CodeLayering

TableOfContents([2])

Status

Not yet completely written; please feel free to expand on content and idea

Proposal

Code Layering - for the purpose of enabling a command layer (headless mode) and different front ends (e.g., web-based or SVG). Some may see this as refactoring, but I think we can identify critical feature-based goals that derive from code layering that can be more readily justified as project aims that are typically expected to produce something "new".

Use Cases

• Headless Mode: Something we talked about having for a while. Do people have particular projects that would benefit from this?

• Web-based Front Ends: there is evolutionary pressure for software these days to be more web-based (versus stand-alone or even web start). Can we come up with specific projects that would make use of this?

  • Cytoscape Server: many at ISB would utilize this for larger network analysis projects and several would embed it into internal and external web sites

  • GenMAPP-CS funding is starting in August and we plan to hire someone to work on this sort of development in Cytoscape to expand the client options.

  • WikiPathways.org might be able to embed a special front end of cytoscape for advanced pathway analysis

  • http://t1dbase.org would like to be able to use Cytoscape directly through a web front end (Nat Goodman has directly requested it several times)

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General Notes

Requirements

Backward Compatibility

• Identify critical areas effected by layering:

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Implementation Plan

• Identify collections of classes to be layered
• Layer the code
• Develop new features

Comments

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