Tag: Biological Networks

GeneNet Toolbox – Analysis of Gene Connectivity in Biological Networks

GeneNet Toolbox

:: DESCRIPTION

GeneNet Toolbox for MATLAB available as command-line or with a graphical user interface (GUI), enables biologists to assess connectivity among a set of genes of interest (‘seed-genes’) within a biological network of their choosing.

::DEVELOPER

GeneNet Toolbox team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • MatLab

:: DOWNLOAD

 GeneNet Toolbox

:: MORE INFORMATION

Citation:

GeneNet Toolbox for MATLAB: a flexible platform for the analysis of gene connectivity in biological networks.
Taylor A, Steinberg J, Andrews T, Webber C.
Bioinformatics. 2014 Oct 14. pii: btu669.

Multi-netclust – Finding Connected Clusters in multi-parametric Networks

Multi-netclust

:: DESCRIPTION

Multi-netclust is an efficient tool to detect connected clusters in large biological networks represented by different data matrices.

::DEVELOPER

Wageningen University Bioinformatics group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX

:: DOWNLOAD

 Multi-netclust

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Oct 1;26(19):2482-3. doi: 10.1093/bioinformatics/btq435. Epub 2010 Aug 2.
Multi-netclust: an efficient tool for finding connected clusters in multi-parametric networks.
Kuzniar A1, Dhir S, Nijveen H, Pongor S, Leunissen JA.

SPEM 1.32.0 – S-system Parameter Estimation Method for Biological Networks.

SPEM 1.32.0

:: DESCRIPTION

SPEM can optimize the parameter in S-system models given time series data.

::DEVELOPER

Group of Clinical Genomic Networks

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

 SPEM

:: MORE INFORMATION

Citation

Comput Biol. 2012 Feb;19(2):175-87. doi: 10.1089/cmb.2011.0269.
An S-System Parameter Estimation Method (SPEM) for biological networks.
Yang X, Dent JE, Nardini C.

NetConfer – Exploration and Comparisons of Biological Networks

NetConfer

:: DESCRIPTION

NetConfer is a web based tool designed for comparative analysis of multiple interaction networks. It implements various analysis methods organized as workflows.

::DEVELOPER

NetConfer team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • WEb browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nagpal S, Baksi KD, Kuntal BK, Mande SS.
NetConfer: a web application for comparative analysis of multiple biological networks.
BMC Biol. 2020 May 19;18(1):53. doi: 10.1186/s12915-020-00781-9. Erratum in: BMC Biol. 2020 Oct 22;18(1):147. PMID: 32430035; PMCID: PMC7236966.

Interference 1.0 – Virtual Knock-out experiments on Biological networks, based on the Centralities Interference notion

Interference 1.0

:: DESCRIPTION

Interference is a Cytoscape plug-in for virtual knock-out experiments on complex networks

::DEVELOPER

The Center for BioMedical Computing (CBMC)

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java
  • Cytoscape

:: DOWNLOAD

 Interference

:: MORE INFORMATION

Citation

PLoS One. 2014 Feb 20;9(2):e88938. doi: 10.1371/journal.pone.0088938. eCollection 2014.
Node interference and robustness: performing virtual knock-out experiments on biological networks: the case of leukocyte integrin activation network.
Scardoni G, Montresor A, Tosadori G, Laudanna C.

CommFinder – Visualizing Community Structures in Biological Networks

CommFinder

:: DESCRIPTION

CommFinder is a Cytoscape plugin for finding and visualizing community structures in biological networks. It provides interfaces to several community finding algorithms including Qcut, HQcut, MCL and MCODE.

::DEVELOPER

Jianhua Ruan

:: SCREENSHOTS

CommFinder

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java/ Cytoscape / MatLab

:: DOWNLOAD

 CommFinder

:: MORE INFORMATION

CytoKavosh 1.1 / Kavosh – Finding Network Motifs in Large Biological Networks

CytoKavosh 1.1 / Kavosh

:: DESCRIPTION

CytoKavosh is a Cytoscape plug-in which allows discovering network motifs with less memory and CPU time in comparison with other existing tools. CytoKavosh plug-in uses Kavosh algorithm for finding network motifs and is based on counting all k-size sub-graphs of a given network graph (directed or undirected).

Kavosh is a new algorithm for finding network motifs.

::DEVELOPER

Laboratory of Systems Biology & Bioinformatics (LBB)

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/ Windows / MacOsX
  • Java
  • Cytoscape

:: DOWNLOAD

 CytoKavosh , Kavosh

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2009 Oct 4;10:318. doi: 10.1186/1471-2105-10-318.
Kavosh: a new algorithm for finding network motifs.
Kashani ZR1, Ahrabian H, Elahi E, Nowzari-Dalini A, Ansari ES, Asadi S, Mohammadi S, Schreiber F, Masoudi-Nejad A.

PLoS One. 2012;7(8):e43287. doi: 10.1371/journal.pone.0043287. Epub 2012 Aug 29.
CytoKavosh: a cytoscape plug-in for finding network motifs in large biological networks.
Masoudi-Nejad A1, Ansariola M, Kashani ZR, Salehzadeh-Yazdi A, Khakabimamaghani S.

MODA – Network Motif Discovery in Biological Networks

MODA

:: DESCRIPTION

MODA is an efficient algorithm for network motif discovery in biological networks.

::DEVELOPER

Laboratory of Systems Biology & Bioinformatics (LBB)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 MODA

:: MORE INFORMATION

Citation

Genes Genet Syst. 2009 Oct;84(5):385-95.
MODA: an efficient algorithm for network motif discovery in biological networks.
Omidi S1, Schreiber F, Masoudi-Nejad A.

ModMap – Detecting maps of Modules in Biological Networks

ModMap

:: DESCRIPTION

ModMap is a tool for advanced analysis of biological networks. Given two biological networks, Modmap seeks a set of modules, each representing strongly connected nodes in the first network, that are also strongly interconnected in the second network. The output is a map of the modules and their links. Unlike clustering, where the clusters are built based on one network, here the two networks are used simultaneously to build the map.

::DEVELOPER

Ron Shamir’s lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/ MacOsX
  • Java 

:: DOWNLOAD

 ModMap

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2014 Feb 4.
Constructing module maps for integrated analysis of heterogeneous biological networks.
Amar D1, Shamir R.

BINAT 1.0 – Biological Networks Analysis Tool

BINAT 1.0

:: DESCRIPTION

BiNAT  is a Java plugin for Cytoscape, an open source bioinformatics software platform for analysis and visualizing molecular interaction networks.

::DEVELOPER

DMB (Data Mining Big) Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux/MacOsX/ android
  • java
  • Cytoscape 

:: DOWNLOAD

 BiNAT

:: MORE INFORMATION

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