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Computer Aided Design of Synthetic Biological Systems Using Standardized Parts
Douglas Densmore

Citation
Douglas Densmore. "Computer Aided Design of Synthetic Biological Systems Using Standardized Parts". Talk or presentation, 18, November, 2008.

Abstract
Genomics has reached the stage at which the amount of DNA sequence information in existing databases is quite large. Moreover, synthetic biology now is using these databases to catalog sequences according to their functionality and therefore creating standard biological parts which can be used to create large systems. What is needed now are flexible tools which not only permit access and modification to that data but also allow one to perform meaningful manipulation and use of that information in an intelligent and efficient way. These tools need to be useful to biologists working in a laboratory environment while leveraging the experience of the larger CAD community. This talk will outline some of the major issues facing tool development for synthetic biological systems. These include issues of data management, part standardization, and composite part assembly. In addition to giving an overview and introduction to systems based on standard biological parts, the talk will discuss the Clotho design environment. This is a system specifically created at UC Berkeley to address these issues as well as be an open source, plugin based system to encourage participation by the community as a whole.

Electronic downloads

Citation formats  
  • HTML
    Douglas Densmore. <a
    href="http://chess.eecs.berkeley.edu/pubs/508.html"
    ><i>Computer Aided Design of Synthetic Biological
    Systems Using Standardized Parts</i></a>, Talk
    or presentation,  18, November, 2008.
  • Plain text
    Douglas Densmore. "Computer Aided Design of Synthetic
    Biological Systems Using Standardized Parts". Talk or
    presentation,  18, November, 2008.
  • BibTeX
    @presentation{Densmore08_ComputerAidedDesignOfSyntheticBiologicalSystemsUsing,
        author = {Douglas Densmore},
        title = {Computer Aided Design of Synthetic Biological
                  Systems Using Standardized Parts},
        day = {18},
        month = {November},
        year = {2008},
        abstract = {Genomics has reached the stage at which the amount
                  of DNA sequence information in existing databases
                  is quite large. Moreover, synthetic biology now is
                  using these databases to catalog sequences
                  according to their functionality and therefore
                  creating standard biological parts which can be
                  used to create large systems. What is needed now
                  are flexible tools which not only permit access
                  and modification to that data but also allow one
                  to perform meaningful manipulation and use of that
                  information in an intelligent and efficient way.
                  These tools need to be useful to biologists
                  working in a laboratory environment while
                  leveraging the experience of the larger CAD
                  community. This talk will outline some of the
                  major issues facing tool development for synthetic
                  biological systems. These include issues of data
                  management, part standardization, and composite
                  part assembly. In addition to giving an overview
                  and introduction to systems based on standard
                  biological parts, the talk will discuss the Clotho
                  design environment. This is a system specifically
                  created at UC Berkeley to address these issues as
                  well as be an open source, plugin based system to
                  encourage participation by the community as a
                  whole.},
        URL = {http://chess.eecs.berkeley.edu/pubs/508.html}
    }
    

Posted by Hiren Patel on 19 Nov 2008.
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