Differences between revisions 35 and 90 (spanning 55 versions)
← Revision 35 as of 2007-04-22 14:47:38 →
Size: 2433
Editor: ujdr9rftay
Comment: add "undirected edges" RFC (following Mike Smoot's request)
← Revision 90 as of 2008-07-03 13:40:25 →
Size: 6506
Editor: csik
Comment: note status change of rfc 30: undirected edges
Deletions are marked like this. Additions are marked like this.
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RFCs represent one possible mechanism for soliciting feedback for core Cytoscape features / refactoring. For details on RFCs in general, check out the [http://www.answers.com/main/ntquery?method=4&dsid=2222&dekey=Request+for+Comments&gwp=8&curtab=2222_1&linktext=Request%20for%20Comments Wikipedia Entry: Request for Comments (RFCs)] RFCs represent one possible mechanism for soliciting feedback for core Cytoscape features / refactoring. For details on RFCs in general, check out http://en.wikipedia.org/wiki/Request_for_Comments the Wikipedia Entry: Request for Comments (RFCs)

== RFC Template ==
Creating a new RFC? Use the ["RFC Template"] and add a link to table below.
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 * ["RFC 1"]: Migrating !GraphObjAttributes to !CyAttributes
 * ["RFC 2"]: Improving the quality of the Cytoscape 2.3 release
 * ["RFC 3"]: Migrating the user manual to the wiki
 * [:License clean-up RFC:RFC 4]: Java code license clean-up
 * [:Wiki clean-up RFC:RFC 5]: Wiki clean-up
 * [:HeadlessModeRFC:RFC 6]: Cytoscape headless mode operation
 * [:ImportableFileTypeRFC:RFC 7]: Adding support for additional file types
 * [:MetaNodes RFC:RFC 8]: !MetaNodes
 * [:SimplifiedMetaNodeDataStructureRFC:RFC 9]: Simplified !MetaNode Data Structure
 * [:PreferenceInitializationRFC:RFC 10]: Preferences initialization
 * [:UndoManager RFC:RFC 11]: Cytoscape Undo Manager
 * [:VizMapPropsRFC:RFC 12]: Fixing the loading and saving of the vizmap.props file
 * [:BioDataServerRFC:RFC 13]: New Bio Data Server (Gene Ontology Server)
 * [:QuickFindRFC:RFC 14]: Quick Find Feature
 * [:CytoscapeIcons:RFC 15]: New Icon Set for Cytoscape 2.4
 * [:SimpleTextTableImport:RFC 16]: Text Table Network File Import
 * [:ImportableFileTypeRFC:RFC 17]: Importable File Type
 * [:groupAPI:RFC 18]: Group API (replaces RFC 8 and RFC 9)
 * [:HyperEdgeAPI:RFC 19]: Hyper''''''Edge API
 * [:TextFileImport:RFC 20]: General Text/Excel file import framework
 * [:GuiTesting:RFC 21]: User interface testing framework
 * [:SingleInstanceWebstart:RFC 22]: Creating single instance webstarts
 * [:ImportExportMenus:RFC 23]: Cleaning up the import/export file menus
 * [:VizMapUI:RFC 24]: Visual Mapping GUI Redesign
 * [:BubbleRouterRFC:RFC 25]: Bubble Router Plugin
 * [:PerformanceProfilingRFC:RFC 26]: Performance Profiling
 * [:Pluginwebsite:RFC 27]: Plugin Web site and auto import
 * [:MultilevelLayout:RFC 28]: Multilevel graph layout algorithm
 * [:WebServicesIDMapping:RFC 29]: Web services API for ID mapping/translator service
 * [:UndirectedEdges:RFC 30]: Making undirected edges first-class citizens
 * Please add your next RFC here...
== RFC Template ==
Creating a new RFC? Use the: RfcTemplate 		|| '''Name of RFC''' ||'''Date of RFC Creation''' ||'''Target''' ||'''Status''' ||
|| ''Please add your next RFC here...'' || ''... the date'' || ''... the target release'' || ''... and the status'' ||
|| [:Advanced Network Merge and ID Mapping:RFC 60]: Advanced Network Merge and ID Mapping API || 2008-05-02 || 2.6 || open ||
|| [:Cytoscape Book:RFC 59]: Cytoscape Book || 2008-05-02 || 3.0 || RFC under construction ||
|| [:Pathway walking plugin:RFC 58]: Pathway Walking Plugin || 2007-12-05 || 2.5 || being coded ||
|| [:CytoscapeRewrite:RFC 57]: Cytoscape Rewrite (alt to RFC 46) || 2007-10-30 || 3.0 || open ||
|| [:Visual Style Simplification:RFC 56]: Visual Style Simplification || 2007-10-29 || 3.0 || open ||
|| [:WebFrontEnd:RFC 55]: Web Front End for Cytoscape || 2007-10-24 || 3.0 || open ||
|| [:CytoscapeThemes:RFC 54]: Cytoscape Themes: A Pinch of Syntactic Sugar || 2007-10-24 || 3.0 ||in testing ||
|| [:CytoService:RFC 53]: Subgene''''''Viewer: Cytoscape from Service Provider Perspective || 2007-10-23 || 2.7 ||open ||
|| [:EventHandling:RFC 52]: Event Handling System || 2007-10-23 || 3.0 || open ||
|| [:CytoscapeProject:RFC 51]: Cytoscape Projects || 2007-10-23 || 3.0 || open ||
|| [:TaskManagement:RFC 50]: Task Management || 2007-10-17 || 3.0 || open ||
|| [:GroupViews:RFC 49]: Viewing groups || 2007-09-26 || 2.x || open ||
|| [:CytoscapePluginBundles:RFC 48]: Plugin Themes || 2007-09-13 || 2.6 || being coded ||
|| [:PluginRefactor:RFC 47]: Plugin Interface Refactor || 2007-08-24 || 3.0 || open ||
|| [:CytoscapeLayerRefactor:RFC 46]: Cytoscape Layers Refactor || 2007-08-16 || 3.0 || open ||
|| [:BioWebServiceConnectivity:RFC 45]: Web Services Client Manager and Unified Network/Attribute Import Mechanism || 2007-08-15 || 2.6 || being coded ||
|| [:DependencyManagement:RFC 44]: Build Process/Dependency Management || 2007-08-01 || 3.0 || open ||
|| [:ExcentricLabelRFC:RFC 43]: Excentric Labeling in Cytoscape || 2007-07-26 || 2.x || being coded ||
|| [:TaskMonitorRefactoring:RFC 42]: Task Monitor Refactoring || 2007-07-26 || 3.0 || open ||
|| [:Consolidated graph analysis plugin:RFC 41]: Consolidated Graph Analysis Plugin || 2007-07-24 || 2.x || open ||
|| [:Scripting:RFC 40]: Scripting in Cytoscape || 2007-07-24 || 3.0 || open ||
|| [:DataIntegration:RFC 39]: Data Integration/Web Services || 2007-07-19 || 2.x || being coded ||
|| [:CodeLayering:RFC 38]: Code Layering || 2007-07-18 || 3.0 || open ||
|| [:AttributeNamespaces:RFC 37]: Attribute Namespaces || 2007-06-27 || 3.0 || open ||
|| [:LayoutImprovement:RFC 36]: Layout Improvement || 2007-06-26 || 2.5 || closed ||
|| [:Molecular Interaction Maps:RFC 35]: Molecular Interaction Maps || 2006-10-10 || 3.0 || open ||
|| [:UserTraining:RFC 34]: User Training Strategy || 2007-05-18 || 3.0 || open ||
|| [:Filters UI Redesign:RFC 33]: Filters UI Redesign || 2007-04-25 || 2.6 || being coded ||
|| [:RichLineTypes:RFC 32]: rich linetypes || 2007-04-22 || 3.0 || open ||
|| [:LocalAttributes:RFC 31]: Implement local (per-network) attributes || 2007-04-22 || 3.0 || open ||
|| [:UndirectedEdges:RFC 30]: Making undirected edges first-class citizens || 2007-04-22 || 3.0 || being coded ||
|| [:WebServicesIDMapping:RFC 29]: Web services API for ID mapping/translator service || 2007-04-13 || 2.6 || being coded ||
|| [:MultilevelLayout:RFC 28]: Multilevel graph layout algorithm || 2007-02-15 || 2.6 || being coded ||
|| [:BubbleRouterRFC:RFC 25]: Bubble Router Plugin || 2007-01-19 || 2.6 || being coded ||
|| [:ImportExportMenus:RFC 23]: Cleaning up the import/export file menus || 2007-01-08 || 3.0 || open ||
|| [:GuiTesting:RFC 21]: User interface testing framework || 2006-10-31 || 3.0 || open ||
|| [:HeadlessModeRFC:RFC 6]: Cytoscape headless mode operation || 2006-01-27 || 3.0 || open ||
=== Completed RFCs ===
|| [:Pluginwebsite:RFC 27]: Plugin Web site and auto import || 2007-02-07 || 2.5 || closed ||
|| [:PerformanceProfilingRFC:RFC 26]: Performance Profiling || 2007-02-06 || 2.5 || closed ||
|| [:VizMapUI:RFC 24]: Visual Mapping GUI Redesign || 2006-01-10 || 2.5 || closed ||
|| [:SingleInstanceWebstart:RFC 22]: Creating single instance webstarts || 2006-12-12 || 2.5 || closed ||
|| [:TextFileImport:RFC 20]: General Text/Excel file import framework || 2006-10-11 || 2.5 || closed ||
|| [:HyperEdgeAPI:RFC 19]: Hyper''''''Edge API || 2006-09-12 || 2.5 || closed ||
|| [:groupAPI:RFC 18]: Group API (replaces RFC 8 and RFC 9) || 2006-08-16 || 2.5 || closed ||
|| [:ImportableFileTypeRFC:RFC 17]: Importable File Type || 2006-03-14 || 2.4 || closed ||
|| [:SimpleTextTableImport:RFC 16]: Text Table Network File Import || 2007-01-19? || 2.5 || closed ||
|| [:CytoscapeIcons:RFC 15]: New Icon Set for Cytoscape 2.4 || 2006-07-19 || 2.4 || closed ||
|| [:QuickFindRFC:RFC 14]: Quick Find Feature || 2006-07-05 || 2.4 || closed ||
|| [:BioDataServerRFC:RFC 13]: New Bio Data Server (Gene Ontology Server) || 2006-06-22 || 2.4 || closed ||
|| [:VizMapPropsRFC:RFC 12]: Fixing the loading and saving of the vizmap.props file || 2006-03-07 || 2.4 || closed ||
|| [:UndoManager RFC:RFC 11]: Cytoscape Undo Manager || 2006-01-26 || 2.5 || closed ||
|| [:PreferenceInitializationRFC:RFC 10]: Preferences initialization || 2006-03-22 || 2.4 || closed ||
|| [:SimplifiedMetaNodeDataStructureRFC:RFC 9]: Simplified !MetaNode Data Structure || 2006-01-27 || 2.4 || closed ||
|| [:MetaNodes RFC:RFC 8]: !MetaNodes || 2006-01-18 || 2.4 || closed ||
|| [:ImportableFileTypeRFC:RFC 7]: Adding support for additional file types || 2006-03-14 || 2.4 || closed ||
|| [:Wiki clean-up RFC:RFC 5]: Wiki clean-up || 2006-02-23 || 2.5 || closed ||
|| [:License clean-up RFC:RFC 4]: Java code license clean-up || 2006-02-16 || 2.4 || closed ||
|| ["RFC 3"]: Migrating the user manual to the wiki || 2005-12-25 || 2.4 || closed ||
|| ["RFC 2"]: Improving the quality of the Cytoscape 2.3 release || 2005-11-28 || 2.4 || closed ||
|| ["RFC 1"]: Migrating !GraphObjAttributes to !CyAttributes || 2005-09-30 || 2.3 || closed ||

Request for Comments (RFCs)

About RFCs

RFCs represent one possible mechanism for soliciting feedback for core Cytoscape features / refactoring. For details on RFCs in general, check out http://en.wikipedia.org/wiki/Request_for_Comments the Wikipedia Entry: Request for Comments (RFCs)

RFC Template

Creating a new RFC? Use the ["RFC Template"] and add a link to table below.

RFC Index

Name of RFC

Date of RFC Creation

Target

Status

Please add your next RFC here...

... the date

... the target release

... and the status

[:Advanced Network Merge and ID Mapping:RFC 60]: Advanced Network Merge and ID Mapping API

2008-05-02

2.6

open

[:Cytoscape Book:RFC 59]: Cytoscape Book

2008-05-02

3.0

RFC under construction

[:Pathway walking plugin:RFC 58]: Pathway Walking Plugin

2007-12-05

2.5

being coded

[:CytoscapeRewrite:RFC 57]: Cytoscape Rewrite (alt to RFC 46)

2007-10-30

3.0

open

[:Visual Style Simplification:RFC 56]: Visual Style Simplification

2007-10-29

3.0

open

[:WebFrontEnd:RFC 55]: Web Front End for Cytoscape

2007-10-24

3.0

open

[:CytoscapeThemes:RFC 54]: Cytoscape Themes: A Pinch of Syntactic Sugar

2007-10-24

3.0

in testing

[:CytoService:RFC 53]: SubgeneViewer: Cytoscape from Service Provider Perspective

2007-10-23

2.7

open

[:EventHandling:RFC 52]: Event Handling System

2007-10-23

3.0

open

[:CytoscapeProject:RFC 51]: Cytoscape Projects

2007-10-23

3.0

open

[:TaskManagement:RFC 50]: Task Management

2007-10-17

3.0

open

[:GroupViews:RFC 49]: Viewing groups

2007-09-26

2.x

open

[:CytoscapePluginBundles:RFC 48]: Plugin Themes

2007-09-13

2.6

being coded

[:PluginRefactor:RFC 47]: Plugin Interface Refactor

2007-08-24

3.0

open

[:CytoscapeLayerRefactor:RFC 46]: Cytoscape Layers Refactor

2007-08-16

3.0

open

[:BioWebServiceConnectivity:RFC 45]: Web Services Client Manager and Unified Network/Attribute Import Mechanism

2007-08-15

2.6

being coded

[:DependencyManagement:RFC 44]: Build Process/Dependency Management

2007-08-01

3.0

open

[:ExcentricLabelRFC:RFC 43]: Excentric Labeling in Cytoscape

2007-07-26

2.x

being coded

[:TaskMonitorRefactoring:RFC 42]: Task Monitor Refactoring

2007-07-26

3.0

open

[:Consolidated graph analysis plugin:RFC 41]: Consolidated Graph Analysis Plugin

2007-07-24

2.x

open

[:Scripting:RFC 40]: Scripting in Cytoscape

2007-07-24

3.0

open

[:DataIntegration:RFC 39]: Data Integration/Web Services

2007-07-19

2.x

being coded

[:CodeLayering:RFC 38]: Code Layering

2007-07-18

3.0

open

[:AttributeNamespaces:RFC 37]: Attribute Namespaces

2007-06-27

3.0

open

[:LayoutImprovement:RFC 36]: Layout Improvement

2007-06-26

2.5

closed

[:Molecular Interaction Maps:RFC 35]: Molecular Interaction Maps

2006-10-10

3.0

open

[:UserTraining:RFC 34]: User Training Strategy

2007-05-18

3.0

open

[:Filters UI Redesign:RFC 33]: Filters UI Redesign

2007-04-25

2.6

being coded

[:RichLineTypes:RFC 32]: rich linetypes

2007-04-22

3.0

open

[:LocalAttributes:RFC 31]: Implement local (per-network) attributes

2007-04-22

3.0

open

[:UndirectedEdges:RFC 30]: Making undirected edges first-class citizens

2007-04-22

3.0

being coded

[:WebServicesIDMapping:RFC 29]: Web services API for ID mapping/translator service

2007-04-13

2.6

being coded

[:MultilevelLayout:RFC 28]: Multilevel graph layout algorithm

2007-02-15

2.6

being coded

[:BubbleRouterRFC:RFC 25]: Bubble Router Plugin

2007-01-19

2.6

being coded

[:ImportExportMenus:RFC 23]: Cleaning up the import/export file menus

2007-01-08

3.0

open

[:GuiTesting:RFC 21]: User interface testing framework

2006-10-31

3.0

open

[:HeadlessModeRFC:RFC 6]: Cytoscape headless mode operation

2006-01-27

3.0

open

Completed RFCs

[:Pluginwebsite:RFC 27]: Plugin Web site and auto import

2007-02-07

2.5

closed

[:PerformanceProfilingRFC:RFC 26]: Performance Profiling

2007-02-06

2.5

closed

[:VizMapUI:RFC 24]: Visual Mapping GUI Redesign

2006-01-10

2.5

closed

[:SingleInstanceWebstart:RFC 22]: Creating single instance webstarts

2006-12-12

2.5

closed

[:TextFileImport:RFC 20]: General Text/Excel file import framework

2006-10-11

2.5

closed

[:HyperEdgeAPI:RFC 19]: HyperEdge API

2006-09-12

2.5

closed

[:groupAPI:RFC 18]: Group API (replaces RFC 8 and RFC 9)

2006-08-16

2.5

closed

[:ImportableFileTypeRFC:RFC 17]: Importable File Type

2006-03-14

2.4

closed

[:SimpleTextTableImport:RFC 16]: Text Table Network File Import

2007-01-19?

2.5

closed

[:CytoscapeIcons:RFC 15]: New Icon Set for Cytoscape 2.4

2006-07-19

2.4

closed

[:QuickFindRFC:RFC 14]: Quick Find Feature

2006-07-05

2.4

closed

[:BioDataServerRFC:RFC 13]: New Bio Data Server (Gene Ontology Server)

2006-06-22

2.4

closed

[:VizMapPropsRFC:RFC 12]: Fixing the loading and saving of the vizmap.props file

2006-03-07

2.4

closed

[:UndoManager RFC 11]: Cytoscape Undo Manager

2006-01-26

2.5

closed

[:PreferenceInitializationRFC:RFC 10]: Preferences initialization

2006-03-22

2.4

closed

[:SimplifiedMetaNodeDataStructureRFC:RFC 9]: Simplified MetaNode Data Structure

2006-01-27

2.4

closed

[:MetaNodes RFC 8]: MetaNodes

2006-01-18

2.4

closed

[:ImportableFileTypeRFC:RFC 7]: Adding support for additional file types

2006-03-14

2.4

closed

[:Wiki clean-up RFC 5]: Wiki clean-up

2006-02-23

2.5

closed

[:License clean-up RFC 4]: Java code license clean-up

2006-02-16

2.4

closed

["RFC 3"]: Migrating the user manual to the wiki

2005-12-25

2.4

closed

["RFC 2"]: Improving the quality of the Cytoscape 2.3 release

2005-11-28

2.4

closed

["RFC 1"]: Migrating GraphObjAttributes to CyAttributes

2005-09-30

2.3

closed

RFC_Index (last edited 2015-06-05 00:20:36 by bdemchak)

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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