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BABA. Basic-Algorithms-of-Bioinformatics Applet. Why?. Interactive demos helps a lot to understand a problem Very few interactive works available on the net only for simple dynamic programming limited parameters really ugly source code rarely available. Goals.

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slide1

BABA

Basic-Algorithms-of-Bioinformatics Applet

slide2
Why?
  • Interactive demos helps a lot to understand a problem
  • Very few interactive works available on the net
    • only for simple dynamic programming
    • limited parameters
    • really ugly
    • source code rarely available
goals
Goals
  • Make algorithms fully understandable and interactive:
    • Simple Dynamic Programming Table
    • Needleman & Wunsch
    • Smith & Waterman Local Search
    • Four Russians
  • Easy to use
  • Highlight the important aspects
  • Let the user play with the parameters
implementation
Implementation
  • Java 1.2 compatible
  • Applet running on
    • Browser (on the net)
    • Applet viewer
  • Swing + Graphics 2D: nice to see!
basic layout for other dp algorithms
Basic layout for other DP algorithms
  • Easy to extend!
    • The four algorithms extends
      • The basic graphic grid class
      • The interface
      • The algorithm execution model
  • published under GPL
slide7
Info
  • ~ 8600 lines of code
  • Basic Grid
    • DP Grid
      • NW Grid
        • SW Grid
      • FR Grid
  • Basic DP Algorithm
    • NW Algorithm
      • SW Algorithm
    • Four Russians

Sweeeet

BABA!