Tauras' Assessment and Reflection

Statement of Work

On this project, I worked as a combination of the coder and a general assistant to the other tasks in the project. My particular accomplishments include downloading and updating files for the gene database, completing four import export cycles, modifying GenMAPP builder for our strain and species, and preparing final versions of the ReadMe file, Testing Report, powerpoints, and group report. Throughout the project, I did most of the group update wiki pages.

Working with my teammates, I spent a lot of time working with Kevin to interpret, understand, and analyze the microarray data. Together, we worked to create the gene database schema, determine the amount of significant genes, work in MAPPfinder, and interpret our results. I worked with Alina to complete the gene database testing report and write the introduction to the final report.

I also coordinated individual contributions to the powerpoints and deliverables as well as serving as a final, last step quality control.

Some Primary Files and Wiki Pages

Code changes made to GenMAPP builder: PDF file
The final gene database: Media:Streptococcus_pneumoniae_TIGR4_20131125.gdb
- Other gene databases: IE1 G54, IE1 R6, IE1 TIGR4, IE2 TIGR4, and IE3 TIGR4
Final Testing Report, particularly through TallyEngine results: tATK E4: TIGR4 Testing Report
- Partial Testing Report Files for Other Databases: IE2 and IE3
The ReadMe file: ReadMe_Streptococcus_pneumoniae_TIGR4_20131125.pdf
Gene Schema: Streptococcus_schema_20131210.pdf
Final Report: tATK Group Report

Assessment of Project

Overall Assessment

I would say that this project was mostly successful. The GenMAPP work ran a bit behind schedule due to abnormalities in the data and the time available for in depth analysis was limited, but besides that everything in the project ran rather smoothly, especially the parts having to do with the gene database. We were able to successfully complete the project, found novel results, and everything came together in the end.

Workflow and Teamwork

The three of us working together on this project had a good team chemistry and were all willing to come together to make things work. There were some issues of mass confusion but we were usually able to resolve those. The one issue we had in terms of teamwork was finding times to meet. We all had very busy schedules which made it difficult to find time outside of class, but by working independently and talking sporadically we were able to make progress.

Workflow could have been optimized a lot. During the first couple weeks of the project when we didn't know precisely what we were doing, I wasted a lot of time running unnecessary I-E sequences that would then have to be done again the next week because of something that we had changed. For example, I think it would have been valuable to wait until after we had made the species profile to run the firs export. This would have opened up more time to really understand what is happening in the data before exporting unnecessary files and also would have helped me work with Kevin on the microarray data to start the class and make more progress there. As it was, microarray data took longer than any other part of the project and there was a stressful point to go with two weeks left because everything else was complete but we had no idea how long it would take.

What Worked and Didn't Work

In this project, pretty much everything worked in the end. The main issues were understanding how the microarray data differed from the VC data while doing analysis. Due to different amounts of columns, the commands in the protocol ended up not referring to the proper cells and it was very difficult to determine what had to be done without that guide.

Our team dynamic was very successful and pretty much everything else in the project worked well. From my perspective, working with Dondi on modifying GenMAPP builder was an especially smooth process.

What I would do differently

If I were to do this project again, I would form a better basic understanding of what was happening in the first place. If I knew more about the project dynamics, we could have avoided unnecessary exports and gotten an earlier start on the microarray data which would have saved a lot of time and stress. Additionally, I felt like I really didn't understand anything for the first three weeks and I think I could have solved a lot of my confusion by looking at the project deliverables at that point instead of reading through the independent milestones and project overview.

Evaluation of the Project and Group Report

Content: I consider the project to be of medium to medium high quality. For the group project, the introduction is very well written and the methods/results are easy to follow with an understanding of the field and thorough. The discussion itself seems a little weak in comparison to the rest of the project, likely because there was insufficient time for full indepth analysis. All of the other project deliverables are complete and I am particularly proud of the ReadMe file and Testing Report. More work could have been put into some of the later figures such as the MAPP file which still looks slightly odd.
Organization: Our project is well organized, clear and easy to follow. The group wiki page is slightly more confusing because it was made as we were working through parts of the project at uneven paces, but can be easily interpretted by looking at the template or table of contents at the top of the page.
Completeness: Yes, we did manage to achieve all the project objectives. We managed to do so by finally figuring out what to do in GenMAPP during the last week before the project deadline.

Reflection on the Process

What did you learn?
- With your head (biological or computer science principles)
  - I learned a lot from this project about how different parts of a project come together in multidisciplinary research. Before the project (and honestly halfway through it), I didn't quite grasp how research like this is not a linear line of thought but a convergent one where different lines of work combine in the end and build on each other.
- With your heart (personal qualities and teamwork qualities that make things work or not work)?
  - In terms of personal skills, I learned about the importance of good communication and a clear structure to work in. Many times throughout the project, I had to help Kevin with the microarray information and if there wasn't good communication on the topic I was ultimately unable to help him. Other times when he could cleanly say what the issue was and what he had tried, we were much more successful. I also learned that it's very important to have group members who take initiative and read all the assignments. We had some difficulties early on in accurately completing projects because I was the only one who read the assignment and made sure each part was present. Later as well, there were many cases where Kevin needed help simply because he hadn't completely read the instructions/didn't know what the deliverable product was (although there were also many times the full directions were just confusing). The mindset of making sure everything is important and everybody in the group being obsessed with quality assurance is definitely a teamwork quality I will try to emphasize in future projects.
- With your hands (technical skills)?
  - During the course of this project, I learned how to create a gene database and then how to use that database to interpret microarray data. In particular, I was fascinated by the way Eclipse works as a java editing software and, although I still have no idea what I'm doing in it, the small amount I learned working with the GenMAPP builder code was very valuable. I also learned technical skills related to maintaining a wiki page for a developing project, saving, updating, and organizing project files on my computer, and how to effectively transmit our results to other group members.
What lesson will you take away from this project that you will still use a year from now?
- I don't know where I'll be a year from now (hopefully graduate school) or what I'll be doing, so I'm not sure if I will still use many, if any, of the technical skills from this class. The one thing I know I'll take away is an increased perspective on the research process as not just a series of linear steps but as a multi-headed creation with multiple avenues of approach that can be viewed simultaneously. I also hope to keep in mind that you can gain valuable new information by asking an old question with a new spin or looking for changes with prior research.