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

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 dataHow 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. http://mobyle.pasteur.fr/cgi-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