Harvard:Biophysics 101/2007/04/19

From OpenWetWare

< Harvard:Biophysics 101 | 2007 | 04(Difference between revisions)
Jump to: navigation, search
Current revision (01:57, 26 April 2007) (view source)
 
(4 intermediate revisions not shown.)
Line 6: Line 6:
'''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.
-
* [[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
+
* 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

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.
Personal tools