Difference between revisions of "Cytoscape"

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==Contents==
 
==Contents==
* The platform
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Cytoscape is now [http://cytoscape.org/ available as '''version 3'''] and should be straightforward to download and install.
* Plugins
 
  
 
 
 
 
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==Exercises==
 
==Exercises==
<section begin=exercises />
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<section begin=exercises_I />
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<div class="reference-box">Cytoscape 3 tutorials <small>([http://opentutorials.cgl.ucsf.edu/index.php/Portal:Cytoscape3])</small>
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* [http://opentutorials.cgl.ucsf.edu/index.php/Tutorial:Introduction_to_Cytoscape_3 Introduction to Cytoscape 3: User Interface]
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* [http://opentutorials.cgl.ucsf.edu/index.php/Tutorial:Introduction_to_Cytoscape_3.1-part2 Introduction to Cytoscape 3.1: Part 2 - importing networks]
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* [http://opentutorials.cgl.ucsf.edu/index.php/Tutorial:Introduction_to_Cytoscape_3-part3 Introduction to Cytoscape 3: Part 3 - Web import]
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* [http://opentutorials.cgl.ucsf.edu/index.php/Tutorial:Filtering_and_Editing_in_Cytoscape_3 Cytoscape 3: Filtering and editing]
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</div>
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<div class="reference-box">Cytoscape tutorials <small>([http://wiki.cytoscape.org/Presentations/Basic])</small>
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* Browse over the [http://wiki.cytoscape.org/Presentations/03_Download_Data Cytoscape Downloading Data tutorial]
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* Work through the [http://irefindex.uio.no/wiki/iRefScape '''iRefScape''' &mdash; iRefIndex Cytoscape plugin tutorial:] Installation, data selection and use.
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* Work through the [http://wiki.cytoscape.org/Presentations/04_Expression_Data Cytoscape Basic expression analysis tutorial]
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<section begin=exercises_IV />
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<section begin=exercises_V />
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<section end=exercises_V />
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;Further reading
 
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==Further reading and resources==
 
==Further reading and resources==
 
<div class="reference-box">The [http://wiki.cytoscape.org/Welcome '''Cytoscape wiki''' and manual], and the [http://wiki.cytoscape.org/Cytoscape_User_Manual/Network_Formats Cytoscape manual page on '''network formats'''].</div>
 
<div class="reference-box">The [http://wiki.cytoscape.org/Welcome '''Cytoscape wiki''' and manual], and the [http://wiki.cytoscape.org/Cytoscape_User_Manual/Network_Formats Cytoscape manual page on '''network formats'''].</div>

Latest revision as of 00:49, 12 March 2014

Cytoscape


This page is a placeholder, or under current development; it is here principally to establish the logical framework of the site. The material on this page is correct, but incomplete.


Cytoscape is a program originally written in Trey Ideker's lab at the Institue for Systems Biology, that is now a thriving, open-source community project for the development of a biology-oriented network display and analysis tool.



 

Introductory reading

Kohl et al. (2011) Cytoscape: software for visualization and analysis of biological networks. Methods Mol Biol 696:291-303. (pmid: 21063955)

PubMed ] [ DOI ]


 

Contents

Cytoscape is now available as version 3 and should be straightforward to download and install.

 

Exercises





Further reading
Montojo et al. (2010) GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop. Bioinformatics 26:2927-8. (pmid: 20926419)

PubMed ] [ DOI ]

Merico et al. (2011) Visualizing gene-set enrichment results using the Cytoscape plug-in enrichment map. Methods Mol Biol 781:257-77. (pmid: 21877285)

PubMed ] [ DOI ]

 

Further reading and resources

Platform
Shannon et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13:2498-504. (pmid: 14597658)

PubMed ] [ DOI ]

Cline et al. (2007) Integration of biological networks and gene expression data using Cytoscape. Nat Protoc 2:2366-82. (pmid: 17947979)

PubMed ] [ DOI ]

Killcoyne et al. (2009) Cytoscape: a community-based framework for network modeling. Methods Mol Biol 563:219-39. (pmid: 19597788)

PubMed ] [ DOI ]

Smoot et al. (2011) Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27:431-2. (pmid: 21149340)

PubMed ] [ DOI ]

Plugins
Rivera et al. (2010) NeMo: Network Module identification in Cytoscape. BMC Bioinformatics 11 Suppl 1:S61. (pmid: 20122237)

PubMed ] [ DOI ]

Montojo et al. (2010) GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop. Bioinformatics 26:2927-8. (pmid: 20926419)

PubMed ] [ DOI ]

Oesper et al. (2011) WordCloud: a Cytoscape plugin to create a visual semantic summary of networks. Source Code Biol Med 6:7. (pmid: 21473782)

PubMed ] [ DOI ]

Razick et al. (2011) iRefScape. A Cytoscape plug-in for visualization and data mining of protein interaction data from iRefIndex. BMC Bioinformatics 12:388. (pmid: 21975162)

PubMed ] [ DOI ]

Morris et al. (2011) clusterMaker: a multi-algorithm clustering plugin for Cytoscape. BMC Bioinformatics 12:436. (pmid: 22070249)

PubMed ] [ DOI ]