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

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Abstract

RuleDSD is a tool to support 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 ofa 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.
Original languageEnglish
Title of host publicationProceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies
Subtitle of host publicationVolume 3 BIOINFORMATICS
EditorsElisabetta De Maria, Ana Fred, Hugo Gamboa
Pages158-167
Number of pages10
ISBN (Electronic)978-989-758-398-8
DOIs
Publication statusPublished - 2020
MoE publication typeA4 Article in a conference publication
EventInternational Joint Conference on Biomedical Engineering Systems and Technologies - Valletta, Malta
Duration: 24 Feb 202026 Apr 2020
Conference number: 13
http://www.biostec.org/?y=2020

Conference

ConferenceInternational Joint Conference on Biomedical Engineering Systems and Technologies
Abbreviated titleBIOSTEC
CountryMalta
CityValletta
Period24/02/202026/04/2020
Internet address

Keywords

  • DNA strand displacement
  • DSD modelling and simulation
  • rule-based modeling
  • BioNetGet
  • PySB

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  • Projects

    ALBION: Algorithmic Designs for Biomolecular Nanostructures (ALBION)

    Mohammed, A., Orponen, P., Saman Booy, M., Vo, T., Lohikko, A., Elonen, A. & Korpela, D.

    01/09/201731/08/2021

    Project: Academy of Finland: Other research funding

    Cite this

    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 (pp. 158-167) https://doi.org/10.5220/0008979101580167