Simplified COPASI interface for python
Project description
BasiCO
This project hosts a simplified python interface to COPASI. While all functionality from COPASI is exposed via automatically generated SWIG wrappers, this package aims to add a layer on top of that, to hide most of the complexity away when calling COPASI functions.
Installation
The package works with python 3.7+, provided the following packages are installed:
- python-copasi
- pandas
- numpy
- matplotlib
- PyYAML
that are freely available on pypi, they will be automatically installed when installing via setup.py.
Once done, just have the basico
directory
in the PYTHONPATH
or sys.path
.
Or you could directly install everything you need right from pypi
pip install copasi-basico
from this git repo:
pip install git+https://github.com/copasi/basico.git
Usage
The following modules are available:
model_io
: functionality, for creating / loading / saving models.model_info
: functionality to getting / setting model elements from pandas dataframestask_timecourse
: a wrapper for running time course simulationstask_parameter_estimation
: a wrapper for parameter estimationtask_optimization
: a wrapper for computing optimizations with arbitrary objective functionstask_steadystate
: a wrapper for computing steady statestask_scan
: a wrapper for parameter scans / repeatstask_sensitivities
: a wrapper for computing sensitivitiescompartment_array_tools
: utility for plotting and the like
Documentation is continually updated at: https://basico.readthedocs.org/.
Please use the issue tracker for bug reports and feature requests.
Acknowledgements
This project has been possible thanks to the BMBF funded de.NBI initiative (031L0104A):
License
The packages available on this page are provided under the Artistic License 2.0, which is an OSI approved license. This license allows non-commercial and commercial use free of charge.
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