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

Vinay Gautam; Shiting Long; Pekka Orponen

doi:10.5220/0008979101580167

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

Vinay Gautam, Shiting Long, Pekka Orponen

Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceedings › Scientific › peer-review

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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.

Original language	English
Title of host publication	Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies
Subtitle of host publication	Volume 3 BIOINFORMATICS
Editors	Elisabetta De Maria, Ana Fred, Hugo Gamboa
Publisher	SciTePress
Pages	158-167
Number of pages	10
ISBN (Electronic)	978-989-758-398-8
DOIs	https://doi.org/10.5220/0008979101580167
Publication status	Published - 2020
MoE publication type	A4 Conference publication
Event	International Joint Conference on Biomedical Engineering Systems and Technologies - Valletta, Malta Duration: 24 Feb 2020 → 26 Apr 2020 Conference number: 13 http://www.biostec.org/?y=2020

Conference

Conference	International Joint Conference on Biomedical Engineering Systems and Technologies
Abbreviated title	BIOSTEC
Country/Territory	Malta
City	Valletta
Period	24/02/2020 → 26/04/2020
Internet address	http://www.biostec.org/?y=2020

Keywords

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

Access to Document

10.5220/0008979101580167Licence: CC BY-NC-ND

ruledsd_2020Accepted author manuscript, 296 KBLicence: CC BY-NC-ND

https://www.scitepress.org/PublicationsDetail.aspx?ID=436I3PP3/Ks=&t=1Licence: CC BY-NC-ND

ALBION: Algorithmic Designs for Biomolecular Nanostructures (ALBION)
Orponen, P. (Principal investigator), Saman Booy, M. (Project Member), Vo, T. (Project Member), Granö, H. (Project Member), Hiitola, E. (Project Member), Korpela, D. (Project Member), Lohikko, A. (Project Member), Gautam, V. (Project Member), Mohammed, A. (Project Member) & Elonen, A. (Project Member)
01/09/2017 → 31/08/2021
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). SciTePress. https://doi.org/10.5220/0008979101580167

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title = "RuleDSD: A rule-based modelling and simulation tool for DNA strand displacement systems",

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.",

keywords = "DNA strand displacement, DSD modelling and simulation, rule-based modeling, BioNetGet, PySB",

author = "Vinay Gautam and Shiting Long and Pekka Orponen",

year = "2020",

doi = "10.5220/0008979101580167",

language = "English",

pages = "158--167",

editor = "\{De Maria\}, Elisabetta and Ana Fred and Hugo Gamboa",

booktitle = "Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies",

publisher = "SciTePress",

address = "Portugal",

note = "International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC ; Conference date: 24-02-2020 Through 26-04-2020",

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}

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

RuleDSD: A rule-based modelling and simulation tool for DNA strand displacement systems. / Gautam, Vinay; Long, Shiting; Orponen, Pekka.
Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies: Volume 3 BIOINFORMATICS. ed. / Elisabetta De Maria; Ana Fred; Hugo Gamboa. SciTePress, 2020. p. 158-167.

Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceedings › Scientific › peer-review

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AU - Long, Shiting

AU - Orponen, Pekka

N1 - Conference code: 13

PY - 2020

Y1 - 2020

N2 - 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.

AB - 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.

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BT - Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies

A2 - De Maria, Elisabetta

A2 - Fred, Ana

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PB - SciTePress

T2 - International Joint Conference on Biomedical Engineering Systems and Technologies

Y2 - 24 February 2020 through 26 April 2020

ER -

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

Abstract

Conference

Keywords

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Projects

ALBION: Algorithmic Designs for Biomolecular Nanostructures (ALBION)

Cite this