Laurmagee: Individual Assessment

Statement of Work

• Describe exactly what you did on the project.
• The first step in my role as GenMAPP user was to find an article that contained microarray data on the Rhizobacterium, Sinorhizobium Meliloti. I submitted a few articles for consideration, but ultimately my partner, Miles, found the article we have been using throughout this project. The mentioned article can be found on the following page: [HTML version] and is references below.
• Domínguez-Ferreras, A., Pérez-Arnedo, R., Becker, A., Olivares, J., Soto, M.J., Sanjuán, J. (2006) Transcriptome Profiling Reveals the Importance of Plasmid pSymB for Osmoadaptation of Sinorhizobium meliloti Journal of Bacteriology 188:7617-7625
• From this article, we were able to procure the raw microarray data off of the following website: [Osmotic upshift elicited by salt and sucrose].
• The article that we were studying carried out four different experiments, with different levels of NaCl and sucrose being the manipulated variable. I personally studied the experiment done with 700mm of sucrose. Raw Data File for 700S (1-3): File:Full Raw Data.xls
• The columns of interest in the above data file were collect and scaling and centering was done to produce the log values needed for statistical analysis. Further description can be found on the following page: Laurmagee: Week 13. And the following data file was produced Media:Compiled Ratios and Logs.xls.
• With this new file, statistical analysis could be done on the log values. Fist the Avg_LogFC values were calculated, averaging the log values of the three replicants present at each of the four individual time intervals (t15, t30, t60, t240). Therefore, I had to calculate four of these Avg_LogFC values, one for each time point. From these averages, I was able to calculate the T_stat and P_value for each time interval as well. This process if outlined in the "Statistical Analysis" section of the following journal: Laurmagee: Week 15. This spreadsheet was formatted specifically for GenMAPP standards and the following were produced: Media:SinorhizobiumMeliloti_LM_GenMapp_DataSheet.xls and Media:SinorhizobiumMeliloti_LM_GenMapp_DataSheet.txt. The text file is to be fed into GenMAPP.
• A Sanity Check was done and highlighted on the following page: Laurmagee: Week 15, and it shows the number of microarray dots that were changed significantly in the process of the experiment.
• After this check proved to provide accurate results, I moved on to load my datafile into GenMAPP. However, this is where I found a snag. My GenMAPP file would not load into GenMAPP and the whole program would stop responding immediately after I would input my text file.
• After trying different computer, walking through every aspect of my data file with my partners, and trouble shooting different alternatives, I finally emailed Dr. Dondi, who found the main problem with my dataset. The gene IDs that had been present on my sheet did not follow the same format of those in the Gene Database that was created by my partners. The paralleled IDs were present, but they had extraneous information attached to them, which was inhibiting GenMAPP from recognizing them. The amount of error that the file was collecting was so large that the program had to stop responding entirely, which is why I wasn't getting an error message.
• However, even upon testing the modified data sheet, I found that it was giving me another error message. This time it was telling me my column titles were insufficient. After some research, I found that my text file was not in tab delimited format, despite the fact that I had saved it as such on my MacBook Pro computer. After transferring my previous .xls workbook onto a Windows computer, and saving it as a tab delimited text file, I finally got GenMAPP to accept the following data file: Media:SinorhizobiumMeliloti_LM_GenMapp_FinalFile.txt.
• The GenMAPP and MAPPFiner protocols can be viewed at the bottom of the following journal page: Laurmagee: Week 15.
• The exception file created with the GenMAPP program is included here: [[Media:SinorhizobiumMeliloti_LM_GenMapp_FinalFile.EX.txt] along with the following other three GenMAPP program exports: Media:SinorhizobiumMeliloti_LM_GenMapp_FinalFile.gex, [[Media:ColorSets.mapp]}, Media:SinorhizobiumMeliloti_LM_GenMapp_FinalFile.gmf, which are all detailed on the journal page noted above.
• In addition, the MAPPFinder documents are the following: Media:700S1-3-t15-Decreased-Criterion0-GO.txt, Media:700S1-3-t15-Increased-Criterion0-GO.txt
• Beyond my assigned tasks, I helped my group out in whatever areas were necessary. It was a challenge to keep up with the tasks of my partners, but I was always accessible to offer input or advice.

Assessment of Project

• Give an objective assessment of the success of your project workflow and teamwork.
  1. What worked and what didn't work?
     • I think my group and I should have stressed collaboration more on this project. Since we were all given an independent job to handle, I think it was difficult for us to establish a "team" environment. All four of us were busy outside of class with conflicting schedules, so it was very challenging to find time when we could all meet one another and discuss where we were in our project. I think having each other as check and balances would have been very helpful throughout the project, especially since I made it all the way to my GenMAPP stage of the project without anyone realizing I was using different GeneIDs then those contained in the database.
  2. What would you do differently if you could do it all over again?
     • If I could do the project all over again, I would have spent much less time scaling, centering, and performing statistical analysis on the data and I would spend more time completing my GenMAPP and MAPPFinder analysis to produce more conclusive results. I would also set aside time from the beginning of the project, where Miles and I could meet outside of class, because we had the exact same protocol yet we failed to use each other as a resource.
• Evaluate the Gene Database Project and Group Report in the following areas:
  1. Content: What is the quality of the work?
     • Our quality of work thus far has been admittedly lack luster, due to extenuating circumstances that occurred only days before our project assignments were due. However, I think our final deliverable and our final report will reflect how much we can improved in our quality of work, with the right circumstances.
  2. Organization: Comment on the organization of the project and of your group's wiki pages.
     • Team Name the wiki page is a bit overcrowded, but for the most part is organized. All of our contacts are contained in the first section and then all the files related to the Microarray Paper are contained in the next section. The Coder and QA personnel in my group then organized different sections based off the times when the files had been exported. Our believe that our powerpoint presentation could have been a lot more organized, but I think we were able to fix those flaws in our written report. A common theme with our group, i think, has been as not working as a cohesive unit, so our product come out disorganized and lacking fluidity. I think we remedied this in our final report, but other assignments prior may have reflected this.
  3. Completeness: Did your team achieve all of the project objectives? Why or why not?
     • There were some issues with time constraints, mainly with my portion of the project. I ran into a lot of GenMAPP issues during the end of our time with the project and this set me back many days. As far as final products go, however, I believe that we have completed the necessary items to the best of our ability, which is all I can ask of myself and my group.

Reflection on the Process

• What did you learn?
  1. With your head (biological or computer science principles)
     • I learned a lot about computers in this course. I was coming in with a fair amount of knowledge in the subject of biology, but very little knowledge of computers in general. Therefore, I have been exposed to coding, which was completely new to me, and also using data analysis programs such as GenMAPP which were otherwise foreign to me. Biologically, I learned what it was like to follow a biology based project all the way through data collect to conclusion. I do research on statistics education with Dr. Bargagliotti, in the math department, so i already new the processes of such projects, but had never had an opportunity to follow it through with a biological perspective.
  2. With your heart (personal qualities and teamwork qualities that make things work or not work)?
     • I learned how important working with a team is and how your cohesiveness as a unit can make our break a project. Everyone has busy schedules, but it is important to make the time to meet for collaboration, otherwise things like presentation seem choppy and you are much more prone to making errors. Although this project did assign personal responsibilities, that should not deter from the overall idea that you are a team and your success depends on one another.
  3. With your hands (technical skills)?
     • As I said previously, I learned a lot of computer skills, so whether that be inputing code, generating a .mapp on GenMAPP, or creating data calculation shortcuts in Excel, this was all new directions for my hands. I have never had a class taught primarily on the computer as well, so this was all together a new experience for me. In this project specifically, I learned how important it is to look over every single detail of a spreadsheet before you input it into a data processing program such as GenMAPP. With the issues I was struggling with using the GenMAPP program for hours, I will never make the mistake again of not checking the IDs of my file against those in the gene database.
• What lesson will you take away from this project that you will still use a year from now?
  • I think all of the components that I listed above with stay with my even a year from now. I will definitely remember how to prepare a file for GenMAPP and complete an analysis on that file, but more generally, I will remember to look for the details, especially in research, that i have been tripped up on in this project and in this class as a whole as well. I will also take away the importance of teamwork, especially on such a multifaceted project as this one, and the excitement that can come out of your own research by creating a product that is completely your own.