Synthetic biology open language will fuel progress, Virginia Bioinformatics Institute experts say
July 31, 2014
New standards within the synthetic biology community may help lift the field from pure research to practical applications, according to an international group of researchers, including a computational synthetic biologist at Virginia Tech.
A group of 32 authors from 19 institutions writing in Nature Biotechnology says Synthetic Biology Open Language, a proposed data standard for exchanging previously validated designs, is critical to the evolution of synthetic biology from a research discipline to an engineering practice.
Synthetic biology brings together diverse disciplines such as bioinformatics, molecular biology, chemistry, and engineering. Its goal is to engineer living organisms to fulfill certain functions, much like machines are built to perform specific tasks.
Synthetic Biology Open Language, also known as SBOL, has allowed the synthetic biology community to put its ambitions into action by giving scientists the freedom and flexibility to move data between software tools and projects.
"Since 2007, we have seen a rapid expansion of the number of software applications for synthetic biology," said Jean Peccoud, a professor at the Virginia Bioinformatics Institute. "It is critical to avoid locking our users into software silos corresponding to a proprietary data format. Synthetic Biology Open Language makes it possible for users to freely move data between tools depending on their needs and rapid evolutions of the different software projects."
Development of the language began in April 2008.
Peccoud and a small group of synthetic biologists involved in software development projects realized that their tools needed access to specific data that could not be captured using existing bioinformatics standards.
A series of biannual meetings, along with a vibrant online community, have been instrumental in enabling the community-driven specification of this standard. Virginia Tech hosted the fourth Synthetic Biology Open Language meeting in January 2011.
In addition, Mandy Wilson, a senior software developer in the Peccoud Lab, was elected as one of the three Synthetic Biology Open Language editors in June 2011.
"Fifteen years ago, I was part of the effort to develop a standard for the systems biology community," said Herbert Sauro, an associate professor of bioengineering at the University of Washington and senior author of the article. "The success of the Systems Biology Markup Language has been an inspiration for SBOL. From its inception, SBOL has been supported by several major companies who provide software packages for synthetic biologists. Their participation is critical to the future development of the standard."
The development of such a standard makes possible greater synergy between teams working toward the same objectives in synthetic biology. This could mean even quicker advances in medicine, sustainability, and agriculture.
"The institute's reputation has been built on providing software tools and information portals to various communities of life scientists," said Christopher Barrett, executive director of the Virginia Bioinformatics Institute. "Synthetic biology is one of the fastest growing segments of the life sciences, and we are happy to contribute our expertise and resources to meeting its rapidly evolving computational needs."
The Virginia Bioinformatics Institute's contribution to the development of the Synthetic Biology Open Language was supported by a grant from the National Science Foundation to develop GenoCAD, a computer-assisted design software for synthetic biology (Award EF-0850100).
Peccoud is the chief scientific officer of GenoFAB LLC, a company that provides products and services related to GenoCAD.