Difference between revisions of "TATK Week 12 Status Report"

Revision as of 05:39, 15 November 2013

tATK Week 12 Status Report

Week Goals and Status Report

1. 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.
2. 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
3. For Alina to complete the counting exercise with the initial exports.
   • Began doing the counting exercise but results vary between the different methods.
4. 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.

Immediate Next Steps

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

Deliverables

• PowerPoint presentation in class on Thursday, December 12, 8:00am.
• All other deliverables is no later than Friday, December 13, 4:30pm

Group

• 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)

• PowerPoint presentation (.ppt, given on Thursday, December 12)

Individual

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

Team Reflections

Tauras

1. 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.
2. 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.
3. 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.
4. 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)

Streptococcus pneumoniae

Import Export Cycle 1: tATK Export One: TIGR4 Testing Report

Import Export Cycle 2: tATK E2: TIGR4 Testing Report

Import Export Cycle 3: tATK E3: TIGR4 Testing Report

Import Export Cycle 4: tATK E4: TIGR4 Testing Report

Data Information

• Kmeilak Week 10, Kmeilak Week 11, Kmeilak Week 12, Kmeilak Week 13
• Taur.vil Week 10, Taur.vil Week 11, Taur.vil Week 12, Taur.vil Week 13, Taur.vil Week 14, Taur.vil Week 15
• Ajvree Week 10, Ajvree Week 11, Ajvree Week 12, Ajvree Week 13, Ajvree Week 14, Ajvree Week 15