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