Cbcb:Pop-Lab:Ted-Report

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Revision as of 16:44, 4 June 2009 by Tgibbons (talk | contribs) (Posted 3 weeks of progress reports)
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Summer 2009 Goals

  • Research traditional approaches taken to gene-level analysis of metagenomic data
  • Critically evaluate the traditional approaches in general and in the context of current Pop Lab projects
  • Identify portions of the analysis that can be automated
  • Develop scalable tools to do the automated analysis

May 15, 2009

  • Read VisANT paper and user manual[1]. Determined VisANT will work for manual metabolic pathway analysis of even large scale data sets and can be automated by running in "Batch Mode".
  • Need to read about FastHMM[2]
  • Still need to make "Welcome Wiki" for n00bs (read: new members)

May 22, 2009

  • Made Welcome Wiki
  • Read metagenomics papers
  • Determined that VisANT can be used with Bo's data by importing it as MicroArray data

May 29, 2009

  • Took an early Summer vacation last weekend:
    • Drove to NC to see friend graduate with BS' in CS & Physics
    • Went sailing for the first time at girlfriends' parents' place in VA
  • Refined Welcome Wiki
  • Read metagenomics/pathway reconstruction/analysis papers
  • Organized reading group for Palsson Systems Bio book

June 5, 2009

  • Read metagenomics/pathway reconstruction/analysis papers and first two chapters of Palsson book.
  • Currently building test set for incorporation of Phymm into metagenomics pipeline.
    • A single archeal genome and two pairs of bacterial genomes were chosen for the test set using columns on the NCBI RefSeq Complete Genomes website[3]:
    1. The pairs of bacterial genomes were taken from the Groups: Bacteroidetes/Chlorobi and Firmicutes because they are the two most predominant groups present in the human gut.
    2. I chose genomes with a complete set of NCBI Tools available.
    3. After this I attempted to choose genomes with significantly different GC content.
    4. Finally, preference was given to organisms I recognized from gut microbiome papers/discussions, or failing that, just a really awesome name.
    • The final list is:
      • Bacteroides fragilis NCTC 9343
      • Porphyromonas gingivalis W83
      • Aster yellows witches'-broom phytoplasma AYWB
      • Bacillus subtilis subsp. subtilis str. 168
      • [An as yet unspecified archeal genome]