Team H(oo)KD Week 13 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 |
Contents |
Coder Status Update
Reflection
Quality Assurance Status Update
- The coder, Katrina, and I have completed a full import and export cycle.
Reflection
- 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.
- 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.
- 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.
- 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.
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
- 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.
- What are next week’s target accomplishments?
- By next week we would like to perform GenMAPP and MAPPFinder analysis of the data.
- 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.
- 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.
