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

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

2010

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.

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