A generic algorithm for layout of biological networks

<p>Abstract</p> <p>Background</p> <p>Biological networks are widely used to represent processes in biological systems and to capture interactions and dependencies between biological entities. Their size and complexity is steadily increasing due to the ongoing growth of...

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Main Authors: Dwyer Tim, Schreiber Falk, Marriott Kim, Wybrow Michael
Format: Article
Language:English
Published: BMC 2009-11-01
Series:BMC Bioinformatics
Online Access:http://www.biomedcentral.com/1471-2105/10/375
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spelling doaj-116ec1143a594dd69d52e89145097c5a2020-11-24T22:38:51ZengBMCBMC Bioinformatics1471-21052009-11-0110137510.1186/1471-2105-10-375A generic algorithm for layout of biological networksDwyer TimSchreiber FalkMarriott KimWybrow Michael<p>Abstract</p> <p>Background</p> <p>Biological networks are widely used to represent processes in biological systems and to capture interactions and dependencies between biological entities. Their size and complexity is steadily increasing due to the ongoing growth of knowledge in the life sciences. To aid understanding of biological networks several algorithms for laying out and graphically representing networks and network analysis results have been developed. However, current algorithms are specialized to particular layout styles and therefore different algorithms are required for each kind of network and/or style of layout. This increases implementation effort and means that new algorithms must be developed for new layout styles. Furthermore, additional effort is necessary to compose different layout conventions in the same diagram. Also the user cannot usually customize the placement of nodes to tailor the layout to their particular need or task and there is little support for interactive network exploration.</p> <p>Results</p> <p>We present a novel algorithm to visualize different biological networks and network analysis results in meaningful ways depending on network types and analysis outcome. Our method is based on constrained graph layout and we demonstrate how it can handle the drawing conventions used in biological networks.</p> <p>Conclusion</p> <p>The presented algorithm offers the ability to produce many of the fundamental popular drawing styles while allowing the exibility of constraints to further tailor these layouts.</p> http://www.biomedcentral.com/1471-2105/10/375
collection DOAJ
language English
format Article
sources DOAJ
author Dwyer Tim
Schreiber Falk
Marriott Kim
Wybrow Michael
spellingShingle Dwyer Tim
Schreiber Falk
Marriott Kim
Wybrow Michael
A generic algorithm for layout of biological networks
BMC Bioinformatics
author_facet Dwyer Tim
Schreiber Falk
Marriott Kim
Wybrow Michael
author_sort Dwyer Tim
title A generic algorithm for layout of biological networks
title_short A generic algorithm for layout of biological networks
title_full A generic algorithm for layout of biological networks
title_fullStr A generic algorithm for layout of biological networks
title_full_unstemmed A generic algorithm for layout of biological networks
title_sort generic algorithm for layout of biological networks
publisher BMC
series BMC Bioinformatics
issn 1471-2105
publishDate 2009-11-01
description <p>Abstract</p> <p>Background</p> <p>Biological networks are widely used to represent processes in biological systems and to capture interactions and dependencies between biological entities. Their size and complexity is steadily increasing due to the ongoing growth of knowledge in the life sciences. To aid understanding of biological networks several algorithms for laying out and graphically representing networks and network analysis results have been developed. However, current algorithms are specialized to particular layout styles and therefore different algorithms are required for each kind of network and/or style of layout. This increases implementation effort and means that new algorithms must be developed for new layout styles. Furthermore, additional effort is necessary to compose different layout conventions in the same diagram. Also the user cannot usually customize the placement of nodes to tailor the layout to their particular need or task and there is little support for interactive network exploration.</p> <p>Results</p> <p>We present a novel algorithm to visualize different biological networks and network analysis results in meaningful ways depending on network types and analysis outcome. Our method is based on constrained graph layout and we demonstrate how it can handle the drawing conventions used in biological networks.</p> <p>Conclusion</p> <p>The presented algorithm offers the ability to produce many of the fundamental popular drawing styles while allowing the exibility of constraints to further tailor these layouts.</p>
url http://www.biomedcentral.com/1471-2105/10/375
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