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BioD Developer Promotes Visual Description LanguageforBiologicalInteractions


Five years after setting out to develop BioD, a visual description language for biological systems, Daniel Cook said the time is now ripe for its implementation.

“The wave that I’ve been anticipating is now coming,” said Cook, a researcher affiliated with the University of Washington. “A lot of people now see the need for these sorts of tools to handle the complexity of large biological systems.”

Describing it as a prototype for a “graphical description language for systems biology,” Cook said that BioD uses a common set of symbols to convey biological interactions.

The prototype, described in a recent issue of Genome Biology, uses a limited vocabulary of icons and arrows to represent complex biological systems as discrete models that can be posted and linked on the Internet. Object icons stand for common biological structures, events, and processes. Arrows represent the actions that the functional properties of one object can have on the functional properties of other objects and actions.

Cook began building the language from the ground up in recognition of the fact that “in large part, we don’t know enough to write mathematical equations for the biological functions we want to understand, and ultimately we may never know enough.”

While mathematical modeling is a valuable tool, Cook said, it has limited applications in biology. Instead, he approached the problem linguistically and hit upon BioD as “a literal language to express concepts and ideas about how biology works, but in such a manner that the model can be refined and made more rigorous in stages so ultimately you can do a mathematical model.”

Cook is currently developing a BioD editor in Java that will act as a graphics program to draw diagrams — much like a CAD language for simulating and analyzing biological systems. He expects to make the editor “reasonably functional” within the next six months and is considering its release as freeware.

Cook has received some seed money from an undisclosed pharmaceutical company for the BioD project and is seeking further support through grants from the National Institutes of Health and other funding sources, he said.

— BT

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