Difference between revisions of "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 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.
* [[Harvard:Biophysics_101/Notebook:ZS/2007-4-22|Zach]] Finish CDC prevalence / consolidate CDS mutation code from earlier / (tasks people need help on? email me  and I can help out)
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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]]
 
* [[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
* [[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.
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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.

Latest revision as of 21:57, 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 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.