==Statement of Work==

==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  

* 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  

#*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]].

#*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]]

#[[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 genMAPPbuilder) to josh. Next I committed my code to github.  

#*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]]

#[[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

#*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==

==Assessment of Project==