These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.
23. A model of TLR4 signaling and tolerance using a qualitative, particle-event-based method: introduction of spatially configured stochastic reaction chambers (SCSRC). An G Math Biosci; 2009 Jan; 217(1):43-52. PubMed ID: 18950646 [TBL] [Abstract][Full Text] [Related]
25. Computational modeling of signal transduction networks: a pedagogical exposition. Prasad A Methods Mol Biol; 2012; 880():219-41. PubMed ID: 23361987 [TBL] [Abstract][Full Text] [Related]
26. Rule-based modeling of signal transduction: a primer. Sekar JA; Faeder JR Methods Mol Biol; 2012; 880():139-218. PubMed ID: 23361986 [TBL] [Abstract][Full Text] [Related]
27. Specification, annotation, visualization and simulation of a large rule-based model for ERBB receptor signaling. Creamer MS; Stites EC; Aziz M; Cahill JA; Tan CW; Berens ME; Han H; Bussey KJ; Von Hoff DD; Hlavacek WS; Posner RG BMC Syst Biol; 2012 Aug; 6():107. PubMed ID: 22913808 [TBL] [Abstract][Full Text] [Related]
28. Rule-based spatial modeling with diffusing, geometrically constrained molecules. Gruenert G; Ibrahim B; Lenser T; Lohel M; Hinze T; Dittrich P BMC Bioinformatics; 2010 Jun; 11():307. PubMed ID: 20529264 [TBL] [Abstract][Full Text] [Related]
29. Using rxncon to Develop Rule-Based Models. Romers J; Thieme S; Münzner U; Krantz M Methods Mol Biol; 2019; 1945():71-118. PubMed ID: 30945243 [TBL] [Abstract][Full Text] [Related]
30. MONALISA for stochastic simulations of Petri net models of biochemical systems. Balazki P; Lindauer K; Einloft J; Ackermann J; Koch I BMC Bioinformatics; 2015 Jul; 16():215. PubMed ID: 26156221 [TBL] [Abstract][Full Text] [Related]
32. The efficiency of reactant site sampling in network-free simulation of rule-based models for biochemical systems. Yang J; Hlavacek WS Phys Biol; 2011 Oct; 8(5):055009. PubMed ID: 21832806 [TBL] [Abstract][Full Text] [Related]
36. Modeling signaling networks with different formalisms: a preview. MacNamara A; Henriques D; Saez-Rodriguez J Methods Mol Biol; 2013; 1021():89-105. PubMed ID: 23715981 [TBL] [Abstract][Full Text] [Related]
37. Strategy-Driven Exploration for Rule-Based Models of Biochemical Systems with PORGY. Andrei O; Fernández M; Kirchner H; Pinaud B Methods Mol Biol; 2019; 1945():43-70. PubMed ID: 30945242 [TBL] [Abstract][Full Text] [Related]
38. Using RuleBuilder to Graphically Define and Visualize BioNetGen-Language Patterns and Reaction Rules. Suderman R; Fricke GM; Hlavacek WS Methods Mol Biol; 2019; 1945():33-42. PubMed ID: 30945241 [TBL] [Abstract][Full Text] [Related]