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dc.contributor.authorKonur, Savas
dc.contributor.authorMierla, L.M.
dc.contributor.authorFellermann, H.
dc.contributor.authorLadroue, C.
dc.contributor.authorBrown, B.
dc.contributor.authorWipat, A.
dc.contributor.authorTwycross, J.
dc.contributor.authorDun, B.P.
dc.contributor.authorKalvala, S.
dc.contributor.authorGheorghe, Marian
dc.contributor.authorKrasnogor, N.
dc.date.accessioned2021-09-15T10:31:46Z
dc.date.available2021-09-15T10:31:46Z
dc.date.issued2021-08-02
dc.identifier.citationKonur S, Mierla L, Fellermann H et al (2021) Toward full-stack in silico synthetic biology: integrating model specification, simulation, verification, and biological compilation. ACS Synthetic Biology. 10(8): 1931-1945.en_US
dc.identifier.urihttp://hdl.handle.net/10454/18588
dc.descriptionYesen_US
dc.description.abstractWe present the Infobiotics Workbench (IBW), a user-friendly, scalable, and integrated computational environment for the computer-aided design of synthetic biological systems. It supports an iterative workflow that begins with specification of the desired synthetic system, followed by simulation and verification of the system in high- performance environments and ending with the eventual compilation of the system specification into suitable genetic constructs. IBW integrates modelling, simulation, verification and bicompilation features into a single software suite. This integration is achieved through a new domain-specific biological programming language, the Infobiotics Language (IBL), which tightly combines these different aspects of in silico synthetic biology into a full-stack integrated development environment. Unlike existing synthetic biology modelling or specification languages, IBL uniquely blends modelling, verification and biocompilation statements into a single file. This allows biologists to incorporate design constraints within the specification file rather than using decoupled and independent formalisms for different in silico analyses. This novel approach offers seamless interoperability across different tools as well as compatibility with SBOL and SBML frameworks and removes the burden of doing manual translations for standalone applications. We demonstrate the features, usability, and effectiveness of IBW and IBL using well-established synthetic biological circuits.en_US
dc.description.sponsorshipThe work of S.K. is supported by EPSRC (EP/R043787/1). N.K., A.W., and B.B. acknowledge a Royal Academy of Engineering Chair in Emerging Technologies award and an EPSRC programme grant (EP/N031962/1).en_US
dc.language.isoenen_US
dc.relation.isreferencedbyhttps://doi.org/10.1021/acssynbio.1c00143en_US
dc.rights© 2021 The Authors. Published by American Chemical Society. This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License. (http://creativecommons.org/licenses/by-nc-nd/4.0/).en_US
dc.subjectSynthetic biologyen_US
dc.subjectComputational biologyen_US
dc.subjectIn silicoen_US
dc.subjectModellingen_US
dc.subjectSimulationen_US
dc.subjectVerificationen_US
dc.subjectBiocompilationen_US
dc.subjectHigh performance computingen_US
dc.subjectSBOLen_US
dc.subjectSBMLen_US
dc.titleToward full-stack in silico synthetic biology: integrating model specification, simulation, verification, and biological compilationen_US
dc.status.refereedYesen_US
dc.date.Accepted2021
dc.date.application2021-08-02
dc.typeArticleen_US
dc.type.versionPublished versionen_US
refterms.dateFOA2021-09-15T10:33:20Z
dc.openaccess.statusGreenen_US


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