Using PSAMM for the curation and analysis of genome-scale metabolic models
Document Type
Article
Date of Original Version
1-1-2018
Abstract
PSAMM is an open source software package that supports the iterative curation and analysis of genome-scale models (GEMs). It aims to integrate the annotation and consistency checking of metabolic models with the simulation of metabolic fluxes. The model representation in PSAMM is compatible with version tracking systems like Git, which allows for full documentation of model file changes and enables collaborative curations of large, complex models. This chapter provides a protocol for using PSAMM functions and a detailed description of the various aspects in setting up and using PSAMM for the simulation and analysis of metabolic models. The overall PSAMM workflow outlined in this chapter includes the import and export of model files, the documentation of model modifications using the Git version control system, the application of consistency checking functions for model curations, and the numerical simulation of metabolic models.
Publication Title, e.g., Journal
Methods in Molecular Biology
Volume
1716
Citation/Publisher Attribution
Dufault-Thompson, Keith, Jon Lund Steffensen, and Ying Zhang. "Using PSAMM for the curation and analysis of genome-scale metabolic models." Methods in Molecular Biology 1716, (2018): 131-150. doi: 10.1007/978-1-4939-7528-0_6.