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.
Installation
Currently, we do not provide Python wheels for this package and therefore Installing from source is a bit more involved. The quickest way to run the software is from the provided Docker image:
docker run --rm -it davidtourigny/dfba:latestInstalling 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 .Dependencies
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
Be aware that some of these packages have their own dependencies that must therefore be installed also (e.g. GLPK depends on GMP and pybind11 requires pytest).
Alternatively, a Dockerfile is provided for building a Docker image to run the software from an interactive container. The Docker image can be built in one step by issuing the command:
make buildfrom the root of this repository. It can then be started using:
make runDocumentation
Documentation for dfba is provided at readthedocs
Additional contributors
Jorge Carrasco Muriel (visualization and documentation)
Funding
David S. Tourigny is a Simons Foundation Fellow of the Life Sciences Research Foundation.
Copyright
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+).
2 maintainers
Release files for dfba 0.1.8
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
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| dfba-0.1.8.tar.gz | 63.1 kB | Details |
Release files / dfba-0.1.8.tar.gz
| Download URL | dfba-0.1.8.tar.gz |
|---|---|
| Size | 63.1 kB |
| Tags | Source |
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