Storing and Sharing Synthetic Biology Designs

Curtis Madsen

This is a presentation given on 20 January, 2016, at the Open Tools and Infrastructure for Biology 2016 held at Newcastle University.

Synthetic biology is a growing field that combines ideas from biology and engineering. It is, however, often difficult to utilize the extensive amount of biological data for design in synthetic biology. The Newcastle SBOL Stack allows researchers to store, retrieve, exchange and publish SBOL data. It’s a Sesame RDF database designed to publish a library of synthetic parts, collaborate with others, and much more.

Data in the SBOL Stack can be accessed via SPARQL queries that produce either tables or graphs. The graph response is in the standard RDF triple format. As the SBOL language is based on RDF, these queries can return SBOL data. Querying the stack can be done with a simplified, non-SPARQL, query where you simply pass a triple to the Stack.

The SBOL Stack contains the option to further search the selected nodes in the results of a graph query. This is useful for someone interested in searching for more data on a particular element. For example, interactions with other elements and the DNA sequence of an element. The Stack includes an ontology (SynBiOnt) of genetic features, gene products and their annotations, gene regulatory networks, metabolic pathways and so on. Biological entities can be mapped to SBOL objects using this ontology.

One of the strengths of the Stack is its ability to register many Sesame RDF databases and perform federated queries for data integration. Repositories that contain any RDF info about biological parts can be included in the federated query.

The SBOL stack automatically retrieves the most up to date data each time a query is made. It can also take advantage of the cloud-based messaging system POLEN developed for the Flowers Consortium.

The SBOLhub is a front-end Web application that uses the Stack as its back end. Allows upload of entire SBOL documents along with metadata. Users can then share their designs and make them public. Each record can be viewed and obtain images using VisBOL. This can be used as reference data for synthetic biology publications. Uploading to VisBOL will allow the creation of an SVG image. VisBOL is available now, and they’re just working on a further visualization tool called TurBOL, which they call “The SBOL IDE”.

Phoenix is an automated design-build-test tool developed for synthetic biology experiments. He has been working on this most recently while at Boston University (he has been in Newcastle University prior to this).

Please note that this post is merely my notes on the presentation. I may have made mistakes: these notes are not guaranteed to be correct. Unless explicitly stated, they represent neither my opinions nor the opinions of my employers. Any errors you can assume to be mine and not the speaker’s. I’m happy to correct any errors you may spot – just let me know!

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