Main logo
tutorial arrow
Create your own tool library
Bookmark tools and put favorites into folders to find them easily.

CellNetOptimizer CellNOpt


An open-source R software package for building predictive logic models of signaling networks by training networks derived from prior knowledge to signaling (typically phosphoproteomic) data. CellNOptR features different logic formalisms, from Boolean models to differential equations, in a common framework. These different logic model representations accommodate state and time values with increasing levels of detail. Models built with CellNOptR are useful tools to understand how signals are processed by cells and how this is altered in disease. They can be used to predict the effect of perturbations (individual or in combinations), and potentially to engineer therapies that have differential effects/side effects depending on the cell type or context.

User report

tutorial arrow
Vote up tools and offer feedback
Give value to tools and make your expertise visible
Give your feedback on this tool
Sign up for free to join and share with the community

0 user reviews

0 user reviews

No review has been posted.

CellNOpt forum

tutorial arrow
Communicate with other users
Participate in the forum to get support for using tools. Ask questions about technical specifications.
Take part in the discussion
Sign up for free to ask question and share your advices

No open topic.

CellNOpt classification

CellNOpt specifications

Software type:
Restrictions to use:
Input format:
Output format:
Programming languages:
MATLAB, Python, R
Computer skills:
Command line interface
Input data:
A prior knowledge network (PKN) describing signed and directed interactions between proteins as a graph, biochemical data relating to the changes in the modification state (typically phosphorylation) of proteins following stimulation under various conditions
Output data:
The summary of the analysis, hyperlinked to diagnostic graphs, and the trained networks
Operating system:
Unix/Linux, Mac OS, Windows
GNU General Public License version 3.0
GraphViz, RBGL, graph, methods, hash, ggplot, RCurl, Rgraphviz, XML

CellNOpt distribution


tutorial arrow
Upload and version your source code
Get a DOI for each update to improve tool traceability. Archive your releases so the community can easily visualize progress on your work.
Facilitate your tool traceability
Sign up for free to upload your code and get a DOI

No versioning.


CellNOpt support



tutorial arrow
Promote your skills
Define all the tasks you managed and assign your profile the appropriate badges. Become an active member.
Promote your work
Sign up for free to badge your contributorship



European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, UK; Biological Engineering Department, Massachusetts Institute of Technology, Cambridge, MA, USA

Funding source(s)

This work was supported by the Institute for Collaborative Biotechnologies (contract no. W911NF-09-D-0001 from the U.S. Army Research Office), EU-7FP-BioPreDyn and the EMBL EIPOD program.

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.