PyCoTools

PyCoTools is a python package that was developed as an alternative interface into COPASI, simulation software for modelling biochemical systems. The PyCoTools paper can be found here and describes in detail the intentions and functionality of PyCoTools. There are some important differences between the PyCoTools version that is described in the publication and the current version. The first is that PyCoTools is now a python 3 only package. If using Python 2.7 you should create a virtual Python 3.6 environment using conda or virtualenv. My preference is conda. The other major difference is the interface to COPASI’s parameter estimation task which is described in the tutorials and examples.

Installation

Use:

$ pip install pycotools3

Remember to source activate your python 3.6 environment if you need to.

Note

Copasi (currently version 4.24) is distributed with pycotools3. The first time you use import pycotools3, the import statement will take some time to execute. This is because there is a configuration step that takes place. This will only happen once and then its business as usual thereafter.

To install from source:

$ git clone https://github.com/CiaranWelsh/pycotools3.git
$ cd pycotools3
$ python setup.py install

The procedure is the same in linux, mac and windows.

Documentation

This is a guide to PyCoTools version >2.0.1.

Support

Users can post a question on stack-overflow using the pycotools tag. I get email notifications for these questions and will respond.

People

PyCoTools has been developed by Ciaran Welsh in Daryl Shanley’s lab at Newcastle University.

Caveats

  • Non-ascii characters are minimally supported and can break PyCoTools
  • Do not use unusual characters or naming systems (i.e. A reaction name called “A -> B” will break pycotools)
  • In COPASI we can have (say) a global quantity and a metaboltie with the same name because they are different entities. This is not supported in Pycotools and you must use unique names for every model component

Citing PyCoTools

If you made use of PyCoTools, please cite this article using:

  • Welsh, C.M., Fullard, N., Proctor, C.J., Martinez-Guimera, A., Isfort, R.J., Bascom, C.C., Tasseff, R., Przyborski, S.A. and Shanley, D.P., 2018. PyCoTools: a Python toolbox for COPASI. Bioinformatics, 34(21), pp.3702-3710.

And also please remember to cite COPASI:

  • Hoops, S., Sahle, S., Gauges, R., Lee, C., Pahle, J., Simus, N., Singhal, M., Xu, L., Mendes, P. and Kummer, U., 2006. COPASI—a complex pathway simulator. Bioinformatics, 22(24), pp.3067-3074.

and tellurium:

  • Medley, J.K., Choi, K., König, M., Smith, L., Gu, S., Hellerstein, J., Sealfon, S.C. and Sauro, H.M., 2018. Tellurium notebooks—An environment for reproducible dynamical modeling in systems biology. PLoS computational biology, 14(6), p.e1006220.