Harvard:Biophysics 101/2007/04/19

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Current revision (00:57, 26 April 2007) (view source)
 
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'''Plans'''
'''Plans'''
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* [http://openwetware.org/wiki/Harvard:Biophysics_101/2007/Notebook:Christopher_Nabel/2007-4-19 Chris] Write SNP sequence parser and integrate QC code.  Propose ideas for OMIM DOA hits.
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* [[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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* ...
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* Zach Finish CDC prevalence [[Harvard:Biophysics_101/Notebook:ZS/2007-4-22| 4-24 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]]
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* [[TChan/Notebook/2007-4-22 |Tiff]] Learn how to & parse HTML and XML to extract info from MedStory searches
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* [[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|4-24 Progress]]; [[Harvard:Biophysics_101/2007/Notebook:Resmi Charalel/2007-4-26|4-26 Progress]]
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* [[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
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*[[Harvard:Biophysics_101/2007/Notebook:Denizkural/2007-4-24|Deniz]] Bringing in the news, trials, news and such and keep working on the ranking.
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* [[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.

Current revision

  • 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 4-24 completion / consolidate CDS mutation code from earlier (delayed) / determine CDS from a gene input or blast search 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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