RuleDSD: A Rule-based Modelling and Simulation Tool for DNA Strand Displacement Systems

Vinay Gautam, Shiting Long, Pekka Orponen

2020

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 systems 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.

Paper Citation

in Harvard Style

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) - Volume 3: BIOINFORMATICS; ISBN 978-989-758-398-8, SciTePress, pages 158-167. DOI: 10.5220/0008979101580167

in Bibtex Style

@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) - Volume 3: BIOINFORMATICS},
year={2020},
pages={158-167},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0008979101580167},
isbn={978-989-758-398-8},
}

in EndNote Style

TY - CONF

JO - Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2020) - Volume 3: BIOINFORMATICS
TI - RuleDSD: A Rule-based Modelling and Simulation Tool for DNA Strand Displacement Systems
SN - 978-989-758-398-8
AU - Gautam V.
AU - Long S.
AU - Orponen P.
PY - 2020
SP - 158
EP - 167
DO - 10.5220/0008979101580167
PB - SciTePress