PSAMM

Curation and Analysis of Metabolic Models

Latest release: PSAMM 0.31 (June 30, 2017)

View on GitHub

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.

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. doi:10.1371/journal.pcbi.1004732

Getting started

The tutorial will show you how to get started with metabolic model curation using PSAMM.

View the tutorial

Install

Installing the base PSAMM package is as simple as

pip install psamm

Pip automatically fetches the latest version from the Python Package Index. See the documentation for more information on installing PSAMM.

Documentation

Read our comprehensive online documentation hosted by Read the Docs.

View the documentation

GitHub project

Our project is open source software, developed with Python and hosted publicly as a GitHub project.

News

See the NEWS file for detailed information on the latest updates to PSAMM.

Model collection

We have converted more than 50 published model to the PSAMM YAML format to demonstrate the capabilities of PSAMM to help with model curation. The models are hosted in a repository on GitHub .