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 Web Start version (separate Java Runtime Environment required)

Download and launch Pathway Editor Web Start version (no database connection; separate Java Runtime Environment required)

Download Pathway Editor installer program (includes Java Runtime Environment):

Windows
Windows (no database connection)
Mac (64 bit Mac OS X version)
Mac (64 bit Mac OS X version) (no database connection)

Download BioPAX Level 3 files of 25 LIPID MAPS Pathways

- created using the Pathway Editor acting on downloaded path files from our Pathway database

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

On Safari and Chrome browsers, the Pathway Editor does not automatically start up when the Pathway Editor is downloaded. In these cases, the Pathway Editor may be started by double-clicking the .jnlp file icon in a Finder window or typing the following in a terminal window:
javaws http://www.lipidmaps.org/pathways/PathwayEditor.jnlp

LINUX
The Web Start version has been tested on the following versions of LINUX:

  • LINUX Ubuntu release 12.04 64-bit virtual machine containing 3.9 GB memory and 4 Intel Xeon 2GHz CPU with a Java 6 version of Open JDK, and
  • LINUX CentOS (Red Hat) release 6.5 virtual machine with 65 GB memory and 22 Intel Xeon 2 GHz CPU, with Oracle Java 7.

An installed version of the Pathway Editor for LINUX is not available at this time.

On CentOS installations, the OpenJDK Java which is installed by default may not contain Java Web Start. Java 7, which contains Web Start, may be installed by following the directions on http://www.java.com/en/download/help/linux_install.xml.

The version of Java that is used to run the Web Start version may be set in the browser. However, given difficulties associated with finding Java settings in browser menus, the Web Start version may be downloaded and started from a terminal window by entering the text
javaws http://www.lipidmaps.org/pathways/PathwayEditor.jnlp

UNIX and other platforms
The Pathway Editor has not been tested on UNIX and other platforms.



Software requirements:

The Pathway Editor uses Java Web Start 1.6 or later version and JOGL(Java Open Graphics Language) (JOGL is downloaded as part of the Pathway Editor). If you use the Web Start version, please install a Java Runtime Environment.

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, 3:99 doi: 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.