Simplified COPASI interface for python

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  • License: Artistic License (Artistic-2.0)
  • Author: COPASI Team
  • Tags copasi, sbml, systems, biology
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Project description

Python package Documentation Status Quality Gate Status Binder DOI codecov

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.

COPASI Logo

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 dataframes
  • task_timecourse: a wrapper for running time course simulations
  • task_parameter_estimation: a wrapper for parameter estimation
  • task_optimization: a wrapper for computing optimizations with arbitrary objective functions
  • task_steadystate: a wrapper for computing steady states
  • task_scan: a wrapper for parameter scans / repeats
  • task_sensitivities: a wrapper for computing sensitivities
  • compartment_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):

de.NBI logo

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.

Project details

Verified details

These details have been verified by PyPI
Maintainers
Avatar for frankbergmann.myopenid.com from gravatar.com frankbergmann.myopenid.com

Unverified details

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Project links
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  • License: Artistic License (Artistic-2.0)
  • Author: COPASI Team
  • Tags copasi, sbml, systems, biology
Classifiers

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