[Biopython] PythonCyc for Pathway Tools

[Mario Latendresse]

Hello All,

This is not a Biopython specific posting, yet I believe it may interest 
many Biopython users.

PythonCyc allows you to interact with Pathway Tools 
<http://bioinformatics.ai.sri.com/ptools/> using the Python programming 
language.
The latest version of Pathway Tools (19.0) was just released (for all 
release notes of Pathway Tools, please see Released Notes 
<http://bioinformatics.ai.sri.com/ptools/release-notes.html>).
Please see below for more details on a complete API documentation and a 
tutorial for PythonCyc.

-- Mario Latendresse
Computer Scientist
SRI International


  PythonCyc: A Python Interface for Pathway Tools

It is now possible to use the Python programming language to query and 
modify an organism database (i.e., a PGDB) of Pathway Tools via the 
newly developed PythonCyc package. You will need a recent version of 
Pathway Tools, that is, version 18.5 (November 2014) or version 19.0 
(March 2015), to use PythonCyc.

  * PythonCyc is hosted on GitHub
    <http://github.com/latendre/PythonCyc>. To use PythonCyc, you will
    have to download it from GitHub and install it on your local computer.
  * The PythonCyc tutorial
    <https://github.com/latendre/PythonCyc/blob/master/doc/tutorial.md>
    describes how to install PythonCyc and the main functionalities
    available.
  * PythonCyc has over 150 functions to interact with Pathway Tools. In
    particular, you can extract and manipulate all data from PGDBs and
    modify your own PGDBs by using the well-known Python programming
    language.
  * You can access MetaFlux, a Flux Balance Analysis tool, via PythonCyc.
  * The complete PythonCyc API documentation
    <http://pythoncyc.readthedocs.org> is available online.


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