Proposal

The goal of the QuickStart Plugin is to provide a splash screen that appears when Cytoscape starts and that prompts users in basic Cytoscape tasks like importing networks and attributes.

Background

Cytoscape has many mechanisms for getting data network and attribute data into Cytoscape, however loading networks and mapping attributes onto networks is still challenging, especially for novice users. It is particularly difficult to map network identifiers to attributes.

Use Cases

• A biologist has done and experiment and has 100 genes of interest with measurements for multiple conditions and would like to see that data projected onto an existing network.

Design Concept

• The splash screen should have 3 primary icons: one for networks, one for attributes, and one for analysis.
• Clicking on any of the icons will start a "wizard" that prompts users through various possible decisions. For example:
  1. A user clicks the load attributes button.
  2. The user is presented with a file dialog (we might expand this later to provide a webservice option through GEO or something).
  3. Depending on the file type, we do different things:
     • If it's a 2.x style attribute file, then just open the file.
     • If it's an excel file, present a parsing gui similar to what we have now for excel.
  4. Add a window that asks users to identify the type of the key (e.g. gene id, pdb id, whatever). This will be an important bit of information that will help us map identifiers onto networks.
  5. Once the attributes are loaded, return a modified start screen (or continue in the wizard?). The screen should (ideally) be modified such that the next obvious step is to load a network.
  6. The user should be presented with an option to load their own network or import one from somewhere else.
  7. If they load their own network, then they should be presented with the usual dialog, just like a normal import.
  8. If they want us to load a network for them, then they will need to answer some questions about the type of network to load.
     • What species?
     • Any other criteria?
     • Load a network from a pre-determined, fast, reliable web service. (Should users have the option to use their attribute data as a query or should we just load a whole species network?)
  9. Once the network is loaded, they should be asked to identify the type of the key used for nodes in the network. This will be used to map the attributes to the network.
  10. Once network and attributes are loaded map the attribute data onto the network.
  11. Now that we have network and attribute data, return to a modified start screen. The screen should be modified so that it now highlights the available analysis options.
  12. The user now selects the analysis or visualization task they'd like to proceed with (filter, layout, vizmap, etc.).
  13. Cytoscape is now in its normal operating phase.
• This workflow should also work in reverse, which is to say: load a network, then load data, then do analysis.
• We should even allow users to select the analysis they want to do, then be prompted to load the necessary prerequisites for that analysis.

• There should be a button that always allows users to return to the QuickStart screen.

Project Dependencies

• This will be 3.0 project.
• This will depend on the Task framework.
• We've refactored the data import dialogs to be a bit simpler.

Comments

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