Difference between revisions of "CH391L/S13/CAD"

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==Synthetic Biology CAD Tools ==
 
==Synthetic Biology CAD Tools ==
 
Simulation Software
 
Simulation Software
*[http://www.tinkercell.com/ Tinker Cell]
+
*[http://www.tinkercell.com/ Tinker Cell]<cite>TinkerCell2009</cite>
*[http://synbioss.sourceforge.net/ SynBioSS]
+
*[http://synbioss.sourceforge.net/ SynBioSS]<cite>SynBioSS2010</cite>
 
Design Tools
 
Design Tools
*[https://public-registry.jbei.org/static/vesa/VectorEditor.html VectorEditor]
+
*[https://public-registry.jbei.org/static/vesa/VectorEditor.html VectorEditor]<cite>VectorEditor2012</cite>
 
*[http://clothocad.org Clotho]
 
*[http://clothocad.org Clotho]
 
*[https://www.dna20.com/genedesigner2/ Gene Designer 2.0]<cite>GeneDesigner2006</cite>
 
*[https://www.dna20.com/genedesigner2/ Gene Designer 2.0]<cite>GeneDesigner2006</cite>
*[http://www.genomecompiler.com/ Genome Compiler]<cite>TinkerCell2009</cite>
+
*[http://www.genomecompiler.com/ Genome Compiler]
  
  
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#GeneDesigner2006 pmid=16756672
 
#GeneDesigner2006 pmid=16756672
 
//Gene Designer:a synthetic biology tool for constructing artificial DNA segments
 
//Gene Designer:a synthetic biology tool for constructing artificial DNA segments
 +
#SynBioSS2010 pmid=20639523
 +
//SynBioSS designer: a web-based tool for the automated generation of kinetic models for synthetic biological constructs
 +
#VectorEditor2012 pmid=22718978
 +
//Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools.
 
</biblio>
 
</biblio>

Revision as of 00:48, 3 February 2013

Representing Synthetic Biology Designs

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

Simulation Software

Design Tools


References

  1. Galdzicki M, Rodriguez C, Chandran D, Sauro HM, and Gennari JH. Standard biological parts knowledgebase. PLoS One. 2011 Feb 24;6(2):e17005. DOI:10.1371/journal.pone.0017005 | PubMed ID:21390321 | 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. TinkerCell: modular CAD tool for synthetic biology. J Biol Eng. 2009 Oct 29;3:19. DOI:10.1186/1754-1611-3-19 | PubMed ID:19874625 | HubMed [TinkerCell2009]
    TinkerCell: modular CAD tool for synthetic biology
  4. Weeding E, Houle J, and Kaznessis YN. SynBioSS designer: a web-based tool for the automated generation of kinetic models for synthetic biological constructs. Brief Bioinform. 2010 Jul;11(4):394-402. DOI:10.1093/bib/bbq002 | PubMed ID:20639523 | 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. Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools. Nucleic Acids Res. 2012 Oct;40(18):e141. DOI:10.1093/nar/gks531 | PubMed ID:22718978 | 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. Gene Designer: a synthetic biology tool for constructing artificial DNA segments. BMC Bioinformatics. 2006 Jun 6;7:285. DOI:10.1186/1471-2105-7-285 | PubMed ID:16756672 | HubMed [GeneDesigner2006]
    Gene Designer:a synthetic biology tool for constructing artificial DNA segments
All Medline abstracts: PubMed | HubMed