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Essays Biochem. 2008;45:211-22. doi: 10.1042/BSE0450211.

Standards and ontologies in computational systems biology.

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  • 1Department of Bioengineering, William H. Foege Building, Seattle, WA 98195-5061, U.S.A.


With the growing importance of computational models in systems biology there has been much interest in recent years to develop standard model interchange languages that permit biologists to easily exchange models between different software tools. In the present chapter two chief model exchange standards, SBML (Systems Biology Markup Language) and CellML are described. In addition, other related features including visual layout initiatives, ontologies and best practices for model annotation are discussed. Software tools such as developer libraries and basic editing tools are also introduced, together with a discussion on the future of modelling languages and visualization tools in systems biology.

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