TableOfContents([2])

About this Document

This document summarizes the results of the RFC 2 discussion during the 2005 Cytoscape Retreat.

• Section 1 documents the final group ideas. Ideas which garnered the most ideas are shown first.
• Section 2 documents individual ideas from Cytoscape retreat attendees.

Section 1: Final Group Ideas

Idea 1: Gather Feedback from Cytoscape Users

Total Number of Votes: 6

Summary:

• Cytoscape has thousands of users. We should develop a feedback and information gathering mechanism for this large user base.
• Feature prioritization should be based on user feedback.
• Display statistics on the Cytoscape site about most liked, wanted, and disliked features.
• Organize user meetings, perhaps in combination with another meeting users might attend.
• Provide easy mechanism to make feature requests, submit new ideas.
• Create a User FAQ

• Create a User Q&A forum online for new users (Cytoscape discuss seems very programmer oriented)

• Conduct user survey.

Idea 2: Create Development Coordinators

Total Number of Votes: 6

Summary:

• Partition and assign rotating responsibility for development areas.
• "Development coordinators" will be tasked with centralizing and facilitating communication between areas.
• Posts held for 1-2 years.
• May need one top-level coordinator to arbitrate development coordinators and cover misc. tasks.

Idea 3: Be Clear About Use-Cases and Long-Term Vision

Total Number of Votes: 4

Summary:

• Implement a process for defining use-cases, and building community consensus.
• Adopt a Mozilla-like process for development to reach these goals.
• Implement this for 2.3; maybe not possible for long-term vision.

Idea 4: Adopt a more Systematic Development Process

Total Number of Votes: 3

Summary:

• User requirements gathering (talk to our users more)
• Technical specs and documentation
• Coding
• Testing
• User Feedback
• Documentation for the end-user

Idea 5: Create a new Project Coordinator / Architect

Total Number of Votes: 1

Summary:

• Full-time position
• Central contact for both developers and users.
• Authority to make decisions, but answerable to core developers, PIs, and community.
• Must know the code.

Idea 6: User-Driven Functionality

Total Number of Votes: 1

Summary:

• Solicit feedback from biological users in outreach efforts (e.g. external demos, tutorials) in a systematic form, as follows:
  • ask a structured set of questions, including, "Why are you using the software?", "Can you perform this function now?", and so forth.
  • ask if users would be willing to weigh in again 6 months later.
• Have a designated Cytostaffer whose role is to assess feedback and identify key functionality to address major concerns, and works closely with core developers to communicate and track targeted developments.
• Track development efforts on the wiki, and open it up to users.

Section 2: Ideas from Individual Retreat Participants

Nerius Landys

We seem to be easy swayed by problems reported by users, etc. This forces us to focus on short-term development goals rather than long-term goals. To see Cytoscape really break through, we should be focusing on what Cytoscape will become five years from now.

Chris Workman

Rotating officres for development areas (MVC might be a natural breakdown). "Development coordinators" help to centralize and facilitate flow of information. An office would also be need to coordinate the development coordinators. Posts held for 1-2 years.

Allan Kuchinsky

Collaborate with usability / UI research groups at universities. Do student usability review projects; use Cytoscape UI as a vehicle, e.g. for heuristic walk-throughs.

Mike Smoot

Create a project manager / chief architect. Must know the code; must have authority to decide what goes in / stays out and have veto power over PIs. Should be dedicated to Cytoscape work - not a part-time gig.

Michael Creech

Define a process for reviewing and determining Cytoscape core additions / modifications made by the community.

Janette Jones

Create a project administrator. Two functions to oversee: understand timings and linkages / codependencies of modules and also synthesize feedback from the user community (ie. keep track of who they are; organize scheduled feedback from them, and feed that back to the Cytoscape developers.

Patrick Warren

Open a structured route for user feedback, e.g. online pools for feature prioritization, online user feedback form, etc.

Gary Bader

Create a clear group-based process for biological use-case driven core feature prioritization and implementation review. Be clear about our use-cases (bio-focused); use this to prioritize new features; review by group of new core features; do this early in the release cycle. Right now, we are not clear about our use cases.

Scooter Morris

Adopt (and refine) a working open-source model. Mozilla defines 'module owners" who take directions / responsibility for sections of the code base. Developers submit their code for review, and depending on the module, super-review. Module owners can change over time, but provides a single point to collect ideas about module directions.

Alex Pico

Designate a project manager to oversee all development efforts and organize / visualize how it all fits together in the context of specific user cases.

Melissa Cline

Identify holes in existing functionality through outreach to external users. Solicit feedback in external demos, tutorials, etc. directed at biological users. Select 2-3 key holes to address in 2.3. Track efforts on key holes through the wiki; with participation from users.

Guy Warner

Develop Cytoscape to address the emerging needs of users. Improve usability. Ensure Cytoscape keep pace with its users. Make the simple things even easier.

Benno Schwikowski

The lack of concrete persons taking charge of one or the other aspect of the project has been a growing weakness of the project. Without affecting the current levels of identification with the project, we could designate -- possibly by election -- people what take active charge and responsibility for a number of specific higher-level issues, e.g. software architecture, user interface, etc.

Willem Ligtenberg

Split project up in more layers. Core (kernel) = graph model plus renderer. Visualization = makes the core usable, but nothing more. Plugins = (Programs) allow you to do exactly what you want.

Benjamin Gross

Create a new rotating position for "Chief Architect". Nobody has an entire picture of the code base. Too much refactoring going on.

Keiichiro Ono

Start from documents, not from coding (UML, etc.) Since there is no comprehensive documentation for developers, it's hard to maintain other's code.)

Iliana Avila

Be a lot more user oriented.

Amy Wiles

Improve user input as to what feature they would like to see / ability to get help on Cytoscape usage. Perhaps a simple FAQ or online Q&A that would not be emailed out to everyone to aid new users. Currently, mailing list seems very programmer oriented.

Andrew Kossenkov

You can't open files if they are not in the machine you're working on. Make it possible to get files from remote servers.

Adeleye Yeyejide

Improved interaction with user: Plugin development, feature requests, how new features are determined. Survey of users and what they require. Someone should be in charge of interacting with potential users.

Aditya Vailaya

Cytoscape has had 1,000s of downloads. We should be gathering feedback from this large user base. Have a feature prioritization / gathering via Cytoscape discuss / announce lists; collate statistics over the next month or so. Development of prioritized features.

Trey Ideker

More structured organization of core developers. Stricter cvs control; avoid sweeping core changes; appoint chief developer; build website clearing house; adopt procedures as a group. Improve task scheduling, coordination, responsibility, and timeliness.