Object-oriented software for dynamic flux-balance simulations.
This project provides an object-oriented software package for dynamic flux-balance analysis (DFBA) simulations using implementations of the direct method or Algorithm 1 described in the paper Harwood et al., 2016. The main algorithms for solving embedded LP problems are written in C++ and use the GNU Linear Programming Kit (GLPK) and the Suite of Nonlinear and Differential/Algebraic Equation Solvers (SUNDIALS) CVODE or IDA. Extension modules to cobrapy are provided for easy generation and simulation of DFBA models.
docker run --rm -it davidtourigny/dfba:latest
Installing from source
Currently this package is compatible with most UNIX-like operating systems. Provided the following Dependencies are installed, the module can be installed from the root of the repository using the command:
pip install .
A version of Python 3.6 or higher is required
You need cmake for the build process
You will need git to clone this repository to access the scripts and build files
You need a working compiler with C++11 support, for example, by installing build-essential on Debian-derived Linux systems
from the root of this repository. It can then be started using:
Documentation for dfba is provided at readthedocs
Jorge Carrasco Muriel (visualization and documentation)
David S. Tourigny is a Simons Foundation Fellow of the Life Sciences Research Foundation.
Copyright © 2018,2019 Columbia University Irving Medical Center, New York, USA
Copyright © 2019 Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark
Free software distributed under the GNU General Public License v3 or later (GPLv3+).
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