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CellNOpt specifications


Unique identifier OMICS_06007
Name CellNOpt
Alternative name CellNetOptimizer
Software type Package/Module
Interface Command line interface
Restrictions to use None
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
Input format SIF, MIDAS
Output data The summary of the analysis, hyperlinked to diagnostic graphs, and the trained networks
Output format HTML
Operating system Unix/Linux, Mac OS, Windows
Programming languages MATLAB, Python, R
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.20.0
Stability Stable
GraphViz, RBGL, graph, methods, hash, ggplot, RCurl, Rgraphviz, XML
Maintained No



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Publication for CellNetOptimizer

CellNOpt in publications

PMCID: 5747350
PMID: 29226804
DOI: 10.1016/j.cels.2017.11.002

[…] us to generate dynamic mechanistic models based on a qualitative understanding of the processes, but without having a detailed chemical knowledge about all the underlying mechanisms (). within the cellnetoptimizer (cellnopt) framework, the same prior-knowledge network was trained with the experimental data from different cell lines to obtain cell-line-specific models (). […]

PMCID: 5557587
PMID: 28813442
DOI: 10.1371/journal.pone.0182186

[…] of phosphorylation measurements from a hepatocellular carcinoma cell line (hepg2) at 0, 30 and 180 minutes after perturbation., to preprocess the network, we used cellnoptr, the r version of cellnopt []. basically, the network was compressed to remove as many non-observable/non-controllable species as possible. subsequently, we generated all gates that were compatible with the network; […]

PMCID: 5572374
PMID: 28681552
DOI: 10.1002/psp4.12225

[…] data and how to analyze the resulting model to obtain insights of relevance for systems pharmacology. our workflow uses the free tools omnipath (network reconstruction from the literature), cellnopt (model fit to experimental data), maboss (model analysis), and cytoscape (visualization)., finding effective drugs and understanding how they work still pose considerable challenges […]

PMCID: 5573916
PMID: 28186392
DOI: 10.1002/wsbm.1379

[…] tools such as celldesigner, copasi, and pybios, all of which include methods for parameter estimation and model analysis. boolean or logic‐based models can be created and simulated by, e.g., cellnetoptimizer, a software suite which allows to train a set of possible logical models against experimental data., until recently, experimental data for parameter estimation of signaling pathway […]

PMCID: 5120272
PMID: 27876821
DOI: 10.1038/srep36812

[…] without the need to tune parameters., our work is similar in spirit to logic regression (lr), sparse combinatorial inference (sci), markov logic networks, combinatorial association logic (cal), cellnetoptimizer and genetic programming for association studies (gpas), which all employ combinatorial logic to explicitly incorporate interactions in their models. the most important aspect […]

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

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