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Authors: Vinay Gautam ; Shiting Long and Pekka Orponen

Affiliation: Department of Computer Science, Aalto University, 00076 Aalto, Finland

Keyword(s): DNA Strand Displacement, DSD Modelling and Simulation, PySB, Rule-based Model, BioNetGen.

Abstract: RuleDSD is a tool to support the rule-based modelling and simulation of DNA Strand Displacement (DSD) systems. It constitutes a software pipeline programmed in Python and integrated with PySB, a standard framework for rule-based modelling of biochemical systems. The input to RuleDSD is a domain-level model of a DSD system, where each initial DNA complex is described at the level of named pairing domains. The RuleDSD pipeline converts these domain-level descriptions into a canonical graph representation, and based on this performs a full state-space enumeration of DNA species reachable by applying the basic rules of DNA strand displacement reactions to the ensemble of initial species. The resulting chemical reaction network is then converted into a BioNetGen model and imported into the PySB framework for deterministic or stochastic simulation and analysis. Altogether, RuleDSD thus provides a customised front-end for rule-based modelling and simulation of DNA Strand Displacement system s using the BioNetGen simulation engine, and opens up further possibilities for harnessing the well-established rule-based modelling methods and tools that can easily be utilised through the PySB wrapper. (More)

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Paper citation in several formats:
Gautam, V.; Long, S. and Orponen, P. (2020). RuleDSD: A Rule-based Modelling and Simulation Tool for DNA Strand Displacement Systems. In Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2020) - BIOINFORMATICS; ISBN 978-989-758-398-8; ISSN 2184-4305, SciTePress, pages 158-167. DOI: 10.5220/0008979101580167

@conference{bioinformatics20,
author={Vinay Gautam. and Shiting Long. and Pekka Orponen.},
title={RuleDSD: A Rule-based Modelling and Simulation Tool for DNA Strand Displacement Systems},
booktitle={Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2020) - BIOINFORMATICS},
year={2020},
pages={158-167},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0008979101580167},
isbn={978-989-758-398-8},
issn={2184-4305},
}

TY - CONF

JO - Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2020) - BIOINFORMATICS
TI - RuleDSD: A Rule-based Modelling and Simulation Tool for DNA Strand Displacement Systems
SN - 978-989-758-398-8
IS - 2184-4305
AU - Gautam, V.
AU - Long, S.
AU - Orponen, P.
PY - 2020
SP - 158
EP - 167
DO - 10.5220/0008979101580167
PB - SciTePress

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