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

1. 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.
2. 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.
3. 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.
4. 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 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

1. 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.
2. 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.
3. 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?
  1. 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.
  2. 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.
  3. 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?
  1. • 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.