BioPAX support in CellDesigner.
BACKGROUND
BioPAX is a standard language for representing and exchanging models of biological processes at the molecular and cellular levels. It is widely used by different pathway databases and genomics data analysis software. Currently, the primary source of BioPAX data is direct exports from the curated pathway databases. It is still uncommon for wet-lab biologists to share and exchange pathway knowledge using BioPAX. Instead, pathways are usually represented as informal diagrams in the literature. In order to encourage formal representation of pathways, we describe a software package that allows users to create pathway diagrams using CellDesigner, a user-friendly graphical pathway-editing tool and save the pathway data in BioPAX Level 3 format.


BACKGROUND
The plug-in is freely available and can be downloaded at ftp://ftp.pantherdb.org/CellDesigner/plugins/BioPAX/  CONTACT:  huaiyumi@usc.edu


BACKGROUND
Supplementary data are available at Bioinformatics online.
Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA. huaiyumi@usc.edu
Huaiyu
H
Mi
Anushya
A
Muruganujan
Emek
E
Demir
Yukiko
Y
Matsuoka
Akira
A
Funahashi
Hiroaki
H
Kitano
Paul D
PD
Thomas
D000818:Animals; D019295:Computational Biology; D016208:Databases, Factual; D006801:Humans; D053858:Metabolic Networks and Pathways; D008954:Models, Biological; D015398:Signal Transduction; D012984:Software