The re-use of previously validated designs is critical to the evolution of synthetic biology from a research discipline to an engineering practice. Here we describe the Synthetic Biology Open Language (SBOL), a proposed data standard for exchanging designs within the synthetic biology community. SBOL represents synthetic biology designs in a communitydriven, formalized format for exchange between software tools, research groups and commercial service providers. The SBOL Developers Group has implemented SBOL as an XML/RDF serialization and provides software libraries and specification documentation to help developers implement SBOL in their own software. We describe early successes, including a demonstration of the utility of SBOL for information exchange between several different software tools and repositories from both academic and industrial partners. As a community-driven standard, SBOL will be updated as synthetic biology evolves to provide specific capabilities for different aspects of the synthetic biology workflow.Synthetic biology treats biological organisms as a new technological medium with a unique set of characteristics, such as the ability to self-repair, evolve and replicate. These characteristics create their own engineering challenges, but offer a rich and largely untapped source of potential applications across a broad range of sectors 1,2 . Applications such as biomolecular computing 3 , metabolic engineering 4 , or reconstruction and exploration of natural cell biology 5,6 commonly require the design of new genetically encoded systems. As engineers, synthetic biologists most often base their designs on previously described 'DNA segments' (see Supplementary Table 1 for definitions of selected terms) to meet their design requirements. Reuse of the DNA sequence for these segments involves their exchange between laboratories and their hierarchical composition to form devices and systems with higher level function.Every engineering field relies on a set of 'standards' 7 that practitioners follow to enable the exchange and reuse of designs for 'systems' , 'devices' and 'components' . Similarly, the representation of synthetic biology designs using computer-readable 'data standards' has the potential to facilitate the forward engineering of novel biological systems from previously characterized devices and components. For example, such standards could enable synthetic biology companies to offer catalogs of devices and components by means of computerreadable data sheets, just as modern semiconductor companies do for electronics. Such standards could also enable a synthetic biologist to develop portions of a design using one software tool, refine the design using another tool, and finally transmit it electronically to a colleague or commercial fabrication company.In order for synthetic biology designs to scale up in complexity, researchers will need to make greater use of specialized design tools and parts repositories. Seamless inter-tool communication would, for example, allow the separation of gene...

The Joint BioEnergy Institute Inventory of Composable Elements (JBEI-ICEs) is an open source registry platform for managing information about biological parts. It is capable of recording information about ‘legacy’ parts, such as plasmids, microbial host strains and Arabidopsis seeds, as well as DNA parts in various assembly standards. ICE is built on the idea of a web of registries and thus provides strong support for distributed interconnected use. The information deposited in an ICE installation instance is accessible both via a web browser and through the web application programming interfaces, which allows automated access to parts via third-party programs. JBEI-ICE includes several useful web browser-based graphical applications for sequence annotation, manipulation and analysis that are also open source. As with open source software, users are encouraged to install, use and customize JBEI-ICE and its components for their particular purposes. As a web application programming interface, ICE provides well-developed parts storage functionality for other synthetic biology software projects. A public instance is available at public-registry.jbei.org, where users can try out features, upload parts or simply use it for their projects. The ICE software suite is available via Google Code, a hosting site for community-driven open source projects.

SUMMARYThe glycosyltransferases (GTs) are an important and functionally diverse family of enzymes involved in glycan and glycoside biosynthesis. Plants have evolved large families of GTs which undertake the array of glycosylation reactions that occur during plant development and growth. Based on the Carbohydrate-Active enZymes (CAZy) database, the genome of the reference plant Arabidopsis thaliana codes for over 450 GTs, while the rice genome (Oryza sativa) contains over 600 members. Collectively, GTs from these reference plants can be classified into over 40 distinct GT families. Although these enzymes are involved in many important plant specific processes such as cell-wall and secondary metabolite biosynthesis, few have been functionally characterized. We have sought to develop a plant GTs clone resource that will enable functional genomic approaches to be undertaken by the plant research community. In total, 403 (88%) of CAZy defined Arabidopsis GTs have been cloned, while 96 (15%) of the GTs coded by rice have been cloned. The collection resulted in the update of a number of Arabidopsis GT gene models. The clones represent full-length coding sequences without termination codons and are Gateway â compatible. To demonstrate the utility of this JBEI GT Collection, a set of efficient particle bombardment plasmids (pBullet) was also constructed with markers for the endomembrane. The utility of the pBullet collection was demonstrated by localizing all members of the Arabidopsis GT14 family to the Golgi apparatus or the endoplasmic reticulum (ER). Updates to these resources are available at the JBEI GT Collection website http://www.addgene.org/.