RuleDSD: A rule-based modelling and simulation tool for DNA strand displacement systems

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Journal Title
Journal ISSN
Volume Title
Conference article in proceedings
Date
2020
Major/Subject
Mcode
Degree programme
Language
en
Pages
10
158-167
Series
Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies
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 Ru1eDSD is a domain-level model of a DSD system, where each initial DNA complex is described at the level of named pairing domains. The Ru1eDSD 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, Ru1eDSD 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 model ling methods and tools that can easily be utilised through the PySB wrapper.
Description
Keywords
DNA strand displacement, DSD modelling and simulation, rule-based modeling, BioNetGet, PySB
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Citation
Gautam , V , Long , S & Orponen , P 2020 , RuleDSD: A rule-based modelling and simulation tool for DNA strand displacement systems . in E De Maria , A Fred & H Gamboa (eds) , Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies : Volume 3 BIOINFORMATICS . SciTePress , pp. 158-167 , International Joint Conference on Biomedical Engineering Systems and Technologies , Valletta , Malta , 24/02/2020 . https://doi.org/10.5220/0008979101580167