3. Fundamentals of cell modeling

Table of contents

• 3.1. Data aggregation
  • 3.1.1. Common data types and data sources
  • 3.1.2. Finding data sources
  • 3.1.3. Finding relevant data for models
  • 3.1.4. Data aggregation tools
  • 3.1.5. Determining the consensus of multiple observations
  • 3.1.6. Exercise
• 3.2. Input data organization
  • 3.2.1. Schema
  • 3.2.2. Software tools
  • 3.2.3. Exercises
• 3.3. Model design
  • 3.3.1. Software tools
  • 3.3.2. Exercises
• 3.4. Model calibration
  • 3.4.1. Key concepts
  • 3.4.2. Calibration data
  • 3.4.3. Approximate, multi-stage parameter estimation
  • 3.4.4. Exercise
• 3.5. Model representation
  • 3.5.1. Custom numerical simulation code
  • 3.5.2. Standard numerical simulation packages
  • 3.5.3. Enumerated modeling languages
  • 3.5.4. Ruled-based modeling languages
  • 3.5.5. Rule-based modeling API
  • 3.5.6. High-level rule-based modeling language
• 3.6. Model annotation
  • 3.6.1. Component-level semantic annotations of species, reactions, and parameters
  • 3.6.2. Model-level semantic annotations
  • 3.6.3. Model provenance annotations
  • 3.6.4. Simulation algorithm annotations
  • 3.6.5. Exercises
• 3.7. Model composition
  • 3.7.1. Model composition procedure
  • 3.7.2. Software tools
  • 3.7.3. Exercises
• 3.8. Mathematical representations and simulation algorithms
  • 3.8.1. Boolean/logical models
  • 3.8.2. Ordinary differential equations (ODEs)
  • 3.8.3. Stochastic simulation
  • 3.8.4. Network-free simulation
  • 3.8.5. Flux balance analysis (FBA)
  • 3.8.6. Hybrid/multi-algorithmic simulation
  • 3.8.7. Reproducing stochastic simulations
  • 3.8.8. Simulation descriptions
  • 3.8.9. Software tools
  • 3.8.10. Exercises
• 3.9. Model testing
  • 3.9.1. Testing composite models
  • 3.9.2. Exercise
• 3.10. Logging simulation results
• 3.11. Organizing simulation results
  • 3.11.1. Exercise
• 3.12. Quickly analyzing large simulation results
• 3.13. Rule-based Modeling with BioNetGen, BNGL, and RuleBender
  • 3.13.1. Description of Rule-based Modeling, BioNetGen, BNGL, and RuleBender
  • 3.13.2. BNGL and RuleBender Basic Functionality
  • 3.13.3. Exercises
  • 3.13.4. Molecular sites, their states, and bonds