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

• SynthBioCHESS.pdf · application/pdf · 1486 kbytes

• 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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