A Proposal for a Language Combining Biochemical Rules and Topological Structure for Systems Biology

Anasthasie Compaore, Pascale Gall

Abstract

For about twenty years, rule-based modelling has been widely used for Systems Biology issues. Most existing languages focus on biochemical reactions primarily, and to a lest extent, on the cell structure in compartments. BIOCHAM and Pathway Logic Assistant (PLA) are representative examples of such rule-based languages. They are equipped with tools providing great analysis capabilities. We propose to provide such biochemical languages with annotations relating to the compartments in which the biochemical reactions take place. We will make sure that biochemical rules always indicate the nature of the compartments involved and the neighbourhood relations between them. At the end, it suffices to specialize the generic rules according to a particular topological structure in order to obtain sets of localized rules. Thus, resulting models can be analysed by using either BIOCHAM or PLA.

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Paper Citation


in Harvard Style

Compaore A. and Gall P. (2019). A Proposal for a Language Combining Biochemical Rules and Topological Structure for Systems Biology.In Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 3: BIOINFORMATICS, ISBN 978-989-758-353-7, pages 310-317. DOI: 10.5220/0007689303100317


in Bibtex Style

@conference{bioinformatics19,
author={Anasthasie Compaore and Pascale Gall},
title={A Proposal for a Language Combining Biochemical Rules and Topological Structure for Systems Biology},
booktitle={Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 3: BIOINFORMATICS,},
year={2019},
pages={310-317},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0007689303100317},
isbn={978-989-758-353-7},
}


in EndNote Style

TY - CONF

JO - Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 3: BIOINFORMATICS,
TI - A Proposal for a Language Combining Biochemical Rules and Topological Structure for Systems Biology
SN - 978-989-758-353-7
AU - Compaore A.
AU - Gall P.
PY - 2019
SP - 310
EP - 317
DO - 10.5220/0007689303100317