Tag: Cytoscape

Cerebral 2.8.2 / CerebralWeb 1.0 – Cytoscape Molecular Interaction Viewer

Cerebral 2.8.2 / CerebralWeb 1.0

:: DESCRIPTION

Cerebral (Cell Region-Based Rendering And Layout) is a Java plugin for the widely used open-source Cytoscape molecular interaction viewer.

CerebralWeb is a light-weight JavaScript plug-in that extends Cytoscape.js to enable fast and interactive visualisation of molecular interaction networks stratified based on subcellular localisation or other custom annotation.

::DEVELOPER

Cerebral team

:: SCREENSHOTS

Cerebral

:: REQUIREMENTS

  • Windows/Linux/ MacOsX
  • Java
  • Cytoscape

:: DOWNLOAD

 Cerebral

:: MORE INFORMATION

Citation

Barsky A, Gardy JL, Hancock REW, and Munzner T. (2007)
Cerebral: a Cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation.
Bioinformatics 23(8):1040-2.

Database (Oxford). 2015 May 7;2015. pii: bav041. doi: 10.1093/database/bav041. Print 2015.
CerebralWeb: a Cytoscape.js plug-in to visualize networks stratified by subcellular localization.
Frias S1, Bryan K1, Brinkman FS1, Lynn DJ

CySBGN 1.2 – SBGN diagrams in Cytoscape

CySBGN 1.2

:: DESCRIPTION

CySBGN is a Cytoscape plug-in that extends the use of Cytoscape visualization and analysis features to SBGN maps. CySBGN adds support to Cytoscape to import, export, visualize, validate and analyse SBGN maps.

::DEVELOPER

Saez-Rodriguez Group

:: SCREENSHOTS

CySBGN

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java
  • Cytoscape

:: DOWNLOAD

 CySBGN

:: MORE INFORMATION

Citation

Goncalves, E. J. V., Iersel, M. V., & Saez-Rodriguez, J. (2013).
CySBGN: A Cytoscape plug-in to integrate SBGN maps.
BMC Bioinformatics, 14(1), 17. doi:10.1186/1471-2105-14-17

chemViz2 1.1.0 – Cheminformatics Plugin for Cytoscape

chemViz2 1.1.0

:: DESCRIPTION

UCSF chemViz is a Cytoscape plugin that extends the capabilities of Cytoscape into the domain of cheminformatics. chemViz displays 2D diagrams of compounds specified by InCHI or SMILES strings. chemViz can also calculate Tanimoto similarities of compounds and use the values to create chemical similarity networks. Part of such a network is shown above. The 2D diagrams can be presented as scalable independent windows or as part of a table also showing Cytoscape attributes and calculated compound descriptors, including number of hydrogen bond donors, number of hydrogen bond acceptors, molecular weight, ALogP, molecular refractivity, number of Rule of Five violations, and several more. Any of the calculated descriptors can be mapped onto Cytsocape attributes where they can be used by the VizMapper and saved with the session.

::DEVELOPER

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

:: SCREENSHOTS

chemViz

:: REQUIREMENTS

:: DOWNLOAD

  chemViz

:: MORE INFORMATION

FunMod 2.8.3 – Cytoscape plugin for Identifying Functional Modules in undirected Protein-protein Networks

FunMod 2.8.3

:: DESCRIPTION

FunMod is an innovative Cytoscape version 2.8 plugin that is able to mine undirected protein-protein networks and to infer sub-networks of interacting proteins intimately correlated with relevant biological pathways.

::DEVELOPER

the Systems Biology Research Group at the Department of Control and Computer Engineering of Politecnico di Torino.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Java
  • Cytoscape

:: DOWNLOAD

 FunMod

:: MORE INFORMATION

Citation

FunMod: a Cytoscape plugin for identifying functional modules in undirected protein-protein networks.
Natale M, Benso A, Di Carlo S, Ficarra E.
Genomics Proteomics Bioinformatics. 2014 Aug;12(4):178-86. doi: 10.1016/j.gpb.2014.05.002.

CyNeo4j 1.3 – A Cytoscape app to connect to a Neo4j database

CyNeo4j 1.3

:: DESCRIPTION

CyNeo4j allows users to connect to a Neo4j server to use the server as a storage for large graphs, a calculation platform through plugins in Neo4j or query the graph with Cypher.

::DEVELOPER

CyNeo4j team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java
  • Cytoscape
  • Neo4j
:: DOWNLOAD

 CyNeo4j

:: MORE INFORMATION

Citation

cyNeo4j: connecting Neo4j and Cytoscape.
Summer G, Kelder T, Ono K, Radonjic M, Heymans S, Demchak B.
Bioinformatics. 2015 Aug 12. pii: btv460.

BiNoM 2.5 – Cytoscape plug-in for Manipulating and Analysing biological networks

BiNoM 2.5

:: DESCRIPTION

BiNoM (Biological Network Manager )is a Cytoscape plugin, developed to facilitate the manipulation of biological networks represented in standard systems biology formats (SBML, SBGN, BioPAX) and to carry out studies on the network structure. BiNoM provides the user with a complete interface for the analysis of biological networks in Cytoscape environment.

::DEVELOPER

Computational Systems Biology of Cancer group in Bioinformatics Laboratory of Institut Curie (Paris).

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 BiNoM

:: MORE INFORMATION

Citation:

BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats.
Bonnet E, Calzone L, Rovera D, Stoll G, Barillot E, Zinovyev A.
BMC Syst Biol. 2013 Mar 1;7:18. doi: 10.1186/1752-0509-7-18.

Zinovyev A., Viara E., Calzone L., Barillot E.
BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks. 2008.
Bioinformatics 24(6):876-877

CySBML 1.4.1 – Cytoscape Plugin for SBML

CySBML 1.4.1

:: DESCRIPTION

CySBML is a Cytoscape plugin for the import and work with SBML files in Cytoscape providing the visualisation of SBML network annotations within the network context. SBML models can be imported from BioModels.net or via file or urls. One click access to the annotation resources is provided. SBML validation information about the imported files is available.

::DEVELOPER

Matthias König

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 CySBML

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Sep 15;28(18):2402-3. doi: 10.1093/bioinformatics/bts432. Epub 2012 Jul 5.
CySBML: a Cytoscape plugin for SBML.
König M, Dräger A, Holzhütter HG.

FluxViz/CyFluxViz 1.00 – Cytoscape Plugin for Flux Visualization

FluxViz/CyFluxViz 1.00

:: DESCRIPTION

FluxViz is an open-source Cytoscape plug-in for the visualization of flux distributions in molecular interaction networks.FluxViz was used for the visualization and analysis of the metabolic network of the human hepatocyte

::DEVELOPER

Matthias König

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

FluxViz

:: MORE INFORMATION

Citation:

Genome Inform. 2010 Jul;24(1):96-103.
Fluxviz – cytoscape plug-in for visualization of flux distributions in networks.
König M, Holzhütter HG.

enhancedGraphics 1.5.4 – Cytoscape app for enhanced Node Graphics

enhancedGraphics 1.5.4

:: DESCRIPTION

enhancedGraphics is a Cytoscape app that implements a series of enhanced charts and graphics that may be added to Cytoscape nodes.

::DEVELOPER

enhancedGraphics team

:: SCREENSHOTS

enhancedGraphics

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java
  • Cytoscape

:: DOWNLOAD

 enhancedGraphics

:: MORE INFORMATION

Citation

enhancedGraphics: a Cytoscape app for enhanced node graphics.
Morris JH, Kuchinsky A, Ferrin TE, Pico AR.
F1000Res. 2014 Jul 1;3:147. doi: 10.12688/f1000research.4460.1

PINBPA 1.1.9 – Cytoscape app for Network Analysis of GWAS data

PINBPA 1.1.9

:: DESCRIPTION

PINBPA (Protein interaction network-based pathway analysis) for genome-wide association studies (GWAS) has been developed as a Cytoscape app, to enable analysis of GWAS data in a network fashion.

::DEVELOPER

PINBPA team

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java
  • Cytoscape

:: DOWNLOAD

 PINBPA

:: MORE INFORMATION

Citation

PINBPA: Cytoscape app for network analysis of GWAS data.
Wang L, Matsushita T, Madireddy L, Mousavi P, Baranzini S.
Bioinformatics. 2014 Sep 25. pii: btu644