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List of software and libraries for pathway/graph analysis
''last updated October 2014 -- so needs reviewing''
=Mindmapping=
==Commercial Apps==
* [https://literatureandlatte.com Scapple](https://www.literatureandlatte.com/forum/viewtopic.php?f=42&t=20583) from the makers of Scrivener.
* [https://www.delineato.com/ Delineato]
* [https://mindnode.com/ MindNode] + iOS.
* [https://www.conceptdraw.com/ ConceptDraw]
* [https://www.thinkbuzan.com/us/products/imindmap iMindMap] Tony Buzan claims to have invented mindmapping.
* [https://www.ithoughts.co.uk iThoughts] for iOS
* [https://www.novamind.com NovaMind]
* [https://www.mindmaple.com/Products/iPad/ MindMaple] for iOS and windows.
* [https://www.mythoughtsformac.com MyThoughts]
* [https://www.matchware.com/en/ MindView]
* [https://www.mindgenius.com/Products/MindGenius-for-iPad.aspx MindGenius] for iOS and Windows.
* [https://aged-and-distilled.com/napkin/ Napkin] diagramming and annotation
* [https://www.yworks.com yWorks] diagramming libraries/software components
==Web Apps==
* [https://coggle.it/ Coggle]
* [https://www.mindmeister.com/ MindMeister]
* [https://www.mindomo.com Mindomo] by subscription. Also as a desktop version that requires Adobe Air.
* [https://www.mindjet.com/ Mindjet] by subscription. Also as a desktop version.
==OpenSource/Freeware==
* [https://www.xmind.net/ XMind]
* [https://freeplane.sourceforge.net/wiki/index.php/Main_Page Freemind](https://freemind.sourceforge.net/wiki/index.php/Main_Page) and * [FreePlane]
* [https://vue.tufts.edu/ Vue] - Visual Understanding Environment from Tufts.
* [https://www.ihmc.us CmapTools](https://cmap.ihmc.us) from the Florida * [Institute for Human and Machine Cognition]
==Articles & Reviews==
Lifehacker on [https://lifehacker.com/five-best-mind-mapping-tools-476534555 5 best mindmapping tools]
=Biological Networks=
* [https://nemo-cyclone.sourceforge.net/graphs.php Cyclone]
* [https://www.cytoscape.org Cytoscape] software for visualising biological networks
* [https://www.systems-biology.org/002/ CellDesigner]
* [https://www.genome.jp/kegg/pathway.html Kegg Pathway Database] handdrawn?
* [https://www.pathvisio.org/ PathVisio] Java
* [https://www.proteinlounge.com/epath3d/default.asp ePath3d] commerial Windows $500/3years subscripton
Microsoft research cell modeling software?
==SMBL viewers and editors==
* [https://www.ebi.ac.uk/biomodels-main/ BioModels Database]
* [https://arcadiapathways.sourceforge.net Arcadia ]: a visualization tool for metabolic pathways
* [https://sbml.org Systems Biology Language]
* [https://www.sbgn.org Systems Biology Graphical Notation]
=Graph Visualization=
Wikipedia: * [https://en.wikipedia.org/wiki/Force-directed_graph_drawing Force-directed graph drawing]
* [https://graphviz.org GraphViz] "Graphviz is a package of open-source tools initiated by AT&T Labs Research for drawing graphs specified in DOT language scripts. It also provides libraries for software applications to use the tools. Graphviz is free software licensed under the Eclipse Public License."
* [https://gephi.org/features/ Gephi] "Gephi is an interactive visualization and exploration platform for all kinds of networks and complex systems, dynamic and hierarchical graphs.
Runs on Windows, Linux and Mac OS X. Gephi is open-source and free."
* [https://tulip.labri.fr/TulipDrupal/ Tulip] "Written in C++ the framework enables the development of algorithms, visual encodings, interaction techniques, data models, and domain-specific visualizations. One of the goal of Tulip is to facilitates the reuse of components and allows the developers to focus on programming their application. This development pipeline makes the framework efficient for research prototyping as well as the development of end-user applications."
=Graph Libraries=
* [https://www.boost.org Boost C++ Graph Library]
* [https://jung.sourceforge.net JUNG] Java Universal Network/Graph Framework
* [https://github.com/tinkerpop Gremlin](https://github.com/tinkerpop/gremlin) graph traversal language from * [TinkerPop]- Gremlin, Pixy, Blueprints, etc.
* [https://stchang.github.io/graph/graph.html Racket Generic Graph Library]
Charles E. Leiserson, Clifford Stein, Thomas H. Cormen, and Ronald Rivest, Introduction to Algorithms, 2nd ed.. 2001.
* [https://graphml.graphdrawing.org GraphXML file format] "a comprehensive and easy-to-use file format for graphs. It consists of a language core to describe the structural properties of a graph and a flexible extension mechanism to add application-specific data...based on XML"
* [https://www.fim.uni-passau.de/index.php?id=17297&L=1 GML file format] "GML supports attaching arbitrary information to graphs, nodes and edges, and is therefore able to emulate almost every other format."
List of Pathway Analysis Software (view source)
Revision as of 14:40, 26 June 2021
, 14:40, 26 June 2021copied from a stray markdown notes file
List of software and libraries for pathway/graph analysis
''last updated October 2014 -- so needs reviewing''
=Mindmapping=
==Commercial Apps==
* [https://literatureandlatte.com Scapple](https://www.literatureandlatte.com/forum/viewtopic.php?f=42&t=20583) from the makers of Scrivener.
* [https://www.delineato.com/ Delineato]
* [https://mindnode.com/ MindNode] + iOS.
* [https://www.conceptdraw.com/ ConceptDraw]
* [https://www.thinkbuzan.com/us/products/imindmap iMindMap] Tony Buzan claims to have invented mindmapping.
* [https://www.ithoughts.co.uk iThoughts] for iOS
* [https://www.novamind.com NovaMind]
* [https://www.mindmaple.com/Products/iPad/ MindMaple] for iOS and windows.
* [https://www.mythoughtsformac.com MyThoughts]
* [https://www.matchware.com/en/ MindView]
* [https://www.mindgenius.com/Products/MindGenius-for-iPad.aspx MindGenius] for iOS and Windows.
* [https://aged-and-distilled.com/napkin/ Napkin] diagramming and annotation
* [https://www.yworks.com yWorks] diagramming libraries/software components
==Web Apps==
* [https://coggle.it/ Coggle]
* [https://www.mindmeister.com/ MindMeister]
* [https://www.mindomo.com Mindomo] by subscription. Also as a desktop version that requires Adobe Air.
* [https://www.mindjet.com/ Mindjet] by subscription. Also as a desktop version.
==OpenSource/Freeware==
* [https://www.xmind.net/ XMind]
* [https://freeplane.sourceforge.net/wiki/index.php/Main_Page Freemind](https://freemind.sourceforge.net/wiki/index.php/Main_Page) and * [FreePlane]
* [https://vue.tufts.edu/ Vue] - Visual Understanding Environment from Tufts.
* [https://www.ihmc.us CmapTools](https://cmap.ihmc.us) from the Florida * [Institute for Human and Machine Cognition]
==Articles & Reviews==
Lifehacker on [https://lifehacker.com/five-best-mind-mapping-tools-476534555 5 best mindmapping tools]
=Biological Networks=
* [https://nemo-cyclone.sourceforge.net/graphs.php Cyclone]
* [https://www.cytoscape.org Cytoscape] software for visualising biological networks
* [https://www.systems-biology.org/002/ CellDesigner]
* [https://www.genome.jp/kegg/pathway.html Kegg Pathway Database] handdrawn?
* [https://www.pathvisio.org/ PathVisio] Java
* [https://www.proteinlounge.com/epath3d/default.asp ePath3d] commerial Windows $500/3years subscripton
Microsoft research cell modeling software?
==SMBL viewers and editors==
* [https://www.ebi.ac.uk/biomodels-main/ BioModels Database]
* [https://arcadiapathways.sourceforge.net Arcadia ]: a visualization tool for metabolic pathways
* [https://sbml.org Systems Biology Language]
* [https://www.sbgn.org Systems Biology Graphical Notation]
=Graph Visualization=
Wikipedia: * [https://en.wikipedia.org/wiki/Force-directed_graph_drawing Force-directed graph drawing]
* [https://graphviz.org GraphViz] "Graphviz is a package of open-source tools initiated by AT&T Labs Research for drawing graphs specified in DOT language scripts. It also provides libraries for software applications to use the tools. Graphviz is free software licensed under the Eclipse Public License."
* [https://gephi.org/features/ Gephi] "Gephi is an interactive visualization and exploration platform for all kinds of networks and complex systems, dynamic and hierarchical graphs.
Runs on Windows, Linux and Mac OS X. Gephi is open-source and free."
* [https://tulip.labri.fr/TulipDrupal/ Tulip] "Written in C++ the framework enables the development of algorithms, visual encodings, interaction techniques, data models, and domain-specific visualizations. One of the goal of Tulip is to facilitates the reuse of components and allows the developers to focus on programming their application. This development pipeline makes the framework efficient for research prototyping as well as the development of end-user applications."
=Graph Libraries=
* [https://www.boost.org Boost C++ Graph Library]
* [https://jung.sourceforge.net JUNG] Java Universal Network/Graph Framework
* [https://github.com/tinkerpop Gremlin](https://github.com/tinkerpop/gremlin) graph traversal language from * [TinkerPop]- Gremlin, Pixy, Blueprints, etc.
* [https://stchang.github.io/graph/graph.html Racket Generic Graph Library]
Charles E. Leiserson, Clifford Stein, Thomas H. Cormen, and Ronald Rivest, Introduction to Algorithms, 2nd ed.. 2001.
* [https://graphml.graphdrawing.org GraphXML file format] "a comprehensive and easy-to-use file format for graphs. It consists of a language core to describe the structural properties of a graph and a flexible extension mechanism to add application-specific data...based on XML"
* [https://www.fim.uni-passau.de/index.php?id=17297&L=1 GML file format] "GML supports attaching arbitrary information to graphs, nodes and edges, and is therefore able to emulate almost every other format."