[BiO BB] Blue Gene/L

Boris Steipe boris.steipe at utoronto.ca
Tue Dec 2 16:47:29 EST 2003

> Spencer Covington wrote:
> My school ( Arizona State University ) has recently acquired a supercomputer (
> an IBM Blue Gene/L ).  I am preparing to begin a M.S. in Computational
> Bioscience ( Genomics / Bioinformatics ) in the fall.  Would like to design a
> project to run on this computer.  What kinds of projects should I consider ?

I find this quite amusing. This almost sounds like a troll: multi-million $$$
solution, deprecating at a significant perecentage each month, waiting for a
problem. I've heard similar machines play wicked chess though.

Seriously: think about a project to improve MM-forcefields for partially folded
proteins with an aim to improve the radius of convergence in folding

This is a problem that has 
- an objective function that is hard to compute ( radius of convergence is
essentially the largest RMSD which you may be off from the native structure and
still find it through minimization, i.e. not combinatorial search)
- yet parallelizes well across processors
- raises interesting issues in combinatorial optimization
- has important applications
- and needs to keep a lot of stuff in memory at the same time (explicit solvent,
atoms etc.) and thus is probably not well suited for distributed applications.

Best regards,


Prof. Boris Steipe
University of Toronto
Program in Proteomics & Bioinformatics
Departments of Biochemistry & Molecular and Medical Genetics

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