Visualisation of BioPAX Networks using BioLayout Express3D

Wright, D. W. , Angus, T., Enright, A. J. and Freeman, T. C. (2014) Visualisation of BioPAX Networks using BioLayout Express3D. F1000Research, 3, 246. (doi:10.12688/f1000research.5499.1) (PMID:25949802) (PMCID:PMC4406191)

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Abstract

BioLayout Express3D is a network analysis tool designed for the visualisation and analysis of graphs derived from biological data. It has proved to be powerful in the analysis of gene expression data, biological pathways and in a range of other applications. In version 3.2 of the tool we have introduced the ability to import, merge and display pathways and protein interaction networks available in the BioPAX Level 3 standard exchange format. A graphical interface allows users to search for pathways or interaction data stored in the Pathway Commons database. Queries using either gene/protein or pathway names are made via the cPath2 client and users can also define the source and/or species of information that they wish to examine. Data matching a query are listed and individual records may be viewed in isolation or merged using an ‘Advanced’ query tab. A visualisation scheme has been defined by mapping BioPAX entity types to a range of glyphs. Graphs of these data can be viewed and explored within BioLayout as 2D or 3D graph layouts, where they can be edited and/or exported for visualisation and editing within other tools.

Item Type:Articles
Additional Information:T.C.F. is funded by an Institute Strategic Grant from the Biotechnology and Biological Sciences Research Council (BBSRC) [grant number BB/JO1446X/1] and development of BioLayout Express3D is funded by BBSRC grant BB/I001107/1.
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Wright, Mr Derek
Authors: Wright, D. W., Angus, T., Enright, A. J., and Freeman, T. C.
College/School:College of Medical Veterinary and Life Sciences > Institute of Infection Immunity and Inflammation
Journal Name:F1000Research
Publisher:F1000Research
ISSN:2046-1402
ISSN (Online):2046-1402
Copyright Holders:Copyright © 2014 Wright DW et al
First Published:First published in F1000Research 3:246
Publisher Policy:Reproduced under a Creative Commons License

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