Cbcb:Pop-Lab:Ted-Report: Difference between revisions
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(Posted 3 weeks of progress reports) |
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* Read metagenomics/pathway reconstruction/analysis papers and first two chapters of Palsson book. | * Read metagenomics/pathway reconstruction/analysis papers and first two chapters of Palsson book. | ||
* Currently building test set for incorporation of Phymm into metagenomics pipeline. | * Currently building test set for incorporation of Phymm into metagenomics pipeline. | ||
** A single | ** A single archaeal genome was chosen from the findings of Mihai's 2006 Science paper analyzing the human distal gut. | ||
** Two pairs of bacterial genomes were chosen for the test set using columns on the NCBI RefSeq ''Complete Genomes'' website[http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi]: | |||
*# 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. | *# 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. | ||
*# I chose genomes with a complete set of NCBI ''Tools'' available. | *# I chose genomes with a complete set of NCBI ''Tools'' available. | ||
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*# Finally, preference was given to organisms I recognized from gut microbiome papers/discussions, or failing that, just a really awesome name. | *# 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: | ** The final list is: | ||
*** Methanobrevibacter_smithii_ATCC_35061 (archaeal) | |||
*** Bacteroides fragilis NCTC 9343 | *** Bacteroides fragilis NCTC 9343 | ||
*** Porphyromonas gingivalis W83 | *** Porphyromonas gingivalis W83 | ||
*** Aster yellows witches'-broom phytoplasma AYWB | *** Aster yellows witches'-broom phytoplasma AYWB | ||
*** Bacillus subtilis subsp. subtilis str. 168 | *** Bacillus subtilis subsp. subtilis str. 168 | ||
Revision as of 20:24, 4 June 2009
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 archaeal genome was chosen from the findings of Mihai's 2006 Science paper analyzing the human distal gut.
- Two pairs of bacterial genomes were chosen for the test set using columns on the NCBI RefSeq Complete Genomes website[3]:
- 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.
- I chose genomes with a complete set of NCBI Tools available.
- After this I attempted to choose genomes with significantly different GC content.
- 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:
- Methanobrevibacter_smithii_ATCC_35061 (archaeal)
- Bacteroides fragilis NCTC 9343
- Porphyromonas gingivalis W83
- Aster yellows witches'-broom phytoplasma AYWB
- Bacillus subtilis subsp. subtilis str. 168