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, a 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
• A deeper introduction of SBOL can be found here
Biological Parts Repositories
Components of molecular DNA originate from samples found in nature; they can also be synthesized from raw chemical ingredients using DNA synthesis technology. Once an interesting piece of DNA has been isolated and studied in the lab, it is usually saved as a physical sample. Often, another inquisitive researcher will be interested in combining this DNA component with others to study it in a different context or produce a new and useful biological function. Similar to how software programmers share and re-use each other’s code, this sharing process is essential to synthetic biology. Biological parts repositories serve as a common resource where synthetic biologist can go to obtain physical samples of DNA associated with important data about those samples. The Synthetic Biology Open Language was invented to help make management and sharing of designs for biological parts easy and efficient. As DNA synthesis costs drop the designs and sequence of parts in SBOL format will become more important than the actual physical DNA itself
Examples of Biological Parts Repositories:
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.