Team H(oo)KD Week 13 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 Update

• When first performing an import/export cycle for the gene database, I ran into Java heap space errors, which I tried to reconcile by manually increasing the maximum heap space allocated for gmbuilder. Through this process, I found that 32-bit gmbuilder has a limit for what the maximum heap space can be set to.
• For the first import/export cycle, I imported the files into the database created in pgAdminIII using 64-bit gmbuilder with increased maximum heap space and performed the export in 32-bit gmbuilder without changing the heap space.
• Tally Engine did not produce the same counts for the UniProt file and the OBO-XML file for this first exported database. We believe that this is a result of duplicate entries being formed when I imported the UniProt, OBO-XML, and GOA files multiple times when I was working out the heap space error.
• A new database was created in pgAdminIII and a new import/export cycle in 32-bit gmbuilder was performed with this new database.
• Hilda and I were able to find the gene link pattern, which I was able to add to the custom species profile for C. trachomatis. With this final edit, I was able to build a new version of gmbuilder.
• Using the new build, I exported a new gene database.
• Hilda and I then performed quality assurance testing with the newest version of the C. trachomatis gene database. In so doing, we found that two genes were counted in Access and xmlpipedb match that were not counted by TallyEngine and pgAdminIII.

• In addition, Hilda and I also found in using xmlpipedb match that some of the genes have the gene ID pCTA_#### rather than CTA_####.
• Next week, we may need to consult with Dr. Dahlquist regarding what may be causing this discrepancy in the gene counts.
• The plan then for next week is to try to run GenMAPP with the microarray data (or at least a dummy file with the gene IDs from the data and some fake numbers) and the new gene database.

Ksherbina (talk) 23:44, 21 November 2013 (PST)

Reflection

1. What were the week’s key accomplishments?
   • This week's key accomplishments included finishing the custom species profile and then creating a new build of gmbuilder. With this new build, we were able to produce a gene database for C. trachomatis and run through the quality assurance testing for the database.
   • In addition, we were able to access the microarray data as well as normalize it using a software from Affymetrix.
2. What are next week’s target accomplishments?
   • For next week, the plan is to finish formatting the microarray data so that we know what chip corresponds to which experimental conditions that were tested by Omsland et al.
   • In addition, we want to try running GenMAPP using the microarray data (or at least a dummy fie with the gene IDs from the data and some fake values) with the latest version of the gene database.
3. What team strengths were seen this week?
   • I think our biggest strength was catching up to where the professors expected us to be in our project at this time.
   • We also were able to help each other with different tasks to make sure that we were all on the same page.
4. What team weaknesses were seen this week?
   • Unlike last week, we were not able to meet as a whole group this week outside of class time to check up on our progress and work out some of the difficulties that we were having with some tasks.

Ksherbina (talk) 00:00, 22 November 2013 (PST)

Quality Assurance Status Update

• The coder, Katrina, and I have completed a full import and export cycle. We were able to look at the Tally Engine, XMLPipeDB Match, SQL, and Microsoft Access in order to check our gene ID counts on Katrina's laptop. Fortunately, our numbers matched for the Tally Engine which assured us that our export of our database was essentially successful. The XMLPipeDB Match gave us 911 total unique matches, while in the SQL query the count was 917 and in ACCESS there were 919 unique gene ID matches. Therefore, there is certainly a discrepancy with the SQL query and the Tally Engine in which 917 gene IDs are being found, but are not adding up with the amount found in ACCESS and XMLPipeDB Match. We will look into the discrepancies next week.

Reflection

1. What were the week’s key accomplishments?
   • Within this week we were able to complete an import and export cycle of the files and database, respectively. We were also able to distinguish our specific gene IDs from the microarray data and we will work on categorizing the RBs and EBs with Rifampicin and without Rifampicin, so that we can make sense of which genes correlate to what category. We have also used the Tally Engine, XMLPipeDB Match, SQL, and Microsoft Access to compare our gene ID counts. Although we are facing some count discrepancies, we are in the midst of finding answers to these problems by looking closely at the formatting of the gene IDs.
2. What are next week’s target accomplishments?
   • We are hoping to Perform GenMAPP and MAPPFinder Analysis as well as figure out the discrepancies that were faced this week.
3. What team strengths were seen this week?
   • The team was very committed to putting our heads together and come up with solutions to our obstacles that we faced. We work well in helping each other out and brainstorming to find potential answers to our particular wrinkles that we encounter.
4. What team weaknesses were seen this week?
   • The team did not really meet all together in a group due to our conflicting class schedule, but Katrina was able to meet with both Dillon and I independently and fill us in as to what was discussed in the previous meeting.

HDelgadi (talk) 23:40, 21 November 2013 (PST)

GenMAPP User Status Update

Status Report

Milestone 2 Read the microarray paper to understand the experiment.

• Read Microarray Paper to understand experiment and find relations between raw data and article.

Create a table or list that shows the correspondence between the samples in the experiment and the files you have downloaded.

• Downloaded sdrf file and opened in excel to determine list that shows correspondence between samples in experiment and raw data file downloaded.

Determine how many biological or technical replicates, and which samples were labeled with Cy3 or Cy5.

• Determined 4 replicates based on article and data.

Create a Master Raw Data file that contains the IDs and columns of data required for further analysis.

• Created Master Spreadsheet and uploaded it to team wiki.

Consult with Dr. Dahlquist on how to process the data (normalization, statistics).

• Consulted with Dr. Dahlquist on how to process data and recorded steps in Project Notebook.

Reflection

1. What were the week’s key accomplishments?
   • The key accomplishments (for my position in the group) were understanding how to run the dChip software and convert and collect the raw data used into a workable format.
2. What are next week’s target accomplishments?
   • By next week we would like to perform GenMAPP and MAPPFinder analysis of the data.
3. What team strengths were seen this week?
   • Every member on our team accomplishes their role in an efficient and effective manner. If one member needs help with their role, the others are more than willing to help.
4. What team weaknesses were seen this week?
   • The Affymetrix data and use of the dChip software were confusing at first, but easily resolved once Dr. Dahlquist was consulted.

-Dwilliams (talk) 21:27, 21 November 2013 (PST)