Meeting Log 17-05-19

[davisbk]

General Notes

General Plan

1. Start with wild type(s) - these have evolved over X million generations (X = {3, 5, 10}) and are now stable.
2. For each wild type, alter a parameter (e.g. mutation rate, selection pressure, population size, etc.) and let the organisms evolve for another 10,000 (100,000?) generations
3. Use statistical analysis to evaluate results.
   • Trace phylogeny of most fit individual(s) and examine factors leading to fitness
   • Evaluate average genome size
   • etc.
4. Write down all commands used for aevol and Bash.
5. Use Bash scripts wherever possible -> increases reproducibility
6. Write something for the report every week (don't leave it all for the last minute)

Brian's To Do

• [x] Create GitHub repository

  • Give it an organized structure
    • Root-> readme.txt with scientific question
    • doc-> Documentation
    • src-> All source code
    • data-> All input data
      • WT1 -> Wild type 1
        • param -> Different parameter settings for this wild type
      • WT2 -> Wild type 2
        • param -> Different parameter settings for this wild type
      • etc.
    • results -> Results from different parameters
      • WT1
      • mutation up - > results from increasing mutation rate
      • neutral -> results from leaving mutation rate
      • mutation down -> results from decreasing mutation rate
      • etc.
      • WT2
      • etc.
    • .
    • .
    • .
    • etc.

• [X] Write meeting protocol for weekly meeting of 5-17-19

• [x] Complete Bash tutorial here

• [x] Complete git tutorial here

• [ ] Get Linux set up

• [x] Read paper "How to Reduce a Genome?"

• [ ] Begin writing thesis paper (Introduction)

Dr. Batut's To Do

• [x] Give Brian access to aevol gitlab repository
• [x] Give Brian access to Gitter
• [x] Look into a room for Brian to work in

[bebatut]

Thanks for this protocol!

Can you create yourself an account on https://gitlab.inria.fr/ and then send me your username there? Thanks! Then I can give you access to the GitLab repo

[bebatut]

Can you also link your GitHub account on Gitter (https://gitter.im/)? Then you can search for me (bebatut) to discuss there