List of Pathway Analysis Software

List of software and libraries for pathway/graph analysis

last updated October 2014 -- so needs reviewing

Mindmapping

Commercial Apps

• Scapple(https://www.literatureandlatte.com/forum/viewtopic.php?f=42&t=20583) from the makers of Scrivener.

• Delineato

• MindNode + iOS.

• ConceptDraw

• iMindMap Tony Buzan claims to have invented mindmapping.

• iThoughts for iOS

• NovaMind

• MindMaple for iOS and windows.

• MyThoughts

• MindView

• MindGenius for iOS and Windows.

• Napkin diagramming and annotation

• yWorks diagramming libraries/software components

Web Apps

• Coggle

• MindMeister

• Mindomo by subscription. Also as a desktop version that requires Adobe Air.

• Mindjet by subscription. Also as a desktop version.

OpenSource/Freeware

• XMind

• Freemind(https://freemind.sourceforge.net/wiki/index.php/Main_Page) and * [FreePlane]

• Vue - Visual Understanding Environment from Tufts.

• CmapTools(https://cmap.ihmc.us) from the Florida * [Institute for Human and Machine Cognition]

Articles & Reviews

Lifehacker on 5 best mindmapping tools

Biological Networks

Pathway Visualization

• Cyclone

• Cytoscape software for visualising biological networks

• CellDesigner

• Kegg Pathway Database handdrawn?

• PathVisio Java

• ePath3d commerial Windows $500/3years subscripton

Microsoft research cell modeling software

Microsoft Automatic Graph Layout

Synthesizing Biological Theories "The Scenario-Based Tool aims to provide a scalable and intuitive tool for biological modeling, where the main modeling construct is a “scenario”, a story about the system. "

SMBL viewers and editors

• BioModels Database

• Arcadia : a visualization tool for metabolic pathways

• Systems Biology Language

• Systems Biology Graphical Notation

Graph Visualization

Wikipedia: * Force-directed graph drawing

• 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."

• 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."

• 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

• Boost C++ Graph Library

• JUNG Java Universal Network/Graph Framework

• Gremlin(https://github.com/tinkerpop/gremlin) graph traversal language from * [TinkerPop]- Gremlin, Pixy, Blueprints, etc.

• Racket Generic Graph Library

Charles E. Leiserson, Clifford Stein, Thomas H. Cormen, and Ronald Rivest, Introduction to Algorithms, 2nd ed.. 2001.

• 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"

• GML file format "GML supports attaching arbitrary information to graphs, nodes and edges, and is therefore able to emulate almost every other format."