Team H(oo)KD Week 15 Status Report

Team H(oo)KD

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.

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

1. 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.
2. 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.
3. With next week being finals week, we will have several meetings leading up to the final presentation in order to work on the paper, the presentation, and deliverables to make sure we meet the final deadline.

Ksherbina (talk) 23:02, 5 December 2013 (PST)

Quality Assurance Status Report

Katrina, the Coder, and I were able to work on separating the gene IDs so that statistical analysis could be performed by Dillon, the GenMAPP User, along with including this information into GenMAPP. The process of separating the IDs were tricky, but with Katrina's advice and some google searches I was able to manage separating the IDs, although I must admit it took Katrina 5 minutes to separate the IDs whereas it took me about close to an hour to figure out how to maneuver my way into figuring out how to go about this process. In any case, once this was done, Dillon (GenMAPP User) was able to generate the statistical analysis and the three of us proceeded to applying the data into GenMAPP. Luckily, we did not receive any errors throughout this transition to GenMAPP, so an exceptions file did not need to be generated. Moreover, we are now able to proceed with the project, so we will meet and start on our paper by Saturday. I will also proceed to complete the relational database schema for the gene database by Saturday. Katrina and I looked at the schema today and asked Dr. Dionisio questions about the schema to make sure we understood its format.

Reflection

1. What worked?

   Our schedules were able to match much better this week, so we were all able to meet without any problems.

2. What didn't work?

   We had hoped to start on the paper this week, but unfortunately we faced difficulties with the microarray data and gmbuilder, so we were not able to get far enough in the process to run GenMAPP earlier in the week.

3. What will I do next to fix what didn't work?

   We have resolved the problems we faced, so we will make sure to begin the paper as soon as possible (by Saturday) and if there are any questions we will contact Dr. Dionisio and Dr. Dahlquist immediately.

HDelgadi (talk) 00:05, 6 December 2013 (PST)

GenMAPP User Status Report

This week, after fixing the initial issues that we had with running the statistics on the C. trachomatis raw data, I was able to create the final excel spreadsheet that was to be used in GenMAPP. With the help of the coder and QA in formatting the gene ID's for the "for GenMAPP" sheet in the excel master spreadhseet, I was able to create a sheet with all of the information necessary to run the data in GenMAPP.

• I used the database the Katrina (coder) created and proceeded to use the tab delimited file of the final excel spreadsheet to run the dataset in GenMAPP.
• We had no errors.
• After running GenMAPP, I used the LogFC changes and P values of the Rifampicin/No Rifampicin EB to RB data to create a color set. The color set was then saved as a .gex file on our team page.
• After completing this, Katrina and I used MAPPFinder to find the changes in some of the metabolic and catabolic pathways of the genes used.
• We are currently in the process of creating a map for the changes in these pathways.

Reflection

1. ) This week, I spent a lot of time sorting out a lot of little problems. When it came to some of the things that required collaboration of multiple group members, Katrina and I were able to get the work done fairly efficiently and we both spent a lot of time making sure that everything ran smoothly.
2. ) There wasn't anything that didn't work per se, although we did not get as much done as we were hoping for, we are going to continue working on the project over the course of the weekend.
3. ) Next week we will really be focusing our time and energy into ensuring that everything is done correctly and that the paper is done as well as possible. I personally, will also contribute time to cleaning up my electronic lab notebook, streamlining some of the steps and making the page itself more readable (I have already begun to improve some of the formatting on my page). Ultimately, next week will consist of tying off any loose ends and ensuring that everything is running how it should be running.

-Dwilliams (talk) 22:07, 5 December 2013 (PST)