Algorithm Animation for Bioinformatics Algorithms Animating graph algorithms on the web. You’ll see later why there’s a cat.

Prelude Graph G = (V,E)‏ Abstractions for real-life problems Algorithms Graphs consisting of a set of vertices and edges that connect them. Each edge may have a weight associated with them. Graphs used to stand for real-life problems. No need to go into detail.

Prelude (cont'd)‏ How to teach graph algorithms? Visualization? http://en.wikipedia.org/wiki/Dijkstra%27s_algorithm Graphs may be a tad difficult to teach to students. How do we teach these algorithms? Try to give students an intuitive understanding. But try not to make the presentation dry. Otherwise, nothing is accomplished. Visualization Go through the algorithm and connect significant events to certain visual cues. You might have seen this on Wikipedia

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 Gato = Graph Animation Toolbox Open source At least two major components Gred Create/delete edges/vertices., add edge weights Gato Upload graphs and algorithms that operate on graphs Walk through each step of the algorithm and see what happens to graph at each step Animates as you step through On next slide, example to show what I mean

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. 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) After a user is done animating an algorithm, he/she may export the animation itself to an SVG. This type of file can be viewed by most internet browsers. It is essentially an animation. As of now, the SVG file doesn’t have the same interactivity as Gato. It’s missing buttons, doesn’t show procession through algorithm, doesn’t support directed graphs. For half of the project, try make code to create a fully functional SVG counterpart.

Gato on iPad After that’s done, I’ll try to make it accessible by iPad. Just because it’s awesome. Maybe add some iPad specific functionality, like tilting to fast-forward/rewind.

Thanks - That’s everything I wanted to cover.