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Graphical rule-based representation of signal-transduction networks., , and . SAC, page 133-140. ACM, (2005)Prediction of metabolic reactions based on atomic and molecular properties of small-molecule compounds, , , and . Bioinformatics, (2011)Design of gene circuits: lessons from bacteria, , and . Nature Reviews Genetics, 5 (1): 34--42 (Jan 1, 2004)TRuML: A Translator for Rule-Based Modeling Languages., and . BCB, page 372-377. ACM, (2017)GetBonNie for building, analyzing and sharing rule-based models., , , , and . Bioinform., 25 (11): 1457-1460 (2009)Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2., , , , , , , , , and 4 other author(s). J. Integr. Bioinform., (2020)BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains., , , and . Bioinform., 20 (17): 3289-3291 (2004)Systems Biology Approaches for Developing Artificial Pathogen Detection Networks., , , and . ALIFE, page 93. MIT Press, (2010)Graph Theory for Rule-Based Modeling of Biochemical Networks., , , and . Trans. Comp. Sys. Biology, (2006)Modeling the Effect of APC Truncation on Destruction Complex Function in Colorectal Cancer Cells., and . PLoS Comput. Biol., (2013)