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
- GLPK version 4.65 is required or can be installed using build_glpk.sh
- SUNDIALS version 5.0.0 or higher is required or can be installed using build_sundials.sh
- pybind11 is required or can be installed using build_pybind11.sh
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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