INDRA documentation
===================

INDRA (the Integrated Network and Dynamical Reasoning Assembler) assembles
information about biochemical mechanisms into a common format that can be used
to build several different kinds of explanatory models.  Sources of mechanistic
information include pathway databases, natural language descriptions of
mechanisms by human curators, and findings extracted from the literature by
text mining.  Mechanistic information from multiple sources is de-duplicated,
standardized and assembled into sets of mechanistic *Statements* with
associated evidence.  Sets of Statements can then be used to assemble both
executable rule-based models (using `PySB`_) and a variety of different types
of network models.

License and funding
-------------------

INDRA is made available under the `MIT License
<https://opensource.org/licenses/MIT>`_. Users are asked to acknowledge DARPA
grant W911NF-14-1-0397, “Programmatic modelling for reasoning across complex
mechanisms,” Peter Sorger and Dexter Pratt PIs.

.. _PySB: http://pysb.org

Contents:

.. toctree::
   :maxdepth: 3

   installation.rst
   getting_started.rst
   modules/index
   tutorials/index

Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`


INDRA documentation
===================

INDRA (the Integrated Network and Dynamical Reasoning Assembler) assembles
information about biochemical mechanisms into a common format that can be used
to build several different kinds of explanatory models.  Sources of mechanistic
information include pathway databases, natural language descriptions of
mechanisms by human curators, and findings extracted from the literature by
text mining.  Mechanistic information from multiple sources is de-duplicated,
standardized and assembled into sets of mechanistic *Statements* with
associated evidence.  Sets of Statements can then be used to assemble both
executable rule-based models (using `PySB`_) and a variety of different types
of network models.

License and funding
-------------------

INDRA is made available under the 2-clause `BSD license
<https://opensource.org/licenses/BSD-2-Clause>`_. Users are asked to
acknowledge DARPA grant W911NF-14-1-0397, “Programmatic modelling for 
reasoning across complex mechanisms,” Peter Sorger and Dexter Pratt PIs.

.. _PySB: http://pysb.org

Contents:

.. toctree::
   :maxdepth: 3

   installation.rst
   getting_started.rst
   modules/index
   tutorials/index

Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`


Fix license mismatch in docs
Fix license mismatch in docs
