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Open Access Open Badges Research

A basis for a visual language for describing, archiving and analyzing functional models of complex biological systems

Daniel L Cook12*, Joel F Farley2 and Stephen J Tapscott1

Author Affiliations

1 Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA

2 RainTown, 331 N 72nd St, Seattle, WA 98103, USA

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Genome Biology 2001, 2:research0012-research0012.10  doi:10.1186/gb-2001-2-4-research0012

Published: 22 March 2001



We propose that a computerized, internet-based graphical description language for systems biology will be essential for describing, archiving and analyzing complex problems of biological function in health and disease.


We outline here a conceptual basis for designing such a language and describe BioD, a prototype language that we have used to explore the utility and feasibility of this approach to functional biology. Using example models, we demonstrate that a rather limited lexicon of icons and arrows suffices to describe complex cell-biological systems as discrete models that can be posted and linked on the internet.


Given available computer and internet technology, BioD may be implemented as an extensible, multidisciplinary language that can be used to archive functional systems knowledge and be extended to support both qualitative and quantitative functional analysis.