Kevin's Assessment and Reflection

Statement of Work

I compiled the raw data downloaded from array express

1. Associated Data Files
2. Array Design
3. Raw Data
4. Processed Data
5. Sample and Data Relationship

into one excel file 20131119_teamATK_KM_compiledrawdata.xls, log transformed the data, scaled and centered it, and ran Tstat and Pvalue calculations on the data as described in the V. cholerae instructions. V. cholerae 1 However, averages were performed first on the technical replicates corresponding to the same biological replicate, and then on each time period. Furthermore, Tstats and Pvalues were calculated by replicate rather than as one total calculation.

This data was imported into GenMAPP to create a gene database for S. pneumoniae, and color sets were created according to the instructions for V. cholerae V. cholerae 2. MAPPFinder was run, and a filtered ranked list was produced 20131210_tATK_filteredresults.xls. The sugar transmembrane transporter activity pathway was selected for further investigation, and a mapp of the genes in that pathway was produced using MAPPFinder 20131211_tATK_sugar_transmembrane_transporter_activity.mapp tATK jpeg MAPP. The function of each gene was determined based on the UniProt page for that particular gene, and a compiled list may be found here Media:Pathway_Gene_Info.xls. This information was incorporated into the report and presentation.

Assessment of Project

• The project workflow went well overall. There was some confusion concerning my role and how to change the V. cholerae instructions for the data set from this experiment, but once imported into GenMAPP everything ran smoothly. The work Tauras and Alina produced was excellent, and we worked together very well and efficiently to produce our final products.
• We worked well as a team, group meetings were productive, and most things went smoothly. I had some troubles interpreting the data before the column headers were acquired, and difficulty understanding how to apply the statistics tests and data transformations, but those issues were worked out with help from Dr. Dahlquist and Dr. Dionisio.
• I would work earlier on and focus more on getting the data ready for GenMAPP so that results rather than methods could receive more of my time.
• Gene Database Project and Group Report Assessment

1. Content: the work is of high quality, but relatively limited in scope. Only one pathway at one time point was analyzed. It would have been much more interesting to see that pathway at multiple time points, or to see different pathways in conjunction with the sugar transmembrane transporter activity pathway that was examined.
2. Organization: Our group was generally well organized, but our wiki pages were messy as we all were uploading and posting haphazardly. We generally fixed these issues of disorganization in retrospect, and some pages are still quite messy.
3. Completeness: Our team achieved all of the project objectives because we were motivated, put in the time and effort, and asked for help from the professors or each other when necessary.

Reflection on the Process

• I learned how to transform data, to use programs that allow one to easily organize and understand an enormous volume of otherwise incomprehensible data. I also learned how to integrate computer information and programs with my biologist's understanding of processes and workings of life. I had the opportunity to improve upon my teamwork skills that allowed this project to be successful relatively smoothly.
• I will take away the importance and power of interdisciplinary approaches to research, as well as the importance of effective teamwork and planning.