TATK Week 12 Status Report

tATK Week 12 Status Report

Week Goals and Status Report

To complete initial exports of databases for the 3 strains
- First attempts on all 3 were uploaded using gmbuildder 2.0b71. R6 was not successful and Tauras will repeat it over the weekend. The other two seem to have produced clear data, but the data is being processed for quality assurance by Alina.
For the coder (Tauras) to create a first draft for a working species-fix for gmbuilder.
- This was completed during class time on Thursday working with Dr. Dionisio
For Alina to complete the counting exercise with the initial exports.
- Began doing the counting exercise but results vary between the different methods.
For Kevin to understand the construction of the microarray data and start to organize it.
- Very much a work in progress. The data is very disorganized and Kevin (and Dr. Dahlquist) are struggling to make headway. After class Thursday, they have some idea how it may be organized, but not much is clear.

Export R6 again
Tauras and Alina work together to finish the gmbuilder species profile
Determine how the output data is configured and what modifications need to be made
For Kevin to understand the microarray data

Formally write out the ID systems (QA, Milestone 1 part 3)
Characterize regular expression patterns to detect IDs (QA, Milestone 2)
Complete through GenMapp Milestone 2 (should be possible if we can make sense of the raw data)
Run export of multiple strains at the same time

GenMAPP Gene Database for assigned species (.gdb)
ReadMe file to accompany the Gene Database (.pdf)
- Sample ReadMe in Word format: ReadMe_Vc-Std_External_20101022.zip
- Include Gene Database Schema diagram in ReadMe
  - Sample schema in Adobe Illustrator format: Vibrio_schema_20101022.zip
Gene Database Testing Report for final submitted Gene Database (print from wiki to .pdf file)

Processed and analyzed DNA microarray dataset (.xls)
GenMAPP Expression Dataset file (.gex)
Filtered MAPPFinder Results (.xls)
Sample MAPP file of a relevant biological pathway for your species (.mapp)
Group Report describing the creation of the Gene Database and the biological analysis of the data (.doc or .pdf)

Assessment and reflection on process
- Statement of work
- Assessment of the work done
- What was learned

The key accomplishments this week were: 1) doing a first export for each of our three data sets, 2) learning how to edit gmbuilder, and 3) Kevin starting to work with the experimental data and understand how it's put together.
Next week, we hope to 1) test whether the first export was successful, work to resolve errors, and try to run an export for all 3 sub-strains at once and 2) for Kevin to actually understand what is going on with the raw research data and why it is organized so weirdly.
This week, we saw that we worked well had as a group, could divide labor well, and that everybody was competent enough to make progress working independently and with group members.
The largest weakness we have is scheduling. It's often hard for us to meet, so we'll have to plan our outside of class meetings well ahead of time. We also have an issue of direction, I observed that without a firm idea of purpose and an immediate goal, none of us work that efficiently necessitating firm direction and clear intermediate goals.

Taur.vil (talk) 21:07, 14 November 2013 (PST)