Discrete-Event Simulation
Applied to Biochemical Pathways

• DiMSim: A Discrete-Event Simulator of Metabolic Networks
• iSimBioSys: A Discrete Event Simulation Platform for `in silico' Study of Biological Systems
• Petri Net Based Model Validation in Systems Biology
• Biopathways Representation and Simulation on Hybrid Functional Petri Net
• Structural Modeling and Analsis of Signaling Pathways Based on Petri Nets
• Qualitative Analysis of Biochemical Reaction Systems
• Discrete Event Multi-level Models for Systems Biology
• Time Petri Nets for Modeling and Analysis of Biochemical Networks
• From Petri Nets ot Differential Equations - an Integrative Approach for Biochemical Network Analysis

Hybrid Petri Nets

• Bibliography on Hybrid Petri Nets
• Discrete Event Simulation of Fluid Stochastic Petri Nets

Data/Text Mining for Model Calibration

• Reconstructing Biochemical Pathways from Time Course Data
• The Role of Control and System Theory in Systems Biology
• Parameter Estimation in Biochemical Pathways: A Comparison of Global Optimization Methods
• Assigning Numbers to the Arrows: Parameterizing a Gene Regulation Network by using Accurate Expression Kinetics
• SABIO-RK: Integration and Curation of Reaction Kinetics Data

Modeling Enzymatic Reactions

• Enzyme Kinetics
• Biochemistry in Silico
• Michealis-Menten Approximation (and Briggs-Haldane)

Ontologies for Systems Biology

• Adding Semantics in Kinetic Models of Biochemical Pathways
• Systems Biology Ontology (SBO)

Biochemical Pathway Databases

• KEGG
  • Metabolic Pathways
  • Glycan Biosynthesis and Metabolism
  • N-Glycan Biosynthesis
• BioCyc
• Glycan Biosynthetic Pathways

Biochemical Reaction Kinetics Databases

• SABIO-RK
• BRENDA
• Kinetikon