.. PyBNF documentation master file, created by
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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.

.. _BNGL: http://www.bionetgen.org
.. _SBML: http://sbml.org/Main_Page

.. toctree::
   :maxdepth: 2
   :caption: Contents:

   installation
   quickstart
   config
   config_keys
   algorithms
   advanced
   algorithm_development
   cluster
   examples
   troubleshooting
   
PyBNF Module Reference
----------------------

Detailed documentation of the PyBNF code base for advanced users

.. toctree::
   :maxdepth: 2
   :caption: Contents:
   
   modules/index.rst