Harvard:Biophysics 101/2007/Project

Project Sections

• ATTENTION: Everyone needs to post their code to one place. Let's say everyone post a link from here that works to their code and then I'll be able to combine it all. --User:Katie Fifer
• 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

• Relevant file: Python25/Lib/site-packages/Bio/Blast/NCBIWWW.py
• Discussion on BLAST SNP can proceed on the discussion page.
• Seq--> BlastSNP --> rs# (former hard, latter easy)

• Modifying BioPython BLAST

Parsing XML from #2 in python

• Deniz
• OMIM download

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, Medstory. (Deniz)
• Linking out of XML (Xiaodi)
• MedStory (Mike?)

Unassigned

1. not in SNP db... then what? - I'd like to point out new efforts that aim to replace OMIM, called the "Human Variome Project" -- Deniz
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.