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

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dc.contributor Aalto-yliopisto fi
dc.contributor Aalto University en
dc.contributor.author Gautam, Vinay
dc.contributor.author Long, Shiting
dc.contributor.author Orponen, Pekka
dc.contributor.editor De Maria, Elisabetta
dc.contributor.editor Fred, Ana
dc.contributor.editor Gamboa, Hugo
dc.date.accessioned 2020-04-28T06:31:40Z
dc.date.available 2020-04-28T06:31:40Z
dc.date.issued 2020
dc.identifier.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 Science And Technology Publications , pp. 158-167 , International Joint Conference on Biomedical Engineering Systems and Technologies , Valletta , Malta , 24/02/2020 . https://doi.org/10.5220/0008979101580167 en
dc.identifier.isbn 978-989-758-398-8
dc.identifier.other PURE UUID: 351ab53c-135a-4407-a5b6-ca5dc2a03224
dc.identifier.other PURE ITEMURL: https://research.aalto.fi/en/publications/351ab53c-135a-4407-a5b6-ca5dc2a03224
dc.identifier.other PURE LINK: https://www.scitepress.org/PublicationsDetail.aspx?ID=436I3PP3/Ks=&t=1
dc.identifier.other PURE FILEURL: https://research.aalto.fi/files/42115430/ruledsd_2020.pdf
dc.identifier.uri https://aaltodoc.aalto.fi/handle/123456789/43847
dc.description.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. en
dc.format.extent 10
dc.format.extent 158-167
dc.format.mimetype application/pdf
dc.language.iso en en
dc.relation.ispartof International Joint Conference on Biomedical Engineering Systems and Technologies en
dc.relation.ispartofseries Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies en
dc.rights openAccess en
dc.title RuleDSD: A rule-based modelling and simulation tool for DNA strand displacement systems en
dc.type A4 Artikkeli konferenssijulkaisussa fi
dc.description.version Peer reviewed en
dc.contributor.department Department of Computer Science
dc.contributor.department Professorship Orponen Pekka
dc.subject.keyword DNA strand displacement
dc.subject.keyword DSD modelling and simulation
dc.subject.keyword rule-based modeling
dc.subject.keyword BioNetGet
dc.subject.keyword PySB
dc.identifier.urn URN:NBN:fi:aalto-202004282861
dc.identifier.doi 10.5220/0008979101580167
dc.type.version acceptedVersion


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