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= Community Structure Layout = '''Gang Su''' |
'''GLay[Temporary Name] Brief Description ''' |
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| ''Bioinformatics Program, University of Michigan, Ann Arbor'' | '''Gang Su, Allan Kuchinsky, Scooter Morris and David J. States ''' |
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| '''__Biological Use Case__''': This plugin is aimed to find community structures in large biological networks, which may infer protein complexes and biological pathways. We also utilize the community structure information to improve visualization of large interaction networks. | '''Motivation''': Cytoscape is a comprehensive software foundation for visualizing and analysis of various scaled biological networks. The major objective of this Google Summer of Code project is to develop a plugin for Cytoscape, integrating community detection algorithms into this platform to provide interactive and flexible clustering functions and optimize visualization for large networks with the clustering data. We have three specific aims: 1. Implement community detection algorithms into the plugin. Provide an interface for the user to execute the clustering algorithm; fast select/activate/browse clusters. 2. Re-layout the network with the clustering data. Nodes belong to the same cluster should be agglomerated together and separated apart from the other clusters. Clusters should have the ability to be expanded/collapsed for the ease of user focus on a specific subset of the network. 3. This plugin should be able to cooperate with other plugins, such MIMi and MCode to enhance usage potential. |
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| '''__Recipe__''' | '''Background''': Community structure detection is to find clusters in a network that maximizes intra-cluster edge density and minimizes inter-cluster edge density. When applied to biological interaction networks, community structure detection algorithms are able to recover structures like protein complexes, biological pathways or molecule cocompartmentation. Cytoscape is an active open-source software foundation built on Java for visualization of biological interaction networks. |
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''__Cytoscape version__'': Version number (2.6.1) ''__Plugins to Load__'': attachment:GLay.jar , MetaNodePlugin2.jar ''__Plugins to Load__'': attachment:GLay.jar , attachment:MetaNodePlugin2.jar ''__GUI steps__'': Describe each step (story), the GUI action to take, and probable remarks || ''Story'' || ''Action'' || ''Remarks'' || || First of all, you need to load Glay. After you placed all the plugins jars in the folder, load Glay from the plugins tab. Also please load the preferred network. Here we used galFiltered.sif attachment:screen1.jpg || || || || Then, you may tune the parameters. Right now we have two clustering algorithms and two layout algorithms. Just go with the default. attachment:4screen2.jpg || || || || Next, you may interact with all the clusters from the cluster browsing panel; you may select multiple clusters from by holding the shift key. This will 'activate' clusters my changing visual styles. attachment:screen3.jpg || || || || Clusters can be expanded or collapsed by right click on the nodes to bring up the contextual menu. attachment:screen4.jpg || || || || Toolticons can be used to perform various tasks. attachment:screen5.jpg || || || Here's a miniposter for FYI attachment:GLayMiniPoster.jpg '''__Data / Session Files__''': Attach (preferably) a session file or else the data files used in the workflow '''__Presentation__''': attachment:Presentation.ppt '''__Webstart__''': Attach a webstart '''__Video__''': Video Tutorial: http://www.youtube.com/watch?v=W79Kb28348g, http://www.youtube.com/watch?v=OD3fUF62Gd8 |
'''Plugin Description''': The current alpha build of the plugin require Cytoscape 2.6.1 and MetaNodePlugin2 from Scooter Morris to function. This plugin could take the active network in the cytoscape viewport as the input, perform either Fast-Greedy algorithm or modified Fast-Greedy algorithm with consolidation ratio. The user may also to cast forcedirected layout globally or cast force-directed layout on top of cluster metaNodes for better visualization of large networks. The clusters can be expanded/collapsed by metaNodePlugin2 and browsed in the provided cluster navigation panel; the cluster members can be fast selected/activated/deactivated/zoomed in/out from the provided tool-cons. A screenshot below explains some of the functions. When the clusters are activated, the visual style is changed instead of selection so that the user could still maintain the current selection from other operations or plugins. |
GLay[Temporary Name] Brief Description
Gang Su, Allan Kuchinsky, Scooter Morris and David J. States
Motivation: Cytoscape is a comprehensive software foundation for visualizing and analysis of various scaled biological networks. The major objective of this Google Summer of Code project is to develop a plugin for Cytoscape, integrating community detection algorithms into this platform to provide interactive and flexible clustering functions and optimize visualization for large networks with the clustering data. We have three specific aims: 1. Implement community detection algorithms into the plugin. Provide an interface for the user to execute the clustering algorithm; fast select/activate/browse clusters. 2. Re-layout the network with the clustering data. Nodes belong to the same cluster should be agglomerated together and separated apart from the other clusters. Clusters should have the ability to be expanded/collapsed for the ease of user focus on a specific subset of the network. 3. This plugin should be able to cooperate with other plugins, such MIMi and MCode to enhance usage potential.
Background: Community structure detection is to find clusters in a network that maximizes intra-cluster edge density and minimizes inter-cluster edge density. When applied to biological interaction networks, community structure detection algorithms are able to recover structures like protein complexes, biological pathways or molecule cocompartmentation. Cytoscape is an active open-source software foundation built on Java for visualization of biological interaction networks.
Plugin Description: The current alpha build of the plugin require Cytoscape 2.6.1 and MetaNodePlugin2 from Scooter Morris to function. This plugin could take the active network in the cytoscape viewport as the input, perform either Fast-Greedy algorithm or modified Fast-Greedy algorithm with consolidation ratio. The user may also to cast forcedirected layout globally or cast force-directed layout on top of cluster metaNodes for better visualization of large networks. The clusters can be expanded/collapsed by metaNodePlugin2 and browsed in the provided cluster navigation panel; the cluster members can be fast selected/activated/deactivated/zoomed in/out from the provided tool-cons. A screenshot below explains some of the functions. When the clusters are activated, the visual style is changed instead of selection so that the user could still maintain the current selection from other operations or plugins.