Harvard:Biophysics 101/2007/Notebook:Christopher Nabel/2007-4-19

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Contents

Tasks Due Today

Parse SNP Sequence for Quality Control

Last Tuesday, I wrote the basic script for this task, but I didn't have a parser. Xiaodi had previous written a parser that can process XML data from SNP. We met last night to figure out what I'd need to do to download the sequence from the XML file. I have figured out how to write the code necessary to pull down the sequence: all I need to do is insert a line of code to get the sequence by the tag name corresponding to the sequence.

Outline for Hits That Don't Appear in OMIM

I thought about this for today, and it still isn't quite clear what the best plan of action is. I'm going to think more about this and present a concrete idea for next Tuesday.

Upcoming Tasks

For Tuesday

  • Write a script to parse out sequence data from dbSNP
  • Combine the quality control script with current version of the program (probably to be done with our project leader, Katie)
  • Present four scenarios for hits that have no OMIM entry

For Thursday

  • Explore what opportunities we have to interface with GeneCard
  • Write a disclaimer about the recommendations made by our program--as we discussed today in class, there are a few legal/ethical dilemmas that could arise from lay persons taking the recommendations of our program to extremes. I think a disclaimer should appear in two places: the written introduction to what our program is/does and at the screen where we return any potential recommendations (such as Tiffany's interface to Medline).
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