| Researchers at the NSF-funded
Synthetic Biology Engineering Research Center (SynBERC) at the University
of California, Berkeley continue to develop new open source tools and standards
to help drive the field of synthetic biology. The open source nature
of these tools and standards—i.e., the analytical methods, design software,
and data will be available to the non-profit research community and to
companies that are members of the Center’s industrial consortium—is a key
characteristic of the ERC’s mission to not only advance the field, but
to do so in a way that others in academia and business can also help further
to deliver benefits across society.
Several of these open source
advances have been led by Adam Arkin, a computational biologist at the
University of California, Berkeley, including: BioSPICE
(Biological Simulation Program for Intra- and Inter-Cellular Evaluation),
a framework and software toolset for modeling and simulation of spatio-temporal
processes in living cells; tools for the comparison of genome structure
(operon, regulon, etc.) across sequenced microbes; and specifications for
a standard for transport of a model as part of the original design team
for the Systems Biology Markup Language
(SBML), a computer-readable format for representing models of biological
processes.
SynBERC Strategic Director
Drew Endy, an Assistant Professor of Bioengineering at Stanford University,
leads another team of researchers that is a prolific developer of open
source tools, including: the BioBricks
Foundation, a 501(c)3 not-for-profit that encourages the development
and responsible use of technologies based on BioBrick™ standard DNA parts
that encode basic biological functions; specifications for a device-independent
signal carrier for gene expression-based devices (i.e., PoPS, or polymerase
per second, a term for quantifying the input/output signals in genetic
circuits); specifications for abstraction hierarchies for the Protein:DNA
Parts (PDP) and Post-Translational Parts (PTP) families; and the first
specification datasheet for a biological device. In addition to the
work done by the BioBricks Foundation, Massachusetts Institute of Technology
Senior Research Scientist Tom Knight has developed the first BioBrick™
parts and assembly strategy. |
