Michal Galdzicki

The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology

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 community-driven, 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.

Standard Biological Parts Knowledgebase

We have created the Knowledgebase of Standard Biological Parts (SBPkb) as a publically accessible Semantic Web resource for synthetic biology (sbolstandard.org). The SBPkb allows researchers to query and retrieve standard biological parts for research and use in synthetic biology. Its initial version includes all of the information about parts stored in the Registry of Standard Biological Parts (partsregistry.org). SBPkb transforms this information so that it is computable, using our semantic framework for synthetic biology parts. This framework, known as SBOL-semantic, was built as part of the Synthetic Biology Open Language (SBOL), a project of the Synthetic Biology Data Exchange Group. SBOL-semantic represents commonly used synthetic biology entities, and its purpose is to improve the distribution and exchange of descriptions of biological parts. In this paper, we describe the data, our methods for transformation to SBPkb, and finally, we demonstrate the value of our knowledgebase with a set of sample queries. We use RDF technology and SPARQL queries to retrieve candidate “promoter” parts that are known to be both negatively and positively regulated. This method provides new web based data access to perform searches for parts that are not currently possible.

Multiple ontologies in action: Composite annotations for biosimulation models

There now exists a rich set of ontologies that provide detailed semantics for biological entities of interest. However, there is not (nor should there be) a single source ontology that provides all the necessary semantics for describing biological phenomena. In the domain of physiological biosimulation models, researchers use annotations to convey semantics, and many of these annotations require the use of multiple reference ontologies. Therefore, we have developed the idea of composite annotations that access multiple ontologies to capture the physics-based meaning of model variables. These composite annotations provide the semantic expressivity needed to disambiguate the often-complex features of biosimulation models, and can be used to assist with model merging and interoperability. In this paper, we demonstrate the utility of composite annotations for model merging by describing their use within SemGen, our semantics-based model composition software. More broadly, if orthogonal reference ontologies are to meet their full potential, users need tools and methods to connect and link these ontologies. Our composite annotations and the SemGen tool provide one mechanism for leveraging multiple reference ontologies.

SBOL Visual: A Graphical Language for Genetic Designs.

Synthetic Biology Open Language (SBOL) Visual is a graphical standard for genetic engineering. It consists of symbols representing DNA subsequences, including regulatory elements and DNA assembly features. These symbols can be used to draw illustrations for communication and instruction, and as image assets for computer-aided design. SBOL Visual is a community standard, freely available for personal, academic, and commercial use (Creative Commons CC0 license). We provide prototypical symbol images that have been used in scientific publications and software tools. We encourage users to use and modify them freely, and to join the SBOL Visual community: http://www.sbolstandard.org/visual.

Essential information for synthetic DNA sequences

Jean Peccoud1, J Christopher Anderson2, Deepak Chandran3, Douglas Densmore4, Michal Galdzicki5, Matthew W Lux1, Cesar A Rodriguez6, Guy-Bart Stan7 & Herbert M Sauro3 1Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, USA. 2Department of Bioengineering, QB3: California Institute for Quantitative Biological Research, University of California, Berkeley, California, USA. 3Department of Bioengineering, University of Washington, Seattle, Washington, USA. 4Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts, USA.5Biomedical and Health Informatics, University of Washington, Seattle, Washington, USA. 6BIOFAB, Emeryville, California, USA. 7Department of Bioengineering and Centre for Synthetic Biology and Innovation, Imperial College London, London, UK. e-mail: peccoud@vt.edu

A C library for retrieving specific reactions from the BioModels database

SUMMARY We describe libSBMLReactionFinder, a C library for retrieving specific biochemical reactions from the curated systems biology markup language models contained in the BioModels database. The library leverages semantic annotations in the database to associate reactions with human-readable descriptions, making the reactions retrievable through simple string searches. Our goal is to provide a useful tool for quantitative modelers who seek to accelerate modeling efforts through the reuse of previously published representations of specific chemical reactions. AVAILABILITY AND IMPLEMENTATION The library is open-source and dual licensed under the Mozilla Public License Version 2.0 and GNU General Public License Version 2.0. Project source code, downloads and documentation are available at http://code.google.com/p/lib-sbml-reaction-finder.

Reply to Intellectual property issues and synthetic biology standards.

25 property rights covering technical standards. Inevitably, there will be trade-offs in the time and resources needed for developing technical standards versus the time and resources needed to identify and evaluate property rights that may be essential for practicing those standards. As such, it will be important to establish policies for meaningful disclosure that are not overly burdensome and will not unduly hinder the standards development process. We, together with the BioBricks Foundation and others in the synthetic biology community, would welcome additional work by legal professionals to analyze, establish and share opinions regarding the ‘freedom to operate’ for SBOL v1.1 and other standards from a property rights perspective. These opinions could, for example, be made available to the public by posting on the BioBricks Foundation’s website. By engaging in a careful and active process of public documentation and disclosure of SBOL’s development, and by working with legal experts that could assist in identifying potential third-party rights (thereby enabling workarounds if needed), we hope to realize our goal of keeping the SBOL standard free to use for all.

Data Model Standardization for Synthetic Biomolecular Circuits and Systems

While biological engineers strive to capture the biophysical theory essential in predicting how a newly designed synthetic organism will behave, the current state of this knowledge is far from ideal. To facilitate the research towards this goal, specifically through the application of computational tools, the data required to engineer biological systems should be electronically accessible and interpretable. The challenge to represent such information computationally is complicated by the enormous diversity and size of biological data. There is a plethora of biological components, interacting physically and chemically, with implications for behavior at multiple time and spatial scales. The many scientists working to move the synthetic biology field forward have to communicate their research findings and should understand each other despite their diverse academic backgrounds. The challenge and demand for data standardization arises from the need to collaborate in order to engineer ever more complex biomolecular circuits and to understand and control biological systems. The bioinformatics field provides us with a history of experience in its attempts to facilitate collaboration in the biomedical research community. We draw on the lessons from the application of information technology solutions to inform and inspire the new efforts in synthetic biology. Furthermore, we acknowledge fundamental differences in the nature of the two fields and discuss the need to standardize data models for the purpose of engineering and design of novel biomolecular circuits and systems.