Most of the details on this site are geared towards developers who wish to understand the specification, development and implementation of SBOL in their own software. This page however will introduce the purpose of SBOL to the wider community. What is SBOL? Here are four scenarios that SBOL is designed to solve:
SBOL comprises of an object model and a serialization of SBOL to a file. The file then becomes a machine-readable format form representing designs in synthetic biology. The supported serialization is RDF/XML. In addition, export and import to GenBank format will also be supported. SBOL is neutral with respect to programming languages and software encoding. By supporting SBOL for reading and writing synthetic biology designs, different software tools can directly communicate and store the same representation of these designs. This removes an impediment to sharing engineered systems and permits other researchers and commercial enterprises to start with an unambiguous representation of the design. The adoption of SBOL offers many benefits, including: (1) enabling the use of multiple tools without rewriting designs for each tool, (2) enabling designs to be shared and published in a form other researchers can use even in a different software environment, and (3) ensuring the survival of design (and the intellectual effort put into them) beyond the lifetime of the software or the reseachers that were used to create them. To use SBOL you should use the libSBOL library. Currently the libSBOL library is written in Java and can import and export an early XML format. The library is currently been re-factored to read and write RDF/XML. There is also a C/C++ based library written by Deepak Chandran that can export and import RDF, this will also be modified to read and write RDF/XML. Ultimately there will be two libraries, one for Java developers and a C/C++ library for all other languages. Each library will be able to import and export RDF/XML. SBOL's development started in 2008 with a small grant from Microsoft. Since then it has grown to include a wide consortium of individuals, public institutions and commercial enterprises both in the US and Europe. SBOL is built around the idea of a core that is used to unambiguously specify a DNA molecule. Around the core are extensions that are used to increase the kind and amount of information transmitted by the language. There are three extensions under development and three more under consideration. For example, one extension includes data and information on the performance of DNA components. The examples page illustrates a variety of DNA designs specified using the core. * Round-tripping: Round-tripping is the repeated conversion back and forth of data between different software tools such that the data is always preserved. For example a document might be saved in Microsoft Word, imported into WordPerfect, changed, saved then imported again into Word without loss of any of the important information. |