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[Click on the figure to see the entire screenshot]
ChiBE: Chisio BioPAX Editor
Chisio BioPAX Editor, or simply ChiBE, is a free editing and visualization tool for pathway models represented by the BioPAX format, based on Chisio.
The tool features user-friendly display, viewing, and editing of pathway models. Pathway views are rendered in a feature-rich format, and may be laid out and edited with state-of-the-art layout and visualization technologies. In addition, facilities for querying a set of integrated pathways in Pathway Commons are provided. Furthermore, visualization of experimental data overlaid on pathway views is supported in ChiBE.
ChiBE is a Java application running on Windows XP/Vista and Linux. It was built using Chisio 1.0 and Eclipse GEF 3.1 for graph visualization, Paxtools for accessing and manipulating BioPAX files, and PATIKAmad for experiment data analysis.
Software
ChiBE is distributed under Eclipse Public License.
The sources of ChiBE are maintained in a sourceforge project, and distributed under Eclipse Public License. The project's Subversion repository is
Highlights
Following are sample screenshots showing tool highlights.
Sample Pathways
Following are images of pathway models produced by ChiBE taken from some prominent databases.
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Release Notes for Version 1.1
Credits Developed with
The requirements of ChiBE were determined by Ozgun Babur and Ugur Dogrusoz of BCBI, and Emek Demir and Chris Sander of MSKCC. Design and development of the software were mainly performed by Ozgun Babur with help from Ugur Dogrusoz.
Please cite the following article if you make use of our software:
O. Babur, U. Dogrusoz, E. Demir, and C. Sander, "ChiBE: interactive visualization and manipulation of BioPAX pathway models", Bioinformatics, 26(3), pp. 429-431, 2010.