Document Type



Life Sciences | Medicine and Health Sciences


Multi-state molecules and multi-component complexes are commonly involved in cellular signaling. Accounting for molecules that have multiple potential states, such as a protein that may be phosphorylated on multiple residues, and molecules that combine to form heterogeneous complexes located among multiple compartments, generates an effect of combinatorial complexity. Models involving relatively few signaling molecules can include thousands of distinct chemical species. Several software tools (StochSim, BioNetGen) are already available to deal with combinatorial complexity. Such tools need information standards if models are to be shared, jointly evaluated and developed. Here we discuss XML conventions that can be adopted for modeling biochemical reaction networks described by user-specified reaction rules. These could form a basis for possible future extensions of the Systems Biology Markup Language (SBML).


Proc IEEE Int Symp Bioinformatics Bioeng. Author manuscript; available in PMC 2011 February 16. Published in final edited form as: Proc IEEE Int Symp Bioinformatics Bioeng. 2007 November 5: 987–994. doi: 10.1109/BIBE.2007.4375678 PMCID: PMC3039882 NIHMSID: NIHMS262289