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? _algorithm

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

Bioinformatics and Gato

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

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

Why animate bioinformatics? Educate biologists so they’ll use the correct tools and options.  bin/portal.py?form=dnapars

Phylogenetic Trees : Demo

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)

Gato on iPad

Thanks