Alina's Assessment and Reflection

Statement of Work

Identification of Gene IDs

• Used Microsoft Access to investigate files of original 3 strains (TIGR4, R6, G54)
• Identified/checked gene ID formats for consistency and looked for orderedlocus totals
• Format/total for TIGR4 strain of interest were as follows:
  • TIGR4: SP_#### Orderedlocus: 2126

Updating of Gene Database Testing Reports

• Was responsible for running counts (XMLPipeDB Match, Tally Engine, SQL)for all export testing reports
• Performed visual inspections within gdb files
  • Systems table
  • UniProt table
  • RefSeq table
  • OriginalRowCounts
• Used snipping tool to provide screenshots for most results in testing
• (Did not update GenMAPP aspects, left to Kevin)
• Compared found Gene ID formats with corresponding online resources (UniProt, RefSeq)
• Investigated Ensembl (MOD) to compare gene totals
• Export Reports contributed to:
  • [1] [2] [3]

Electronic Notebooks: Week12 Week13 Week14 Week15

XML/Exception File Comparison

• Used XMLPipeDB Match in order to search Uniprot XML file for species IDs with format SP_[0-9][0-9][0-9][0-9] and got 2126 results.
• This was saved as a text file in order to make compatible for Excel. This file and exceptions file were put in adjacent columns and Excel match function was used. All results found to be #N/A.
• Excel File: ID Comparison

Visual Representation of Data Information

• Helped Kevin with visual representating replicate information from microarray paper
• Used Paint program to create diagram

• Provide references or links to artifacts of your work, such as:
  • Wiki pages
  • Other files or documents
  • Code or scripts

Assessment of Project

• Give an objective assessment of the success of your project workflow and teamwork.
  • As a group we were very successful when it came to completing tasks and working together as a team. All members were committed to the tasks they were given and we had no problems getting together to work on the project. We had no problems with one another individually, and all group members were as supportive and as helpful as possible. Had it not been for the slight hiccup in terms of analyzing the microarray data, the workflow would have been very smooth.
• What worked and what didn't work?
  • We had a little trouble getting the microarray data in a form we could use, but other than that most of our testing went flawlessly. All of our counts matched our expected value, and our ID exceptions/errors from the database could not be fixed due to their absence in our original file. Our team stayed on track despite the delay for the microarray data, but we were able to work efficiently enough to catch up once the data was in order.
• What would you do differently if you could do it all over again?
  • I think I would try and learn more about the coder's tasks. While I did work side by side with my team, I feel I could have immersed myself a little more and not focused so much on just completing particular tasks. Another thing I would improve on is the detail content within the electronic journal. In some cases this semester I could have given more information on what I actually did, instead of just summarizing.
• Evaluate the Gene Database Project and Group Report in the following areas:
• Content: What is the quality of the work?
  • The work we completed is high quality, due to the care and diligence my team put into making it the best they possibly could. The group had no problem asking each other questions or asking the professors questions when they needed clarification or advice on certain topics. The work really reflects the effort that was put into it.
• Organization: Comment on the organization of the project and of your group's wiki pages.
  • Overall, I think the content on our wiki was pretty organized, despite having our respective information somewhat scattered in our journals. It all came together once we compiled everything into the testing reports and project. The team template really made it easy to navigate through all our team pages and keep track of our information. The project is also well-organized, with a flow of information that makes sense.
• Completeness: Did your team achieve all of the project objectives? Why or why not?
  • My team was very on-the-ball when it came to completing objectives. The team worked very hard at making sure everything was done, and done correctly, using whatever resources were available.

Reflection on the Process

• What did you learn?
  • With your head (biological or computer science principles)

The different projects from the groups supplied me with some new knowledge about species I previously was not too familiar with. It was interesting to learn about what kinds of studies are being done on the different species using the skills and information about databases and the programs that go into creating them.

• With your heart (personal qualities and teamwork qualities that make things work or not work)?

A personal quality that I found I need to improve on is my public speaking ability. While I am able to perform fairly well, and perhaps better than quite a few of my peers, I still do not feel as confident as I should while talking about a topic in front of a group. Interacting with my group and seeing how well we worked together in comparison to some of the other groups gave me some insight into what working in real-life teams might be like, and you may not always get to work with people that have the team's success in mind.

• With your hands (technical skills)?

I got a chance to work with a lot of programs that I probably would have never even heard of had I not taken this class. The coding process was difficult, but I found it rewarding to try my hand at something I had never experienced. It was insightful to apply concepts I am familiar with in biology to a new frontier I have never stepped foot in.

• What lesson will you take away from this project that you will still use a year from now?

I will take the lessons I learned from being involved in a long term project and apply them to future group projects I will have to be involved with. Hopefully I will get to apply my new awareness of biological databases and use it for future research or in other future endeavours.