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

Konur, Savas; Mierla, Laurentiu; Fellermann, Harold; Ladroue, Christophe; Brown, Bradley; Wipat, Anil; Twycross, Jamie; Dun, Boyang Peter; Kalvala, Sara; Gheorghe, Marian; Krasnogor, Natalio

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, 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.

Citation

Konur, S., Mierla, L., Fellermann, H., Ladroue, C., Brown, B., Wipat, A., Twycross, J., Dun, B. P., Kalvala, S., Gheorghe, M., & Krasnogor, N. (2021). Toward Full-Stack In Silico Synthetic Biology: Integrating Model Specification, Simulation, Verification, and Biological Compilation. ACS Synthetic Biology, 10(8), 1931-1945. https://doi.org/10.1021/acssynbio.1c00143

• Journal Article Type: Article
• Acceptance Date: Aug 2, 2021
• Online Publication Date: Aug 2, 2021
• Publication Date: Aug 20, 2021
• Deposit Date: Mar 31, 2025
• Publicly Available Date: Apr 3, 2025
• Journal: ACS Synthetic Biology
• Electronic ISSN: 2161-5063
• Publisher: American Chemical Society
• Peer Reviewed: Peer Reviewed
• Volume: 10
• Issue: 8
• Pages: 1931-1945
• DOI: https://doi.org/10.1021/acssynbio.1c00143
• Keywords: Algorithms; Circuits; Genetics; Imaging probes; Molecules
• Public URL: https://nottingham-repository.worktribe.com/output/20554331
• Publisher URL: https://pubs.acs.org/doi/10.1021/acssynbio.1c00143