Tag: Pathvisio

PathVisio 3.3.0 – a tool to Edit and Analyze Biological Pathways

PathVisio 3.3.0

:: DESCRIPTION

PathVisio is a free open-source biological pathway analysis software that allows you to draw, edit and analyze biological pathways.

::DEVELOPER

PathVisio team

:: SCREENSHOTS

PathVisio

::REQUIREMENTS

  • Linux / Solaris / MacOS X
  • Java

:: DOWNLOAD

 PathVisio

:: MORE INFORMATION

Citation

PathVisio 3: an extendable pathway analysis toolbox.
Kutmon M, van Iersel MP, Bohler A, Kelder T, Nunes N, Pico AR, Evelo CT.
PLoS Comput Biol. 2015 Feb 23;11(2):e1004085. doi: 10.1371/journal.pcbi.1004085.

Presenting and exploring biological pathways with PathVisio
Iersel, Martijn P van, Thomas Kelder, Alexander R Pico, Kristina Hanspers, Susan Coort, Bruce R Conklin, and Chris Evelo
BMC Bioinformatics 2008, 9:399

PathVisioRPC – XML-RPC interface for Pathway Analysis tool PathVisio

PathVisioRPC

:: DESCRIPTION

PathVisioRPC is an XML-RPC interface for the pathway analysis tool PathVisio. It allows you to use PathVisio functions to create pathways and visualise and analyse data on pathways in your familiar analytical environment (R, Python, Perl, C++, so on …)

:: SCREENSHOTS

N/A

::DEVELOPER

PathVisioRPC team

::REQUIREMENTS

  • Linux / Solaris / MacOS X
  • Java
  • R

:: DOWNLOAD

 PathVisioRPC

:: MORE INFORMATION

Citation

Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment.
Bohler A, Eijssen LM, van Iersel MP, Leemans C, Willighagen EL, Kutmon M, Jaillard M, Evelo CT.
BMC Bioinformatics. 2015 Aug 23;16:267. doi: 10.1186/s12859-015-0708-8.

PathVisio-MIM 2.0.11 – Pathvisio Plugin which Adds the Ability to Draw MIM Glyph

PathVisio-MIM 2.0.11

:: DESCRIPTION

PathVisio-MIM is a software of MIM (Molecular Interaction Map) plugin for PathVisio allows users to produce diagrams of bioregulatory systems according to an implementation of notation first developed by Kurt Kohn in 1999. The plugin has two main features: 1) it provides users with the glyphs necessary to draw MIM diagrams and 2) it allows users to import and export to the MIM Markup Language (MIMML) format, a format developed to exchange MIM diagrams between MIM compatible tools and used to validate MIM diagrams. Diagrams produced using the MIM PathVisio plugin can be exported into several image formats including PDF, PNG, SVG, and TIFF.

::DEVELOPER

PathVisio-MIM Team

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 PathVisio-MIM

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Aug 1;27(15):2165-6. Epub 2011 Jun 2.
PathVisio-MIM: PathVisio plugin for creating and editing Molecular Interaction Maps (MIMs).
Luna A, Sunshine ML, van Iersel MP, Aladjem MI, Kohn KW.