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dfba-0.1.8
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مشاهده بیشترتوضیحات
Object-oriented software for dynamic flux-balance simulations.
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | dfba-0.1.8 |
| نام | dfba |
| نسخه کتابخانه | 0.1.8 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | David S. Tourigny, Moritz E. Beber |
| ایمیل نویسنده | dst2156@cumc.columbia.edu, morbeb@biosustain.dtu.dk |
| آدرس صفحه اصلی | https://gitlab.com/davidtourigny/dynamic-fba |
| آدرس اینترنتی | https://pypi.org/project/dfba/ |
| مجوز | GNU GPL v3+ |
=============================
Dynamic Flux Balance Analysis
=============================
.. image:: https://img.shields.io/pypi/v/dfba.svg
:target: https://pypi.org/project/dfba/
:alt: Current PyPI Version
.. image:: https://img.shields.io/pypi/pyversions/dfba.svg
:target: https://pypi.org/project/dfba/
:alt: Supported Python Versions
.. image:: https://img.shields.io/pypi/l/dfba.svg
:target: http://www.gnu.org/licenses/
:alt: GPLv3+
.. image:: https://gitlab.com/davidtourigny/dynamic-fba/badges/master/pipeline.svg
:target: https://travis-ci.org/davidtourigny/dynamic-fba/commits/master
:alt: Pipeline Status
.. image:: https://gitlab.com/davidtourigny/dynamic-fba/badges/master/coverage.svg
:target: https://gitlab.com/davidtourigny/dynamic-fba/commits/master
:alt: Coverage Report
.. image:: https://img.shields.io/badge/code%20style-black-000000.svg
:target: https://github.com/ambv/black
:alt: Black
.. _`Harwood et al., 2016`: https://link.springer.com/article/10.1007/s00211-015-0760-3
.. _GLPK: https://www.gnu.org/software/glpk/
.. _SUNDIALS: https://computation.llnl.gov/projects/sundials
.. _Python: https://www.python.org/
.. _cobrapy: https://github.com/opencobra/cobrapy
.. _optlang: https://github.com/biosustain/optlang
.. _symengine: https://github.com/symengine/symengine
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
============
.. _GLPK: https://www.gnu.org/software/glpk/
.. _SUNDIALS: https://computation.llnl.gov/projects/sundials
.. _Python: https://www.python.org/
.. _cobrapy: https://github.com/opencobra/cobrapy
.. _optlang: https://github.com/biosustain/optlang
.. _symengine: https://github.com/symengine/symengine
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 <https://docs.docker.com/>`_ image:
.. code-block:: console
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:
.. code-block:: console
pip install .
Dependencies
~~~~~~~~~~~~
.. _`build_glpk.sh`: https://gitlab.com/davidtourigny/dynamic-fba/tree/master/scripts/build_glpk.sh
.. _`build_pybind11.sh`: https://gitlab.com/davidtourigny/dynamic-fba/tree/master/scripts/build_pybind11.sh
.. _`build_sundials.sh`: https://gitlab.com/davidtourigny/dynamic-fba/tree/master/scripts/build_sundials.sh
.. _Dockerfile: https://gitlab.com/davidtourigny/dynamic-fba/tree/master/Dockerfile
.. _`pybind11`: https://github.com/pybind/pybind11
* A version of Python_ 3.6 or higher is required
* You need `cmake <https://cmake.org/>`_ for the build process
* You will need `git <https://git-scm.com/>`_ 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 <https://gmplib.org/>`_
and pybind11_ requires `pytest <https://docs.pytest.org/en/latest/>`_).
Alternatively, a Dockerfile_ is provided for building a `Docker <https://docs.docker.com/>`_
image to run the software from an interactive container. The `Docker <https://docs.docker.com/>`_ image can be
built in one step by issuing the command:
.. code-block:: console
make build
from the root of this repository. It can then be started using:
.. code-block:: console
make run
Documentation
=============
Documentation for dfba is provided at `readthedocs <https://dynamic-fba.readthedocs.io>`_
Authors
=======
* David S. Tourigny
* Moritz E. Beber
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+) <http://www.gnu.org/licenses/>`_.
زبان مورد نیاز
| مقدار | نام |
|---|---|
| >=3.6 | Python |
نحوه نصب
نصب پکیج whl dfba-0.1.8:
pip install dfba-0.1.8.whl
نصب پکیج tar.gz dfba-0.1.8:
pip install dfba-0.1.8.tar.gz