Harvard:Biophysics 101/2007/Project

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=Path 1: Using OMIM=
=Path 1: Using OMIM=
==Sequence -> RS Number (BLAST SNP)==
==Sequence -> RS Number (BLAST SNP)==
-
* Xiaodi
+
===RS Number -> Disease Name (OMIM)===
 +
* Xiaodi (and Katie?): [[Harvard:Biophysics_101/2007/Notebook:Katie_Fifer/2007-4-15|code]] prints and outputs to file pickled version of the OMIM output for our sequence
 +
 
===RS Number -> Mesh Terms (PubMed)===
===RS Number -> Mesh Terms (PubMed)===
* Cynthia
* Cynthia
-
===RS Number -> Disease Name (OMIM)===
 
===RS Number (OMIM) -> PubMed PMIDs===
===RS Number (OMIM) -> PubMed PMIDs===
====PubMed PMIDs -> Mesh Terms====
====PubMed PMIDs -> Mesh Terms====
-
* Resmi: [[Harvard:Biophysics_101/2007/Notebook:Resmi_Charalel/2007-4-24|code]] (1) parses OMIM XML to (2) get PubMed PMIDs to (3) get Mesh Terms  
+
* Resmi: [[Harvard:Biophysics_101/2007/Notebook:Resmi_Charalel/2007-4-26|code]] (1) parses OMIM XML to (2) get PubMed PMIDs to (3) get Mesh Terms  
Line 26: Line 27:
=====Disease Name -> Useful Patient Info (Medical search engines)=====
=====Disease Name -> Useful Patient Info (Medical search engines)=====
-
* Deniz:  
+
* Deniz: [[Harvard:Biophysics_101/2007/Notebook:Denizkural/2007-4-3|examples of coding]] which returns news updates in several formats
-
* Tiff: [[TChan/Notebook/2007-4-24|code]] (1) displays relevant URLs, (2) returns lists of drugs, clinical trials, experts, etc.
+
* Tiff: [[TChan/Notebook/2007-4-24|code]] (a) displays relevant URLs (, (b) returns lists of drugs, clinical trials, experts, etc.
-
* Resmi: [[Harvard:Biophysics_101/2007/Notebook:Resmi_Charalel/2007-4-5|code]] (1) displays PubMed reviews
+
* Resmi: [[Harvard:Biophysics_101/2007/Notebook:Resmi_Charalel/2007-4-5|code]] displays PubMed review citations in text form
 +
* Cynthia: [[Harvard:Biophysics_101/2007/Notebook:CChi/2007-4-24|code]] displays PubMed article citations in text form
 +
 
 +
=====All displayable data -> Web Interface=====
 +
* Xiaodi: [[Harvard:Biophysics_101/2007/Notebook:Xiaodi_Wu/2007-4-17|code and description]] displays (some - still need to integrate some remaining scripts) preceding data in a web interface
-
=====Disease Name -> PMIDs=====
 
-
* (Uncertain about whether or not this was the point of the code?)
 
-
* Resmi: [[Harvard:Biophysics_101/2007/Notebook:Resmi_Charalel/2007-4-19|code]] returns Mesh Terms
 
=Path 2: Using GenBank and PolyPhen=
=Path 2: Using GenBank and PolyPhen=
==Sequence -> Gene Name (BLAST)==
==Sequence -> Gene Name (BLAST)==
-
* Zach
+
* Zach(?): [[Harvard:Biophysics_101/2007/Notebook:Katie_Fifer/2007-4-19|code]] returns relevant (normal) BLAST data, including the gene name/ID (?)
===Gene Name -> Mutations (GenBank)===
===Gene Name -> Mutations (GenBank)===
Line 48: Line 50:
* Xiaodi
* Xiaodi
-
====Disease Name -> Useful Patient Info (Medical search engines)====
+
=====Disease Name -> Useful Patient Info (Medical search engines)=====
-
* Deniz and Tiff
+
* Deniz: [[Harvard:Biophysics_101/2007/Notebook:Denizkural/2007-4-3|examples of coding]] which returns news updates in several formats
 +
* Tiff: [[TChan/Notebook/2007-4-24|code]] (a) displays relevant URLs (, (b) returns lists of drugs, clinical trials, experts, etc.
 +
* Resmi: [[Harvard:Biophysics_101/2007/Notebook:Resmi_Charalel/2007-4-5|code]] displays PubMed review citations in text form
 +
* Cynthia: [[Harvard:Biophysics_101/2007/Notebook:CChi/2007-4-24|code]] displays PubMed article citations in text form

Revision as of 21:44, 30 April 2007

Biophysics 101: Genomics, Computing, and Economics

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Contents

Overview

  • Project Goal: To develop tools to aid in analysis of personal DNA sequences.

We would like to develop software and documentation that will help people get from sequence to diagnosis. At the moment, we are focusing on identifying and classifying SNPs, but we will broaden this identification to other things like large deletions or insertions or repeats when we have more expertise. We are attempting to harness the power of other already existing tools, and we would also like to make this tool one that others can build upon. Specifically, our program will eventually be able to determine location based on BLAST, determine any SNPs based on NCBI SNP, and give a prognosis based on OMIM and online medical databases.


Path 1: Using OMIM

Sequence -> RS Number (BLAST SNP)

RS Number -> Disease Name (OMIM)

  • Xiaodi (and Katie?): code prints and outputs to file pickled version of the OMIM output for our sequence


RS Number -> Mesh Terms (PubMed)

  • Cynthia


RS Number (OMIM) -> PubMed PMIDs

PubMed PMIDs -> Mesh Terms

  • Resmi: code (1) parses OMIM XML to (2) get PubMed PMIDs to (3) get Mesh Terms


Mesh Terms -> Disease Name (in-house code, prevalence algorithm)
  • Deniz
Disease Name -> Useful Patient Info (Medical search engines)
  • Deniz: examples of coding which returns news updates in several formats
  • Tiff: code (a) displays relevant URLs (, (b) returns lists of drugs, clinical trials, experts, etc.
  • Resmi: code displays PubMed review citations in text form
  • Cynthia: code displays PubMed article citations in text form
All displayable data -> Web Interface
  • Xiaodi: code and description displays (some - still need to integrate some remaining scripts) preceding data in a web interface


Path 2: Using GenBank and PolyPhen

Sequence -> Gene Name (BLAST)

  • Zach(?): code returns relevant (normal) BLAST data, including the gene name/ID (?)

Gene Name -> Mutations (GenBank)

  • Xiaodi

Gene Name -> ??? (PolyPhen)

  • Mike

Mutations -> Disease Name (OMIM)

  • Xiaodi
Disease Name -> Useful Patient Info (Medical search engines)
  • Deniz: examples of coding which returns news updates in several formats
  • Tiff: code (a) displays relevant URLs (, (b) returns lists of drugs, clinical trials, experts, etc.
  • Resmi: code displays PubMed review citations in text form
  • Cynthia: code displays PubMed article citations in text form


Diagram

Project Diagram

Project-in-Progress

Project-in-Progress notes have been moved to their own page.

Project Ideas

Project ideas have been moved to their own page.
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