Harvard:Biophysics 101/2007/04/19

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* [[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
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* [[Harvard:Biophysics_101/2007/Notebook:Resmi Charalel/2007-4-19|Resmi]]  Finish code to parse out keywords from Pubmed and think about how we can process non-OMIM hits.  [[Harvard:Biophysics_101/2007/Notebook:Resmi Charalel/2007-4-24|See Here For Progress]]
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* [[Harvard:Biophysics_101/2007/Notebook:Resmi Charalel/2007-4-19|Resmi]]  Finish code to parse out keywords from Pubmed and think about how we can process non-OMIM hits.  [[Harvard:Biophysics_101/2007/Notebook:Resmi Charalel/2007-4-24|4-24 Progress]]; [[Harvard:Biophysics_101/2007/Notebook:Resmi Charalel/2007-4-26|4-26 Progress]]  
* [[Harvard:Biophysics_101/2007/Notebook:Xiaodi Wu/2007-4-19|Xiaodi]] Genbank file parsing to work around issues with OMIM; will hopefully fetch genes of note and characterize SNPs
* [[Harvard:Biophysics_101/2007/Notebook:Xiaodi Wu/2007-4-19|Xiaodi]] Genbank file parsing to work around issues with OMIM; will hopefully fetch genes of note and characterize SNPs
*[[Harvard:Biophysics_101/2007/Notebook:Denizkural/2007-4-24|Deniz]] Bringing in the news, trials, news and such and keep working on the ranking.
*[[Harvard:Biophysics_101/2007/Notebook:Denizkural/2007-4-24|Deniz]] Bringing in the news, trials, news and such and keep working on the ranking.
* [[Harvard:Biophysics_101/2007/Notebook:MichaelWang/2007-4-19|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.
* [[Harvard:Biophysics_101/2007/Notebook:MichaelWang/2007-4-19|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.

Revision as of 23:41, 25 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 / consolidate CDS mutation code from earlier / determine CDS from a gene input or blast search
  • 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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