Differences between revisions 30 and 47 (spanning 17 versions)
Revision 30 as of 2007-05-26 14:01:28
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Revision 47 as of 2007-05-27 13:42:42
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||Free for Academic use ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES ||NO ||NO ||NO ||NO ||NO ||<bgcolor="#33ff00">YES ||
||Free for Commercial use ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES ||
NO ||NO ||NO ||NO ||NO ||<bgcolor="#33ff00">YES ||
||Open Source ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES ||
NO ||NO ||NO ||NO ||NO ||NO ||
||nbr Curated Pathways || ||96? || || || || || || || ||
||nbr species supported || ||11 || || || || || || || ||
||User-defined Pathways ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES || || || || || ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES ||
||Inferred Pathways ||<bgcolor="#33ff00">YES || || || ||<bgcolor="#33ff00">YES || || || || ||
||Pathway overrepresentation analysis ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES || || || || || || || ||
||Gene Ontology overrepresentation ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES || || || || || || || ||
||Automated Graph Layout ||<bgcolor="#33ff00">YES || || || || || || || || ||
||Free for Academic use ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES ||<bgcolor="#ff3333">NO ||<bgcolor="#ff3333">NO ||<bgcolor="#ff3333">NO ||<bgcolor="#ff3333">NO ||<bgcolor="#00ff00">YES ||<bgcolor="#33ff00">YES ||
||Free for Commercial use ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES ||<bgcolor="#ff3333">
NO ||<bgcolor="#ff3333">NO ||<bgcolor="#ff3333">NO ||<bgcolor="#ff3333">NO ||<bgcolor="#ff3333">NO ||<bgcolor="#33ff00">YES ||
||Open Source ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES ||<bgcolor="#ff3333">
NO ||<bgcolor="#ff3333">NO ||<bgcolor="#ff3333">NO ||<bgcolor="#ff3333">NO ||<bgcolor="#ff3333">NO ||<bgcolor="#ff3333">NO ||
||nbr Curated Pathways || ||96? ||949 ||2100 || || ||500 || || ||
||nbr species supported || ||11 ||10 ||17 || || || || || ||
||User-defined Pathways ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES || || ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES ||
||Inferred Pathways ||<bgcolor="#33ff00">YES || || || ||<bgcolor="#33ff00">YES || ||<bgcolor="#33ff00">YES ||YES || ||
||Pathway overrepresentation analysis ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES || || || ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES || || ||
||Gene Ontology overrepresentation ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES || || ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES || || ||
||Automated Graph Layout ||<bgcolor="#33ff00">YES || || || ||<bgcolor="#33ff00">YES || || ||YES || ||
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||Graphical Overlays ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES || || ||<bgcolor="#33ff00">YES || || || || ||
||User-defined overlays ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES || || || || || || || ||
||Graphical Overlays ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES || ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES || ||<bgcolor="#33ff00">YES ||YES || ||
||User-defined overlays ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES || ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES || ||<bgcolor="#33ff00">YES ||YES || ||
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||Multiple visual styles ||<bgcolor="#33ff00">YES || || || || || || || || ||
||advance search/filter ||<bgcolor="#33ff00">YES || || || || || || || || ||
||customizable gene/protein database || ||<bgcolor="#33ff00">YES || || || || || || ||
||nbr input/output spigots || || || || || || || || || ||
||statistical network analysis ||<bgcolor="#33ff00">plugins || || || || || || ||<bgcolor="#33ff00">YES || ||
||Multiple visual styles ||<bgcolor="#33ff00">YES || || ||<bgcolor="#33ff00">YES || || || || || ||
||advance search/filter ||<bgcolor="#33ff00">YES || || || ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES || || ||
||customizable gene/protein database || ||<bgcolor="#33ff00">YES || || || || ||<bgcolor="#33ff00">YES || ||
||rich graphical annotation || ||<bgcolor="#33ff00">YES || || || || || ||
|| ||
||nbr input/output spigots ||15 ||?? || ||12 ||16 || ||many ||4 || ||
||layers ||coming || || || || || || ||YES || ||
||
statistical network analysis ||<bgcolor="#33ff00">plugins || || ||shortest path || ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES ||<bgcolor="#33ff00">YES || ||

TableOfContents

Software applications

Programming Libraries

Layouts

Other link directories

Network Visualization

Competitive Landscape

Feature

Cytoscape

GenMAPP

Pathway Commons

Jubilant

Ariadne

Ingenuity

GeneGo

pajek

CellDesigner

Free for Academic use

YES

YES

YES

NO

NO

NO

NO

YES

YES

Free for Commercial use

YES

YES

YES

NO

NO

NO

NO

NO

YES

Open Source

YES

YES

YES

NO

NO

NO

NO

NO

NO

nbr Curated Pathways

96?

949

2100

500

nbr species supported

11

10

17

User-defined Pathways

YES

YES

YES

YES

YES

YES

YES

Inferred Pathways

YES

YES

YES

YES

Pathway overrepresentation analysis

YES

YES

YES

YES

Gene Ontology overrepresentation

YES

YES

YES

YES

YES

Automated Graph Layout

YES

YES

YES

Interactive Graph Layout

YES

Graphical Overlays

YES

YES

YES

YES

YES

YES

User-defined overlays

YES

YES

YES

YES

YES

YES

SQL defined coloring criteria

YES

Multiple visual styles

YES

YES

advance search/filter

YES

YES

YES

YES

customizable gene/protein database

YES

YES

rich graphical annotation

YES

nbr input/output spigots

15

??

12

16

many

4

layers

coming

YES

statistical network analysis

plugins

shortest path

YES

YES

YES

quantitative simulation

YES

YES

Network_analysis_links (last edited 2009-09-06 11:30:19 by c-98-207-16-44)

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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