Team H(oo)KD Week 15 Status Report
From LMU BioDB 2013
| Project Manager/Coder: Katrina Sherbina | Quality Assurance: Hilda Delgadillo | GenMAPP User: Dillon Williams |
| Project Guidelines: | Gene Database Project | Report Guidelines | |
| Team Journal Assignments | Week 12 Status Report | Week 13 Status Report | Week 15 Status Report |
| Individual Status Reports: | HDelgadi Project Notebook | dwilliams Project Notebook | Ksherbina Project Notebook |
| Useful Links: | Class Page | Team Home Page |
| Final Product | Project Deliverables |
Refer to the calendar on the team home page to see the milestones for this week.
Contents |
Coder Status Report
The following was accomplished during Weeks 14-15:
- Determined why TallyEngine counted 917 genes in the gene database for C. trachomatis while the count was 919 when viewing the gene database in Access.
- Apparently, one ordered locus ID (CTA_0406/CTA_0407/CTA_0408) is actually a combination of three ordered locus IDs each of which were predicted to correspond to a different gene before it was found that all three IDs actually correspond to the same gene. TallyEngine does not separate the ordered locus IDs while Access does.
- In consulting with Dr. Dahlquist and Dr. Dionisio, we decided to leave this as is and describe the discrepancy in the final testing report, which is recorded in my project journal under November 27-28, 2013.
- Customized the Tally Engine for C. trachomatis and committed the changes to SourceForge.
Ksherbina (talk) 22:41, 5 December 2013 (PST)
Reflection
- The Quality Assurance person (Hilda) and I were able to finish working on the gene database and figuring out how to separate the gene IDs from the Affymetrix IDs appened to the gene IDs in the microarray data. This allowed as to devote the rest of our time to working with Dillon to perform the GenMAPP and MAPPFinder analysis. Lucky for us, no exceptions file was generated when running GenMAPP with the microarray data with the modified IDs and the gene database for C. trachomatis.
- When we originally set the milestones, we had planned to start working on both the paper and the presentation this week. Unfortunately, we had not advanced far enough in finalizing the database and performing GenMAPP analysis at the beginning of the week to be able to do this.
