Tag: Biological Network

MixNet 1.1.2 / MixeR 1.9 – Analyzes Biological Networks using Mixture Models

MixNet 1.1.2 / MixeR 1.9

:: DESCRIPTION

MixNet (Erdös-Renyi Mixture for Networks) is the first publicly available computer software that analyzes biological networks using mixture models.This model is based on the hypothesis that real networks are made of classes which show specific connectivity patterns.

The MixeR allows the use of the basical options of MixNet software and the post-treatment of the results.

::DEVELOPER

SSB group.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • C Complier / R package

:: DOWNLOAD

 MixNet / MixeR

:: MORE INFORMATION

Citation

Picard, F., Miele, V., Daudin,J-J., Cottret,L., Robin, S.,
Deciphering the connectivity structure of biological networks using MixNet,
MC Bioinformatics. 2009 Jun 16;10 Suppl 6:S17. doi: 10.1186/1471-2105-10-S6-S17.

SimTrek 2.0 – Cytoscape plugin for Ontology-based Similarity Assessment of Biological Networks

SimTrek 2.0

:: DESCRIPTION

SimTrek is a Cytoscape plugin for ontology-based similarity assessment of biological networks.

::DEVELOPER

SimTrek team

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

SimTrek

:: MORE INFORMATION

Citation

Wang H, Zheng H, Azuaje F (2010)
Ontology- and graph-based similarity assessment in biological networks,
Bioinformatics (2010)doi: 10.1093/bioinformatics/btq477

BioLayout 3.4 – Biological Network Visualisation and Analysis

BioLayout 3.4

:: DESCRIPTION

BioLayout is a powerful open-source visual analytics platform designed and developed to aid the interpretation of large and complex biological datasets rendered as network.

::DEVELOPER

BioLayout team 

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX /  Linux
  • Java

:: DOWNLOAD

 BioLayout

:: MORE INFORMATION

Citation

Theocharidis A., van Dongen S., Enright A.J. and Freeman T.C.
Network Visualisation and Analysis of Gene Expression Data using BioLayout Express3D.
Nature Protocols 2009; Vol.4 No.10:1535-50.

FastGGM 20151105 – Algorithm for the inference of Gaussian Graphical Model in Biological Networks

FastGGM 20151105

:: DESCRIPTION

FastGGM is an R package for efficiently studying conditional dependence among variables, which is well known as the Gaussian graphical model (GGM).

::DEVELOPER

Chen Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R
:: DOWNLOAD

 FastGGM

:: MORE INFORMATION

Citation

Wang T, Ren Z, Ding Y, Fang Z, Sun Z, MacDonald ML, Sweet RA, Wang J, Chen W.
FastGGM: An Efficient Algorithm for the Inference of Gaussian Graphical Model in Biological Networks.
PLoS Comput Biol. 2016 Feb 12;12(2):e1004755. doi: 10.1371/journal.pcbi.1004755. PMID: 26872036; PMCID: PMC4752261.

BinAligner 1.0.0 – Bioinformatics software for BIological Network ALIGNment

BinAligner 1.0.0

:: DESCRIPTION

BinAligner is a bioinformatics software for biological network alignment, which uses a mixture of global and local algorithm for netowrk alignment.

:: DEVELOPER

Systems Biology Laboratory, College of Veterinary Medicine,Mississippi State University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • C++ Compiler

:: DOWNLOAD

 BinAligner

:: MORE INFORMATION

Citation

Yang J, Li J, Grünewald S, Wan X.
BinAligner: a heuristic method to align biological networks.
Manuscript 2012.

NaviCluster 2.0 – Interactive, Multi-Scale Navigation for Large and Complicated Biological Networks

NaviCluster 2.0

:: DESCRIPTION

NaviCluster is developed as an interactive, multi-scale navigation tool for large and complicated biological networks.

::DEVELOPER

NaviCluster team

:: SCREENSHOTS

NaviCluster

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java

:: DOWNLOAD

 NaviCluster

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Apr 15;27(8):1121-7. doi: 10.1093/bioinformatics/btr083. Epub 2011 Feb 23.
Interactive, multiscale navigation of large and complicated biological networks.
Praneenararat T1, Takagi T, Iwasaki W.

NetDecoder – Network-based Platform to Decode Context-Specific Biological Networks and Gene Activities

NetDecoder

:: DESCRIPTION

NetDecoder is a novel network biology-based computational platform designed to integrate transcriptomes, interactomes and gene ontologies to identify phenotype-specific subnetworks.

::DEVELOPER

Hu Li Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Max OS X
  • JAVA

:: DOWNLOAD

 NetDecoder

:: MORE INFORMATION

Citation:

NetDecoder: a network biology platform that decodes context-specific biological networks and gene activities.
da Rocha EL, Ung CY, McGehee CD, Correia C, Li H.
Nucleic Acids Res. 2016 Mar 14. pii: gkw166.

NetSets – Compositional Assessment of Biological Networks through Venn and Network Diagrams

NetSets

:: DESCRIPTION

NetSets is a (server-independent) JavaScript framework that integrates popular Venn and Network diagrams in a single application.

::DEVELOPER

NetSets team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • WEb browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nagpal S, Kuntal BK, Mande SS.
NetSets.js: a JavaScript framework for compositional assessment and comparison of biological networks through Venn-integrated network diagrams.
Bioinformatics. 2021 May 1;37(4):580-582. doi: 10.1093/bioinformatics/btaa723. PMID: 32805035.

visANT 5.53 – Integrative Visual Analysis Tool for Biological Networks & Pathways

visANT 5.53

:: DESCRIPTION

visANT is an integrative visual analysis tool for biological networks and pathways. VisANT is implemented as a java applet which can be run in most common browsers and has been test with Netscape, Internet Explorer with different versions on different platforms.

::DEVELOPER

VisANT Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux
  • JAVA

:: DOWNLOAD

visANT

:: MORE INFORMATION

Citation

Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0.
Granger BR, Chang YC, Wang Y, DeLisi C, Segrè D, Hu Z.
PLoS Comput Biol. 2016 Apr 15;12(4):e1004875. doi: 10.1371/journal.pcbi.1004875

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W225-31. doi: 10.1093/nar/gkt401. Epub 2013 May 28.
VisANT 4.0: Integrative network platform to connect genes, drugs, diseases and therapies.
Hu Z1, Chang YC, Wang Y, Huang CL, Liu Y, Tian F, Granger B, Delisi C.

SPICi – Fast Biological Network Clustering Algorithm

SPICi

:: DESCRIPTION

SPICi (Speed and Performance In Clustering) is a fast local network clustering algorithm. SPICi runs in time O(Vlog V +E) and space O(E), where V and E are the number of vertices and edges in the network. It also has state-of the-art performance with respect to the quality of the clusters it uncovers.

::DEVELOPER

Mona Singh

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SPICi

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Apr 15;26(8):1105-11. doi: 10.1093/bioinformatics/btq078. Epub 2010 Feb 24.
SPICi: a fast clustering algorithm for large biological networks.
Jiang P1, Singh M.