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I am trying to use PySB with Anaconda3 and Windows7. I have added the relevant depedencies (numpy, scipy, sympi, perl) to a working environment. However I am struggling with the BioNetGen program. I have downloaded it, and added the path to BNG, but I cannot add it to my environment.

Here is what I have tried:

>conda search bionetgen

Using Anaconda Cloud api site http....
Fetching package metadata...

Then nothing happens.

>pip install bionetgen
Collecting bionetgen

Then error message:

Could not find a version that satisfies the requirement bionetgen (from versions: )
No matching distribution found for bionetgen

Finally, I tried:

>easy_install bionetgen
Processing bionetgen...
error: could not find a setup script in C:\....

However I can open the BioNetGen programme manually and get the gui so I assume it has installed correctly. I just don't know how to add it to anaconda. Is the problem that BioNetGen runs on perl?

There is a Virtual Box available for visualisation the pysb models but I would prefer to install dependencies manually.

Thanks for any help!

josijosi
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  • I do not think this is question for the Python community. Perhaps you should read the documentation of BioNetGen, and figure out how the connection to Python works. I am also not aware that BioNetGen is a Python package. – Kartik Aug 06 '16 at 08:22
  • Here you are: http://bionetgen.org/index.php/Using_the_BNGConsole#An_example_using_Python According to this, you need the `pexpect` package, which can be `pip` installed, according to their docs: https://pexpect.readthedocs.io/en/stable/install.html – Kartik Aug 06 '16 at 08:25

1 Answers1

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Yes, BioNetGen itself is written in Perl and thus can't be installed via pip or other Python package managers. You need to download the BioNetGen command-line interface for your platform and then follow the instructions in the PySB installation documentation to install it where PySB can find it:

Rename the unzipped BioNetGen-x.y.z folder to just BioNetGen and move it into /usr/local/share (Mac or Linux) or C:\Program Files (Windows). If you would like to put it somewhere else, set the BNGPATH environment variable to the full path to the BioNetGen-x.y.z folder.

You mention the BioNetGen "GUI" which leads me to believe you've downloaded the RuleBender GUI interface rather than the command-line tools. The PySB docs don't explicitly state that you need the command-line tools -- we will definitely rectify this oversight.

Jeremy Muhlich
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