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Computer-aided design in synthetic biology: a system designer approach

Published: 26 October 2011 Publication History

Abstract

The development of computer-aided design tools for synthetic biology is currently a hot research topic. However the field is not mature enough to provide a generic, adaptable and reliable tool for potential applications. The purpose of this paper is to present a system designers approach. We highlight, through the work carried out by our team in recent years, the potential, but also the difficulties, of structuring an assisted design flow for synthetic biology. For this task, our idea is to build the design flow for synthetic biology on the foundations of the Electronic Design Automation tools that have proven their efficiency during the past 30 years. Although the overall approach of the microelectronics can be adapted to synthetic biology, some specific steps have to be created from scratch.

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  • (2024)Designing Lab Prototype of Synthetic p53 Protein-Based Tumor Suppressor Pathway2024 1st International Conference on Cognitive, Green and Ubiquitous Computing (IC-CGU)10.1109/IC-CGU58078.2024.10530855(1-6)Online publication date: 1-Mar-2024
  • (2020)A biological multiplexer, designs, and simulationsThe Journal of Supercomputing10.1007/s11227-019-03138-4Online publication date: 13-Apr-2020
  • (2012)A game-of-life like simulator for design-oriented modeling of BioBricks in synthetic biology2012 Annual International Conference of the IEEE Engineering in Medicine and Biology Society10.1109/EMBC.2012.6347230(5462-5465)Online publication date: Aug-2012

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        cover image ACM Other conferences
        ISABEL '11: Proceedings of the 4th International Symposium on Applied Sciences in Biomedical and Communication Technologies
        October 2011
        949 pages
        ISBN:9781450309134
        DOI:10.1145/2093698
        Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

        Sponsors

        • Universitat Pompeu Fabra
        • IEEE
        • Technical University of Catalonia Spain: Technical University of Catalonia (UPC), Spain
        • River Publishers: River Publishers
        • CTTC: Technological Center for Telecommunications of Catalonia
        • CTIF: Kyranova Ltd, Center for TeleInFrastruktur

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        Association for Computing Machinery

        New York, NY, United States

        Publication History

        Published: 26 October 2011

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        Author Tags

        1. computer-aided design tools
        2. design flow
        3. hardware description language
        4. microelectronics
        5. synthetic biology

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        ISABEL '11
        Sponsor:
        • Technical University of Catalonia Spain
        • River Publishers
        • CTTC
        • CTIF

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        • (2024)Designing Lab Prototype of Synthetic p53 Protein-Based Tumor Suppressor Pathway2024 1st International Conference on Cognitive, Green and Ubiquitous Computing (IC-CGU)10.1109/IC-CGU58078.2024.10530855(1-6)Online publication date: 1-Mar-2024
        • (2020)A biological multiplexer, designs, and simulationsThe Journal of Supercomputing10.1007/s11227-019-03138-4Online publication date: 13-Apr-2020
        • (2012)A game-of-life like simulator for design-oriented modeling of BioBricks in synthetic biology2012 Annual International Conference of the IEEE Engineering in Medicine and Biology Society10.1109/EMBC.2012.6347230(5462-5465)Online publication date: Aug-2012

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