Graph theory for rule-based modeling of biochemical networks
Transactions on Computational Systems Biology VII
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The Systems Biology Markup Language (SBML) is an XML-based exchange format for computational models of biochemical networks. SBML Level 2, whose definition was established in June 2003, includes several enhancements to the original Level 1. This paper includes a brief overview of Level 2. Several proposals are under development to extend SBML to create Level 3. These include diagrams, 2-D and 3-D spatial characteristics, arrays, model composition and multi-component chemical species. This paper describes the current proposals for the last two features.