LEAD SCIENTIST ON PROTEOME PROJECT ON WORKING WITH BIG BLUE

By By Derrick Harris, Editor

November 15, 2004

Special Section — World Community Grid

LEAD SCIENTIST ON PROTEOME PROJECT ON WORKING WITH BIG BLUE
By Derrick Harris, Editor

GRIDtoday spoke with Dr. Rich Bonneau from the Institute for Systems Biology, lead scientist on on the Human Proteome Folding Project, about how Grid computing will help his cause, and what it was like working with United Devices and industry bigshot IBM.


GRIDtoday: How did IBM go about choosing the Human Proteome Folding Project as the first project on the World Community Grid? Was there a selection process?

RICH BONNEAU: United Devices approached ISB and together ISB and UD approached IBM and other potential cooperate sponsors. IBM was by far the most open-minded and the ball started rolling (this was spring of 2003).

Gt: How familiar with were you with Grid computing before the project came into being? How familiar are you now?

BONNEAU: In graduate school we were familiar with [email protected] and dreamed that we would one day use such a strategy. But we're scientists, not programmers, so we focused mostly on developing the algorithm. A few years ago, when we realized that we (myself, Charlie Strauss, David Baker, etc. ) needed to scale up the Rosetta-annotation if we were going to annotate genomes. We've also always known that our algorithm is “embarrassingly parallel” and potentially perfect for distributed computing. When UD and IBM agreed to take on the project, that was the last step in a very long development process leading from showing we can fold small proteins to folding the human proteome.

Gt: How much time do you estimate will be saved by using Grid technology versus predicting the shapes of proteins using the conventional method?

BONNEAU: The method, Rosetta, is the same on the Grid or on our in-house cluster. What is different is that it would take 10-100,000 years to fold all the proteins we want to fold on our in-house cluster. On the Grid, we can do it in three-six months, without the Grid we can't think about it with current hardware and even a lavish budget.

Gt: How is the Human Proteome Folding Project related to the Human Genome Project?

BONNEAU: It is a logical next step: (A) The human genome project gave us the genome sequence; (B) lots of people worked hard to annotate the human genome and find the genes; (C) several proteins in the genome remain unannotated (they have no know function or structure); and (D) we try to fold those mystery proteins to get clues about their function in the cell.

Gt: What kind of results can we expect to see as the process moves along? What cures could possibly emerge from this research, and what is the timeline for producing real, tangible results?

BONNEAU: There is no silver bullet in biomedical research. What we want to do is take the 30-50 percent of protein domains that are of unknown function and begin the process of figuring out what roles they play in the human animal. Lots of these proteins are involved in disease, so we expect to facilitate large numbers (thousands) of functional insights into human proteins that play roles in disease. This will take the form of a large database that biologists can navigate to find information about the proteins they are interested in. Another important point is that biologists use lots of different kinds of information and we'll be integrating the data from this project with several other sources of bioinfo.

Gt: Do you believe that being involved with such a high-profile project will result in further funding or other benefits for ISB?

BONNEAU: This project is great for all parties involved. ISB has the problem and IBM and UD are showing that they can enable biotech research in big ways with their IT infrastructure know-how. I was a little afraid of working with Big Blue at first, but they've been great. In fact I want to thank Bill Bovermann, Viktors Berstis and Rick Alther of IBM. They are the guys that took Rosetta from us and put it up on the Grid. This process is called “boarding” an application and is made much faster by United Devices Software.

Gt: What other research is ISB conducting right now? How do you foresee ISB using Grid computing (either public or private) on future research endeavors?

BONNEAU: ISB is a big place, intellectually speaking, and is at the forefront of lots of stuff. Leroy Hood has more medals and prizes than you could fit in a Toyota van and was the inventor of the first DNA sequencer. There is cutting edge research going on in fields such as Cancer Biology, Alzheimer's, Biotechnology development, computational Biology, immunology, etc. ISB also has affiliations with lots of other places. www.systemsbiology.org will give you our party line, which is that we're working to get from current medicine (you go to the doctor and say “ahhhh”) to quantitative, predictive, preventative, systems-wide medicine. So don't look at one part of the system, look at the whole thing (all 30,000-plus parts screaming around inside us). You can imagine that it is easier said than done, but we're making progress and it is an exciting time in biotech.

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