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Clustered Graph Hierarchical Layout Algorithm for Systems Biology Models

by Pratik Erande, Noshir Tarapore, Vrushali Inamdar
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International Journal of Computer Applications
Foundation of Computer Science (FCS), NY, USA
Volume 96 - Number 24
Year of Publication: 2014
Authors: Pratik Erande, Noshir Tarapore, Vrushali Inamdar
10.5120/16945-7012

Pratik Erande, Noshir Tarapore, Vrushali Inamdar . Clustered Graph Hierarchical Layout Algorithm for Systems Biology Models. International Journal of Computer Applications. 96, 24 ( June 2014), 28-35. DOI=10.5120/16945-7012

@article{ 10.5120/16945-7012,
author = { Pratik Erande, Noshir Tarapore, Vrushali Inamdar },
title = { Clustered Graph Hierarchical Layout Algorithm for Systems Biology Models },
journal = { International Journal of Computer Applications },
issue_date = { June 2014 },
volume = { 96 },
number = { 24 },
month = { June },
year = { 2014 },
issn = { 0975-8887 },
pages = { 28-35 },
numpages = {9},
url = { https://ijcaonline.org/archives/volume96/number24/16945-7012/ },
doi = { 10.5120/16945-7012 },
publisher = {Foundation of Computer Science (FCS), NY, USA},
address = {New York, USA}
}
%0 Journal Article
%1 2024-02-06T22:22:41.930043+05:30
%A Pratik Erande
%A Noshir Tarapore
%A Vrushali Inamdar
%T Clustered Graph Hierarchical Layout Algorithm for Systems Biology Models
%J International Journal of Computer Applications
%@ 0975-8887
%V 96
%N 24
%P 28-35
%D 2014
%I Foundation of Computer Science (FCS), NY, USA
Abstract

In this article we describe a complete method to the layout clustered graph in hierarchical fashion. We have adopted Sugiyama[11] framework for hierarchical layout and modified its phases to produce the clustered graph layout. The algorithm is based on Sanders compound graph layout algorithm. Our main contribution is positioning of nodes with different sizes without any node overlap while maintaining straight lines for long edges. Experimental results show that the executiontime and quality of the produced drawings with respect to commonly accepted layoutcriteria are quite satisfactory. This algorithm is intended to integrate as a part of system biology software Cell-in-Silico, for drawing biological pathways with compartmental constraints and arbitrary nesting of graphs and molecular complexes.

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Index Terms

Computer Science
Information Sciences

Keywords

Clustered Graph Hierarchical Layout Biological Graphs Node Size Complex Species.

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