RuleMonkey: Software for stochastic simulation of rule-based models

Keyphrases

• Rule-based Model 100%
• Stochastic Simulation 100%
• BioNetGen 33%
• Network Simulation 33%
• Simulation Method 22%
• Reaction Network 22%
• Protein-protein Interaction 11%
• Reaction Rules 11%
• Biochemical Reaction Networks 11%
• Null Events 11%
• Molecular Interactions 11%
• Model Specification 11%
• Modeling Approach 11%
• System Level 11%
• Freely Available 11%
• Global Applications 11%
• Simulation Engine 11%
• Network Generation 11%
• Sharing Rule 11%
• Building Rules 11%
• Network Size 11%
• Biochemical Systems 11%
• Computationally Expensive 11%
• Standalone Applications 11%
• Web-based Environment 11%
• Compliant Tools 11%
• Rejection-Free 11%
• Gillespie Method 11%
• Simulation Procedure 11%
• Level Dynamics 11%
• Benchmark Problems 11%
• Association Reaction 11%
• Specification Language 11%
• Network Dynamics 11%
• Intramolecular Association 11%
• Reaction Systems 11%

Biochemistry, Genetics and Molecular Biology

• Dynamics 100%
• Protein-Protein Interaction 50%
• Molecular Interaction 50%
• Rule-Based Modeling 50%