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BiNoM specifications

Information


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
Requirements
Cytoscape
Maintained Yes

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Maintainer


  • person_outline Andrei Zinovyev

Publications for Biological Network Manager

BiNoM citations

 (11)
library_books

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

2017
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 […]

call_split

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

2016
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 […]

library_books

Qualitative dynamics semantics for SBGN process description

2016
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 % […]

library_books

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

2015
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 […]

library_books

Logic modeling and the ridiculome under the rug

2012
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. […]

library_books

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

2012
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 […]

Citations

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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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