Harvard:Biophysics 101/2007/Notebook:Christopher Nabel/2007-4-19: Difference between revisions
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(New page: ==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 t...) |
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==Upcoming Tasks== | ==Upcoming Tasks== | ||
===For Tuesday=== | ===For [http://openwetware.org/index.php?title=Harvard:Biophysics_101/2007/Notebook:Christopher_Nabel/2007-4-24 Tuesday]=== | ||
* Write a script to parse out sequence data from dbSNP | * 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) | * Combine the quality control script with current version of the program (probably to be done with our project leader, Katie) |
Revision as of 04:32, 24 April 2007
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).