Harvard:Biophysics 101/2007/Project: Difference between revisions

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* Could someone who typed this up today please add the other sections that are being worked on? '''--[[User:TChan|TChan]], 12:47 20 March 2007'''
* Could someone who typed this up today please add the other sections that are being worked on? '''--[[User:TChan|TChan]], 12:47 20 March 2007'''


:* The following is from the information that Zach typed up in class (Located  [[Harvard:Biophysics_101/2007/Notebook:Xiaodi_Wu/2007-3-20 | here]]) '''--[[User:Hetmann|Hetmann]], 5:32 20 March 2007'''
==OMIM Parsing==
* Resmi, Cynthia, and Hetmann


==BLAST SNP to OMIM==
==BLAST SNP to OMIM==
* Zach, Mike, and Tiffany
===BioPython Modification===
===BioPython Modification===
* Relevant file: [[Image:NCBIWWWforBLASTSNPmodif-TC32007.py|Python25/Lib/site-packages/Bio/Blast/NCBIWWW.py]]
* Relevant file: [[Image:NCBIWWWforBLASTSNPmodif-TC32007.py|Python25/Lib/site-packages/Bio/Blast/NCBIWWW.py]]
* Discussion on BLAST SNP can proceed on the [[Talk:Harvard:Biophysics_101/2007/Project|discussion page]].
* Discussion on BLAST SNP can proceed on the [[Talk:Harvard:Biophysics_101/2007/Project|discussion page]].
* Seq--> BlastSNP --> rs# (former hard, latter easy)
:* Modifying BioPython BLAST
==Parsing XMP from #2 in python==
* Deniz
* OMIM download
:* Zach - did you mean XML?  I have XML in my notes... '''--[[User:Hetmann|Hetmann]], 5:32 20 March 2007'''
==Integration==
* Katie
* PM / encourage documentation
==OMIM XML Parse==
* Xiaodi - completed?
* rs-->OMIM XML parse -> phenotype text
Chris
*if one gets multiple SNPs, which is revelant?
*linking to PubMED after finding disease
Kay


==Beyond OMIM==
* Tiffany, Resmi, Deniz, Xiaodi, Mike (''note: ask if API exists'')
:* Wikipedia (Mike) http://meta.wikimedia.org/wiki/API
:* Webmd (Tiff)
:* Emedicine (Resmi)
:* Google (Deniz)
:* Linking out of XML (Xiaodi)
:* MedStory (Mike?)


==Unassigned==
#not in SNP db... then what?
#OMIM DOA
#systematically nonsyn. -> mutation not in OMIM or dbSNP?
#other dbs: genecard (spec. conservation, pop. freq)
#looking into linking gene expression w/ GEO?




=Project Ideas=
=Project Ideas=
Project ideas have been moved to their [[Harvard:Biophysics_101/2007/ProjectIdeas|own page]].
Project ideas have been moved to their [[Harvard:Biophysics_101/2007/ProjectIdeas|own page]].

Revision as of 14:32, 20 March 2007

Biophysics 101: Genomics, Computing, and Economics

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Project Sections

  • Could someone who typed this up today please add the other sections that are being worked on? --TChan, 12:47 20 March 2007
  • The following is from the information that Zach typed up in class (Located here) --Hetmann, 5:32 20 March 2007

OMIM Parsing

  • Resmi, Cynthia, and Hetmann

BLAST SNP to OMIM

  • Zach, Mike, and Tiffany

BioPython Modification

  • Modifying BioPython BLAST

Parsing XMP from #2 in python

  • Deniz
  • OMIM download
  • Zach - did you mean XML? I have XML in my notes... --Hetmann, 5:32 20 March 2007

Integration

  • Katie
  • PM / encourage documentation

OMIM XML Parse

  • Xiaodi - completed?
  • rs-->OMIM XML parse -> phenotype text


Chris

  • if one gets multiple SNPs, which is revelant?
  • linking to PubMED after finding disease

Kay

Beyond OMIM

  • Tiffany, Resmi, Deniz, Xiaodi, Mike (note: ask if API exists)

Unassigned

  1. not in SNP db... then what?
  2. OMIM DOA
  3. systematically nonsyn. -> mutation not in OMIM or dbSNP?
  4. other dbs: genecard (spec. conservation, pop. freq)
  5. looking into linking gene expression w/ GEO?


Project Ideas

Project ideas have been moved to their own page.

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