An overview of several standardization efforts for systems biology

Abstract

A computational model represents a modeler's understanding of the structure and function of parts of a biological system. As the overall number of quantitative models continues to grow, and they become ever more sophisticated, they collectively represent a significant accumulation of knowledge about the structural and functional organization of biological systems. Enabling effective sharing of such quantitative models is the driving vision behind SBML and several related efforts that I will describe in this presentation. •SBML (the Systems Biology Markup Language) is a machine-readable exchange format for computational models in systems biology. •MIRIAM (Minimum Information Requested in the Annotation of Models) is a set of guidelines for model annotation. •SBO (Systems Biology Ontology) is an ontology of mathematical concepts used in computational models. •MIASE (Minimum Information About a Simulation Experiment) is a set of guidelines for making simulation results reproducible. •SBGN (Systems Biology Graphical Notation) is a standard for graphical drawings of biological networks. All of these efforts are, at their core, a means of improving our ability to communicate our discoveries and understanding.

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