cobamp 0.1.0rc1

cobamp - pathway analysis methods for genome-scale metabolic models

CoBAMP

CoBAMP (Constraint-Based Analysis of Metabolic Pathways) is a Python package containing pathway analysis methods for use with constraint-based metabolic models. The main purpose is to provide a framework that is both modular and flexible enough to be integrated in other packages (such as cobrapy, framed or cameo) that already implement generic data structures for metabolic models.

A (MI)LP solver is required for most of the methods. Current methods are implemented using CPLEX as a solver, although future versions will use a unifying solver platform, such as optlang.

Current methods include:

• Elementary flux modes: K-Shortest algorithm

• Minimal cut sets: MCSEnumerator approach

• Elementary flux patterns: K-Shortest algorithm

Documentation

Documentation available at https://cobamp.readthedocs.io/

Instalation from PyPI (stable releases)

::

pip install cobamp

Credits and License

Developed at the Centre of Biological Engineering, University of Minho

Released under the GNU Public License (version 3.0).