CellNOptR in Cytoscape
This results in a point and click interface where users can run the same steps as they would using an R script without having to actually write any code. Given that this is a front-end to the R algorithms, consistency is ensured between the results obtained through the GUI and those obtained through the corresponding scripts.
Install CytoCopteR either through Cytoscape plug-ins manager or by downloading CytoCopteR jar file:
CytoCopteR v1.2 (8.7 MB) Latest version (01/08/2013)
Open 'C:\Program Files\Cytoscape_v2.8.3\plugins' and copy the downloaded CytoCopteR-v1.2.jar to this directory.
Make sure you have R installed.
Note: We recommend to use R version 2.15 for full support of CellNOptR features
Open R console.
Type the following commands in R console to install Rserve:
install.packages("Rserve") # This command only needs to be typed once library(Rserve) Rserve(args="--vanilla")
On Windows Rserve may also stop working if an error is encountered.
Make sure you have Cytoscape installed.
Note: We recommend to use Cytoscape version 2.8.3
Install CytoCopteR plugin.
Note: CytoCopteR can be installed automatically through 'Plugins' -> 'Manage Plugins' OR manually through 'Plugins' -> 'Install plugin from file' and selecting CytoCopteR jar file.
IMPORTANT: Before using CytoCopteR on Ubuntu you need to type on Terminal:
sudo apt-get install libcairo2-dev
sudo apt-get install libxt-dev
Small demonstration highlighting the basic features of CytoCopteR
To illustrate the use of CytoCopteR you can use an imaginary but biologically plausible prior knowledge network (PKN). This network includes a subset of intracellular signaling networks known to be activated downstream of EGF and TNFa stimulation. It is available at BioModels ("Download SBML" and then "SBML V3 L1").
The accompanying in silico data (MIDAS file format) replicates biologically plausible behavior that has been seen in such networks, such as the transient behavior of ERK activation and the oscillatory dynamics of NFkB translocation from the cytoplasm to the nucleus.
CytoCopteR Tutorial is available here: CytoCopteR Tutorial
An additional scripting tutorial demonstrating the use of logic models with increasing levels of detail is available here: R Script Tutorial