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

2. 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.

3. Prelude (cont'd)‏ How to teach graph algorithms? Visualization?
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

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
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

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.

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)
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.

11. 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.

12. Thanks
- That’s everything I wanted to cover.