| The emergence of open source
software – which differs from most commercial software because the computer
programming code is published openly and designed to allow others to build
improvements and complementary programs – has been heralded by academics
and independent programmers for a number of reasons. Chief among them in
the academic world is the open and collaborative approach to designing
and often using for free, or limited cost, programs that aid in research
and development of cutting-edge developments in science and technology.
Researchers at the NSF-funded
Synthetic Biology Engineering Research Center (SynBERC), based at the University
of California, Berkeley, have worked to develop open source tools and standards
to drive the field of synthetic biology forward.
These open source innovations
include: Biological Simulation Program for Intra- and Inter-Cellular Evaluation
(Bio-SPICE), a network informatics tools for simulating and analyzing natural
and designed biological networks and their comparison to data, by SynBERC
researcher Adam Arkin; VIMSS Comparative Genomics database VIMSSDB, tools
for comparing genome structure across sequenced microbes, also by Arkin;
the BioBricks Foundation not-for-profit that promotes technical standards
for the use of BioBricks (a set of standard biological parts that researchers
can use to program living organisms, akin to computer programming); the
first assembly strategy for BioBrick parts, led by MIT’s Tom Knight; specifications
for device-independent signal carrier for gene expression-based devices,
by Stanford University’s Drew Endy; specifications for abstraction hierarchies
for the Protein:DNA Parts and Post-Translational Parts families, also led
by Endy; and specifications for a standard for transport of models as part
of the original SBML design team, by Arkin.
SynBERC’s continued leadership
in the development of more open source tools is a powerful driver of the
synthetic biology community’s technological capabilities, as well as its
capacity to develop even more powerful open source tools. |
