Documentation for FreeFlux
==========================

FreeFlux is a Python package for \ :sup:`13`\C metabolic flux analysis (\ :sup:`13`\C MFA) of biological systems at isotopic steady state or isotopically nonstationary state (INST) state. Functionally, FreeFlux is capable of:

- Metabolic flux estimation
- Simulation of labeling patterns of metabolite (fragments)
- Constraint-based optimizations, such as flux balance analysis (FBA) and flux variability analysis (FVA)

.. toctree::
   :numbered:
   :maxdepth: 2
   :caption: Contents:
   
   installation
   quickstart
   mdv
   building_model
   ss_simulating
   ss_fitting
   inst_simulating
   inst_fitting
   fba
   API </autoapi/freeflux/index.rst>

Indices and tables
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* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`