Harvard:Biophysics 101/2007/04/19: Difference between revisions
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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 | ||
* [[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| | * [[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 20:41, 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.
