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

Vinay Gautam, Shiting Long, Pekka Orponen

Tutkimustuotos: Artikkeli kirjassa/konferenssijulkaisussaConference contributionScientificvertaisarvioitu

60 Lataukset (Pure)

Abstrakti

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.

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 helmik. 202026 huhtik. 2020
Konferenssinumero: 13
http://www.biostec.org/?y=2020

Conference

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

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