 20151212 HMH.xlsx | criterion 1]]
* Sample MAPP file of a relevant biological pathway for your species (''.mapp'')
* [[Gene Database Project Deliverables#Group Report | Group Report]] describing the creation of the Gene Database and the biological analysis of the data (''.doc'', ''.docx'', or ''.pdf'')
* [[Media:Biol Data Final Presentation.pdf | PowerPoint presentation]] given on Tuesday, December 15

[[Gene Database Project Deliverables]]
[[Category:Heavy Metal HaterZ]]
[[Category:Group Projects]]

Gene Database Testing Report - Heavy Metal HaterZ

2015-12-15T04:16:08Z

Malverso: /* Export Information */ gdb

{{Heavy Metal HaterZ}}
==Export Information==

Version of GenMAPP Builder: '''3 build 5'''

Computer on which export was run: '''HP Compaq 8300 Elite SFF FC'''

Postgres Database name: '''S. Oneidensis'''

UniProt XML filename: [[Media:SOneidensisUNIPROT.gz | '''SOneidensisUNIPROT''']]
* UniProt XML version: '''UniProt release 2015_10 - October 14, 2015'''
* [http://www.uniprot.org/uniprot/?query=taxonomy:211586 UniProt XML download link]
* Time taken to import: '''3.18 minutes'''
** Note: ''n/a''

GO OBO-XML filename: [[Media:Go daily-termdb.obo-xml.gz | '''go daily-termdb.obo-xml''']]
* GO OBO-XML version (The version information can be found in the file properties after the file downloaded from the [http://beta.geneontology.org/page/download-ontology GO Download page] has been unzipped):
* [http://geneontology.org/page/download-ontology#Legacy_Downloads GO OBO-XML download link]
* Time taken to import: '''7.16 minutes'''
* Time taken to process: '''4.27 minutes'''
** Note: ''n/a''

GOA filename: [[Media:ShewanellaOneidensisGOA.zip | '''ShewanellaOneidensisGOA''']]
* GOA version (News on [http://www.ebi.ac.uk/GOA/ this page] records past releases; current information can be found in the Last modified field on the [ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/ FTP site]): '''October 14, 2015 - GOA Proteome Sets 124'''
* [ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/106.S_oneidensis.goa GOA download link]
* Time taken to import: '''0.05 minutes'''
** Note: ''n/a''

Name of .gdb file: [[Media:So-Std_HMH_20151214.zip | '''So-Std_HMH_20151214.gdb''']]
* Time taken to export: '''1 hour and 18 minutes'''
** Start time: '''3:48pm'''
** End time: '''5:06pm'''
** Note: ''n/a''

==TallyEngine==

* Run the TallyEngine in GenMAPP Builder and record the number of records for UniProt and GO in the XML data and in the Postgres databases.
** Choose the menu item Tallies > Run XML and Database Tallies for UniProt and GO...
** Take a screenshot of the results. Upload the image to the wiki and display it on this page.
** '''4196''' IDs
** For more information, [[How_Do_I_Count_Thee%3F_Let_Me_Count_The_Ways | see this page.]]

[[Image:TallyEngineSOneidensis.PNG | center | 540px]]

== Using XMLPipeDB match to Validate the XML Results from the TallyEngine==

[[How_Do_I_Count_Thee%3F_Let_Me_Count_The_Ways | Follow the instructions found on this page to run XMLPipeDB match.]]

Are your results the same as you got for the TallyEngine? Why or why not?
* Initially, we got '''4196''' IDs for both XML and Postgres DB from TallyEngine but got '''4079''' IDs by using XMLPipeDB match. This result was from using the following command:
java -jar xmlpipedb-match-1.1.1.jar "SO_[0-9][0-9][0-9][0-9]" < SOneidensisUNIPROT

* After checking the .gdb file and looking through the Gene IDs, I found that some IDs were in the form "SO_A####" so I ran a new command accounting for this:
java -jar xmlpipedb-match-1.1.1.jar "SO_A?[0-9][0-9][0-9][0-9]" < SOneidensisUNIPROT
* This gave a total number of '''4207''' IDs.

== Using SQL Queries to Validate the PostgreSQL Database Results from the TallyEngine==

For more information, [[How_Do_I_Count_Thee%3F_Let_Me_Count_The_Ways | see this page.]]

You can also look for counts at the SQL level, using some variation of a ''select count(*)'' query. This requires some knowledge of which table received what data. Here’s an initial tip: the ''gene/name'' tags in the XML file land in the ''genenametype'' table. A query on this table counting values from this table that were marked as ''ordered locus'' in the XML file matching the pattern ''SO_[0-9][0-9][0-9][0-9]'' would look like this:

select count(*) from genenametype where type = 'ordered locus' and value ~ 'SO_[0-9][0-9][0-9][0-9]';
* However, once I found that some IDs were in the form "SO_A####" I tweaked the pattern to account for those IDs:
select count(*) from genenametype where type = 'ordered locus' and value ~ 'SO_A?[0-9][0-9][0-9][0-9]';

In ''pgAdmin III'', you can issue these queries by clicking on the pencil/SQL icon in the toolbar, typing the query into the ''SQL Editor'' tab, then clicking on the green triangular ''Play'' button to run.

Are your results the same as reported by the TallyEngine? Why or why not?
* Initially, we got a count of '''4068''' IDs using SQL, which differed from the '''4196''' IDs from TallyEngine.
* After tweaking the pattern to account for IDs with that extra ''A'', we got a grand total of '''4196''' IDs, which matches with what TallyEngine gave us.

==OriginalRowCounts Comparison==

Within the .gdb file, look at the OriginalRowCounts table to see if the database has the expected tables with the expected number of records. Compare the tables and records with a benchmark .gdb file.

Benchmark .gdb file: [http://sourceforge.net/projects/xmlpipedb/files/V.%20cholerae%20Gene%20Database/V.%20cholerae%2020101022/Vc-Std_External_20101022.zip/download 2010 benchmark file]

Copy the OriginalRowCounts table from the benchmark and new gdb and paste them here:

[[Media:OriginalRowCounts.pdf | Original Row Counts Table]]

[[Media:OriginalRowCounts2010.pdf | 2010 Benchmark Original Row Counts Table]]

See Analysis section for more on the comparison and the discrepancy found because of this comparison.

Note: Using Microsoft Access, we found ''7664'' IDs, which was actually double the number of IDs present because of duplicated IDs that did not have an underscore.

==Visual Inspection==

Perform visual inspection of individual tables to see if there are any problems.

* Look at the Systems table. Is there a date in the Date field for all gene ID systems present in the database?
** No. For the current version, a good number of gene ID systems in the database do not have a value for the date field. Some systems that lack a date include: GenBank, UniGene, WormBase, and EcoGene.
* Open the UniProt, RefSeq, and OrderedLocusNames tables. Scroll down through the table. Do all of the IDs look like they take the correct form for that type of ID?
** For the UniProt table, the IDs start with either ''Q8'' or ''K4'' and have some string of four letters/numbers trailing that. For the RefSeq tables, the IDs have forms that start with either ''NP_'' or ''WP_'', with the ''WP_'' forms having 9 numbers afterwards and the ''NP_'' forms having 6 numbers afterwards. For the OrderedLocusNames table, the IDs either start with <code>SO_</code> or <code>SO_A</code>.

Note: ''n/a''

==Analysis==

Consolidating the counts of gene IDs from the various methods, I got:

* 4196 IDs from Tally Engine
* ''4207'' IDs from xmlpipedb-match
java -jar xmlpipedb-match-1.1.1.jar "SO_A?[0-9][0-9][0-9][0-9]" < SOneidensisUNIPROT
* 4196 IDs from PostgreSQL
select count(*) from genenametype where type = 'ordered locus' and value ~ 'SO_A?[0-9][0-9][0-9][0-9]';
* 4196 IDs from Microsoft Access (Noted that there were 4068 IDs in the form <code>SO_####</code> and 128 IDs in the form <code>SO_A####</code>)

Notice that there is a small but significant discrepancy in that there seems to be eleven more IDs when using xmlpipedb-match. This is troubling because of the fact that the other three methods seemed to confirm a total count of 4196. So, I used Microsoft Excel to compare the list of gene IDs from the actual .gdb file and the list I got back from xmlpipedb-match. As you can see on [[Media:Comparing gdb and xmlpipedb-match.xlsx | this document]], there are 11 IDs in the xmlpipedb-match column that are not found in the gdb column. This discrepancy was further pointed out by the use of some <code>match</code> functions to see where an ID was missing from either list. Below are the two match functions I used in the document:
=MATCH(A2, B$2:B$4208, 0)
=MATCH(B2, A$2:A$4208, 0)
Below are the eleven IDs in question:
SO_3699 NO-KD
SO_1312 NO-KD
SO_4269 NO-KD if they are all part of "Protein-protein interaction databases", then you can safely leave them out
SO_2875 NO-MA
SO_4532 NO-MA
SO_4580 NO-MA
SO_2662 NO-MA
SO_4423 NO-MA
SO_3156 NO-MA
SO_2967 NO-MA
SO_2024 NO-MA
//I looked these up on www.uniprot.org and all were found to be only in "Protein-protein interaction databases"

Look up the IDs at [http://www.uniprot.org UniProt web site] and then search for them on the UniProt record web page. If they are part of the "STRING" protein-protein interaction database, then you can safely leave them out. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:55, 3 December 2015 (PST)''

None of these IDs are in our MOD.
We searched for these IDs in the microarray statistical analysis sheet and did not find the following IDs:
SO_4269, SO_2875, SO_4580

As of 12/01/15, we are waiting on input from Professor Dahlquist to see if we will adjust our GenMAPP Builder to account for these 11 IDs.
* A manual inspection was done on the [[Media:SOneidensisUNIPROT.gz | '''SOneidensisUNIPROT''']] XML file and it looks like these 11 IDs are contained within entries that are missing a gene tag, which explains why the other methods only picked up 4196 IDs.

==.gdb Use in GenMAPP==

While the above sections perform quality assurance on the exported Gene Database via verifying ID counts, the "proof in the pudding" is to actually use the Gene Database in GenMAPP. You can follow the instructions in [http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols Part 2 of the ''Vibrio cholerae'' Microarray Data Analysis] to verify that the Gene Database works in GenMAPP. In this case, the emphasis is not on the findings of the data analysis itself, but that the Gene Database functions appropriate in GenMAPP.

For assistance with using the GenMAPP program, the GenMAPP Help is very extensive. To access it within GenMAPP, go to the menu item Help > GenMAPP Help and either browse or search for your topic of interest.

Note: ''n/a''

===Putting a gene on the MAPP using the GeneFinder window===

* In the main GenMAPP Drafting Board window, left-click on the icon for "Gene" in the upper left corner of the window. Click on the Drafting Board to place the Gene on the MAPP. Now, right-click on the gene to access the GeneFinder window. Type or paste a gene ID into the Gene ID field. Select the appropriate Gene ID system from the drop-down menu and click the Search button. For example, for ''Vibrio cholerae'', you could search for the ID "VC0028", which is an OrderedLocusNames ID. Once the ID has been found, click the OK button to return to the Drafting Board window.
** For the Final Project, you will need to try a sample ID from each of the gene ID systems, not just OrderedLocusNames.
* Open the Backpage by left-clicking on the gene box on the Drafting Board to see if all of the cross-referenced IDs that are supposed to be there are there.

Note: I tried out the search for a gene ID and was able to bring up the Backpage for that ID. The cross-referenced IDs that were supposed to show up were indeed on the page.

===Creating an Expression Dataset in the Expression Dataset Manager===

* How many of the IDs were imported out of the total IDs in the microarray dataset? How many exceptions were there? Look in the EX.txt file and look at the error codes for the records that were not imported into the Expression Dataset. Do these represent IDs that were present in the UniProt XML, but were somehow not imported? or were they not present in the UniProt XML?

Note: The Expression Dataset Manager reported that there were 1441 errors during the conversion. From looking over the error codes, I found that these genes were the ones we expected to ignore, like the IDs with an added 'F.'

===Coloring a MAPP with expression data===

Note: I was able to successfully color the MAPP by coloring the increased and decreased Log Fold Changes.

===Running MAPPFinder===

Note: After the results had been calculated, a Gene Ontology browser opened showing my results. All of the Gene Ontology terms that have at least 3 genes measured and a p value of less than 0.05 were highlighted yellow. A term with a p value less than 0.05 is considered a "significant" result. Browsed through the tree to see the results.

Documents produced from this run-through can be found here: [[Media:MAPPFinder Relevant Files.zip | Gene Database Testing docs]]

Heavy Metal HaterZ Deliverables

2015-12-15T03:57:37Z

Malverso: /* Gene Database */ gdb

{{Template:Heavy Metal HaterZ}}

== Group Files and Datasets ==

===Gene Database===

* [[Media:So-Std_HMH_20151214.zip | GenMAPP Gene Database for assigned species]]
* ReadMe file to accompany the Gene Database (''.pdf'')
** [[Media:ReadMe So-Std 20151214.pdf | Shewanella onedensis ReadMe]]
* [[Media:Gene Database Testing Report - Heavy Metal HaterZ.pdf | Gene Database Testing Report]] for final submitted Gene Database
* Processed and analyzed DNA microarray dataset (''.xls'' or ''.xlsx'')
* [[Media:CompiledRawData ForGenMAPP 20151208 HMH.txt | Data file]] used for import into GenMAPP
* [[Media:CompiledRawData ForGenMAPP 20151210 HMH.gex | GenMAPP Expression Dataset file]]
* [[Media:CompiledRawData ForGenMAPP 20151210 HMH.EX.txt | Exceptions file]] of data imported into GenMAPP
* Raw MAPPFinder results files:
** [[Media:MAPPFINDER 20151212-Criterion0-GO.txt | criterion 0]]
** [[Media:MAPPFINDER 20151212-Criterion1-GO.txt | criterion 1]]
* [[Media:CompiledRawData ForGenMAPP 20151210 HMH.zip | ''.gmf'' file]]
* Filtered MAPPFinder Results (''.xls'' or ''.xlsx'')
**[[Media:MAPPFINDER 20151212-Criterion0-GO.xlsx | criterion 0]]
**[[Media:MAPPFINDER 20151212-Criterion1-GO 20151212 HMH.xlsx | criterion 1]]
* Sample MAPP file of a relevant biological pathway for your species (''.mapp'')
* [[Gene Database Project Deliverables#Group Report | Group Report]] describing the creation of the Gene Database and the biological analysis of the data (''.doc'', ''.docx'', or ''.pdf'')
* PowerPoint presentation (''.ppt'', ''.pptx'', or ''.pdf'', given on Tuesday, December 15)

[[Gene Database Project Deliverables]]
[[Category:Heavy Metal HaterZ]]
[[Category:Group Projects]]

Heavy Metal HaterZ Deliverables

2015-12-15T03:48:12Z

Malverso: /* Group Files and Datasets */ took out stuff

{{Template:Heavy Metal HaterZ}}

== Group Files and Datasets ==

===Gene Database===

* [[File:So-Std_HMH_20151214.zip | GenMAPP Gene Database for assigned species]]
* ReadMe file to accompany the Gene Database (''.pdf'')
** [[Media:ReadMe So-Std 20151214.pdf | Shewanella onedensis ReadMe]]
* [[Media:Gene Database Testing Report - Heavy Metal HaterZ.pdf | Gene Database Testing Report]] for final submitted Gene Database
* Processed and analyzed DNA microarray dataset (''.xls'' or ''.xlsx'')
* [[Media:CompiledRawData ForGenMAPP 20151208 HMH.txt | Data file]] used for import into GenMAPP
* [[Media:CompiledRawData ForGenMAPP 20151210 HMH.gex | GenMAPP Expression Dataset file]]
* [[Media:CompiledRawData ForGenMAPP 20151210 HMH.EX.txt | Exceptions file]] of data imported into GenMAPP
* Raw MAPPFinder results files:
** [[Media:MAPPFINDER 20151212-Criterion0-GO.txt | criterion 0]]
** [[Media:MAPPFINDER 20151212-Criterion1-GO.txt | criterion 1]]
* [[Media:CompiledRawData ForGenMAPP 20151210 HMH.zip | ''.gmf'' file]]
* Filtered MAPPFinder Results (''.xls'' or ''.xlsx'')
**[[Media:MAPPFINDER 20151212-Criterion0-GO.xlsx | criterion 0]]
**[[Media:MAPPFINDER 20151212-Criterion1-GO 20151212 HMH.xlsx | criterion 1]]
* Sample MAPP file of a relevant biological pathway for your species (''.mapp'')
* [[Gene Database Project Deliverables#Group Report | Group Report]] describing the creation of the Gene Database and the biological analysis of the data (''.doc'', ''.docx'', or ''.pdf'')
* PowerPoint presentation (''.ppt'', ''.pptx'', or ''.pdf'', given on Tuesday, December 15)

[[Gene Database Project Deliverables]]
[[Category:Heavy Metal HaterZ]]
[[Category:Group Projects]]

Heavy Metal HaterZ Deliverables

2015-12-15T03:47:44Z

Malverso: /* Group Files and Datasets */ readme

{{Template:Heavy Metal HaterZ}}

== Group Files and Datasets ==

===Gene Database===

* [[File:So-Std_HMH_20151214.zip | GenMAPP Gene Database for assigned species]]
* ReadMe file to accompany the Gene Database (''.pdf'')
** [[Media:ReadMe So-Std 20151214.pdf | Shewanella onedensis ReadMe]]
** Include Gene Database Schema diagram in ReadMe
*** Sample schema in Adobe Illustrator format: [[Media:Vibrio_schema_20101022.zip | Vibrio_schema_20101022.zip]]
* [[Media:Gene Database Testing Report - Heavy Metal HaterZ.pdf | Gene Database Testing Report]] for final submitted Gene Database
* Processed and analyzed DNA microarray dataset (''.xls'' or ''.xlsx'')
* [[Media:CompiledRawData ForGenMAPP 20151208 HMH.txt | Data file]] used for import into GenMAPP
* [[Media:CompiledRawData ForGenMAPP 20151210 HMH.gex | GenMAPP Expression Dataset file]]
* [[Media:CompiledRawData ForGenMAPP 20151210 HMH.EX.txt | Exceptions file]] of data imported into GenMAPP
* Raw MAPPFinder results files:
** [[Media:MAPPFINDER 20151212-Criterion0-GO.txt | criterion 0]]
** [[Media:MAPPFINDER 20151212-Criterion1-GO.txt | criterion 1]]
* [[Media:CompiledRawData ForGenMAPP 20151210 HMH.zip | ''.gmf'' file]]
* Filtered MAPPFinder Results (''.xls'' or ''.xlsx'')
**[[Media:MAPPFINDER 20151212-Criterion0-GO.xlsx | criterion 0]]
**[[Media:MAPPFINDER 20151212-Criterion1-GO 20151212 HMH.xlsx | criterion 1]]
* Sample MAPP file of a relevant biological pathway for your species (''.mapp'')
* [[Gene Database Project Deliverables#Group Report | Group Report]] describing the creation of the Gene Database and the biological analysis of the data (''.doc'', ''.docx'', or ''.pdf'')
* PowerPoint presentation (''.ppt'', ''.pptx'', or ''.pdf'', given on Tuesday, December 15)

[[Gene Database Project Deliverables]]
[[Category:Heavy Metal HaterZ]]
[[Category:Group Projects]]

File:ReadMe So-Std 20151214.pdf

2015-12-15T03:46:53Z

Malverso:

Heavy Metal HaterZ Deliverables

2015-12-15T03:44:58Z

Malverso: updated .gdb

{{Template:Heavy Metal HaterZ}}

== Group Files and Datasets ==

===Gene Database===

* [[File:So-Std_HMH_20151214.zip| GenMAPP Gene Database for assigned species]]
* ReadMe file to accompany the Gene Database (''.pdf'')
** Shewanella onedensis ReadMe
** Include Gene Database Schema diagram in ReadMe
*** Sample schema in Adobe Illustrator format: [[Media:Vibrio_schema_20101022.zip | Vibrio_schema_20101022.zip]]
* [[Media:Gene Database Testing Report - Heavy Metal HaterZ.pdf | Gene Database Testing Report]] for final submitted Gene Database
* Processed and analyzed DNA microarray dataset (''.xls'' or ''.xlsx'')
* [[Media:CompiledRawData ForGenMAPP 20151208 HMH.txt | Data file]] used for import into GenMAPP
* [[Media:CompiledRawData ForGenMAPP 20151210 HMH.gex | GenMAPP Expression Dataset file]]
* [[Media:CompiledRawData ForGenMAPP 20151210 HMH.EX.txt | Exceptions file]] of data imported into GenMAPP
* Raw MAPPFinder results files:
** [[Media:MAPPFINDER 20151212-Criterion0-GO.txt | criterion 0]]
** [[Media:MAPPFINDER 20151212-Criterion1-GO.txt | criterion 1]]
* [[Media:CompiledRawData ForGenMAPP 20151210 HMH.zip | ''.gmf'' file]]
* Filtered MAPPFinder Results (''.xls'' or ''.xlsx'')
**[[Media:MAPPFINDER 20151212-Criterion0-GO.xlsx | criterion 0]]
**[[Media:MAPPFINDER 20151212-Criterion1-GO 20151212 HMH.xlsx | criterion 1]]
* Sample MAPP file of a relevant biological pathway for your species (''.mapp'')
* [[Gene Database Project Deliverables#Group Report | Group Report]] describing the creation of the Gene Database and the biological analysis of the data (''.doc'', ''.docx'', or ''.pdf'')
* PowerPoint presentation (''.ppt'', ''.pptx'', or ''.pdf'', given on Tuesday, December 15)

[[Gene Database Project Deliverables]]
[[Category:Heavy Metal HaterZ]]
[[Category:Group Projects]]

Heavy Metal HaterZ Files

2015-12-15T03:43:36Z

Malverso: added .gdb file

==All Files==
*All files will be listed here.
*Appropriate way to title files:
**FileName_YYYYMMDD_HMH

===Gene Database===
*[[File:So-Std_HMH_20151214.zip]]

===Initial Flow Chart===
*Initial flow chart for experimental design - [[File:Experimental Design Flow Chart 20151115 HMH.pptx]]

===Journal Club Presentation Power Points===
*Microarray Paper Presentation - [[File:SoMicroarrayPaperPresentation 20151117 HMH.pptx]]
*Genome Paper Presentation - [[File:GenomePPT_20151123_HMH.pdf]]

===Data Processing Notes from Dr. Dahlquist===
*Page 1 of Notes - [[Media:DrDDataProcessNotes1 20151119 HMH.JPG]]
*Page 2 of Notes - [[Media:DrDDataProcessNotes2 20151119 HMH.JPG]]

===GenMapp Builder===
*[[File:ShewanellaOneidensisGMBuilder_20151201_HMH.zip]]

===Statistical Analysis Excel Sheets===
*Prior to Splitting:
*#[[File:UpdatedCompiledRawData Shewanella RARL 20151201 HMH.xlsx]]
*#[[File:UpdatedCompiledRawData 20151206 HMH.xlsx]]
* After splitting, use this one:
*# [[Media:UpdatedCompiledRawData_Shewanella_RARL_20151201_HMH_forsplitting.xlsx | UpdatedCompiledRawData_Shewanella_RARL_20151201_HMH_forsplitting.xlsx]]
*Following the splitting, averages taken and ttests done to data sets:
*#[[File:StatisticalAnalysis Shewanella RARL 20151207 HMH.xlsx]]
*#[[File:UpdatedCompiledRawData Shewanella RARL 20151201 ES HMH forsplitting.xlsx]]
*#* [[Media:UpdatedCompiledRawData_Shewanella_RARL_20151201_ES_HMH_forsplitting_KD.xlsx | UpdatedCompiledRawData_Shewanella_RARL_20151201_ES_HMH_forsplitting_KD.xlsx]]
*#* I made corrections to Emily's file because there are 5408 genes, not 5408. I think that both files have the same results not and you can move on to the next step. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 15:22, 9 December 2015 (PST)''
*Ready for GenMAPP
**[[File:UpdatedCompiledRawData WithGenMAPP 20151210 ES HMH.xlsx]]
*.txt file for GenMAPP
**[[File:CompiledRawData ForGenMAPP 20151208 HMH.txt]]
* Ranked List from MAPPFinder: [[File:Ranked list from MAPPFinder.PNG]]

===Sanity Check Table===
*[[File:Sanity Check Chart 20151212 HMH.xlsx]]

===MAPPFinder Documents===
*gdb file - [[File:So-Std 20151201special.zip]]
*[[File:ColorSetforExpressionData F60C60 20151210 HMH.gex]]
*GenMAPP with all comparisons - [[File:FilesForComparison AllTrials WithGenMAPP 20151212 ES HMH.gex]]
*Filtered GO terms for increased - [[File:MAPPFINDER 20151212-Criterion0-GO 20151212 HMH.xlsx]]
**[[File:MAPPFINDER 20151212-Criterion0-GO 20151212 HMH.txt]]
*Filtered GO terms for decreased - [[File:MAPPFINDER 20151212-Criterion1-GO 20151212 HMH.xlsx]]
**[[File:MAPPFINDER 20151212-Criterion1-GO 20151212 HMH.txt]]
*Screenshots showing significant results - [[File:CompiledScreenShots 20151212 HMH.docx]]
*MAPP for Fatty Acid Degradation - [[File:Fatty Acid Degradation Soneidensis 20151213 HMH.mapp]]
**Screenshot of results - [[File:Fatty Acid Degradation 20151213 HMH.PNG]]
*MAPP for Ribosome - [[File:Ribosomal Soneidensis 20151213 HMH.mapp]]
**Screenshot of results - [[File:Ribosomal Pathway 20151213 HMH.PNG]]

[[Category:Heavy Metal HaterZ]]
[[Category:Group Projects]]

File:So-Std HMH 20151214.zip

2015-12-15T03:41:34Z

Malverso:

Malverso Week 15

2015-12-15T03:40:09Z

Malverso: updated electronic journal

==Electronic Journal==
*Josh and I ran some of the statistical analysis data from the GenMAPP users through creating a new expression dataset and generated an exception file which found some issues with our database.
* At first there was an exception for every single gene, because we did not compensate for the underscore in the ID. After manually inserting the underscore after the 'SO', we were able to find the actual errors.
*We noted that there are 5408 genes listed in their data, but only 4196 genes in our database.
*There are also 760 gene IDs that are in the form SO_####F, which are genes that don't exist in our database.
*There are 681 gene IDs that are in a 'normal' form (either SO_#### or SO_A####) but do not exist in our database.
*For some of the gene IDs that have 'F's, there are multiple genes of the same ID.
*We failed at trying to find a way to search uniprot for all 1441 missing ID's, so decided to do a spot check, seearching for about 1 out of every 100 gene ID's on uniprot. None of which returned any results.
*We also searched for the some of the 'F' IDs in our MOD and none of them returned results either.
*We concluded that even though 1441 is a large number, the exception scoul dbe safely ignored.
*I did, however, have to make another customization to genMapp to be able to handle the underscores.
*In class on 12/10/15, we worked on figuring out the corrections for our GenMAPP code and made a new dataset using the finished data from the GenMAPP users.
*Using the manually underscored dated, we were able to run MAPPFinder successfully and generated all of the necessary files for our deliverables.
*I wrote the customization by copy and pasting the code from the vibrio cholerae customization and then customizing that to add an underscore to the data.
*Ran new export according to https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Running_GenMAPP_Builder with newly customized code (The power outage erased my records of how long the various exports took but my .gdb file was saved in the ThawSpace which is a plus)
*I tested the new .gdb file with the unmodified data ID's and found that every ID still resulted in an error.\
*To figure out my problem I opened the .gdb file with Microsoft Access and looked in the ordered Locus names to see that there was a copy of each gene ID (Which was expected), but also that the copy of the ID names had two underscores in them instead of none.
*I redid the code by adding this line:
newId = "SO" + substrings[i].substring(3,substrings[i].length());
*Then I re-exported the gene database. The links can be foound on our gene database testing report page.
**Uniprot took 3.13 minutes.
**OBO.XML took 7.05 minutes.
**Processing the GO terms took 4.76 minutes.
**GOA took .06 minutes.
**The export took 1 hour and 35 minutes.
*The new .gdb file can be located on the files and deliverables page.

{{Template:Malverso}}

Heavy Metal HaterZ

2015-12-15T03:35:20Z

Malverso: /* Week 15 Assignment */ updated status report

{{Heavy Metal HaterZ}}
==Week 15 Assignment==
===Goals===
*Finish Deliverables
*Prepare for the presentation
===Status Report===
*Mary - Finished second customization for the S.oneidensis profile. I need to push it to github with support from Dr.Dionisio.

==Week 14 Assignment==
===Goals===
*Coder/QA
**Analyze the initial exports and make any necessary changes to the custom species profile to capture all of the IDs for your species
*GenMAPP Users
**Finish statistical analysis of compiled microarray data
**Prepare file for GenMAPP
===Status Report===
*Mary- I finished customizing the genMappBuilder and uploaded it onto this wiki so htat Josh could test to see if it works, which it does for the most part. A few genes aren't picked up that are not in the MOD but present elsewhere.
* Josh- Completed the export using the customized GenMAPP Builder from Mary. Checked the .gdb file and everything checked out. Used GenMAPP to see if the gene ID links worked and they did. Made more progress on the Gene Database Testing Report.
*Emily - I worked on manipulating the data to import it into GenMAPP and while Ron and I initially had some problems, I think we worked them out and are ready to continue this coming week.
*Ron - Worked on manipulation of the data along with Emily to prepare data for GenMAPP. Difficulties arose when it came to performing particular calculations and having data match with Emily's, but I think that they have been resolved with the help of Dr. Dahlquist; thus, we are closer to having a GenMAPP ready file.

====Reflections====
#What worked?
#What didn't work?
#What will I do next to fix what didn't work?

*Mary:
*#Dr.Dionisio's instructions were very clear so I was able to customize the genMappBuilder and it is working like it should.
*#There are still 11 "lost" genes that may need to be "found" somehow with my code, even though they are not located within the MOD.
*#First I need to determine if those genes are necessary for genMapp to catch, and then i will need to re-customize the code if so.

*Josh:
*# Our customized export seemed to work, since we got the 4196 count for Ordered Locus Names for which we were looking.
*#The 11 IDs we found that did not have gene tags in the XML file are a small issue for us. None of them exist in our model organism database, but 8 of them are present in our microarray data.
*#We are waiting on input from Professor Dahlquist regarding our next steps with these 11 IDs. Once we find out, we will act accordingly and possibly edit our code.

*Emily
*#It was very helpful to have Dr. Dahlquist's instructions for manipulating our data, so I was able to calculate the Pvalues and adjust them using the two tests.
*#Ron and I had to do a lot of work late this week to make our data match, but we worked together well and were able to solve the problems we encountered.
*#I will redo the Pvalues and the two adjustment calculations. Then I will get the data ready for GenMAPP.

*Ron
*#Dr. Dahlquist's instructions and feedback helped with ensuring the manipulation of the data was done accurately.
*#It was difficult to calculate the averages from the split data since the equations wouldn't copy down the entire column due to blank spaces within the data; in addition, calculating the p-values was difficult. In addition, there was a lot of work to be done since issues were encountered with the data and the equations.
*#Hopefully, after all the feedback and instructions Emily and I will be able to do all the necessary calculations and statistical analysis to have a file ready for GenMAPP by the end of this week.

==Week 12 Assignment==
===Goals===
*Coder/QA
**Prepare for journal club presentation
**Perform an initial Gene Database export and Gene Database Testing Report
*GenMAPP Users
**Compile the raw data in preparation for normalization and statistical analysis.
===Status Report===
*Emily: uploaded and formatted all microarray files after they were repleted with ferrous sulfate
*Mary: Prepared for genome paper journal club presentation. I also pushed the code from github onto a computer in the lab, which included downloading eclipse and git for windows on the lab computer.
*Josh: Prepared for genome paper presentation with Mary. Completed the initial import/export cycle and made significant progress on the Gene Database Testing Report.
*Ron: Similar to Emily, downloaded the microarray raw data files, followed the procedure given by Dr. Dahlquist for data processing (I worked with the files related to iron depletion with the iron chelator), and I uploaded the files to the wiki.

==Week 11 Assignment : Journal Club Presentation==
===Presentation Slides===
*These can also be accessed by going to our [[Heavy Metal HaterZ Files | Files]] page.

*[[File:Genome_Paper_Presentation_20151124_HMH.pptx]]
*[[File:SoMicroarrayPaperPresentation 20151117 HMH.pptx]]

===Goals===
*Prepare for journal club presentations
*Begin initial tasks on your research project
**Coder/QA
***Set up coding/testing environment
***Determine the regular expression for the ordered locus ID for your species
***Identify the appropriate model organism database for your species.
***Perform an initial Gene Database export and Gene Database Testing Report
**GenMAPP Users
***Describe the experimental design of the microarray data, including treatments, number of replicates (biological and/or technical), dye swaps.
***Determine the sample and data relationships, i.e., which files in the data correspond to which samples in the experimental design.
***Compile the raw data in preparation for normalization and statistical analysis.
===Status Report===
*Emily: worked on journal club presentation and created flow chart diagrams for the experimental design
*Mary: Completed journal club presentation slides with Josh. I downloaded eclipse on my personal laptop, so along with the use of the lab computers my coding/testing environment should be set up. I determined with Josh the regular expression of the ordered locus ID for our species. I was not able to, however, perform an initial export yet.
*Ron: Completed journal club presentation slides with Emily and uploaded slides in HMH Files pages. [[Media:SoMicroarrayPaperPresentation 20151117 HMH.pptx | Link to Microarray Paper Presentation here.]] Looked over sample and data relationships file from ArrayExpress entry (E-GEOD-15334) and converted .txt file into .xlsx file. I have not been able to compile raw data with Emily, as we still need clarification on which files are to be used for statistical analysis.
*Josh: Completed the genome paper presentation with Mary and did more research on our organism. Haven't done an initial import/export cycle yet. Planning to complete that later this week.

==Week 10 Assignment : Annotated Bibliography==

===Our Genome Paper===

Heidelberg, J. F., Paulsen, I. T., Nelson, K. E., Gaidos, E. J., Nelson, W. C., Read, T. D., ... & Fraser, C. M. (2002). Genome sequence of the dissimilatory metal ion–reducing bacterium Shewanella oneidensis. ''Nature biotechnology, 20''(11), 1118-1123. doi:10.1038/nbt749
*The [http://www.ncbi.nlm.nih.gov/pubmed/?term=Genome+sequence+of+the+dissimilatory+metal+ion%E2%80%93reducing+bacterium+Shewanella+oneidensis abstract] from PubMed.
*The full text of the article in PubMedCentral : Not available.
*The [http://www.nature.com/nbt/journal/v20/n11/full/nbt749.html full text] of the article from the publisher web site. 
*The [http://www.nature.com/nbt/journal/v20/n11/pdf/nbt749.pdf full PDF version] of the article from the publisher web site.
*Who owns the rights to the article?
**The Nature Publishing Group, which is the publisher of this article, according to this [https://s100.copyright.com/AppDispatchServlet?publisherName=NPG&publication=Nature%20Biotechnology&title=Genome%20sequence%20of%20the%20dissimilatory%20metal%20ion-reducing%20bacterium%20Shewanella%20oneidensis&author=John%20F.%20Heidelberg,%20Ian%20T.%20Paulsen,%20Karen%20E.%20Nelson,%20Eric%20J.%20Gaidos,%20William%20C.%20Nelson%20et%20al.&contentID=10.1038/nbt749&publicationDate=10/07/2002&volumeNum=20&issueNum=11&numPages=6&pageNumbers=pp1118-1123 site].
*Do the authors own the rights under a Creative Commons license?
**Yes, according to this [http://oaspa.org/member/nature-publishing-group-palgrave-macmillan/ site].
*Is the article available “Open Access”?
**According to [http://oaspa.org/membership/members/ this site], the article is available "Open Access".
*What organization is the publisher of the article? What type of organization is it?
**According to the site above, this publisher is a "Professional OA Publisher (Large)".
*Is this article available in print or online only?
**Online only. It was published online in November, 2002.
*Has LMU paid a subscription or other fee for your access to this article?
**No.
*We performed a search in the ISI Web of Science/Knowledge database by typing in the title "Genome sequence of the dissimilatory metal ion–reducing bacterium Shewanella oneidensis" to the search bar.
**Three articles came up as results. The first two articles title's did not exactly match, and were cited under 15 times each. The third article was the article we were searching for.
*How many articles does this article cite?
**This article has 41 cited references within the Web of Science Core Collection, according to this [https://apps.webofknowledge.com/full_record.do?product=UA&search_mode=GeneralSearch&qid=3&SID=3Evs6J6HvCojNOHG6K3&page=1&doc=3 site].
*How many articles cite this article?
**It has been cited 1079 times in all databases, and 426 within the Web of Science Core Collection, according to this [https://apps.webofknowledge.com/full_record.do?product=UA&search_mode=GeneralSearch&qid=3&SID=3Evs6J6HvCojNOHG6K3&page=1&doc=3 site].
*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?
**Examples of titles that reference the genome paper:
***Environmental genome shotgun sequencing of the Sargasso Sea
***Deciphering the evolution and metabolism of an anammox bacterium from a community genome
***Genome of Geobacter sulfurreducens: Metal reduction in subsurface environments
***More can be found by clicking this [https://apps.webofknowledge.com/summary.do?product=WOS&parentProduct=UA&search_mode=CitingArticles&qid=8&SID=3Evs6J6HvCojNOHG6K3&page=1&action=sort&sortBy=LC.D;PY.D;AU.A.en;SO.A.en;VL.D;PG.A&showFirstPage=1 link].
**These papers include studying within in the species, finding out the genomes of other species, as well as the metabolic versatility of microorganisms and metal ion reduction in environments. This shows that a sequenced genome can aide in experiments of many kinds.

===Our Microarray Paper===
*Dataset can be found at this [https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-15334/?keywords=&organism=Shewanella+oneidensis&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array= link].


====E-GEOD-15334: Yang et. al (2009)====

This paper is suitable for your project. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 09:41, 10 November 2015 (PST)''

Yang, Y., Harris, D. P., Luo, F., Xiong, W., Joachimiak, M., Wu, L., ... & Zhou, J. (2009). Snapshot of iron response in Shewanella oneidensis by gene network reconstruction. ''BMC genomics, 10''(1), 131.
*The link to the abstract from [http://www.ncbi.nlm.nih.gov/pubmed/?term=Yang%2C+Y.%2C+Harris%2C+D.+P.%2C+Luo%2C+F.%2C+Xiong%2C+W.%2C+Joachimiak%2C+M.%2C+Wu%2C+L.%2C+...+%26+Zhou%2C+J.+%282009%29.+Snapshot+of+iron+response+in+Shewanella+oneidensis+by+gene+network+reconstruction.+BMC+genomics%2C+10%281%29%2C+131. PubMed].
*The link to the full text of the article in [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2667191/ PubMedCentral]
*The link to the full text of the article (HTML format) from the publisher [http://www.biomedcentral.com/1471-2164/10/131 web site].
*The link to the full [http://www.biomedcentral.com/content/pdf/1471-2164-10-131.pdf PDF] version of the article from the publisher web site.
*Who owns the rights to the article?
**The article is Open Access and the authors own the rights under a Creative Commons license.
*What organization is the publisher of the article? What type of organization is it?
**BMC Genomics is the publisher, which is a scientific society
*Is this article available in print or online only?
**It is online only
*Has LMU paid a subscription or other fee for your access to this article?
**No
*How many articles does this article cite?
**This paper sites 48 other articles
*How many articles cite this article?
**3
***Roles of UndA and MtrC of ''Shewanella putrefaciens'' W3-18-1 in iron reduction
***Global transcriptional response of ''Caulobacter crescentus'' to iron availability
***Molecular ecological network analysis
*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?
**This article has mostly been used to look at the iron response of other strains or organisms. It may have been used for comparison's sake or to modify the original methodology to fit the new experiment.
*Link to microarray data
**Found it on [https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-15334/ ArrayExpress]
**This contains the raw data that we will use for our research
*What experiment was performed? What was the "treatment" and what was the "control" in the experiment?
**Strains of ''Shewanella oneidensis'' were put under iron depletion and repletion conditions. The control would be a regular strain of the organism, while the treatments would be either increasing or decreasing the iron levels.
*Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each?
**4 biological replicates of each treatment condition were performed

2015-12-01T23:39:00Z

Malverso:

File:Shewanellaoneidensis GMBuilder.zip

2015-12-01T23:35:42Z

Malverso:

Heavy Metal HaterZ

2015-11-24T22:24:27Z

Malverso: fixed spelling error in ppt

{{Heavy Metal HaterZ}}

==Week 12 Assignment==
===Goals===
*Coder/QA
**Prepare for journal club presentation
**Perform an initial Gene Database export and Gene Database Testing Report
*GenMAPP Users
**Compile the raw data in preparation for normalization and statistical analysis.
===Status Report===
*Emily: uploaded and formatted all microarray files after they were repleted with ferrous sulfate
*Mary: Prepared for genome paper journal club presentation. I also pushed the code from github onto a computer in the lab, which included downloading eclipse and git for windows on the lab computer.
*Josh: Prepared for genome paper presentation with Mary. Completed the initial import/export cycle and made significant progress on the Gene Database Testing Report.
*Ron: Similar to Emily, downloaded the microarray raw data files, followed the procedure given by Dr. Dahlquist for data processing (I worked with the files related to iron depletion with the iron chelator), and I uploaded the files to the wiki.

==Week 11 Assignment : Journal Club Presentation==
===Presentation Slides===
*These can also be accessed by going to our [[Heavy Metal HaterZ Files | Files]] page.

*[[File:Genome_Paper_Presentation_20151124_HMH.pptx]]
*[[File:SoMicroarrayPaperPresentation 20151117 HMH.pptx]]

===Goals===
*Prepare for journal club presentations
*Begin initial tasks on your research project
**Coder/QA
***Set up coding/testing environment
***Determine the regular expression for the ordered locus ID for your species
***Identify the appropriate model organism database for your species.
***Perform an initial Gene Database export and Gene Database Testing Report
**GenMAPP Users
***Describe the experimental design of the microarray data, including treatments, number of replicates (biological and/or technical), dye swaps.
***Determine the sample and data relationships, i.e., which files in the data correspond to which samples in the experimental design.
***Compile the raw data in preparation for normalization and statistical analysis.
===Status Report===
*Emily: worked on journal club presentation and created flow chart diagrams for the experimental design
*Mary: Completed journal club presentation slides with Josh. I downloaded eclipse on my personal laptop, so along with the use of the lab computers my coding/testing environment should be set up. I determined with Josh the regular expression of the ordered locus ID for our species. I was not able to, however, perform an initial export yet.
*Ron: Completed journal club presentation slides with Emily and uploaded slides in HMH Files pages. [[Media:SoMicroarrayPaperPresentation 20151117 HMH.pptx | Link to Microarray Paper Presentation here.]] Looked over sample and data relationships file from ArrayExpress entry (E-GEOD-15334) and converted .txt file into .xlsx file. I have not been able to compile raw data with Emily, as we still need clarification on which files are to be used for statistical analysis.
*Josh: Completed the genome paper presentation with Mary and did more research on our organism. Haven't done an initial import/export cycle yet. Planning to complete that later this week.

==Week 10 Assignment : Annotated Bibliography==

===Our Genome Paper===

Heidelberg, J. F., Paulsen, I. T., Nelson, K. E., Gaidos, E. J., Nelson, W. C., Read, T. D., ... & Fraser, C. M. (2002). Genome sequence of the dissimilatory metal ion–reducing bacterium Shewanella oneidensis. ''Nature biotechnology, 20''(11), 1118-1123. doi:10.1038/nbt749
*The [http://www.ncbi.nlm.nih.gov/pubmed/?term=Genome+sequence+of+the+dissimilatory+metal+ion%E2%80%93reducing+bacterium+Shewanella+oneidensis abstract] from PubMed.
*The full text of the article in PubMedCentral : Not available.
*The [http://www.nature.com/nbt/journal/v20/n11/full/nbt749.html full text] of the article from the publisher web site. 
*The [http://www.nature.com/nbt/journal/v20/n11/pdf/nbt749.pdf full PDF version] of the article from the publisher web site.
*Who owns the rights to the article?
**The Nature Publishing Group, which is the publisher of this article, according to this [https://s100.copyright.com/AppDispatchServlet?publisherName=NPG&publication=Nature%20Biotechnology&title=Genome%20sequence%20of%20the%20dissimilatory%20metal%20ion-reducing%20bacterium%20Shewanella%20oneidensis&author=John%20F.%20Heidelberg,%20Ian%20T.%20Paulsen,%20Karen%20E.%20Nelson,%20Eric%20J.%20Gaidos,%20William%20C.%20Nelson%20et%20al.&contentID=10.1038/nbt749&publicationDate=10/07/2002&volumeNum=20&issueNum=11&numPages=6&pageNumbers=pp1118-1123 site].
*Do the authors own the rights under a Creative Commons license?
**Yes, according to this [http://oaspa.org/member/nature-publishing-group-palgrave-macmillan/ site].
*Is the article available “Open Access”?
**According to [http://oaspa.org/membership/members/ this site], the article is available "Open Access".
*What organization is the publisher of the article? What type of organization is it?
**According to the site above, this publisher is a "Professional OA Publisher (Large)".
*Is this article available in print or online only?
**Online only. It was published online in November, 2002.
*Has LMU paid a subscription or other fee for your access to this article?
**No.
*We performed a search in the ISI Web of Science/Knowledge database by typing in the title "Genome sequence of the dissimilatory metal ion–reducing bacterium Shewanella oneidensis" to the search bar.
**Three articles came up as results. The first two articles title's did not exactly match, and were cited under 15 times each. The third article was the article we were searching for.
*How many articles does this article cite?
**This article has 41 cited references within the Web of Science Core Collection, according to this [https://apps.webofknowledge.com/full_record.do?product=UA&search_mode=GeneralSearch&qid=3&SID=3Evs6J6HvCojNOHG6K3&page=1&doc=3 site].
*How many articles cite this article?
**It has been cited 1079 times in all databases, and 426 within the Web of Science Core Collection, according to this [https://apps.webofknowledge.com/full_record.do?product=UA&search_mode=GeneralSearch&qid=3&SID=3Evs6J6HvCojNOHG6K3&page=1&doc=3 site].
*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?
**Examples of titles that reference the genome paper:
***Environmental genome shotgun sequencing of the Sargasso Sea
***Deciphering the evolution and metabolism of an anammox bacterium from a community genome
***Genome of Geobacter sulfurreducens: Metal reduction in subsurface environments
***More can be found by clicking this [https://apps.webofknowledge.com/summary.do?product=WOS&parentProduct=UA&search_mode=CitingArticles&qid=8&SID=3Evs6J6HvCojNOHG6K3&page=1&action=sort&sortBy=LC.D;PY.D;AU.A.en;SO.A.en;VL.D;PG.A&showFirstPage=1 link].
**These papers include studying within in the species, finding out the genomes of other species, as well as the metabolic versatility of microorganisms and metal ion reduction in environments. This shows that a sequenced genome can aide in experiments of many kinds.

===Our Microarray Paper===
*Dataset can be found at this [https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-15334/?keywords=&organism=Shewanella+oneidensis&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array= link].


====E-GEOD-15334: Yang et. al (2009)====

This paper is suitable for your project. ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 09:41, 10 November 2015 (PST)''

Yang, Y., Harris, D. P., Luo, F., Xiong, W., Joachimiak, M., Wu, L., ... & Zhou, J. (2009). Snapshot of iron response in Shewanella oneidensis by gene network reconstruction. ''BMC genomics, 10''(1), 131.
*The link to the abstract from [http://www.ncbi.nlm.nih.gov/pubmed/?term=Yang%2C+Y.%2C+Harris%2C+D.+P.%2C+Luo%2C+F.%2C+Xiong%2C+W.%2C+Joachimiak%2C+M.%2C+Wu%2C+L.%2C+...+%26+Zhou%2C+J.+%282009%29.+Snapshot+of+iron+response+in+Shewanella+oneidensis+by+gene+network+reconstruction.+BMC+genomics%2C+10%281%29%2C+131. PubMed].
*The link to the full text of the article in [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2667191/ PubMedCentral]
*The link to the full text of the article (HTML format) from the publisher [http://www.biomedcentral.com/1471-2164/10/131 web site].
*The link to the full [http://www.biomedcentral.com/content/pdf/1471-2164-10-131.pdf PDF] version of the article from the publisher web site.
*Who owns the rights to the article?
**The article is Open Access and the authors own the rights under a Creative Commons license.
*What organization is the publisher of the article? What type of organization is it?
**BMC Genomics is the publisher, which is a scientific society
*Is this article available in print or online only?
**It is online only
*Has LMU paid a subscription or other fee for your access to this article?
**No
*How many articles does this article cite?
**This paper sites 48 other articles
*How many articles cite this article?
**3
***Roles of UndA and MtrC of ''Shewanella putrefaciens'' W3-18-1 in iron reduction
***Global transcriptional response of ''Caulobacter crescentus'' to iron availability
***Molecular ecological network analysis
*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?
**This article has mostly been used to look at the iron response of other strains or organisms. It may have been used for comparison's sake or to modify the original methodology to fit the new experiment.
*Link to microarray data
**Found it on [https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-15334/ ArrayExpress]
**This contains the raw data that we will use for our research
*What experiment was performed? What was the "treatment" and what was the "control" in the experiment?
**Strains of ''Shewanella oneidensis'' were put under iron depletion and repletion conditions. The control would be a regular strain of the organism, while the treatments would be either increasing or decreasing the iron levels.
*Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each?
**4 biological replicates of each treatment condition were performed

File:Genome Paper Presentation 20151124 HMH.pptx

2015-11-24T22:23:55Z

Malverso: