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BiNoM specifications


Unique identifier OMICS_18219
Name BiNoM
Alternative name Biological Network Manager
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU Lesser General Public License version 3.0
Computer skills Medium
Version 2.0
Stability Stable
Maintained Yes




No version available


  • person_outline Andrei Zinovyev

Publications for Biological Network Manager

BiNoM citations


Modeling of the jasmonate signaling pathway in Arabidopsis thaliana with respect to pathophysiology of Alternaria blight in Brassica

Sci Rep
PMCID: 5711873
PMID: 29196636
DOI: 10.1038/s41598-017-16884-3

[…] Jasmonate signaling model generated in CellDesigner was exported in SBML format, which was imported in the Cytoscape 2.8.3 using Biological Network Manager (BiNoM). BiNoM is a Cytoscape plug in to support the operation on biological networks represented in standard systems biology formats (SBML, SBGN, BioPAX) and to carry out s […]


Sexual Dimorphism and Aging in the Human Hyppocampus: Identification, Validation, and Impact of Differentially Expressed Genes by Factorial Microarray and Network Analysis

PMCID: 5050216
PMID: 27761111
DOI: 10.3389/fnagi.2016.00229
call_split See protocol

[…] ed from Q-GDEMAR were large, the interactions within the networks were filtered to isolate the sub-network so-called “strongly-connected component” (SCC; Dorogovtsev et al., ). This was done by using Binom (Bonnet et al., ). In turn, the SCCs were further reduced to a minimal core of dense, regulatory sub-networks by using Pathicular (Joshi et al., ). Finally, both the augmented and reduced-size n […]


Qualitative dynamics semantics for SBGN process description

BMC Syst Biol
PMCID: 4910245
PMID: 27306057
DOI: 10.1186/s12918-016-0285-0

[…] r. Therefore the notion of component is not adequate from a dynamics qualitative semantics point of view.In [], the authors decompose the RB/E2F map into 16 network modules using the Cytoscape plugin BiNoM [] as follows. First, modules are built by decomposing the RB/E2F map network into subnetworks, each focusing on a particular molecular entity. The resulting subnetworks that have more than 30 % […]


The gastrin and cholecystokinin receptors mediated signaling network: a scaffold for data analysis and new hypotheses on regulatory mechanisms

BMC Syst Biol
PMCID: 4513977
PMID: 26205660
DOI: 10.1186/s12918-015-0181-z

[…] and 431 reactions, considerably extending previously compiled knowledge on CCK2R signaling [, ] including CCK1R downstream events.Partitioning the total CCKR signaling map into sub-networks using the BiNoM tool [] resulted in 18 modules that coordinate with each other to elicit the diverse intracellular signaling responses to gastrin and/or CCK. Finally, we used the CCKR map as a scaffold for prot […]


Logic modeling and the ridiculome under the rug

BMC Biol
PMCID: 3503555
PMID: 23171629
DOI: 10.1186/1741-7007-10-92

[…] h can be used as a starting point for models. The sheer scope of such information makes the use of it in its entirety as a PKN very difficult. Serious pre-processing by specialized tools (such as the BiNoM [] or CytoCopteR plugins for Cytoscape) is needed, and ideally these have to be integrated with both databases and modeling tools. […]


Gene regulatory network analysis supports inflammation as a key neurodegeneration process in prion disease

BMC Syst Biol
PMCID: 3607922
PMID: 23068602
DOI: 10.1186/1752-0509-6-132

[…] had to identify genes involved in regulatory feed-back loops, or circuits, and genes regulated by them. For the first task we looked for strongly connected components (SCCs) in the raw network using Binom plugin [] in Cytoscape [].An SCC is a network of nodes, where each node can be accessed directly or indirectly from every other node within the network or, in other words, if there exists a path […]


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BiNoM institution(s)
Institut Curie, Paris, France; INSERM, Paris, France; Mines ParisTech, Fontainebleau, France
BiNoM funding source(s)
Supported by the European Union Seventh Framework Programme (FP7/2007-2013) ASSET project under grant agreement number FP7-HEALTH-2010-259348 and by the grant “Projet Incitatif et Collaboratif Computational Systems Biology Approach for Cancer” from Institut Curie.

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