What is Synthetic Biology?
Synthetic biology is a new frontier in biological research where scientists and engineers design and create living systems to carry out useful tasks. In the last half century, the fundamental biochemical pieces and processes that comprise the phenomena of life have been isolated and studied by scientists in the laboratory. This reductionist approach to molecular biology has yielded enormous insight into the basic molecular units that govern life, such as genes encoded on DNA. Today, a new approach, synthetic biology, is possible in which basic units of biochemistry are re-assembled into new living systems, using platform technologies such as DNA synthesis, genome engineering, simulation tools, and computer-aided-design. In the future, important technologies like solar energy, biofuels, and medicines may be synthesized out of “wetware.”
What is SBOL?
The design process is fundamental to synthetic biology. The SBOL standard empowers and enables a design-oriented, forward-engineering approach for synthetic biology in the following ways:
• Facilitates storage of genetic designs in repositories
• Helps synthetic biologists and genetic engineers electronically exchange designs with each other and with biofabrication centers
• Supports development of Genetic Design Automation (GDA) software tools for synthetic biologists
• Represents hierarchically assembled genetic compositions
• Represents abstract genetic compositions without an explicit nucleotide sequence
• Allows expression of genetic designs in publications and thus aids scientific reproducibility
• Captures elements of a design that move beyond DNA Sequences to include RNA, proteins, small molecules and molecular interactions
• SBOL is extensible to allow other kinds of data to be attached to the core data model. This includes, for example, experimental data, host information and mathematical models
• Introductory slides on SBOL can be found here
SBOL vs. GenBank
With the emergence of large-scale DNA sequencing technology in the last few decades, there has also emerged a need to manage and share vast amounts of sequence data. For researchers in the biological sciences, the public GenBank database, data standard, and file format has become a familiar friend. However, there are several reasons why the GenBank standard is insufficient for satisfying the needs of synthetic biologists. While the GenBank standard is used to primarily describe sequences that correspond to an existing DNA sample, the SBOL standard promotes forward-engineering of novel sequences. In other words, SBOL makes it easy to assemble novel sequences from DNA components using computer-aided design and genetic design automation. Moreover, SBOL is able to capture elements of intended design about proteins and small molecules for example, as well as the interactions between them.
Current support for the development of the SBOL standard is provided by the NSF through Collaborative awards #1355909, #1356401, and #1522074 and EPSRC grant #EP/J02175X/1. Other sponsorship, support, or endorsements have been provided by the following federal agencies, federal research centers, commercial enterprises, and academic institutions. Please be aware that this list may not be complete, since the number of SBOL supporters is growing rapidly. If your institution supports SBOL, and it is not listed here, please email the SBOL editors.
Turing Ate My Hamster LTD
BU Crossdisciplinary Integration of Design Automation Research (CIDAR)
Imperial College Centre for Synthetic Biology and Innovation (CSynBI)
Newcastle University Center for Synthetic Biology