Algorithm Animation for Bioinformatics Algorithms

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Algorithm Animation for Bioinformatics Algorithms
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Prelude

• Graph G (V,E)?
• Abstractions for real-life problems
• Algorithms

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Prelude (cont'd)?

• How to teach graph algorithms?
• Visualization?
• http//en.wikipedia.org/wiki/Dijkstra27s_algorith
  m

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Gato

• Graph Animation Toolbox
• Features
• Gred (Graph Editor) create your own graph
• Gato
• Upload graphs and algorithms
• Step through algorithms
• Animation
• Color vertices and edges
• Insert and delete labels, edges, and vertices

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Bioinformatics and Gato
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What is Bioinformatics?

• Extracting meaning from gigantic sets of
  biological data

How closely related are humans and chimps? What
genes are regulated in response to lack of
sunlight? Where is the mutation that caused a
specific phenotype? How can we put together an
entire genome for an organism?
Microarray Data
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Algorithms in Bioinformatics

• Multiple sequence alignment
• Need to align sequences before comparing
• Search a database for a specific sequence
• 106,533,156,756 bases in Genbank
• Motif finding
• Used to find promoter regions
• Molecular structure prediction
• Difficult problem
• Phylogenetic tree construction

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Why animate bioinformatics?

• Educate biologists so theyll use the correct
  tools and options.
• http//mobyle.pasteur.fr/cgi-bin/portal.py?formdn
  apars

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Phylogenetic Trees Demo
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Gato on the Web

• Programmed in Python
• Export animation to SVG
• Track history of commands
• Write these to an SVG file
• Work in progress
• Multiple graphs
• Display and highlight code
• Graphical User Interface (GUI)

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Gato on iPad
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Thanks