Arcadia 1.0rc2 – Visualisation Tool for Metabolic Pathways

Arcadia 1.0rc2

:: DESCRIPTION

Arcadia is a light-weight, cross-platform, C++ desktop application designed for visualizing biological networks such as metabolic pathways.Arcadia is a viewer, not an editor: this means a simpler interface, offering multiple perspectives on the same data, with a focus on navigation. Arcadia translates text-based descriptions of biological networks (SBML files) into standardized diagrams (SBGN PD maps). Users can view the same model from different perspectives and easily alter the layout to emulate traditional textbook representations.

::DEVELOPER

Alice Villéger^1,2, Steve Pettifer², Douglas Kell¹
[1] School of Chemistry, [2] School of Computer Science
at the University of Manchester, United Kingdom

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Mac OS X / Windows
C ++ Complier

:: DOWNLOAD

Arcadia

:: MORE INFORMATION

Citation

Alice C. Villéger, Stephen R. Pettifer, Douglas B. Kell (2010)
Arcadia: a visualization tool for metabolic pathways,
Bioinformatics 2010 26(11):1470-1471; doi:10.1093/bioinformatics/btq154

MetaPAT 20070215 – Tool for the Alignment of Metabolic Pathways

MetaPAT 20070215

:: DESCRIPTION

MetaPAT is a tool for the alignment of metabolic pathways.MetaPAT aligns metabolic pathways based on the FIT-MATCH algorithm.METAPAT can also detect alignments which differ only very slightly from higher scoring ones and might thus not be of interest.

::DEVELOPER

Florian Rasche (m3rafl@minet.uni-jena.de)

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux

:: DOWNLOAD

MetaPAT for Linux ; for win

:: MORE INFORMATION

Citation

S. Wernicke and F. Rasche.
Simple and fast alignment of metabolic pathways by exploiting local diversity.
Bioinformatics (2007) 23 (15): 1978-1985

UBViz 0.9R04- Explore Metabolic Pathways in 3D

UBViz 0.9R04

:: DESCRIPTION

UBViz is a software tool designed to make biochemical pathways easier to understand for biologists. Users can visualize and interact with a biochemical pathway from KEGG’s website in 3-D space, and browse all related web pages within one window.

With UBViz’ built-in network functionalities, pathway data are obtained directly from KEGG’s website and automatically processed. As a result, users are guaranteed to view the newest version of the biochemical pathways. UBViz uses the popular XML format as its input, with very little modification UBViz can be easily adapted to view any database which stores pathway information in XML.

::DEVELOPER

Complex Computation Laboratory ,Iowa State University

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Windows /Mac OsX

:: DOWNLOAD

Registration First ; UBViz

:: MORE INFORMATION

Citation

UBViz: a software tool for exploring metabolic pathways in 3-D space
Song Li and Hui-Hsien Chou
BioTechniques Vol. 38, No. 4: pp 540-542 (Apr 2005)