HOLY-II: IMPROVED HIERARCHICALLY ORGANIZED LAYOUT FOR VISUALIZATION OF BIOCHEMICAL COMPLEX PATHWAYS

Jyh-Jong Tsay, Bo-Liang Wu, Guo-Gen Huang

Abstract

Many complex pathways are described as hierarchical structures in which a pathway is recursively partitioned into several sub-pathways, and organized hierarchically as a tree. The hierarchical structure provides a natural way to visualize the global structure of a complex pathway. Recently, a hierarchically organized layout algorithm HOLY which takes the advantages of the hierarchical structures inherent in complex pathways has been proposed. In this paper, we present a new layout algorithm HOLY-II which follows the basic principle of HOLY, but improves HOLY by introducing a new algorithm for joining layouts, one of the crucial tasks in HOLY. Experiment shows that HOLY-II is able to produce layouts which clearly render both the global structures and the local structures of complex pathways, and gives better visualization for many examples from MetaCyc, CADLIVE and HOLY.

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Paper Citation


in Harvard Style

Tsay J., Wu B. and Huang G. (2010). HOLY-II: IMPROVED HIERARCHICALLY ORGANIZED LAYOUT FOR VISUALIZATION OF BIOCHEMICAL COMPLEX PATHWAYS . In Proceedings of the First International Conference on Bioinformatics - Volume 1: BIOINFORMATICS, (BIOSTEC 2010) ISBN 978-989-674-019-1, pages 135-140. DOI: 10.5220/0002725501350140


in Bibtex Style

@conference{bioinformatics10,
author={Jyh-Jong Tsay and Bo-Liang Wu and Guo-Gen Huang},
title={HOLY-II: IMPROVED HIERARCHICALLY ORGANIZED LAYOUT FOR VISUALIZATION OF BIOCHEMICAL COMPLEX PATHWAYS},
booktitle={Proceedings of the First International Conference on Bioinformatics - Volume 1: BIOINFORMATICS, (BIOSTEC 2010)},
year={2010},
pages={135-140},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0002725501350140},
isbn={978-989-674-019-1},
}


in EndNote Style

TY - CONF
JO - Proceedings of the First International Conference on Bioinformatics - Volume 1: BIOINFORMATICS, (BIOSTEC 2010)
TI - HOLY-II: IMPROVED HIERARCHICALLY ORGANIZED LAYOUT FOR VISUALIZATION OF BIOCHEMICAL COMPLEX PATHWAYS
SN - 978-989-674-019-1
AU - Tsay J.
AU - Wu B.
AU - Huang G.
PY - 2010
SP - 135
EP - 140
DO - 10.5220/0002725501350140