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

Tutkimustuotos: Artikkeli kirjassa/konferenssijulkaisussaConference contributionScientificvertaisarvioitu

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Abstrakti

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.
AlkuperäiskieliEnglanti
OtsikkoProceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies
AlaotsikkoVolume 3 BIOINFORMATICS
ToimittajatElisabetta De Maria, Ana Fred, Hugo Gamboa
Sivut158-167
Sivumäärä10
ISBN (elektroninen)978-989-758-398-8
DOI - pysyväislinkit
TilaJulkaistu - 2020
OKM-julkaisutyyppiA4 Artikkeli konferenssijulkaisuussa
TapahtumaInternational Joint Conference on Biomedical Engineering Systems and Technologies - Valletta, Malta
Kesto: 24 helmikuuta 202026 huhtikuuta 2020
Konferenssinumero: 13
http://www.biostec.org/?y=2020

Conference

ConferenceInternational Joint Conference on Biomedical Engineering Systems and Technologies
LyhennettäBIOSTEC
MaaMalta
KaupunkiValletta
Ajanjakso24/02/202026/04/2020
www-osoite

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    Siteeraa tätä

    Gautam, V., Long, S., & Orponen, P. (2020). RuleDSD: A rule-based modelling and simulation tool for DNA strand displacement systems. teoksessa E. De Maria, A. Fred, & H. Gamboa (Toimittajat), Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies: Volume 3 BIOINFORMATICS (Sivut 158-167) https://doi.org/10.5220/0008979101580167