Tools (:py:mod:`indra.tools`)
=============================


Run assembly components in a pipeline (:py:mod:`indra.tools.assemble_corpus`)
-----------------------------------------------------------------------------

.. automodule:: indra.tools.assemble_corpus
    :members:

Real-time feedback for assembly (:py:mod:`indra.tools.live_curation`)
---------------------------------------------------------------------

.. automodule:: indra.tools.live_curation
    :members:

Build a network from a gene list (:py:mod:`indra.tools.gene_network`)
---------------------------------------------------------------------

.. automodule:: indra.tools.gene_network
    :members:

Build an executable model from a fragment of a large network (:py:mod:`indra.tools.executable_subnetwork`)
----------------------------------------------------------------------------------------------------------

.. automodule:: indra.tools.executable_subnetwork
    :members:

Build a model incrementally over time (:py:mod:`indra.tools.incremental_model`)
-------------------------------------------------------------------------------

.. automodule:: indra.tools.incremental_model
    :members:

The RAS Machine (:py:mod:`indra.tools.machine`)
-----------------------------------------------

.. automodule:: indra.tools.machine
    :members:


High-throughput Reading Tools (:py:mod:`indra.tools.reading`)
-------------------------------------------------------------

.. toctree::
   :maxdepth: 3

   reading/pipelines
   reading/interfaces
   reading/tools
   reading/utils

Tools (:py:mod:`indra.tools`)
=============================


Run assembly components in a pipeline (:py:mod:`indra.tools.assemble_corpus`)
-----------------------------------------------------------------------------

.. automodule:: indra.tools.assemble_corpus
    :members:

Real-time feedback for assembly (:py:mod:`indra.tools.live_curation`)
---------------------------------------------------------------------

.. automodule:: indra.tools.live_curation
    :members:

Build a network from a gene list (:py:mod:`indra.tools.gene_network`)
---------------------------------------------------------------------

.. automodule:: indra.tools.gene_network
    :members:

Build an executable model from a fragment of a large network (:py:mod:`indra.tools.executable_subnetwork`)
----------------------------------------------------------------------------------------------------------

.. automodule:: indra.tools.executable_subnetwork
    :members:

Build a model incrementally over time (:py:mod:`indra.tools.incremental_model`)
-------------------------------------------------------------------------------

.. automodule:: indra.tools.incremental_model
    :members:

The RAS Machine (:py:mod:`indra.tools.machine`)
-----------------------------------------------

.. automodule:: indra.tools.machine
    :members:


Remove reading doc files from toctree.
Remove reading doc files from toctree.
