Tag: Cytoscape

structureViz – Link Visualization of Biological Networks in Cytoscape

structureViz

:: DESCRIPTION

UCSF structureViz is a Cytoscape plugin that links visualization of biological networks in Cytoscape with visualization and analysis of molecular structures in UCSF Chimera.

::DEVELOPER

the Resource for Biocomputing, Visualization, and Informatics (RBVI) at UCSF

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

structureViz

:: MORE INFORMATION

Citation:

Bioinformatics. 2007 Sep 1;23(17):2345-7. Epub 2007 Jul 10.
structureViz: linking Cytoscape and UCSF Chimera.
Morris JH1, Huang CC, Babbitt PC, Ferrin TE.

Cytoprophet 1.0 – A Cytoscape plug-in for Protein and Domain Interaction Networks Inference

Cytoprophet 1.0

:: DESCRIPTION

Cytoprophet is a project developed by the Laboratory for Computational Life Sciences at the Computer Science Department of the University of Notre Dame. It is a tool to help researchers to infer new potential protein (PPI) and domain (DDI) interactions. It is implemented as a Cytoscape plugin, where users input a set of proteins and retrieve a network of plausible protein and domain interactions with a score. Three algorithms are used for the estimation of PPI/DDI: Maximum Specificity Set Cover (MSSC) Approach, Maximum Likelihood Estimation (MLE) and the Sum-Product Algorithm (SPA) for protein networks.

::DEVELOPER

Cytoprophet team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Cytoprophet

:: MORE INFORMATION

Citation

Chengbang Huang , Faruck Morcos, Simon P. Kanaan, Stefan Wuchty, Danny Z. Chen, and Jesús A. Izaguirre
Predicting Protein-Protein Interactions from Protein Domains Using a Set Cover Approach.
IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol 4 pp. 78-87. Jan-March 2007

MOSAIC 1.1 – GO network Annotation and Partition in Cytoscape

MOSAIC 1.1

:: DESCRIPTION

Mosaic performs network annotation and interactive partitioning driven by the Gene Ontology. The Mosaic algorithm works by first annotating the network with GO terms, followed by partitioning the network into a series of subnetworks based on the biological process annotation of nodes.

::DEVELOPER

the National Resource for Network Biology (NRNB)

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOsX  /Windows
  • Java
  • Cytoscape

:: DOWNLOAD

 MOSAIC

:: MORE INFORMATION

Citation:

Bioinformatics. 2012 Jul 15;28(14):1943-4. doi: 10.1093/bioinformatics/bts278. Epub 2012 May 9.
Mosaic: making biological sense of complex networks.
Zhang C1, Hanspers K, Kuchinsky A, Salomonis N, Xu D, Pico AR.

DomainGraph 3.01 – Cytoscape Plugin of Analysis and Visualization of Molecular Interaction Networks

DomainGraph 3.01

:: DESCRIPTION

DomainGraph is the successor tool of DomainNetworkBuilder and works as Java plugin for Cytoscape, a free open-source software platform for visualization and analysis of biomolecular networks. This plugin decomposes protein networks into domain-domain interactions and generates a new network of interacting domains. It also allows the integration of exon expression data measured using Affymetrix GeneChip microarrays, which supports the analysis of alternative splicing events and the characterization of their effects on protein and domain interaction networks.

::DEVELOPER

Max-Planck-Institut Informatik

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

  DomainGraph

:: MORE INFORMATION

Citation:

Emig, D., Salomonis, N., Baumbach, J., Lengauer, T., Conklin, BR., Albrecht, M. (2010)
AltAnalyze and DomainGraph: analyzing and visualizing exon expression data.
Nucleic Acids Res. 2010 July 1; 38

CytoSaddleSum 1.5 – Functional Enrichment Analysis plugin for Cytoscape

CytoSaddleSum 1.5

:: DESCRIPTION

CytoSaddleSum provides Cytoscape users with access to the functionality of SaddleSum, a functional enrichment tool based on sum-of-weight scores.

::DEVELOPER

Yi-Kuo Yu

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java
  • Cytoscape
:: DOWNLOAD

 CytoSaddleSum

:: MORE INFORMATION

Citation:

Bioinformatics. 2012 Mar 15;28(6):893-4. doi: 10.1093/bioinformatics/bts041. Epub 2012 Feb 15.
CytoSaddleSum: a functional enrichment analysis plugin for Cytoscape based on sum-of-weights scores.
Stojmirovic A1, Bliskovsky A, Yu YK.

NOA 1.1 – Cytoscape plugin for Network Ontology Analysis

NOA 1.1

:: DESCRIPTION

The NOA (Network Ontology Analysis) plugin for Cytoscape implements the NOA algorithm for network-based enrichment analysis, which extends Gene Ontology annotations to network links, or edges.

NOA Online Version

::DEVELOPER

NOA team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOsX  /Windows
  • Java
  • Cytoscape

:: DOWNLOAD

 NOA

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2011 Jul;39(13):e87. doi: 10.1093/nar/gkr251. Epub 2011 May 4.
NOA: a novel Network Ontology Analysis method.
Wang J1, Huang Q, Liu ZP, Wang Y, Wu LY, Chen L, Zhang XS.

NOA: a cytoscape plugin for network ontology analysis.
Zhang C, Wang J, Hanspers K, Xu D, Chen L, Pico AR.
Bioinformatics. 2013 Aug 15;29(16):2066-7. doi: 10.1093/bioinformatics/btt334.

Cyrface 2.0 – Bridging Cytoscape with R

Cyrface 2.0

:: DESCRIPTION

Cyrface establishes an interface between R and Cytoscape by using different Java-R libraries, e.g. Rserve, RCaller.

::DEVELOPER

Saez-Rodriguez Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R package
  • Java
  • Cytoscape

:: DOWNLOAD

 Cyrface

:: MORE INFORMATION

Citation

F1000Res. 2013 Sep 19;2:192. doi: 10.12688/f1000research.2-192.v1. eCollection 2013.
Cyrface: An interface from Cytoscape to R that provides a user interface to R packages.
Gonçalves E, Saez-Rodriguez J.

Cyni 1.0.0.beta6 – Cytoscape Network Inference Toolbox

Cyni 1.0.0.beta6

:: DESCRIPTION

Cyni (Cytoscape Network Inference Toolbox) is a new Cytoscape App that puts together several tools that allow infering networks from biological data. Each of the tools can be used independently or together to perform several tasks.

::DEVELOPER

Systems Biology Lab, Institut Pasteur, Paris

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java
  • Cytoscape

:: DOWNLOAD

 Cyni

:: MORE INFORMATION

Citation

The Cyni framework for network inference in Cytoscape.
Guitart-Pla O, Kustagi M, Rügheimer F, Califano A, Schwikowski B.
Bioinformatics. 2014 Dec 18. pii: btu812.

cddApp 1.1.4 – Integration between Cytoscape and the NCBI Conserved Domain Database

cddApp 1.1.4

:: DESCRIPTION

cddApp is a Cytoscape3 extension that supports the annotation of protein networks with information about domains and specific functional sites (features) from the National Center for Biotechnology Information (NCBI) Conserved Domain Database (CDD).

::DEVELOPER

the Resource for Biocomputing, Visualization, and Informatics (RBVI) at UCSF

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 cddApp

:: MORE INFORMATION

Citation:

cddApp: A Cytoscape App for Accessing the NCBI Conserved Domain Database.
Morris JH, Wu A, Yamashita RA, Marchler-Bauer A, Ferrin TE.
Bioinformatics. 2014 Sep 10. pii: btu605.

CytoNCA 2.1.6 – Cytoscape Apps for Network Centrality Analysis and Evaluation

CytoNCA 2.1.6

:: DESCRIPTION

CytoNCA is a Cytoscape plugin integrating calculation, evaluation and visualization analysis for multiple centrality measures.

::DEVELOPER

CytoNCA team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java
  • Cytoscape

:: DOWNLOAD

 CytoNCA

:: MORE INFORMATION

Citation

CytoNCA: A cytoscape plugin for centrality analysis and evaluation of protein interaction networks.
Tang Y, Li M, Wang J, Pan Y, Wu FX.
Biosystems. 2014 Nov 15;127C:67-72. doi: 10.1016/j.biosystems.2014.11.005

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