CytoscapeProject

TableOfContents([2])

Proposal

Expand the concept of Session and the presentation of networks in the Control Panel to introduce the concept of a Project. Initially, a Project would include nothing more than the information associated with a session, including a limited amount of information about the files that were loaded to create the session. For example, a Project would "remember" that a network (saved as an XGMML file) was created by reading in a SIF file, and associating three node attribute files and two edge attribute files with it. The goal would be data provenance, not to be able to recreate the initial data sets. Moving forward, Projects could include logs (Cytoscape 3.0 logging), user created scripts, workflows, etc. While the Projects panel might list all available projects, only one project would be opened at a time. As a result, a project could replace a Cytoscape Session as the main mechanism for saving state.

Background

Describe why this project is being proposed and what issues are addressed.

Use Cases

Provide examples of how the products of this project will be used.

Implementation Plan

Outline and describe the process and major issues related to implementing this proposal. Illustrate your plan when possible. Try this free online tool for making diagrams -> [http://www.best4c.com/editor/NetMapApplication.jsp Best4c] (draw; save; then insert hyperlink into this page)

Project Management

Project Timeline

Provide a timeline for implementation. Insert a graphic if you can. Try this free online tool for making project timelines -> [http://www.helpuplan.com/index.asp Help-u-Plan] (create a new chart; modify; right-click to save gif; then attach to this page)

Tasks and Milestones

Outline the major milestones and tasks involved in implementation.

1. Milestone 1: …

   1. Task 1: ...
   2. Task 2: ...

2. Milestone 2: …

Project Dependencies

Outline and projects that depend on this project, link to relevant RFC's and note at what point dependent projects could be started.

Related RFCs

Link to other related RFCs

Issues

List any issues, conflict, or dependencies raised by this proposal

Comments

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