.. Maud documentation master file, created by
sphinx-quickstart on Fri Oct 4 15:14:47 2019.
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
Welcome to Maud's documentation!
================================
Maud is a tool for fitting Bayesian statistical models of metabolic networks.
Maud's distinguishing features include:
- Scientifically accurate representation of phenomena including enzyme kinetics,
allosteric regulation, competitive inhibition, phosphorylation, knockouts and
transported charges.
- Guaranteed consistency with thermodynamic and steady state constraints.
- A statistical model allowing inference consistent with both information from
experiments and pre-experimental background information.
- Prediction of steady state concentrations and fluxes given unseen boundary
conditions.
More practically speaking, Maud is a command line application that uses Stan to
specify and fit a statistical model and Python to interface between Stan and
humans.
.. toctree::
:maxdepth: 1
:caption: How to use Maud:
usage/installation
usage/inputting
usage/post_installation_usage
.. toctree::
:maxdepth: 1
:caption: Theoretical background:
theory/enzyme_kinetics
theory/kinetic_model
theory/statistics
theory/thermodynamics
theory/drains
theory/transported_charges
theory/papers
..
.. toctree::
:maxdepth: 1
:caption: Case studies:
case_studies/ecoli
.. toctree::
:maxdepth: 1
:caption: How Maud works:
how_maud_works/data_model
how_maud_works/computation
Indices and tables
==================
* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`