Paper

B

Mare

Jun 28th

Posted by Andrew in Paper

1 comment

Motif Finder

Exported the datasets ready for using with software (motif finder) that searches for motifs that are overrepresented. (Hypergeometric tests: 1day work). Cytoscape has a plugin.

  • ib_2010_data.1.xml.gz –> .dot (50mb)
  • ib_2010_data.1.xml.gz –> graph htm??? (cant remeber but it was 450mb)

Motif Type C

Trying to define another motif, struggling… similar targets?

B

B

Plan

Results/Code/Other program (June-July 2010)

4 Weeks

  • Week 1 – Code/Motif Finder (i.e. Motif A,B,C… x,y,z instances)
  • Week 2 – Java/Score/FoundExamples
  • Week 3 – Score
  • Week 4 – Score

    Paper (July-August 2010)

    • Intro
    • Background
    • Methods

      • - Definitions of S.M.
      - Searching
      - Scoring

    • Results
      • TypeA
      • TypeB
      • TypeC
    • Discussion
      • Future work
    • Abstract

    Module Webpage

    Jun 3rd

    Posted by Andrew in Paper

    No comments

    Researching interesting papers to start the introduction of the paper:

    Butcher, E.C., Berg, E.L. and Kunkel, E.J. (2004) Systems biology in drug discovery. Nature Biotechnology. 22:1253-1259. [Link]
    Drews, J. (2000) Drug Discovery: A Historical Perspective. Science. 287(5460):1960-1964. [Link]
    Kitano, H. (2002) Computational systems biology. Nature. 420:206-210. [Link]

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