|
Size: 4451
Comment:
|
Size: 5874
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 1: | Line 1: |
| #acl BaderLabGroup:read,write,revert,delete All: We can migrate some of the content from the MCODE site here: http://cbio.mskcc.org/~bader/software/mcode/ |
#acl All:read |
| Line 8: | Line 4: |
| 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. |
| Line 10: | Line 6: |
| 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 boundary and content exploration with real-time results |
* Coming Soon: Run MCODE v1.3 using Java !WebStart 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 |
| Line 15: | Line 14: |
| 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 new [:Software/MCODE/UsersManual: User's Manual] for screen shots, descriptions, and tutorials. | 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. |
| Line 21: | Line 20: |
| == Downloads == Here you will find all MCODE Cytoscape !PlugIn versions that have been produced to date. All available Javadocs and source codes have been made available for download with their respective versions. |
== Latest Download == The current MCODE Cytoscape plugin is MCODE v1.3. With Cytoscape 2.5.1, you can download the latest MCODE version directly from within the software using the Plugin Manager (Plugins > Manage Plugins). MCODE is found under the Analysis category. Otherwise, you may install the plugin manually: [attachment:MCODE_v1_3.zip Download the latest version] * Plugin requires [http://www.cytoscape.org/ Cytoscape v2.5.1 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 == |
| Line 25: | Line 32: |
| * plugin * requires Cytoscape v2.3.2 or later * Javadoc * Source |
* [attachment:MCODE_v1_2.zip Download MCODE v1.2] * requires Cytoscape v2.3 to v2.4 |
| Line 31: | Line 36: |
| * plugin | * [attachment:MCODE_v1_1.zip Download MCODE v1.1] |
| Line 33: | Line 38: |
| * Run using Java WebStart * Javadoc * Source |
|
| Line 38: | Line 40: |
| * plugin | * [attachment:MCODE_v1_0.zip Download MCODE v1.0] |
| Line 40: | Line 42: |
=== Cytoscape === * The Cytoscape installation file, source code, and an array of useful plugins can be downloaded at [http://www.cytoscape.org www.cytoscape.org] |
|
| Line 55: | Line 54: |
| === User's Manual === | === Documentation === |
| Line 57: | Line 56: |
=== 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. |
|
| Line 61: | Line 63: |
| * 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 |
* 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 |
| Line 74: | Line 75: |
| 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. |
| Line 77: | Line 78: |
| 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: [http://chianti.ucsd.edu/svn/csplugins/trunk/mskcc/gbader/MCODEv1.2/ MCODE directory] * Quick-Link: [http://chianti.ucsd.edu/svn/csplugins/trunk/mskcc/gbader/MCODEv1.2/javadoc/index.html Javadoc] * The Cytoscape developer wiki provides some detailed instructions on using SVN: http://cytoscape.org/cgi-bin/moin.cgi/SVN_Access |
| Line 81: | Line 89: |
| == Acknowledgements == | == Credits == |
| Line 83: | Line 91: |
| 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 1.3 is a Cytoscape compatibility update and was produced by Mike Smoot and the Cytoscape development team. |
| Line 85: | Line 93: |
| Version 1.2 was produced by [:VukPavlovic: Vuk Pavlovic] in the Bader Lab. | Version 1.2 was produced by [:VukPavlovic: Vuk Pavlovic] in the Bader Lab. Thanks to Christopher Workman (The Technical University of Denmark) and Carlo Laudanna (University of Verona) for their expert input during beta-testing. 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.
Coming Soon: Run MCODE v1.3 using Java WebStart
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 v1.3.
With Cytoscape 2.5.1, you can download the latest MCODE version directly from within the software using the Plugin Manager (Plugins > Manage Plugins). MCODE is found under the Analysis category.
Otherwise, you may install the plugin manually: [attachment:MCODE_v1_3.zip Download the latest version]
Plugin requires [http://www.cytoscape.org/ Cytoscape v2.5.1 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 v1.2
- [attachment:MCODE_v1_2.zip Download MCODE v1.2]
- requires Cytoscape v2.3 to v2.4
MCODE v1.1
- [attachment:MCODE_v1_1.zip Download MCODE v1.1]
- requires Cytoscape v2.1
MCODE v1.0
- [attachment:MCODE_v1_0.zip Download MCODE v1.0]
- requires Cytoscape v2.0
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: [http://chianti.ucsd.edu/svn/csplugins/trunk/mskcc/gbader/MCODEv1.2/ MCODE directory]
Quick-Link: [http://chianti.ucsd.edu/svn/csplugins/trunk/mskcc/gbader/MCODEv1.2/javadoc/index.html Javadoc]
The Cytoscape developer wiki provides some detailed instructions on using SVN: http://cytoscape.org/cgi-bin/moin.cgi/SVN_Access
Credits
Version 1.3 is a Cytoscape compatibility update and was produced by Mike Smoot and the Cytoscape development team.
Version 1.2 was produced by [:VukPavlovic: Vuk Pavlovic] in the Bader Lab. Thanks to Christopher Workman (The Technical University of Denmark) and Carlo Laudanna (University of Verona) for their expert input during beta-testing.
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.