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We can migrate some of the content from the MCODE site here: http://cbio.mskcc.org/~bader/software/mcode/ attachment:MCODELogo.png 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 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 * Multiple result set management * 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. |
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| We can migrate some of the content from the MCODE site here: http://cbio.mskcc.org/~bader/software/mcode/ |
== Downloads == Here you will find |
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| === MCODE v1.2 === * plugin * requires Cytoscape v2.3.2 or later * Javadoc * Source |
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| == MCODE Cytoscape PlugIn == | === MCODE v1.1 === * plugin * requires Cytoscape v2.1 * Run using Java WebStart * Javadoc * Source |
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| The MCODE Cytoscape PlugIn finds clusters (highly interconnected regions) in any network loaded into Cytoscape. Depending on the type of network, clusters may mean different things. For instance, clusters in a protein-protein interaction network have been shown to be protein complexes and parts of pathways. Clusters in a protein similarity network represent protein families. | === MCODE v1.0 === * plugin * requires Cytoscape v2.0 |
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| MCODE is a relatively fast method of clustering, although it does not currently provide any statistical score on the resulting clusters. It can be used as discovery tool when analyzing a network. See the paper for more information. | === Cytoscape === * The Cytoscape installation file, source code, and an array of useful plugins can be downloaded at [http://www.cytoscape.org www.cytoscape.org] |
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| === Downloads === | ---- == 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. . http://www.biomedcentral.com/1471-2105/4/2 |
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| ==== Installation ==== ==== Introduction ==== ==== Advanced Techniques ==== ==== Tutorials ==== === Contact === |
The User's Manual includes installation instructions, explanations, examples and tutorials. It is available [:Software/MCODE/UsersManual: here]. ---- == Future Developments == * Commandline accessibility * Automation * Robustness assay * BiNGO validation and statistics * Benchmarking: result comparison and validatation using an established cluster result set * Attribute-enhanced clustering: incorporation of additional datasets in the clustering algorithm * Spatial and temporal expression ---- == 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, I would love to hear from you. Please send me an e-mail to [:GaryBader: Gary Bader]. ---- == 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) Version 1.2 was produced by [:VukPavlovic: Vuk Pavlovic] in the Bader Lab. 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. |
We can migrate some of the content from the MCODE site here: http://cbio.mskcc.org/~bader/software/mcode/
attachment:MCODELogo.png
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 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
- Multiple result set management
- 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.
Downloads
Here you will find
MCODE v1.2
- plugin
- requires Cytoscape v2.3.2 or later
- Javadoc
- Source
MCODE v1.1
- plugin
- requires Cytoscape v2.1
Run using Java WebStart
- Javadoc
- Source
MCODE v1.0
- plugin
- requires Cytoscape v2.0
Cytoscape
The Cytoscape installation file, source code, and an array of useful plugins can be downloaded at [http://www.cytoscape.org www.cytoscape.org]
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.
User's Manual
The User's Manual includes installation instructions, explanations, examples and tutorials. It is available [:Software/MCODE/UsersManual: here].
Future Developments
- Commandline accessibility
- Automation
- Robustness assay
- BiNGO validation and statistics
- Benchmarking: result comparison and validatation using an established cluster result set
- Attribute-enhanced clustering: incorporation of additional datasets in the clustering algorithm
- Spatial and temporal expression
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, I would love to hear from you. Please send me an e-mail to [:GaryBader: Gary Bader].
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)
Version 1.2 was produced by [:VukPavlovic: Vuk Pavlovic] in the Bader Lab.
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.