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Authors: Jyh-Jong Tsay 1 ; Bo-Liang Wu 2 and Guo-Gen Huang 2

Affiliations: 1 National Chung Cheng University, Taiwan ; 2 National Chung-Cheng University, Taiwan

Keyword(s): Pathway layout, Forced-directed layout, Hierarchical layout, Pathway visualization.

Related Ontology Subjects/Areas/Topics: Artificial Intelligence ; Bioinformatics ; Biomedical Engineering ; Soft Computing ; Visualization

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 several formats:
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 (BIOSTEC 2010) - BIOINFORMATICS; ISBN 978-989-674-019-1; ISSN 2184-4305, SciTePress, pages 135-140. DOI: 10.5220/0002725501350140

@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 (BIOSTEC 2010) - BIOINFORMATICS},
year={2010},
pages={135-140},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0002725501350140},
isbn={978-989-674-019-1},
issn={2184-4305},
}

TY - CONF

JO - Proceedings of the First International Conference on Bioinformatics (BIOSTEC 2010) - BIOINFORMATICS
TI - HOLY-II: IMPROVED HIERARCHICALLY ORGANIZED LAYOUT FOR VISUALIZATION OF BIOCHEMICAL COMPLEX PATHWAYS
SN - 978-989-674-019-1
IS - 2184-4305
AU - Tsay, J.
AU - Wu, B.
AU - Huang, G.
PY - 2010
SP - 135
EP - 140
DO - 10.5220/0002725501350140
PB - SciTePress