Differences between revisions 27 and 97 (spanning 70 versions)
← Revision 27 as of 2007-01-08 18:00:14 →
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Comment:
← Revision 97 as of 2009-12-22 16:40:46 →
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Comment: Added RFC 64 describing equation attributes.
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
 * 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'' ||
|| [[Cytoscape_2.8/EquationAttributes|RFC 65]]: Add attribute reference equations as attributes|| 2009-12-22 || 2.8 || draft ||
|| [[CytoscapeCommons|RFC 64]]: Cytoscape Commons: a site for plugin development || 2009-04-21 || 3.0 || draft ||
|| [[Cytoscape_3.0/EventHandling|RFC 63]]: Event handling in Cytoscape 3.0 || 2008-11-21 || 3.0 || draft ||
|| [[Cytoscape_3.0/DataProvenance|RFC 62]]: Support for Data Provenance in Cytoscape 3.0 || 2008-11-20 || 3.0 || draft ||
|| [[AutomaticBugReporter|RFC 61]]: Automatic Bug reporter of Cytoscape || 2008-09-19 || 3.0 || open ||
|| [[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

RFC 65: Add attribute reference equations as attributes

2009-12-22

2.8

draft

RFC 64: Cytoscape Commons: a site for plugin development

2009-04-21

3.0

draft

RFC 63: Event handling in Cytoscape 3.0

2008-11-21

3.0

draft

RFC 62: Support for Data Provenance in Cytoscape 3.0

2008-11-20

3.0

draft

RFC 61: Automatic Bug reporter of Cytoscape

2008-09-19

3.0

open

RFC 60: Advanced Network Merge and ID Mapping API

2008-05-02

2.6

open

RFC 59: Cytoscape Book

2008-05-02

3.0

RFC under construction

RFC 58: Pathway Walking Plugin

2007-12-05

2.5

being coded

RFC 57: Cytoscape Rewrite (alt to RFC 46)

2007-10-30

3.0

open

RFC 56: Visual Style Simplification

2007-10-29

3.0

open

RFC 55: Web Front End for Cytoscape

2007-10-24

3.0

open

RFC 54: Cytoscape Themes: A Pinch of Syntactic Sugar

2007-10-24

3.0

in testing

RFC 53: SubgeneViewer: Cytoscape from Service Provider Perspective

2007-10-23

2.7

open

RFC 52: Event Handling System

2007-10-23

3.0

open

RFC 51: Cytoscape Projects

2007-10-23

3.0

open

RFC 50: Task Management

2007-10-17

3.0

open

RFC 49: Viewing groups

2007-09-26

2.x

open

RFC 48: Plugin Themes

2007-09-13

2.6

being coded

RFC 47: Plugin Interface Refactor

2007-08-24

3.0

open

RFC 46: Cytoscape Layers Refactor

2007-08-16

3.0

open

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

2007-08-15

2.6

being coded

RFC 44: Build Process/Dependency Management

2007-08-01

3.0

open

RFC 43: Excentric Labeling in Cytoscape

2007-07-26

2.x

being coded

RFC 42: Task Monitor Refactoring

2007-07-26

3.0

open

RFC 41: Consolidated Graph Analysis Plugin

2007-07-24

2.x

open

RFC 40: Scripting in Cytoscape

2007-07-24

3.0

open

RFC 39: Data Integration/Web Services

2007-07-19

2.x

being coded

RFC 38: Code Layering

2007-07-18

3.0

open

RFC 37: Attribute Namespaces

2007-06-27

3.0

open

RFC 36: Layout Improvement

2007-06-26

2.5

closed

RFC 35: Molecular Interaction Maps

2006-10-10

3.0

open

RFC 34: User Training Strategy

2007-05-18

3.0

open

RFC 33: Filters UI Redesign

2007-04-25

2.6

being coded

RFC 32: rich linetypes

2007-04-22

3.0

open

RFC 31: Implement local (per-network) attributes

2007-04-22

3.0

open

RFC 30: Making undirected edges first-class citizens

2007-04-22

3.0

being coded

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

2007-04-13

2.6

being coded

RFC 28: Multilevel graph layout algorithm

2007-02-15

2.6

being coded

RFC 25: Bubble Router Plugin

2007-01-19

2.6

being coded

RFC 23: Cleaning up the import/export file menus

2007-01-08

3.0

open

RFC 21: User interface testing framework

2006-10-31

3.0

open

RFC 6: Cytoscape headless mode operation

2006-01-27

3.0

open

Completed RFCs

RFC 27: Plugin Web site and auto import

2007-02-07

2.5

closed

RFC 26: Performance Profiling

2007-02-06

2.5

closed

RFC 24: Visual Mapping GUI Redesign

2006-01-10

2.5

closed

RFC 22: Creating single instance webstarts

2006-12-12

2.5

closed

RFC 20: General Text/Excel file import framework

2006-10-11

2.5

closed

RFC 19: HyperEdge API

2006-09-12

2.5

closed

RFC 18: Group API (replaces RFC 8 and RFC 9)

2006-08-16

2.5

closed

RFC 17: Importable File Type

2006-03-14

2.4

closed

RFC 16: Text Table Network File Import

2007-01-19?

2.5

closed

RFC 15: New Icon Set for Cytoscape 2.4

2006-07-19

2.4

closed

RFC 14: Quick Find Feature

2006-07-05

2.4

closed

RFC 13: New Bio Data Server (Gene Ontology Server)

2006-06-22

2.4

closed

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

2006-03-07

2.4

closed

RFC 11: Cytoscape Undo Manager

2006-01-26

2.5

closed

RFC 10: Preferences initialization

2006-03-22

2.4

closed

RFC 9: Simplified MetaNode Data Structure

2006-01-27

2.4

closed

RFC 8: MetaNodes

2006-01-18

2.4

closed

RFC 7: Adding support for additional file types

2006-03-14

2.4

closed

RFC 5: Wiki clean-up

2006-02-23

2.5

closed

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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