PyBNF documentation

PyBNF is a tool for parameter fitting of dynamical systems biology models specified using the BioNetGen rule-based modeling language (BNGL) or the Systems Biology Markup Language (SBML). It currently runs on most Linux and macOS workstations as well as distributed computing systems using the SLURM queueing manager.

Contents:

• Installation
  • Operating System
  • Python
  • PyBNF
  • Installation of External Simulators
• Quick Start
  • Verify installation with simple examples
  • Set up your own fitting job
• Configuring a Fitting Job
  • The Configuration File
  • Model Files
  • Experimental Data Files
  • Constraint files
• Configuration Keys
  • Required Keys
  • Other Path Keys
  • Parameter and Model Specification
  • Simulation Actions
  • Parallel Computing
  • General Options
  • Algorithm-specific Options
• Fitting Algorithms
  • Summary of Available Algorithms
  • General implementation features for all algorithms
  • Differential Evolution
  • Scatter Search
  • Particle Swarm
  • Markov Chain Monte Carlo
  • Simulated Annealing
  • Parallel Tempering
  • Simplex
• Advanced Features
  • Model Checking
  • Bootstrapping
  • Custom Postprocessing
• Algorithm Development
  • Implementation
  • Adding configuration options
  • Pull requests
• Running on a cluster
  • SLURM
  • TORQUE/PBS
  • Manual configuration with node names
  • Manual configuration with Dask
• Examples
  • List of examples included in PyBNF
  • Index of examples by attribute
• Troubleshooting
  • Failed simulations
  • Timed out simulations
  • Unexpected behavior when generating SBML files in COPASI
  • Too many open files
  • Too many threads
  • Jobs still running after PyBNF stops
  • An unknown error occurred
  • Other issues

PyBNF Module Reference

Detailed documentation of the PyBNF code base for advanced users

Contents:

• PyBNF Module References
  • PyBNF entry point (pybnf.pybnf)
  • PyBNF algorithms (pybnf.algorithms)
  • PyBNF cluster setup (pybnf.cluster)
  • PyBNF configuration (pybnf.config)
  • PyBNF constraint specification (pybnf.constraint)
  • PyBNF data container (pybnf.data)
  • PyBNF objective functions (pybnf.objective)
  • PyBNF configuration parsing (pybnf.parse)
  • PyBNF printing functions (pybnf.printing)
  • PyBNF model and parameter containers (pybnf.pset)