CH391L/S13/CAD

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Representing Synthetic Biology Designs

TinkerCell representation of parts in a lactose-inducible GFP part
TinkerCell representation of parts in a lactose-inducible GFP part

The Synthetic Biology Open Language is an open-source standard for representing designs consisting of both DNA sequence information and higher level annotation of parts with defined roles and behaviors [1]. The core specification of this system has been developed as an RFC [2]. Several different synthetic biology CAD software programs use this format. Representation at this higher level of parts can be visualized and simulated in some of these systems (e.g., TinkerCell).

The Eugene Language[3] is an open-source human-readable language designed to facilitate automatic creation of new devices from a collection of parts. Eugene includes a standardized format for specifying devices and parts as well as constraints on how they can be assembled into higher level devices (i.e. genetic toggle switch). Eugene also features functions for automatic generation of functional assemblies into complex devices. Eugene does not support visualization of constructs.

Synthetic Biology CAD Tools

Synthetic Biology Computer Assisted Design (CAD) tools are programs which help to create novel biological constructs. At the most basic, these programs are essentially enhanced DNA editors which provide a user interface to facilitate easier manipulation of the basic “parts” which comprise biological devices. Some of the more advanced programs have a variety of functions including visualization, asserting validity of constructs, and simulations of metabolic networks.

Simulation Software

Design Tools


References

Error fetching PMID 21390321:
Error fetching PMID 19874625:
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  1. Error fetching PMID 21390321: [Galdzicki2011]
    Standard biological parts knowledgebase

  2. http://dspace.mit.edu/handle/1721.1/66172

    [SBOLRFC]

    Synthetic Biology Open Language (SBOL) Version 1.0.0

  3. Error fetching PMID 21559524: [Eugene2011]
    Eugene--a domain specific language for specifying and constraining synthetic biological parts, devices, and systems

  4. Error fetching PMID 19874625: [TinkerCell2009]
    TinkerCell: modular CAD tool for synthetic biology

  5. Error fetching PMID 20639523: [SynBioSS2010]
    SynBioSS designer: a web-based tool for the automated generation of kinetic models for synthetic biological constructs

  6. Error fetching PMID 22718978: [VectorEditor2012]
    Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools.

  7. Error fetching PMID 16756672: [GeneDesigner2006]
    Gene Designer:a synthetic biology tool for constructing artificial DNA segments

All Medline abstracts: PubMed HubMed
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