CH391L/S13/CAD

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==Representing Synthetic Biology Designs ==
==Representing Synthetic Biology Designs ==
[[Image:TinkerCellSBOLRepresentation.png|thumb|350 px|right|TinkerCell representation of parts in a lactose-inducible GFP part]]
[[Image:TinkerCellSBOLRepresentation.png|thumb|350 px|right|TinkerCell representation of parts in a lactose-inducible GFP part]]
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*The [http://www.sbolstandard.org 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 <cite>Galdzicki2011</cite>. The core specification of this system has been developed as an RFC <cite>SBOLRFC</cite>. Several different [http://www.sbolstandard.org/sbolstandard/software-tools-using-sbol 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., [http://www.tinkercell.com/ TinkerCell]).
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*The [http://www.eugenecad.org/ Eugene Language] 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.
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The [http://www.sbolstandard.org 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 <cite>Galdzicki2011</cite>. The core specification of this system has been developed as an RFC <cite>SBOLRFC</cite>. Several different [http://www.sbolstandard.org/sbolstandard/software-tools-using-sbol 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., [http://www.tinkercell.com/ TinkerCell]).
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The [http://www.eugenecad.org/ Eugene Language] 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 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.
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.
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Simulation Software
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'''Simulation Software'''
*[http://www.tinkercell.com/ Tinker Cell]<cite>TinkerCell2009</cite>
*[http://www.tinkercell.com/ Tinker Cell]<cite>TinkerCell2009</cite>
*[http://synbioss.sourceforge.net/ SynBioSS]<cite>SynBioSS2010</cite>
*[http://synbioss.sourceforge.net/ SynBioSS]<cite>SynBioSS2010</cite>
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Design Tools
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'''Design Tools'''
*[https://public-registry.jbei.org/static/vesa/VectorEditor.html VectorEditor]<cite>VectorEditor2012</cite>
*[https://public-registry.jbei.org/static/vesa/VectorEditor.html VectorEditor]<cite>VectorEditor2012</cite>
*[http://clothocad.org Clotho]
*[http://clothocad.org Clotho]

Revision as of 04:09, 3 February 2013

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 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

  1. Galdzicki M, Rodriguez C, Chandran D, Sauro HM, and Gennari JH. . pmid:21390321. PubMed HubMed [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. Chandran D, Bergmann FT, and Sauro HM. . pmid:19874625. PubMed HubMed [TinkerCell2009]
    TinkerCell: modular CAD tool for synthetic biology

  4. Weeding E, Houle J, and Kaznessis YN. . pmid:20639523. PubMed HubMed [SynBioSS2010]
    SynBioSS designer: a web-based tool for the automated generation of kinetic models for synthetic biological constructs

  5. Ham TS, Dmytriv Z, Plahar H, Chen J, Hillson NJ, and Keasling JD. . pmid:22718978. PubMed HubMed [VectorEditor2012]
    Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools.

  6. Villalobos A, Ness JE, Gustafsson C, Minshull J, and Govindarajan S. . pmid:16756672. PubMed HubMed [GeneDesigner2006]
    Gene Designer:a synthetic biology tool for constructing artificial DNA segments

All Medline abstracts: PubMed HubMed
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