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Toward Full-Stack In Silico Synthetic Biology: Integrating Model Specification, Simulation, Verification, and Biological Compilation

Lookup NU author(s): Dr Harold Fellermann, Bradley Brown, Professor Anil Wipat, Professor Natalio KrasnogorORCiD

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Abstract

We 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 modeling, simulation, verification, and biocompilation 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 modeling or specification languages, IBL uniquely blends modeling …

Publication metadata

Author(s): Konur S, Mierla L, Fellermann H, Ladroue C, Brown B, Wipat A, Twycross J, Dun BP, Kalvala S, Gheorghe M, Krasnogor N

Publication type: Article

Publication status: Published

Journal: ACS Synthetic Biology

Year: 2021

Volume: 10

Issue: 8

Pages: 1931-1945

Print publication date: 02/08/2021

Online publication date: 02/08/2021

Acceptance date: 02/08/2002

ISSN (electronic): 2161-5063

Publisher: American Chemical Society

URL: https://doi.org/10.1021/acssynbio.1c00143

DOI: 10.1021/acssynbio.1c00143

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