PSAMM metabolic modeling tools
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
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.
pip to install (it is recommended to use a Virtualenv):
$ pip install psamm
psamm-import tool is developed in a separate repository. After
installing PSAMM the
psamm-import tool can be installed using:
$ pip install git+https://github.com/zhanglab/psamm-import.git
The documentation for PSAMM is available at Read the Docs.
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.
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/>.