Kzebrows Individual Reflection

Statement of Work

In this project I acted as a GenMAPP User and as the Project Manager for the Oregon Trail Survivors. With the group, I helped to locate an appropriate genome and microarray paper for the project and presented on the microarray paper with Erich. I downloaded and created a compiled raw data file with Erich (I did RX samples and he did RP) and normalized log ratios and performed statistical analysis for my half of the data set. I communicated any errors or bugs with the QA and Coder as well as Dr. Dahlquist. I also performed a sanity check on my data and prepared the file for GenMAPP, which I then combined with Erich’s RP data file to create a master file. I created 12 color sets (one for each treatment) and ran the data through MAPPFinder, creating Criterion-Go.txt files that I then filtered and analyzed with Erich in order to compare with the MAPPs he created. I also helped write the final paper and presentation regarding my contributions to the project.

As Project Manager, I made sure that each team member completed their weekly status updates and checked in with them regularly regarding what they were working on. I also cleaned up the team Wiki and Deliverables pages and met with Dr. Dahlquist and Dr. Dionisio as part of the Project Managers guild to give team updates.

Files I contributed to:

• Microarray Journal Club Power Point
• Microarray Compiled Raw Data RP/RX IDLR
• Microarray Corresponding Files Table
• Compiled Raw Microarray Dataset (.xlsx)
• Data Used for Import into GenMAPP (.txt)
• GenMAPP Expression Dataset File (.gex)
• Exceptions file (.EX.txt)
• Raw MAPPFinder results files (-GO.txt)
• .gmf file
• Final PowerPoint Presentation
• ScalingCentering file 12/1 .xlsx

Files I created:

• Filtered MAPPFinder Results .xlsx
• Filtered MAPPFinder Results (common GO terms highlighted) .png
• RX Compiled Raw Data 12/6
• RX .txt format GenMAPP ready 12/6
• RX Compiled Raw Data as of 12/6
• RX .txt format updated as of 12/6
• RX Exceptions file
• RX .gex file
• RX Exceptions file in Excel format (filtered)

Assessment of Project

Our team was generally very good at communicating. We had a group text that everyone was good about responding to. We also frequently met as a group in person—we had Google docs for things like the Power Point presentations and report but mostly worked on them together instead of separately at home, allowing us to collaborate and keep tabs on what each group member was doing. We almost always met on Monday afternoons in the Bio Databases lab to check in and complete the week’s goals as a team.

Unfortunately, because we were all only simultaneously free from work/classes/other obligations on Mondays, sometimes things were left until shortly before the Tuesday deadline at midnight. While we never turned something in late, the quality of our work may have been affected slightly by this rush; however, I see this more as the nature of having a group project than in a flaw with our team itself.

If I could do it all over again I would have our group practice our presentations more. Even if we all understand our place in the team and what we are working on to a tee things like transitions are almost impossible to really get if the presentation hasn’t been practiced more than once or twice. It may have been helpful in retrospect even to practice just the transitions between slides and topics.

Evaluation:

1. Content: The quality of the work is good in terms of our deliverables, although some more time could have been used to finalize the report. All of the necessary information is present and (to my knowledge) all bullet points on the Deliverables page are answered in the report.
2. Organization: Our group’s Wiki page and Deliverables page are both very organized and clean, with links clearly displayed at the top. The Deliverables page has all of the additional versions and builds commented out from previous weeks’ assignments with just the final, official deliverables displayed. What has been asked to be displayed is displayed with the most recent addition at the top but it is not overly cluttered.
3. Completeness: Our team did finish all of the objectives of the project, although the paper proved more difficult to complete. We were able to do so because we communicated frequently and worked together, particularly with our counterpart (QA and coder and both GenMAPP users). It would have been beneficial in retrospect to have begun this project a little earlier and maybe have had an additional week with the paper due before the presentation (instead, we tried to make our presentation and use that as a template for the paper) or have parts of the paper due along the way as part of the assignment, particularly because were working out bugs and making changes up until right before the presentation.

Reflection on the Process

What did you learn?

• With my head: I learned a lot about Shigella flexneri and about microarrays as well as how to analyze them. I've always known that bacterial resistance to antibiotics is an important area of research because of the complications it poses but it was very interesting to learn how specifically a species is circumventing the drug. It really reinforced for me how important research like what we saw in the microarray paper is and how it can be applied.
• With my heart: I learned that even if something is challenging I shouldn't be frustrated just because it's something I am unfamiliar with. If I keep at it I can make a lot of progress. This is especially apparent to me looking back at the first week and creating our Wiki pages--that seems like such a small task now. I also learned that teamwork is most effective when the team members have different strengths, as was true in the Oregon Trail Survivors. If one person didn't understand something someone else undoubtedly did and could explain it or offer a new perspective, which really helped the team to grow as a whole and proceed.
• With my hands: I learned more about Excel than I ever thought I would and now I feel like I can do so much more with Excel, which is something I can definitely take with me into my future career. I also never thought I would learn how to code and how to format a dataset to import into a program or understand how these things worked.

What lesson will you take away from this project that you will still use a year from now?

• This class and this project have taught me a great deal despite being one of the more challenging courses I have taken at LMU. First of all, I learned that no research is perfect and there is always room for improvement. In a more technical aspect it taught me to take everything with a grain of salt and always make sure data is reproducible--this was apparent after seeing some of the groups find very different things in their analysis than in their microarray papers. I also learned how "analysis" can mean so many different things and how crunching the numbers and formatting the data is only half the battle--the real challenge is what you do with the data you get and how you interpret it. I also learned that "getting answers" in a research project will always lead to more questions, which is great because it shows that there is no end to what interdisciplinary work can accomplish.