Harvard:Biophysics 101/2007/04/19

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'''Plans'''
'''Plans'''
* [[Harvard:Biophysics_101/2007/Notebook:Christopher_Nabel/2007-4-19|Chris]] Write SNP sequence parser and integrate QC code.  Propose ideas for OMIM non-hits.
* [[Harvard:Biophysics_101/2007/Notebook:Christopher_Nabel/2007-4-19|Chris]] Write SNP sequence parser and integrate QC code.  Propose ideas for OMIM non-hits.
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* [[Harvard:Biophysics_101/Notebook:ZS/2007-4-22|Zach]] Finish CDC prevalence / consolidate CDS mutation code from earlier / determine CDS from a gene input or blast search [[http://openwetware.org/wiki/Harvard:Biophysics_101/Notebook:ZS/2007-4-26 progress]
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* Zach Finish CDC prevalence [[Harvard:Biophysics_101/Notebook:ZS/2007-4-22| completion], consolidate CDS mutation code from earlier (delayed) / determine CDS from a gene input or blast search [Harvard:Biophysics_101/Notebook:ZS/2007-4-26 | 4-26 almost complete]
* [[TChan/Notebook/2007-4-22 |Tiff]] Learn how to & parse HTML and XML to extract info from MedStory searches
* [[TChan/Notebook/2007-4-22 |Tiff]] Learn how to & parse HTML and XML to extract info from MedStory searches
* [[Harvard:Biophysics_101/2007/Notebook:CChi/2007-4-22|Cynthia]] Think about how to deal with non OMIM hits, as in the context of what was discussed in class on Thursday
* [[Harvard:Biophysics_101/2007/Notebook:CChi/2007-4-22|Cynthia]] Think about how to deal with non OMIM hits, as in the context of what was discussed in class on Thursday

Revision as of 01:56, 26 April 2007

  • Same drill as last week. Post what you plan to do on your personal page, and link to it below with 1-line summary.
  • Remember to organize your links so we can easily review your progress in class.

smd 23:39, 18 April 2007 (EDT)


Plans

  • Chris Write SNP sequence parser and integrate QC code. Propose ideas for OMIM non-hits.
  • Zach Finish CDC prevalence [[Harvard:Biophysics_101/Notebook:ZS/2007-4-22| completion], consolidate CDS mutation code from earlier (delayed) / determine CDS from a gene input or blast search [Harvard:Biophysics_101/Notebook:ZS/2007-4-26 | 4-26 almost complete]
  • Tiff Learn how to & parse HTML and XML to extract info from MedStory searches
  • Cynthia Think about how to deal with non OMIM hits, as in the context of what was discussed in class on Thursday
  • Resmi Finish code to parse out keywords from Pubmed and think about how we can process non-OMIM hits. 4-24 Progress; 4-26 Progress
  • Xiaodi Genbank file parsing to work around issues with OMIM; will hopefully fetch genes of note and characterize SNPs
  • Deniz Bringing in the news, trials, news and such and keep working on the ranking.
  • Michael Still examining the possibility of estimating allele frequency and maybe penetrance based on Hapmap data combined with epi studies of particular SNPs present within a given allele for a sequence. Also starting to code up something that will make a polyphen query to handle sequences not in OMIM but found in BLAST and get back some idea of whether or not the mutation may be deleterious.
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