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CentiBiN specifications

Information


Unique identifier OMICS_12247
Name CentiBiN
Alternative name Centralities in Biological Networks
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Version 1.4.2
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Dirk Koschützki <>

Information


Unique identifier OMICS_12247
Name CentiBiN
Alternative name Centralities in Biological Networks
Interface Web user interface
Restrictions to use None
Programming languages Java
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Dirk Koschützki <>

Publication for Centralities in Biological Networks

CentiBiN in pipeline

2012
PMCID: 3364978
PMID: 22675433
DOI: 10.1371/journal.pone.0038039

[…] . bioinformatic tools are now available for visualizing and characterizing statistical properties of these networks (e.g. the bnarray, genereg and igraph packages of r, and other software such as centibin, graphviz, pajek, and cytoscape)., at present, no therapeutic treatments are available for hlb, and removal of infected trees and insect control are the main management strategies to limit […]


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CentiBiN in publications

 (11)
PMCID: 5449392
PMID: 28559546
DOI: 10.1038/s41598-017-02522-5

[…] degree, closeness, radiality, shortest-path betweenness, current-flow betweenness, current-flow closeness, centroid, page rank, vulnerability, stress and eigenvector were calculated using software centibin, cytoscape 3.2.1, and in-house code, . detailed information about these centralities is given in the supplementary data., the genes were ranked according to their importance in the network […]

PMCID: 5183126
PMID: 28028462
DOI: 10.7717/peerj.2775

[…] and direct interactions among them. the subnetworks of qqppi were constructed and visualized by cytoscape software (). centrality parameters of qqppi networks were analyzed using the cytoscape and centibin softwares (). the following parameters were calculated to determine biologically significant nodes (). degree: the number of links to a given node. the betweenness centrality of node v […]

PMCID: 4369684
PMID: 25848169
DOI: 10.6026/97320630011090

[…] to cause diabetes mellitus from jensenlab (novo nordisk foundation center for protein research, denmark) for this analysis. a protein-protein interaction network was further constructed using a tool centralities in biological networks (centibin) with 1020 nodes after eliminating the duplicates, parallel edges, self -loop edges and unknown human protein reference database (hprd) ids. we used […]

PMCID: 3914352
PMID: 24551850
DOI: 10.1155/2014/686505

[…] with length l 1 ( = 1), l 2 ( = 2),…, l l ( = l), correspondingly;, l: the maximum length corresponding to the furthest path found., the network analysis was implemented in cosbilab-graph [] and centralities in biological networks []. the network mining and text mining were performed by python script []. the network visualization was performed by the software navigator (network analysis, […]

PMCID: 3847089
PMID: 24312583
DOI: 10.1371/journal.pone.0081766

[…] betweenness, current-flow closeness, current-flow betweenness, katz status index, eigen vector, pagerank . we have calculated the above centrality measures for human immunome network using the tool centibin ., the degree centrality measure ranks the potential of an individual node in the network based on its connectivity. (1), here ‘a’ represents the adjacency matrix., eccentricity centrality […]


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CentiBiN institution(s)
Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
CentiBiN funding source(s)
The German Ministry of Education and Research (BMBF) supported part of this work under grants 0312706A and 0313115.

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