Getting Started:

• After unzipping the MetNet package, double-click "MetNet.cmd" if using Windows, or "MetNet" if using Mac OS to run the MetNet Platform. The MetNet launcher window will appear.
• The MetNet launcher window contains a button to open each of the MetNet applications (see figure 1)
• To get more information about an application, click on the help button (the "?" mark) on the lower-right corner of each button.

• To use HiveMind services in BirdsEyeView, choose the desired service from the actions drop down list (figure 2)

• In MetaOmGraph, choose the HiveMind service from the "Actions" menu

• In Cytoscape, click on the "plugins" menu where HiveMind services are listed among other plugins.

Description of Current Services:

• Integrated Components: MetNetDB, BirdsEyeView, MetaOmGraph, PubMedAssistant, PathBinder, Cytoscape, and AtGeneSearch.
  
• Connections established:

1. MetNetDB -> BirdsEyeView
   Based on BirdsEyeViews request, MetNetDB sends data though HiveMind service.
   
   
2. MetNetDB -> MetaOmGraph
   Based on MetaOmGraphs request, MetNetDB sends data (Pathway Names, Gene Names, Gene Annotations, etc...) through HiveMind service.
   
   
3. BirdsEyeView -> MetaOmGraph
   Sends all (or selected) expression data loaded into BirdsEyeView to MetaOmGraph.
   
   
4. MetaOmGraph -> BirdsEyeView
   Sends a subset of MetaOmGraph expression data to BirdsEyeView.
   
   
5. BirdsEyeView -> Cytoscape
1. HiveMind service displays pathways for all genes in BirdsEyeView.
2. User selects one or more pathways.
3. HiveMind service loaded the pathway(s) into Cytoscape. Common genes will be intially selected, and their expression data will be loaded into Cytoscape.
   
   
6. MetaOmGraph -> Cytoscape
   1. HiveMind service displays pathways for all genes in MetaOmGraph.
   2. User selects one or more pathways.
   3. HiveMind service loaded the pathway(s) into Cytoscape. Common genes will be intially selected, and their expression data will be loaded into Cytoscape.
      
      
7. MetaOmGraph -> PubMedAssistant
   1. Search for articles containing selected entity using PubMedAssistant.
      
      
8. MetaOmGraph -> PathBinder
   1. Select two entities from MetaOmGraph.
   2. PathBinder perform search and shows results to user.
      
      
9. MetaOmGraph -> AtGeneSearch
   AtGeneSearch information for selected entities will be displayed, if any exists.
   
   
10. Cytoscape -> AtGeneSearch
    1. Click on menu item "plugins".
    2. Select "AtGeneSearch".
    3. AtGeneSearch information for selected entities will be displayed, if any exists.
       
       
11. Cytoscape -> PubMedAssistant
    Search for articles containing selected entity using PubMedAssistant. This connection is avaliable to users as a plugin that in turn call a HiveMind service.
    
    
12. Cytoscape -> PathBinder
    1. Select two entities from Cytoscape.
    2. Select the attributes to be used in PathBinders search.
    3. PathBinder will use values of selected attributes in search. Result sentences will be displayed.
       
       
13. BirdsEyeView -> AtGeneSearch
    Shows AtGeneSearch information for selected entities.
    
    
14. Cytoscape -> MetaOmGraph
    Sends genes and their expression data from Cytoscape to MetaOmGraph.
    
    
15. Cytoscape -> BirdsEyeView
    Sends genes and their expression data from Cytoscape to BirdsEyeView.
    
    
16. MetNetDB -> Cytoscape
    MetNetDB sends pathway and gene annotation data to Cytoscape.
    
    
17. BirdsEyeView -> PubMedAssistant
    Searchs for articles containing selected entity using PubMedAssistant.
    
    
18. BirdsEyeView -> PathBinder
    1. Select two entities from BirdsEyeView.
    2. Select the attributes to be used in PathBinders search.
    3. PathBinder will use values of selected attributes in search.
    4. Result sentences will be displayed.