An Update on Synbis – the Synthetic Biology Information System

Systematic rational design — also known as design-build-test cycle — has become key in the development of synthetic biology towards an engineering discipline. Typically, the goal is to build a new pathway or modify an existing one, to endow it with a set of qualitative or quantitative properties (for instance a response function to a given chemical species that falls within an acceptable range) , while reliably operating under a list of constraints (host, environmental conditions etc).

A common concept in engineering is that systems can be rapidly produced from the combination of standardized components. For this to happen in synthetic biology, there is a strong need of developing large catalogues of fully characterised parts and make them available in public registries, so they can be picked and reused for design.

Ideally, BioParts should be characterised in a range of contexts (plasmids, hosts, medium…) to the highest standards - using validated protocols ensuring a high level of reproducibility. Also, the catalogues must be available online, offer programmatic access to their data, and support widely-used data standards to integrate with existing and future CAD tools.

We present here the latest developments on SynBIS. SynBIS is an information system developed at the Centre for Synthetic Biology and Innovation (CSynBI) at Imperial College to support its multistage characterisation pipeline of biological parts, effectively:

• supporting the collection of information on constructs, construction and experimental protocols
• supporting and monitoring data acquisition
• automating data analysis, curation and the generation of Biopart datasheets
• compiling all collected and generated data into the SynBIS catalogue

 

As part of the design of SynBIS, we have striven to support and develop best practices in term of data information standards and reproducibility. SynBIS supports established data standards (SBOL for construct description; SBML for modelling) and nascent standards for protocol description. To enable data acquisition at scale, we have developed the first data-acquisition standard in synthetic biology (DICOM-SB) – basing it on the highly successful DICOM standard used in medical informatics.

Finally, we have developed a flexible datasheet model – based on the workflow of a canonical characterisation pipeline and serialised in XML – linking a BioPart to all the data generated in a characterisation experiment: raw data, analysis results (presenting qualitative and quantitative information describing the part’s behaviour) and the metadata required to ensure reproducibility of the experimental and analysis results.

The SynBIS parts catalogue (www.synbis.bg.ic.ac.uk) is an open access resource. It is organised around datasheets (and Biopart performance), and can be searched (beside standard parameters such as name or sequence) by placing conditions on the input-output function of a part.

Characterisation information is offered in human readable formats —HTML5 and pdf — as well as a machine readable formats —SBOL, SBML,XML and DICOM-SB. Direct programmatic access is available through a public API to all analysis, simulation and CAD software tools.