CellNopt homepage|cellnopt.wrapper 1.0.3 documentation

CELLNOPT.WRAPPER documentation

Motivation

The package cellnopt.wrapper provides

  1. A Python interface to CellNOptR and related add-ons (e.g. CNORode, CNORfuzzy). CellNOptR is a R package dedicated to the Optimisation of Signalling Pathways to data (See CellNOpt page). In particular, it uses boolean logic modelling but other formalisms (e.g. ODE) are available.
  2. Ease test suite integration
  3. Enhance the user interface and data mining

Installation

prerequisites

Of course, you will need to install Python (linux and mac users should have it installed already).

We recommend also to install ipython, which provides a more flexible shell alternative to the python shell itself.

installation

cellnopt.wrapper is available on PyPi. The following command should install the package and its dependencies automatically:

easy_install cellnopt.wrapper

Note

easy_install you may need root permission (under linux, use sudo)

cellnopt.wrapper provides facilities to call CellNOptR package, which is a R package available on BioConductor. If CellNOptR is not installed on your system, then the first time that you import cellnopt.wrapper in a Python shell, it will download and install the R package automatically. The version downloaded will depend on the version of cellnopt.wrapper. For instance in version 1.0.3, CellNOptR 1.4.0 will be installed. If you want a newer version, you can install it yourself as follows. First, open a R session. Then simply type:

source("http://bioconductor.org/biocLite.R")
biocLite("CellNOptR")

Recent versions of CellNOptR are available on CellNOpt page in the download section.

known issues

The installation should be smooth. However, the dependencies rpy2 requires R to be installed. So, you will need to install R before hand. We recommend R version 2.15 which is the latest version. It is also compulsary if you want the latest version of CellNOptR (1.4) from bioconductor.

In order to test if rpy2 is installed properly, run this code in a python shell:

import rpy2;
from rpy2 import robjects; robjects.r("version")

If you get this kind of error:

LookupError: 'show' not found

You may find a solution here rpy2 and R compatibility.