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VBI, European Media Laboratory Partner On Pathway Software


Researchers from Virginia Tech’s Virginia Bioinformatics Institute are collaborating with Germany’s European Media Laboratory to develop software that will simulate biochemical networks.

COPASI, or complex pathway simulator, is based on software developed by VBI’s Pedro Mendes and EML’s Ursula Kummer. Mendes sees the collaboration as an opportunity to extend the functionality of a system he’s been developing over the past ten years, GAPASI, or general pathway simulator.

EML will contribute aspects of the new COPASI software, which will simulate dynamics of chemical networks — how chemical concentrations change with time, for example. The current program calculates time courses using a deterministic algorithm, but Mendes says the new software will use a stochastic algorithm as well. They also plan to add a new level of metabolic control analysis to the software.

When fully developed, COPASI will work with Windows, Unix, and Macintosh and will be free for academics. Commercial users would license the software, although Mendes said the commercialization details have not yet been finalized. He expects that licensing would take place through a separate entity.

EML is currently building a biochemical database that stores information about metabolism, which it plans to contribute to the project. Mendes said that, when finished, the database should be compatible with the COPASI program.

Mendes said that the team is reviewing the possibility of making the software open source, although they have no definite plans to do so.

The VBI and EML researchers will meet twice a year as they see COPASI through to completion, although the bulk of the collaboration will be conducted electronically as a distributed team.

—Bernadette Toner

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