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We can migrate some of the content from the MCODE site here: http://cbio.mskcc.org/~bader/software/mcode/ |
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| MCODE is a Cytoscape !PlugIn designed to find clusters in large networks. Clusters are deemed to be more highly interconnected regions within the network and depending on the nature of the network, they may mean different things. For instance, clustering of protein-protein interaction networks has been shown to produce protein complexes and parts of pathways while clusters in protein similarity networks represent protein families. | MCODE is a [http://cytoscape.org Cytoscape] plugin that finds clusters (highly interconnected regions) in a network. Clusters mean different things in different types of networks. For instance, clusters in a protein-protein interaction network are often protein complexes and parts of pathways, while clusters in a protein similarity network represent protein families. [http://cytoscape.org Cytoscape] is freely available network visualization and analysis software. |
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| MCODE is a relatively fast method of clustering. With an intuitive interface, it is suited for both computationally and biologically oriented reserachers. Version 1.2 features include: * Fine-tuning with numerous node-scoring and cluster-finding parameters * Interactive cluster exploration with real-time results * Cluster size manipulation * Logical cluster visualizization using a conservative layouter * Cluster node attribute enumeration for functional consistancy |
* Run using Java WebStart (TODO: create webstart for 1.2) MCODE is a relatively fast method of clustering. With an intuitive interface, it is suited for both computationally and biologically oriented researchers. Current features include: * Fast network clustering * Fine-tuning of results with numerous node-scoring and cluster-finding parameters * Interactive cluster boundary and content exploration |
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| * Data output * Generate sub-networks from clusters * Export as text for spreadsheet purposes Currently, MCODE does not provide any statistical score on the resulting clusters but can be used as a discovery tool in network analysis. Please see the [http://www.biomedcentral.com/1471-2105/4/2 MCODE paper] for more information. |
* Cluster sub-network creation and plain text export Currently, MCODE does not provide any statistical score on the resulting clusters but can be used as a discovery tool in network analysis. Please see the [http://www.biomedcentral.com/1471-2105/4/2 MCODE paper] for more information. Also be sure to consult the [:Software/MCODE/UsersManual: documentation] for screen shots, descriptions, and tutorials. |
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| == Downloads == Here you will find |
== Latest Download == The current MCODE Cytoscape plugin is MCODE v1.2: [attachment:MCODE_v1_2.zip Download the latest version] * Plugin requires [http://www.cytoscape.org/ Cytoscape v2.3.2 or later] and [http://java.sun.com/j2se/1.5.0/index.jsp Java 1.5.0] * See the [:Software/MCODE/UsersManual: documentation] |
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| === MCODE v1.2 === * plugin * requires Cytoscape v2.3.2 or later * Javadoc * Source |
== Previous Versions == |
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| * plugin | * [attachment:MCODE_v1_1.zip Download MCODE v1.1] |
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| * Run using Java WebStart * Javadoc * Source |
* Developers: Source Code |
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| * plugin | * [attachment:MCODE_v1_0.zip Download MCODE v1.0] |
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=== Cytoscape === * The Cytoscape installation file, source code, and an array of useful plugins can be downloaded at [http://www.cytoscape.org www.cytoscape.org] |
* Developers: Source Code |
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| === User's Manual === The User's Manual includes installation instructions, explanations, examples and tutorials. It is available [:Software/MCODE/UsersManual: here]. |
=== Documentation === The [:Software/MCODE/UsersManual: MCODE User's Manual] is both a great place to start learning the basics and a helpful reference for expert users. It includes installation instructions, explanations, definitions, examples and tutorials to help you produce, interpret, output, and validate results. === Cytoscape Tutorials === A great deal of introductory and advanced tutorials are available at the [http://www.cytoscape.org/tut/tutorial.php Cytoscape Tutorial Resource]. '''Section 7: Modules and Complexes''' incorporates MCODE, and several other plugins, in a complex discovery and validation excercise. |
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| * Ability to run MCODE from the command line * Automation of * Robustness tests * Gene function over-representation analysis * Benchmarking: result comparison and validation using cluster benchmark * Attribute-enhanced clustering: consideration of user attributes, like expression data, in the clustering algorithm |
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| If you encounter a bug with this !PlugIn, or have a feature suggestion, please e-mail [:GaryBader: Gary Bader]. Be sure to take a look at the Future Developments section before e-mailing a feature request. | If you encounter a bug with this plugin, or have a feature suggestion, please e-mail [:GaryBader: Gary Bader]. Be sure to take a look at the Future Developments section before e-mailing a feature request. |
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| This software is open-source. If you modify the source code and would like the modification to be included in a subsequent release, I would love to hear from you. Please send me an e-mail to [:GaryBader: Gary Bader]. | This software is open-source. If you modify the source code and would like the modification to be included in a subsequent release, we would love to hear from you. Please send me an e-mail to [:GaryBader: Gary Bader]. === Software Development === If you are a software developer, the MCODE algorithm is easy to incorporate into your own Java software. Just download the source code to get started. * MCODE source code and Javadoc are made available through Subversion (SVN), a version control repository. * SVN Account Access: '''svn+ssh://chianti.ucsd.edu/svn/csplugins/trunk/mskcc/gbader/mcode/''' * The Cytoscape developer wiki provides some detailed instructions on using SVN: http://cytoscape.org/cgi-bin/moin.cgi/SVN_Access *TODO: add links to MCODE source in SVN and Fisheye + link to Cytoscape wiki instructions on how to use SVN to download code. Could also add links to Javadoc - the easiest way to do this may be to check the Javadoc into SVN and link to it (not sure if this will work, but you can test it out) |
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| == Acknowledgements == This software was originally released as a command-line-only program from the Hogue Lab. It was created by [:GaryBader: Gary Bader], currently based in the [:Home:Bader Lab] at the University of Toronto (formerly in the Sander Group,[http://www.cbio.mskcc.org/ Computational Biology Center, Memorial Sloan-Kettering Cancer Center], New York City) |
== Credits == |
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| This software was originally released as a command-line-only program from the Hogue Lab. It was created by [:GaryBader: Gary Bader], currently based in the [:Home:Bader Lab] at the University of Toronto (formerly in the Sander Group, [http://www.cbio.mskcc.org/ Computational Biology Center, Memorial Sloan-Kettering Cancer Center], New York City) |
attachment:MCODELogo.png
MCODE is a [http://cytoscape.org Cytoscape] plugin that finds clusters (highly interconnected regions) in a network. Clusters mean different things in different types of networks. For instance, clusters in a protein-protein interaction network are often protein complexes and parts of pathways, while clusters in a protein similarity network represent protein families. [http://cytoscape.org Cytoscape] is freely available network visualization and analysis software.
Run using Java WebStart (TODO: create webstart for 1.2)
MCODE is a relatively fast method of clustering. With an intuitive interface, it is suited for both computationally and biologically oriented researchers. Current features include:
- Fast network clustering
- Fine-tuning of results with numerous node-scoring and cluster-finding parameters
- Interactive cluster boundary and content exploration
- Multiple result set management
- Cluster sub-network creation and plain text export
Currently, MCODE does not provide any statistical score on the resulting clusters but can be used as a discovery tool in network analysis. Please see the [http://www.biomedcentral.com/1471-2105/4/2 MCODE paper] for more information. Also be sure to consult the [:Software/MCODE/UsersManual: documentation] for screen shots, descriptions, and tutorials.
Latest Download
The current MCODE Cytoscape plugin is MCODE v1.2: [attachment:MCODE_v1_2.zip Download the latest version]
Plugin requires [http://www.cytoscape.org/ Cytoscape v2.3.2 or later] and [http://java.sun.com/j2se/1.5.0/index.jsp Java 1.5.0]
- See the [:Software/MCODE/UsersManual: documentation]
Previous Versions
MCODE v1.1
- [attachment:MCODE_v1_1.zip Download MCODE v1.1]
- requires Cytoscape v2.1
- Developers: Source Code
MCODE v1.0
- [attachment:MCODE_v1_0.zip Download MCODE v1.0]
- requires Cytoscape v2.0
- Developers: Source Code
Literature and Resources
MCODE Publication
Please see the following paper for more information about the algorithm:
- Bader GD, Hogue CW.
- An automated method for finding molecular complexes in large protein interaction networks.
BMC Bioinformatics. 2003 Jan 13;4(1):2.
Documentation
The [:Software/MCODE/UsersManual: MCODE User's Manual] is both a great place to start learning the basics and a helpful reference for expert users. It includes installation instructions, explanations, definitions, examples and tutorials to help you produce, interpret, output, and validate results.
Cytoscape Tutorials
A great deal of introductory and advanced tutorials are available at the [http://www.cytoscape.org/tut/tutorial.php Cytoscape Tutorial Resource]. Section 7: Modules and Complexes incorporates MCODE, and several other plugins, in a complex discovery and validation excercise.
Future Developments
- Ability to run MCODE from the command line
- Automation of
- Robustness tests
- Gene function over-representation analysis
- Benchmarking: result comparison and validation using cluster benchmark
- Attribute-enhanced clustering: consideration of user attributes, like expression data, in the clustering algorithm
Contact
Bugs / Feature Requests
If you encounter a bug with this plugin, or have a feature suggestion, please e-mail [:GaryBader: Gary Bader]. Be sure to take a look at the Future Developments section before e-mailing a feature request.
Collaboration
This software is open-source. If you modify the source code and would like the modification to be included in a subsequent release, we would love to hear from you. Please send me an e-mail to [:GaryBader: Gary Bader].
Software Development
If you are a software developer, the MCODE algorithm is easy to incorporate into your own Java software. Just download the source code to get started.
- MCODE source code and Javadoc are made available through Subversion (SVN), a version control repository.
SVN Account Access: svn+ssh://chianti.ucsd.edu/svn/csplugins/trunk/mskcc/gbader/mcode/
The Cytoscape developer wiki provides some detailed instructions on using SVN: http://cytoscape.org/cgi-bin/moin.cgi/SVN_Access
- TODO: add links to MCODE source in SVN and Fisheye + link to Cytoscape wiki instructions on how to use SVN to download code. Could also add links to Javadoc - the easiest way to do this may be to check the Javadoc into SVN and link to it (not sure if this will work, but you can test it out)
Credits
Version 1.2 was produced by [:VukPavlovic: Vuk Pavlovic] in the Bader Lab.
This software was originally released as a command-line-only program from the Hogue Lab. It was created by [:GaryBader: Gary Bader], currently based in the [:Home:Bader Lab] at the University of Toronto (formerly in the Sander Group, [http://www.cbio.mskcc.org/ Computational Biology Center, Memorial Sloan-Kettering Cancer Center], New York City)
This software is made available under the [http://www.gnu.org/copyleft/lesser.html LGPL] (Lesser General Public License), which means that you can freely use it within your own software, but if you alter the code itself and distribute it, you must make the source code alterations freely available as well.