Moore Notes 1 21 09
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Group Call 1/21/09
- Annual Report
- Kelly sent a template (simpler if we don't use it - will if there is time)
- Be sure to include:
- Any collaborations with people outside project
- Text for meeting objectives (outline is on the wiki)
- Figures and draft/published papers
- Budget: Gail/Jonathan
- Datasets / Back translation problem
- Martin has scripts for back translation
- Discussed what AMPHORA does (e.g. masked vs. not)
- SQL db
- UCD accounts (bobcat, genbeo)
- Simulations
- MetaSim
- pretty easy to use
- might have to do some scripting to generate input files in a high-throughput way
- what is effect of clone length with 454 simulations? Sam will look into this
- main issue is closed source (probably OK)
- ROSE
- Maritn thinks the models are not realistic (single rate on the tree?)
- MetaSim
- Trees
- long list of possible methods (Brenner lab, Bioinformatics paper, Morgan Price, supertree, supermatrix)
- Aaron will get paper from Davis folks
- BioPerl
- Srijak working on using BioPerl to run AMPHORA on Macs