PSAMM metabolic modeling tools

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PSAMM is an open source software that is designed for the curation and analysis of metabolic models. It supports model version tracking, model annotation, data integration, data parsing and formatting, consistency checking, automatic gap filling, and model simulations.

See NEWS_ for information on recent changes. The master branch tracks the latest release while the develop branch is the latest version in development. Please apply any pull requests to the develop branch when creating the pull request.

.. _NEWS: NEWS.md

Install

Use pip to install (it is recommended to use a Virtualenv_):

.. code:: shell

$ pip install psamm

.. _Virtualenv: https://virtualenv.pypa.io/

Documentation

The documentation for PSAMM is available at Read the Docs_.

.. _Read the Docs: https://psamm.readthedocs.org/

Citing PSAMM

If you use PSAMM in a publication, please cite:

Steffensen JL, Dufault-Thompson K, Zhang Y. PSAMM: A Portable System for the Analysis of Metabolic Models. PLOS Comput Biol. Public Library of Science; 2016;12: e1004732. 10.1371/journal.pcbi.1004732_.

.. _10.1371/journal.pcbi.1004732: https://doi.org/10.1371/journal.pcbi.1004732

Software license

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.

See LICENSE_.

.. _LICENSE: LICENSE