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A Python interface to Pathway Tools, 2019 update

Project description

Copyright (c) 2014, SRI International

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

PythonCyc 2.0, January 2020

Overview

An updated version of the original PythonCyc API from Mario Latendresse.

This module has been testes under Python 3.6 and Python 3.8, with examples at https://github.com/networkbiolab/PythonCyc/tree/master/examples

Disclaimer: a number of functions remains broken.

PythonCyc 1.0, November 2014

Overview

The PythonCyc module provides a Python interface to a Pathway Tools application running either locally or remotely. This module has been designed to work on the three platforms supported by Pathway Tools: Linux, Mac OS X, and Windows. Pathway Tools version 18.5 or above is needed to use this module.

This module has been tested under Python 2.6 and 2.7, IPython 2.1 and IPython notebook.

Installation

Please, consult the HTML file tutorial.html under the doc directory of this package for the installation instruction of PythonCyc and how to start Pathway Tools to be able to use PythonCyc.

Documentation

1) For a tutorial on how to use PythonCyc, please consult the HTML file tutorial.html under the doc directory of this package, or go directly to the tutorial by clicking the following link https://github.com/latendre/PythonCyc/blob/master/doc/tutorial.md

  1. For the API documentation of PythonCyc, please consult http://pythoncyc.readthedocs.org.

3) For the latest news about PythonCyc, please consult http://bioinformatics.ai.sri.com/ptools/pythoncyc.html

Author

Mario Latendresse, latendre@AI.SRI.COM

License

See file LICENSE.

Support

For comments and/or bug reports, send an email to ptools-support@ai.sri.com.

Acknowledgments

Thanks to Eli Bogart to have inspired some implementation details of PythonCyc via PyCyc, Tomer Altman for the Pathway Tools API documentation, and Daniel Weaver for suggesting to implement some specific functions and his design, with Kai Chen, of the beautiful PythonCyc logo.

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