Vkuehn Individual Assessment and Reflection

Statement of Work

• Describe exactly what you did on the project.
• Provide references or links to artifacts of your work, such as:
  • Wiki pages
  • Other files or documents
  • Code or scripts

Vkuehn Week 12

• Compiled all of the raw data so that it would be ready to be analysed statistically and normalized
  • Chip raw data files compared to SDRF and organized
  • Named each chip in a way that gave more information to the project (Chip number from sdrf and species)
  • Created the compiled raw data for L. major
• Updated the team page and made wiki improvements
• As the team leader created The Plan to keep our progress organized and documented
  • Created an outline of the project goals and interim deadlines
  • Wrote the updates that had to do with GenMAPP users for the team page

Vkuehn Week 13

• Reread the paper and took notes on the specific meaning behind the microarray data and took notes on relevant information
• Scaled and centered microarray data
• Performed statistical analysis
• Edited the wiki and made formatting improvements on the templates so that the page would be easier to update for everyone
  • • Wrote the updates that had to do with GenMAPP users for the week

Vkuehn Week 15

• Did sanity check on the statistical results from L. major
• imported the mircoarray data to GenMAPP
• Assigned colors to the criteria for GenMAPP
• Ran GenMAPP and GO terms were found
  • Found the ones with links to families and looked up the GO terms so that the mapp could be created
• Created the L. major week 15 Status Report Page
  • Wrote the updates that had to do with GenMAPP users

Final Week

• Wrote my part of paper that corresponds to the journal club for the article and the microarray data compilation and statistical analysis, and made the power point outlining the project and having everyone input their parts Media:Leishmania PowerPoint 12122013.pdf
• Found and analyzed the results from our GenMAPP and the results in the experiment and compared them
• Looked up the GO terms and the genes that were found to have changed significantly using MAPPFinder and UniProt to organize the genes.

  Figured out a way to categorize them for the MAPP File:Arromatic Compound Catabolic Process Comparative Pathway Map.mapp

  • Highlighted similarities
• Created a presentation on Google Drive for the group to input the project to presentation
• Reviewed all of the pages and noted all of the requirements that need to be submitted for the project so nothing slips through, and communicated with the group on last minute deadlines
• Redid the statistical analysis of the L. major p-values and fold changes by filtering the excel file down to the relevant information after the presentation File:LeishmaniaCompiledStatAnalysis(C).txt
• Wrote the conclusion comparing our results to the results of the article and made general conclusive remarks on the group write up, and made final touches throughout the paper. File:LeishmaniaFinalPaper.pdf

Assessment of Project

• Give an objective assessment of the success of your project workflow and teamwork.

  I think our team worked very well together. We were always good about communicating where the different members stood and if there were problems everyone worked together to make sure that they would get resolved so that the team could move to the next step. We were very good about planning all of the goals for the weeks and would stay after to make sure everyone was updated for the goals for the next meeting.

• What worked and what didn't work?

  We all did a good job dividing the workload and the completion of all of the requirements in a timely manner worked well. The set up pf the team page for the initial journal club presentation was hectic and disorganized, but we were still getting familiar with the project.

• What would you do differently if you could do it all over again?

  Made sure to complete even the last step before finals week because this step did not have a lot of instruction and took a lot of time to understand.

• Evaluate the Gene Database Project and Group Report in the following areas:
  1. Content: What is the quality of the work?

     I am personally very impressed with the quality of our work. With such a large project undestanding all of the details of each step can seem overwhelming, but with the way each team member took a part we were each able to understand all of the details and see the big picture.

  2. Organization: Comment on the organization of the project and of your group's wiki pages.

     The organization of the group's wiki could have been improved in my opinion. I think we were in a rush to set it all up in the beginning, so the layout and organization of the information lacked structure. I think that the project was organized though, this just did not translate very well on the wiki page because of the ineffective formatting at the beginning.

  3. Completeness: Did your team achieve all of the project objectives? Why or why not?
  4. Yes, our team achieved all of the project objectives. We worked to fix as many of the errors as we could up to the last minute. There are some genes that still did not make it into the database, but the coders worked hard and successfully reduced this number a lot. Other than that, everything was completed.

Reflection on the Process

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

    I learned the expanse of biological databases and why they are integral to biology today. I also learned the possibilities that these databases provide.

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

    I learned how to manage a long term project so that it does not become unmanageable at the end.

  • With your hands (technical skills)?

    I became more familiar with using computers and learned how to use different ways of manipulating data in different programs.

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

  The knowledge of how to use databases and how to navigate them to find information.

• Template:vkuehn
• Viktoria Kuehn
• Week 1 Assignment
• Class Journal 1
• Week 2 Assignment
• Class Journal 2
• Vkuehn Week 2
• Week 3 Assignment
• Class Journal 3
• Vkuehn Week 3
• Week 4 Assignment
• Class Journal 4
• Vkuehn Week 4
• Week 5 Assignment
• Vkuehn Week 5
• Ensembl Database
• Week 6 Assignment
• Class Journal 6
• Vkuehn Week 6
• Week 7 Assignment
• Class Journal 7
• Vkuehn Week 7
• Week 8 Assignment
• Class Journal 8
• Vkuehn Week 8
• Leishmania major
• Week 9 Assignment
• Class Journal 9
• Vkuehn Week 9
• Week 10 Assignment
• Class Journal 10
• Vkuehn Week 10
• Leishmania major
• Week 11 Assignment
• Vkuehn Week 11
• Leishmania major Genome Reference Article Presentation
• Vkuehn Week 12
• Week 12 Assignment
• Leishmania major Week 12 Status Report
• Vkuehn Week 13
• Week 13 Assignment
• Vkuehn Week 15
• Week 15 Assignment
• Vkuehn Individual Assessment and Reflection