Wiki_clean-up_RFC

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About this document

This is an official Request for Comment (RFC) for reorganizing the wiki. Wikis grow organically and shouldn't be organized until there is content that needs to be organized. The Cytoscape wiki is starting to have quite a bit of content and is starting to get messy, so we should impose a little bit of structure to help keep it useful i.e. easy to find information.

For details on RFCs in general, check out the Wikipedia Entry: Request for Comments (RFCs)

Status

Open for comment as of Feb.23.2006

How to Comment

Add comments in the discussion section at the bottom of the page along with your name and the date.

Proposal

• Put more description about the Cytoscape project on the front page and a clearer connection to cytoscape.org
• Have the following sections:

  • Using Cytoscape (already there, no change, geared towards biologist and computational biologist users)

    • Add all publications to the publications page. This page is easier to update than the website, so may be easier for us to use to track papers that use Cytoscape. This is very important for providing to our granting agencies that Cytoscape is useful and should be funded.
    • Move the network analysis links page up here. Collecting links to other projects is very useful for our grants as well, since we can more easily identify unique Cytoscape features and show the usefulness of network analysis tools in general.

  • Developing with Cytoscape (new section, documentation focused, geared towards computational biologists and software developers)

    • All class documentation, tutorial info, etc. goes here
    • This is what all developers should read when first starting out + link to all developer reference material

  • Cytoscape Community

    • Links to people writing plugins, user meetings, retreats, mailing lists, etc.

  • Cytoscape project coordination (new section that is project admin focused)

    • All admin and RFCs go here

Implementation Plan

• Gary will reorganize, mostly by editing and renaming existing pages

Defered items

• Better integrate the wiki with cytoscape.org
  • Update the CSS for the wiki so that it looks like the main cytoscape.org page and has the same header. This will make it easier for users to get back to the main Cytoscape.org page.

Discussion

• There's also a lot of potential user documentation lurking in various corners of the Wiki. We could start collecting that by adding a Documentation link to the Using Cytoscape section (Melissa Cline).

  • GaryBader - actually, that reminds me that there is a category feature on the wiki that lets you tag pages as falling into a specific category and then links to all those pages can be automatically generated.

• Great idea to have a Cytoscape project coordination page! But the pitfall is that the RFCs will be buried by Cytoscape core team administrative material, such as meeting notes, and there won't be much external participation. What about: one page listing all open RFCs, with a link from Cytoscape Community as well? (Melissa Cline).

• I would vote for a cleaner front page, that is less cluttered and more focused on key links.Perhaps like http://www.bioconductor.org/ Or even as Spartan as GenMAPP; http://www.genmapp.org/ For instance, Cytoscape could have back pages for Publications (could be replaced by a live link to HighWire with a search for Cytoscape (see: middle of page http://www.genmapp.org/Publications.html) Information of all the versions of Cytoscape should be replaced with general description Cytoscape. Information about funding on back page. (Bruce Conklin).