Software
RuleMonkey: software for stochastic simulation of rule-based models
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* Corresponding author: Richard G Posner rposner@tgen.org
1 Clinical Translational Research Division, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
2 Theoretical Biology and Biophysics Group, Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
3 Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
4 Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA
BMC Bioinformatics 2010, 11:404 doi:10.1186/1471-2105-11-404
Published: 30 July 2010Additional files
Additional file 1:
This plain-text file specifies a simulation of the multisite phosphorylation model introduced by Colvin et al. [14]. This simulation is considered in Fig. 2A and Table 1. The file can be processed by RuleMonkey and other BNGL-compatible tools for simulating rule-based models.
Format: BNGL Size: 2KB Download file
Additional file 2:
This plain-text file specifies a simulation of a model for trivalent ligand-bivalent cell-surface receptor interaction (the so-called TLBR model) introduced by Yang et al. [19]. This simulation is considered in Fig. 3. The file can be processed by RuleMonkey and other BNGL-compatible tools for simulating rule-based models.
Format: BNGL Size: 8KB Download file
Additional file 3:
This plain-text file specifies a simulation of a model for trivalent ligand-bivalent cell-surface receptor interaction (the so-called TLBR model) introduced by Yang et al. [19]. This simulation is considered in Fig. 2B and Table 1. The difference between the files testcase2a.bngl and testcase2b.bngl is in parameter values. The file can be processed by RuleMonkey and other BNGL-compatible tools for simulating rule-based models.
Format: BNGL Size: 8KB Download file
Additional file 4:
This plain-text file specifies a simulation of reaction events occurring on disparate time scales. This simulation is considered in Fig. 4 and Table 1. The file can be processed by RuleMonkey and other BNGL-compatible tools for simulating rule-based models.
Format: BNGL Size: 1KB Download file
Additional file 5:
This plain-text file specifies a simulation of a model for pentavalent ligand-trivalent cell-surface receptor interactions. The model is based on assumptions similar to those upon which the TLBR model [19] and the model of Goldstein and Perelson [49] are based. This simulation is considered in Table 1. The file can be processed by RuleMonkey and other BNGL-compatible tools for simulating rule-based models.
Format: BNGL Size: 8KB Download file
Additional file 6:
This plain-text file specifies a simulation of the model of Blinov et al. [45] for early events in epidermal growth factor receptor (EGFR) signaling. This simulation is considered in Table 1. The file can be processed by RuleMonkey and other BNGL-compatible tools for simulating rule-based models.
Format: BNGL Size: 6KB Download file
Additional file 7:
This plain-text file specifies a simulation of the model of Goldstein et al. [46] and Faeder et al. [47] for early events in IgE receptor (FcϵRI) signaling. This simulation is considered in Table 1. The file can be processed by RuleMonkey and other BNGL-compatible tools for simulating rule-based models.
Format: BNGL Size: 3KB Download file
Additional file 8:
This plain-text file specifies a simulation of the model of Nag et al. [44] for crosslinking of phosphorylated LAT molecules by intracellular Grb2-Sos1 complexes. This simulation is considered in Table 1. The file can be processed by RuleMonkey and other BNGL-compatible tools for simulating rule-based models.
Format: BNGL Size: 2KB Download file