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About this Document

This is an official Request for Comment (RFC) for "improving the quality of the Cytoscape 2.3 release."

RFC 2 is divided in three parts:


12/05/05: This document is open for public comment.

Part I: The Interviews


Part II: Results from 2005 Cytoscape Retreat


Part III: Final Proposals

1. First, do no harm

This final list of proposals represents my best attempt at extracting all the many ideas I have heard, and making them as concrete as possible. I (obviously) used some judgement in selecting some ideas over others, and I tried to develop the final list based on the following criteria:

If you disagree with my final list of ideas, or think my ideas are not broad enough, add a comment below.

Add a comment about this idea: /Scope_Comment

2. Focus Cytoscape 2.3 Objectives on Specific Biological Use Cases

During the last two hours of the Cytoscape Retreat, we devised a set of objectives for Cytoscape_2.3. We need to finish up this task and:

Add a comment about this idea: /Finalize_Objectives_Comment

3. Invite User Feedback on Cytoscape 2.3 Objectives

Once we have Cytoscape 2.3 clear in our minds, and clearly written, we should email the cytoscape-discuss mailing list, and invite feedback from the larger community. Each proposed feature should have a comments page where the public can write in comments, and we should also provide a catch-all page where people can easily request new features.

A bit more background on this: many, many people would like us to solicit more feedback from our user community. Rather than just emailing out a generic email or creating an online poll, I think it would be much more effective if we went to our users with a specific plan, and asked them to comment on that plan. Users can then easily add comments to specific features, and the module owners will be responsible for trying to incorporate these comments into their RFC process.

Add a comment about this idea: /User_Feedback_Comment

4. Adopt a Formal RFC Process for Each New Feature / Refactoring in Cytoscape 2.3

Each new feature / refactoring slated for Cytoscape 2.3 will go through a public review process via an RFC posted to the Cytoscape Wiki.

RFC_1 will serve as a starting template for all RFCs.

Depending on the feature, the RFC should include the following:

Once posted to the wiki, the RFC owner should announce it via the cytostaff and cytoscape-discuss mailing lists, and provide a specific deadline for public discussion. RFCs should be open for public comment for at least one week, and should provide a clear mechanism for adding comments. We should make every effort to involve Cytoscape users in the RFC process.

Add a comment about this idea: /RFC_Comment

5. Clarify Roles at the Beginning of Release Work

Rather than wait until the end of a release to determine who is doing what, appoint people right now to key positions. Ideally, we should rotate these roles at each release in order to spread knowledge throughout the group. Here are the most important roles:

Add a comment about this idea: /Roles_Comment

6. Focus on Cytoscape 2.3 Objectives via Wiki and Weekly Conference Calls

At the 2005 Cytoscape Retreat, we came up with a list of goals for Cytoscape_2.3. We need to maintain focus on these goals, and can do so in two ways:

Ethan volunteers to lead up this item.

Add a comment about this idea: /Focus_Comment

7. Create Module Owners for each New Feature / Refactoring in Cytoscape 2.3

Each new feature / proposed refactoring in Cytoscape 2.3 should have one clear module owner, and this module owner must be specified on the Cytoscape_2.3 page. The module owner is responsible for coordinating the RFC process for their proposed module, reviewing any code which affects the proposed module, and serving as a central point of contact for the module.

For example, in Cytoscape 2.3, we might have the following module owners:

Module owners might rotate or change at every release.

Add a comment about this idea: /Module_Owners_Comment

8. Focus on Usability of Visual Styles / Filters

At the Cytoscape Retreat, many individuals expressed interest in "improving the usability of Cytoscape." However, this is such a large task, that we might not get very far. To narrow things down, Cytoscape 2.3 should focus on:

Both of these items were triaged at the Cytoscape retreat as being very important features.

To Allan K's suggestion, we should reach out to and collaborate with usability / UI research groups at universities.

If we are able to substantially improve the usability of the visual styles / filters in Cytoscape 2.3, we can use this as a basis to improve the usability of other features within Cytoscape.

Add a comment about this idea: /Usability_Comment

9. Create a Cytoscape User FAQ

To help new users, create a Cytoscape User FAQ. For simplicity, keep this on the Wiki. This is relatively easy to do, but would be enormously beneficial to end-users.

Add a comment about this idea: /FAQ_Comment

10. Create a Cytoscape Exchange Program

There is simply no substitute for face-to-face communication, and there are very real limits to communicating via email / phone. Each module owner should make every effort to set-up exchange programs e.g. Nerius comes to NY for a few days, and Ben goes to Agilent for a few days, etc. I am not sure how funding for this would work, but we should discuss further.

Add a comment about this idea: /Exchange_Comment

RFC_2 (last edited 2009-02-12 01:04:11 by localhost)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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