Transcript powerpoint presentation

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

Make algorithms fully understandable and
interactive:
Simple Dynamic Programming Table
 Needleman & Wunsch
 Smith & Waterman Local Search
 Four Russians
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Easy to use
 Highlight the important aspects
 Let the user play with the parameters
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Implementation
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Java 1.2 compatible
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Applet running on
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
Browser (on the net)
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Applet viewer
Swing + Graphics 2D: nice to see!
Basic layout for other DP
algorithms
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Easy to extend!


The four algorithms extends
 The
basic graphic grid class
 The
interface
 The
algorithm execution model
published under GPL
Let’s see some action!
Info
~ 8600 lines of code
 Basic Grid
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DP Grid
 NW
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 FR
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Grid
SW Grid
Grid
Basic DP Algorithm
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NW Algorithm
 SW Algorithm
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Four Russians