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Algorithm Animation for Bioinformatics Algorithms

Algorithm Animation for Bioinformatics Algorithms. Prelude. Graph G = (V,E) ‏ Abstractions for real-life problems Algorithms. Prelude (cont'd) ‏. How to teach graph algorithms? Visualization? http://en.wikipedia.org/wiki/Dijkstra%27s_algorithm. Gato. Graph Animation Toolbox Features

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Algorithm Animation for Bioinformatics Algorithms

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  1. Algorithm Animation for Bioinformatics Algorithms

  2. Prelude • Graph G = (V,E)‏ • Abstractions for real-life problems • Algorithms

  3. Prelude (cont'd)‏ • How to teach graph algorithms? • Visualization? • http://en.wikipedia.org/wiki/Dijkstra%27s_algorithm

  4. 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

  5. Bioinformatics and Gato

  6. 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

  7. 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

  8. Why animate bioinformatics? • Educate biologists so they’ll use the correct tools and options. • http://mobyle.pasteur.fr/cgi-bin/portal.py?form=dnapars

  9. Phylogenetic Trees : Demo

  10. 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)

  11. Gato on iPad

  12. Thanks

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