Metadata-Version: 2.1
Name: modelbase
Version: 1.2.3
Summary: A package to build metabolic models
Home-page: https://gitlab.com/ebenhoeh/modelbase
Author: Oliver Ebenhoeh, Marvin van Aalst
Author-email: oliver.ebenhoeh@hhu.de, marvin.van.aalst@hhu.de
Maintainer-email: marvin.van.aalst@hhu.de, janina.mass@hhu.de, anna.matuszynska@hhu.de
License: GPL3
Project-URL: Documentation, https://modelbase.readthedocs.io/en/latest/
Project-URL: Source, https://gitlab.com/ebenhoeh/modelbase
Project-URL: Tracker, https://gitlab.com/ebenhoeh/modelbase/issues
Keywords: modelling ode pde metabolic
Platform: any
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Topic :: Software Development
Classifier: Topic :: Scientific/Engineering
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: POSIX
Classifier: Operating System :: Unix
Classifier: Operating System :: MacOS
Classifier: Operating System :: OS Independent
Requires-Python: >=3.7.0
Description-Content-Type: text/markdown
Requires-Dist: dataclasses
Requires-Dist: matplotlib
Requires-Dist: numpy
Requires-Dist: pandas
Requires-Dist: python-libsbml
Requires-Dist: scipy
Requires-Dist: black
Requires-Dist: sympy

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# modelbase

modelbase is a python package to help you build and analyze dynamic mathematical models of biological systems. It has originally been designed for the simulation of metabolic systems, but can be used for virtually any processes, in which some substances get converted into others.

modelbase incorporates an easy construction method to define 'reactions'. A rate law and the stoichiometry need to be specified, and the system of differential equations is assembled automatically.

modelbase allows 'algebraic modules', which are useful to implement rapid equilibrium or quasi steady-state approximations. In the simplest instance, they allow easy incorporation of conserved quantities.

modelbase also allows a simple construction of isotope-specific models. This class contains a constructor method that automatically construct all isotope specific versions of a particular reaction. Very cool - check it out!

## Release notes
Versions 1.0 and 0.4.0 introduced changes not compatible with the previous official
release 0.2.5. API changes are summarised in [this notebook](docs/source/api-changes.ipynb)

[Version 0.4.5](https://gitlab.com/qtb-hhu/modelbase-software/-/tags/0.4.5) was the prior stable version

[Version 0.2.5](https://gitlab.com/qtb-hhu/modelbase-software/-/tags/initial-release)
is the official release for the submission of the
mansucript "Building mathematical models of biological systems
with modelbase, a Python package for semi-automatic ODE assembly
and construction of isotope-specific models" to the Journal of Open
Research Software.

See changelog.md for details on changes of earlier versions.

## Dependencies
* NumPy
* Scipy
* Matplotlib
* Assimulo
* Sundials

## Installation

```python3
pip install modelbase
```

To enable assimulo support, either conda install the package

```python3
conda install -c conda-forge assimulo
# or
conda install -c chria assimulo
```

or build sundials from source using our [installation guide](https://gitlab.com/qtb-hhu/modelbase-software/blob/master/docs/installation.rst).


## License
[GPL 3](https://gitlab.com/qtb-hhu/modelbase-software/blob/master/LICENSE)

## Documentation
The official documentation is hosted on [ReadTheDocs](https://modelbase.readthedocs.io/en/latest/).

## Issues and support
If you experience issues using the software please contact us through our [issues](https://gitlab.com/qtb-hhu/modelbase-software/issues) page.

## Contributing to modelbase
All contributions, bug reports, bug fixes, documentation improvements, enhancements and ideas are welcome. See our [contribution guide](https://gitlab.com/qtb-hhu/modelbase-software/blob/master/CONTRIBUTING.md) for more information.


