Tag: Network

iCTNet 0.1 – Analyze Integrative Complex Traits Networks

iCTNet 0.1

:: DESCRIPTION

iCTNet (integrated Complex Traits Network) is a large-scale network, assembling human disease-gene association, tissue-gene association, disease-tissue associations, protein-DNA interactions, protein-protein interactions and drug-target information.

::DEVELOPER

iCTNet team

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java
  • Cytoscape

:: DOWNLOAD

 iCTNet

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2011 Sep 26;12:380. doi: 10.1186/1471-2105-12-380.
iCTNet: a Cytoscape plugin to produce and analyze integrative complex traits networks.
Wang L1, Khankhanian P, Baranzini SE, Mousavi P.

EGAN 1.5 – Exploratory Gene Association Networks

EGAN 1.5

:: DESCRIPTION

EGAN is a software tool that allows a bench biologist to visualize and interpret the results of high-throughput exploratory assays in an interactive hypergraph of genes, relationships (protein-protein interactions, literature co-occurrence, etc.) and meta-data (annotation, signaling pathways, etc.). EGAN provides comprehensive, automated calculation of meta-data coincidence (over-representation, enrichment) for user- and assay-defined gene lists, and provides direct links to web resources and literature (NCBI Entrez Gene, PubMed, KEGG, Gene Ontology, iHOP, Google, etc.).

::DEVELOPER

EGAN team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

 EGAN

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Jan 15;26(2):285-6. Epub 2009 Nov 23.
EGAN: exploratory gene association networks.
Paquette J, Tokuyasu T.

GPU-FAN 1.0 – GPU-based Fast Analysis of Networks

GPU-FAN 1.0

:: DESCRIPTION

GPU-FAN is a project to enable fast network analysis on GPUs. It provides a significant performance improvement for centrality computation in large-scale networks.

::DEVELOPER

the Zhang Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GPU-FAN 

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2011 May 12;12:149. doi: 10.1186/1471-2105-12-149.
Fast network centrality analysis using GPUs.
Shi Z1, Zhang B.

CorNet 2.01 – Correlation Network Graphs

CorNet 2.01

:: DESCRIPTION

 CorNet is a R-script largest correlation network graphs for visualizing clusters of intercorrelated genes/transcripts

::DEVELOPER

Bioinformatics at AWI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX / Windows
  • R Package

:: DOWNLOAD

 CorNet

:: MORE INFORMATION

Citation

Hüning AK, Melzner F, Thomsen J, Gutowska MA, Krämer L, Frickenhaus S, Rosenstiel P, Pörtner HO, Philipp E, Lucassen M
Impacts of seawater acidification on mantle gene expression patterns of the Baltic Sea blue mussel: implications for shell formation and energy budget. (2012),
Marine Biology . August 2013, Volume 160, Issue 8, pp 1845-1861 doi: 10.1007/s00227-012-1930-9

SmartCell v4.3 Beta3 – A Cell Network Simulation Program

SmartCell v4.3 Beta3

:: DESCRIPTION

SmartCell is a program developed to provide an idea of the evolution of a network in a whole, single cell. Based on stochastic algorithms, SmartCell needs multiple runs to have mean results.

::DEVELOPER

Serrano’s laboratory

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows
  • JRE

:: DOWNLOAD

 SmartCell

:: MORE INFORMATION

Citation

SmartCell, a framework to simulate cellular processes that combines stochastic approximation with diffusion and localisation: analysis of simple networks.
Ander M, Beltrao P, Di Ventura B, Ferkinghoff-Borg J, Foglierini M, Kaplan A, Lemerle C, Tomás-Oliveira I, Serrano L.
Syst Biol (Stevenage). 2004 Jun;1(1):129-38.

BNW – Bayesian Network Web Server

BNW

:: DESCRIPTION

BNW is a comprehensive web server for Bayesian network modeling of biological data sets. It is designed so that users can quickly and seamlessly upload a dataset, learn the structure of the network model that best explains the data, and use the model to understand and make predictions about relationships between the variables in the model.

::DEVELOPER

Yan Cui’s Lab at University of Tennessee Health Science Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 BNW

:: MORE INFORMATION

Citation:

Bioinformatics. 2013 Nov 1;29(21):2801-3. doi: 10.1093/bioinformatics/btt472. Epub 2013 Aug 21.
Bayesian Network Webserver: a comprehensive tool for biological network modeling.
Ziebarth JD1, Bhattacharya A, Cui Y.

CoMoFinder – Identify Composite Network Motifs in Genome-scale Co-regulatory Networks

CoMoFinder

:: DESCRIPTION

CoMoFinder strives to discover reliable composite network motifs in co-regulatory networks which consist of microRNAs, transcriptional regulators and genes.

::DEVELOPER

Yue Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • JDK

:: DOWNLOAD

 CoMoFinder

:: MORE INFORMATION

Citation:

A novel motif-discovery algorithm to identify co-regulatory motifs in large transcription factor and microRNA co-regulatory networks in human.
Liang C, Li Y, Luo J, Zhang Z.
Bioinformatics. 2015 Mar 18. pii: btv159

nMLSA / MLSA – Network-based / Modular Latent Structure Analysis

nMLSA / MLSA

:: DESCRIPTION

nMLSA is an exploratory data analysis method. Its purpose is to estimate modular latent structures in high-throughput data. It finds co-regulative modules that involve non-coexpressive genes.

MLSA is an exploratory data analysis method. Its purpose is to estimate modular latent structures in high-throughput data. It finds co-regulative modules that involve non-coexpressive genes.

::DEVELOPER

Tianwei Yu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R

:: DOWNLOAD

 nMLSA ,MLSA

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014;15 Suppl 13:S6. doi: 10.1186/1471-2105-15-S13-S6. Epub 2014 Nov 13.
Network-based modular latent structure analysis.
Yu T, Bai Y.

BMC Bioinformatics. 2010 Aug 27;11:440. doi: 10.1186/1471-2105-11-440.
An exploratory data analysis method to reveal modular latent structures in high-throughput data.
Yu T

NetMatchStar 3.2 – An enhanced Cytoscape network querying app

NetMatchStar 3.2

:: DESCRIPTION

NetMatch* is a Cytoscape app that allow user to find all the occurrences of a query graph in a network and check for its significance as a motif with respect to seven different random models. The query can be uploaded or built from scratch using Cytoscape facilities. NetMatch* also allows queries with wildcards.

::DEVELOPER

Fabio Rinnone

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

NetMatchStar

:: MORE INFORMATION

Citation

Version 2. F1000Res. 2015 Aug 5 [revised 2015 Nov 3];4:479. doi: 10.12688/f1000research.6656.2. eCollection 2015.
NetMatchStar: an enhanced Cytoscape network querying app.
Rinnone F, Micale G, Bonnici V, Bader GD, Shasha D, Ferro A, Pulvirenti A, Giugno R.

Bioinformatics. 2007 Apr 1;23(7):910-2. Epub 2007 Feb 3.
NetMatch: a Cytoscape plugin for searching biological networks.
Ferro A, Giugno R, Pigola G, Pulvirenti A, Skripin D, Bader GD, Shasha D.

Cobweb 1.1.1 – Network Exploration and Visualisation

Cobweb 1.1.1

:: DESCRIPTION

Cobweb is a Java applet for real-time network visualization; its strength lies in enabling the interactive exploration of networks.

::DEVELOPER

Structural Bioinformatics Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 Cobweb

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jun 15;27(12):1725-6. doi: 10.1093/bioinformatics/btr195. Epub 2011 Apr 12.
Cobweb: a Java applet for network exploration and visualisation.
von Eichborn J1, Bourne PE, Preissner R.

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