Goksel Misirli g.misirli@keele.ac.uk
A Genetic Circuit Compiler: Generating Combinatorial Genetic Circuits with Web Semantics and Inference
Misirli
Authors
Abstract
A central strategy of synthetic biology is to understand the basic processes of living creatures through engineering organisms using the same building blocks. Biological machines described in terms of parts can be studied by computer simulation in any of several languages or robotically assembled in vitro. In this paper we present a language, the Genetic Circuit Description Language (GCDL) and a compiler, the Genetic Circuit Compiler (GCC). This language describes genetic circuits at a level of granularity appropriate both for automated assembly in the laboratory and deriving simulation code. The GCDL follows Semantic Web practice, and the compiler makes novel use of the logical inference facilities that are therefore available. We present the GCDL and compiler structure as a study of a tool for generating k-language simulations from semantic descriptions of genetic circuits.
Acceptance Date | Nov 8, 2018 |
---|---|
Publication Date | Dec 1, 2018 |
Publicly Available Date | Mar 28, 2024 |
Journal | ACS Synthetic Biology |
Publisher | American Chemical Society |
Pages | 2812-2823 |
DOI | https://doi.org/10.1021/acssynbio.8b00201 |
Keywords | semantic web; inference; program generation; synthetic biology; genetic circuits |
Publisher URL | https://pubs.acs.org/doi/10.1021/acssynbio.8b00201 |
Files
acssynbio.8b00201.pdf
(451 Kb)
PDF
Publisher Licence URL
https://creativecommons.org/licenses/by-nc/4.0/
acs_composing_biological_parts_supplementary.pdf
(571 Kb)
PDF
Publisher Licence URL
https://creativecommons.org/licenses/by-nc/4.0/
You might also like
libSBOLj3: a graph-based library for design and data exchange in synthetic biology.
(2023)
Journal Article
Modelling the fitness landscapes of a SCRaMbLEd yeast genome.
(2022)
Journal Article
Reflections on the 35th BCS Human-Computer Interaction Conference at Keele University
(2022)
Conference Proceeding
Virtual Parts Repository 2: Model-Driven Design of Genetic Regulatory Circuits
(2021)
Journal Article
Synthetic biology open language visual (SBOL visual) version 3.0.
(2021)
Journal Article
Downloadable Citations
About Keele Repository
Administrator e-mail: research.openaccess@keele.ac.uk
This application uses the following open-source libraries:
SheetJS Community Edition
Apache License Version 2.0 (http://www.apache.org/licenses/)
PDF.js
Apache License Version 2.0 (http://www.apache.org/licenses/)
Font Awesome
SIL OFL 1.1 (http://scripts.sil.org/OFL)
MIT License (http://opensource.org/licenses/mit-license.html)
CC BY 3.0 ( http://creativecommons.org/licenses/by/3.0/)
Powered by Worktribe © 2024
Advanced Search