Biology subjects

Swainston, N.

Publications and source records attributed to Swainston, N..

4 recordsLinked to original sources

bioRxiv2017

Selenzyme: Enzyme selection tool for pathway design

Synthetic biology applies the principles of engineering to biology in order to create biological functionalities not seen before in nature. One of the most exciting applications of synthetic biology is the design of new organisms with the ability to produce valuable chemicals including pharmaceuticals and biomaterials in a greener; sustainable fashion. Selecting the right enzymes to catalyze each reaction step in order to produce a desired target compound is, however, not trivial. Here, we present Selenzyme, a free online enzyme selection tool for metabolic pathway design. The user is guided through several decision steps in order to shortlist the best candidates for a given pathway step. The tool graphically presents key information about enzymes based on existing databases and tools such as: similarity of sequences and of catalyzed reactions; phylogenetic distance between source organism and intended host species; multiple alignment highlighting conserved regions, predicted catalytic site, and active regions; and relevant properties such as predicted solubility and transmembrane regions. Selenzyme provides bespoke sequence selection for automated workflows in biofoundries. The tool is integrated as part of the pathway design stage into the design-build-test-learn SYNBIOCHEM pipeline. The Selenzyme web server is available at http://selenzyme.synbiochem.co.uk.

bioinformatics↗

bioRxiv2017

PartsGenie: an integrated tool for optimising and sharing synthetic biology parts

Synthetic biology is typified by developing novel genetic constructs from the assembly of reusable synthetic DNA parts, which contain one or more features such as promoters, ribosome binding sites, coding sequences and terminators. While repositories of such parts exist to promote their reuse, there is still a need to design novel parts from scratch.\n\nPartsGenie, freely available at http://parts.synbiochem.co.uk, is introduced to facilitate the computational design of such synthetic biology parts. PartsGenie has been designed to bridge the gap between optimisation tools for the design of novel parts, the representation of such parts in community-developed data standards such as Synthetic Biology Open Language (SBOL), and their sharing in journal-recommended data repositories.\n\nConsisting of a drag-and-drop web interface, a number of DNA optimisation algorithms, and an interface to the well-used data repository JBEI ICE, PartsGenie facilitates the design, optimisation and dissemination of reusable synthetic biology parts through a single, integrated application. PartsGenie can therefore be used as a single, stand-alone tool, or integrated into larger synthetic biology pipelines that are being developed in the SYNBIOCHEM centre and elsewhere.

synthetic biology↗

bioRxiv2017

A Metabolic Reaction Balancing Web Service for Computational Systems Biology

BackgroundIn metabolic network reconstruction the stoichiometric balancing of reactions is essential to create realistic constraint-based models. At the genome scale, balancing is a repetitive task that consumes valuable curator resource that could be deployed elsewhere. Automatic reaction balancing is possible and could be useful across computational systems biology, but widespread use of the appropriate code has been limited by the diversity of non-interoperable programming languages used in the field. RESTful web services offer a language-agnostic way of binding services together.\n\nResultsReaction balancing can be posed as a mixed integer linear programming problem to identify stoichiometric coefficients and infer commonly missing components. This functionality has been exposed as a web service that consumes a list of reactions as JSON or SBML. The reaction balancing web service has been deployed at http://www.nactem.ac.uk/balancer. Code is available via Github. By way of demonstration the service has been applied to a Chinese hamster ovary cell metabolic reconstruction to bring a further 219 reactions into balance.\n\nConclusionsThe majority of systems biology software cannot access existing automatic reaction balancing tools due to a lack of language-specific bindings. Web services bridge different languages by using widely-spoken web communication protocols, meaning that one binding works for almost all languages. Automatic reaction balancing can now be consumed by any systems biology software via a RESTful web service.

systems biology↗

bioRxiv2017

Identifiers for the 21st century:How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

In many disciplines, data is highly decentralized across thousands of online databases (repositories, registries, and knowledgebases). Wringing value from such databases depends on the discipline of data science and on the humble bricks and mortar that make integration possible; identifiers are a core component of this integration infrastructure. Drawing on our experience and on work by other groups, we outline ten lessons we have learned about the identifier qualities and best practices that facilitate large-scale data integration. Specifically, we propose actions that identifier practitioners (database providers) should take in the design, provision and reuse of identifiers; we also outline important considerations for those referencing identifiers in various circumstances, including by authors and data generators. While the importance and relevance of each lesson will vary by context, there is a need for increased awareness about how to avoid and manage common identifier problems, especially those related to persistence and web-accessibility/resolvability. We focus strongly on web-based identifiers in the life sciences; however, the principles are broadly relevant to other disciplines.

bioinformatics↗