Pathways

Arachidonic AcidMetabolism

Pathway maps drawn using Pathway Editor software, plus
.path files for editing pathways using Pathway Editor

The Pathway Editor is a program for managing, visualizing, and editing signaling and metabolic pathways. Pathways may be created from scratch, accessed by opening a .path file, or downloaded from the LIPID MAPS website via the Pathway Editor application. Time course graphs for both lipids and genes, and data for technical and biological replicates for lipids can be displayed within the Pathway Editor. For lipids, the Pathway Editor also provides links to KEGG and to LMSD records, with lipid structures and annotations. Links to annotations in GeneEntrez and the Mouse Genome Database are provided for genes.

Please see our Pathway Editor tutorial for an overview of Pathway Editor features, including how to start the Pathway Editor, access LIPID MAPS pathways and display LIPID MAPS and user-provided experimental data, create pathways from scratch, and edit and save pathway files and images. Instructions for working with SBML and BioPAX formats are also provided.


Download and launch Pathway Editor


View pathway maps, download LIPID MAPS pathway (*.path) files, and view time course data for lipids and genes.


Pathway Editor System requirements:

PC with Windows XP
1GHz or better Intel or AMD processor
512Mbytes of memory or more
3D graphics accelerator
Fast network connection

Mac with MacOSX 10.4 or later
1GHz or better G4, G5, or Intel processor (universal binary)
512Mbytes of memory or more
3D graphics accelerator
Fast network connection
For Mac OS X 10.6 and above: A Java 1.6 JRE is required. Java 1.7 does not work. If the required JRE is not found, the user must download and install one (http://www.oracle.com/technetwork/java/javase/downloads/index.html)

Software requirements:

The Workbench uses Java WebStart 1.6 or later version and JOGL(Java Open Graphics Language). Please install Java Web Start if you do not have it already (you can tell you do not have Java Web Start if you get a message when you try to install Pathway Editor). This enables you to run Java applications started from a web page. JOGL is downloaded as part of the Pathway Editor program.

References

An editor for pathway drawing and data visualization in the Biopathways Workbench Robert W Byrnes, Dawn Cotter, Andreia Maer, Joshua Li, David Nadeau and Shankar Subramaniam, BMC Systems Biology 2009, 3:99doi:10.1186/1752-0509-3-99.
logo LIPID MAPS is funded by a grant from the National Institute of General Medical Sciences of the National Institutes of Health.