Malverso Assessments & 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 genMAPPbuilder) 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 here. 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?
