401 results found
Sainz de Murieta I, Bultelle M, Kitney R, 2018, A Data Model for Biopart Datasheets, Engineering Biology, Vol: 2, Pages: 7-18
This study introduces a new data model, based on the DICOM-SB (see glossary of terms for definition of acronyms) standard for synthetic biology, that is capable of describing/incorporating the data, metadata and ancillary information from detailed characterisation experiments - to present DNA components (bioparts) in datasheets. The data model offers a standardised mechanism to associate bioparts with data and information about component performance - in a particular biological context (or a range of contexts, e.g. chassis). The data model includes the raw, experimental data for each characterisation run, and the protocol details needed to reliably reproduce the experiment. In addition, it provides metrics (e.g. relative promoter units, synthesis/growth rates etc.) that constitute the main content of a biopart datasheet. The data model has been developed to directly link to DICOM-SB, but also to be compatible with existing data standards, e.g. SBOL and SBML. It has been implemented within the latest version of the API that enables access to the SynBIS information system. The work should contribute significantly to the current standardisation effort in synthetic biology. The standard data model for datasheets is seen as a necessary step towards effective interoperability between part repositories, and between repositories and BioCAD applications.
Claesen S, Stone A, van Rossum M, et al., 2017, Comprehensive web-based broker for bio-technology design and manufacturing, Engineering Biology, Vol: 1, Pages: 100-102, ISSN: 2398-6182
Synthetic biology, particularly in relation to characterisation experiments relating to the description of bio-parts frequently involves the use of a wide range of equipment, including, for example, plate reader's, flow cytometers, and mass spectrometers. This equipment is often from multiple manufacturers. The study describes broker technology that has been developed which has the ability to connect multiple types of equipment into a common information environment; the connectivity from the databases and equipment is achieved using Visbion's ‘cube’ technology that involves military specification encryption for data security. The broker technology uses a new, developing standard, Digital Imaging and Communication in Medicine (DICOM)-SB, that is based on the highly successful international standard for biomedicine, DICOM. The broker uses a version of the DICOM data model that has been specifically designed for synthetic biology and, in particular, characterisation data.
Kitney RI, Freemont PS, 2017, Engineering biology: a key driver of the bio-economy, Engineering Biology, Vol: 1, Pages: 3-6, ISSN: 2398-6182
This study provides a relatively brief overview of the field of synthetic biology/engineering biology for thenon-specialist reader. This is in line with one of the basic aims of the new journalEngineering Biology–which is toopen up the field to a much wider audience than those currently engaged and, particularly, to people working incompanies and disciplines whose technology may be relevant to the field. Consequently, the study contains somedidactic material.
Mısırlı G, Madsen C, de Murieta IS, et al., 2017, Constructing synthetic biology workflows in the cloud, Engineering Biology, Vol: 1, Pages: 61-65
Reynolds CR, Exley K, Bultelle MA, et al., 2017, Debugging experiment machinery through time-course event sequence analysis, Engineering Biology, Vol: 1, Pages: 51-54, ISSN: 2398-6182
This application note describes an open-source web application software package for viewing and analysing time-course event sequences in the form of log files containing timestamps. Web pages allow the visualisation of time-course event sequences as time curves and the comparison of sequences against each other to visualise deviations between the timings of the sequences. A feature allows the analysis of the sequences by parsing selected sections with a support vector machine model that heuristically calculates a value for the likelihood of an error occurring based on the textual output in the log files. This allows quick analysis for errors in files with large numbers of log events. The software is written in ASP.NET with Visual Basic code-behind to allow it to be hosted on servers and integrated into web application frameworks.
Chambers S, Kitney R, Freemont P, 2016, The Foundry: the DNA synthesis and construction Foundry at Imperial College, BIOCHEMICAL SOCIETY TRANSACTIONS, Vol: 44, Pages: 687-688, ISSN: 0300-5127
Clarke LJ, Kitney RI, 2016, Synthetic biology in the UK - An outline of plans and progress, SYNTHETIC AND SYSTEMS BIOTECHNOLOGY, Vol: 1, Pages: 243-257, ISSN: 1389-0166
Coghlan A, Kitney R, 2016, Tiny but mighty, NEW SCIENTIST, Vol: 230, Pages: 7-7, ISSN: 0262-4079
De Murieta IS, Bultelle M, Kitney RI, 2016, Information standards supporting the characterisation of bioparts in synthetic biology
De Murieta IS, Bultelle M, Kitney RI, 2016, A data model for biopart datasheets
Florea M, Hagemann H, Santosa G, et al., 2016, Engineering control of bacterial cellulose production using a genetic toolkit and a new cellulose-producing strain, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 113, Pages: E3431-E3440, ISSN: 0027-8424
Kitney RI, 2016, DICOM-SB at Imperial
This website hosts supporting information for the paper 'Towards the First Data Acquisition Standard in Synthetic Biology' (Sainz de Murieta, Bultelle, Kitney, 2016) .The paper describes the development of a new data acquisition standard for synthetic biology, called DICOM-SB, which is based on the highly successful Digital Imaging and Communications in Medicine (DICOM) standard in medicine. It also introduces a data model that has been specifically developed for synthetic biology. The model is a modular, extensible data model for the experimental process, which can optimize data storage for large amounts of data.
Kitney RI, 2016, Information and communication technology in biodesign and component characterisation
Reynolds CR, Exley K, Bultelle MA, et al., 2016, Business process management of synthetic biology workflows
Rutten PJ, Kitney RI, 2016, Design and characterisation of new to nature inducible promoters
de Murieta IS, Bultelle M, Kitney RI, 2016, Toward the First Data Acquisition Standard in Synthetic Biology, ACS SYNTHETIC BIOLOGY, Vol: 5, Pages: 817-826, ISSN: 2161-5063
Bultelle MA, Sainz De Murieta I, Kitney RI, 2015, Introducing synbis - The synthetic biology information system, Pages: 838-842
Kelwick R, Kopniczky M, Bower I, et al., 2015, A Forward-Design Approach to Increase the Production of Poly-3-Hydroxybutyrate in Genetically Engineered Escherichia coli, PLOS ONE, Vol: 10, ISSN: 1932-6203
Sainz De Murieta I, Bultelle MA, Kitney RI, 2015, A dicom extension supporting data acquisition in synthetic biology, Pages: 948-951
Tay D, Poh CL, Kitney RI, 2015, A novel neural-inspired learning algorithm with application to clinical risk prediction, JOURNAL OF BIOMEDICAL INFORMATICS, Vol: 54, Pages: 305-314, ISSN: 1532-0464
Tay D, Poh CL, Van Reeth E, et al., 2015, The Effect of Sample Age and Prediction Resolution on Myocardial Infarction Risk Prediction, IEEE JOURNAL OF BIOMEDICAL AND HEALTH INFORMATICS, Vol: 19, Pages: 1178-1185, ISSN: 2168-2194
Wong A, Wang H, Poh CL, et al., 2015, Layering genetic circuits to build a single cell, bacterial half adder, BMC Biology, Vol: 13, ISSN: 1741-7007
Background: Gene regulation in biological systems is impacted by the cellular and genetic context-dependenteffects of the biological parts which comprise the circuit. Here, we have sought to elucidate the limitations ofengineering biology from an architectural point of view, with the aim of compiling a set of engineering solutionsfor overcoming failure modes during the development of complex, synthetic genetic circuits.Results: Using a synthetic biology approach that is supported by computational modelling and rigorouscharacterisation, AND, OR and NOT biological logic gates were layered in both parallel and serial arrangements togenerate a repertoire of Boolean operations that include NIMPLY, XOR, half adder and half subtractor logics in asingle cell. Subsequent evaluation of these near-digital biological systems revealed critical design pitfalls thattriggered genetic context-dependent effects, including 5′ UTR interferences and uncontrolled switch-on behaviourof the supercoiled σ54 promoter. In particular, the presence of seven consecutive hairpins immediately downstreamof the promoter transcription start site severely impeded gene expression.Conclusions: As synthetic biology moves forward with greater focus on scaling the complexity of engineeredgenetic circuits, studies which thoroughly evaluate failure modes and engineering solutions will serve as importantreferences for future design and development of synthetic biological systems. This work describes a representativecase study for the debugging of genetic context-dependent effects through principles elucidated herein, therebyproviding a rational design framework to integrate multiple genetic circuits in a single prokaryotic cell.
Casini A, Christodoulou G, Freemont PS, et al., 2014, R2oDNA Designer: Computational Design of Biologically Neutral Synthetic DNA Sequences, ACS SYNTHETIC BIOLOGY, Vol: 3, Pages: 525-528, ISSN: 2161-5063
Dickinson RJ, Kitney RI, 2014, Information driven care pathways and procedures, IFMBE Proceedings, Vol: 41, Pages: 1322-1325, ISSN: 1680-0737
The paper addresses the issue of the implementation of care pathways in electronic form. Within the National Health Service (NHS) of England, Care Pathways are becoming increasingly important. These are typically provided by the Department of Health. The Pathways provided are in the form of paper-based schema. They either have to be implemented via paper forms or, as presented here, in electronic form. In addition, care pathways must be seen in the context of the TModel of health care which comprises the care continuum and the biological continuum. The two care pathways which had been chosen as exemplars are myocardial infarction and stroke. However, the objective of the paper is not to discuss the specific care pathways in detail, but, rather, to describe technology which has been developed for their electronic implementation. The result of this implementation is that all the data and information acquired from the implementation of the care pathway is stored in a single clinical information system (CIS), which has incorporated in it the SQL database. Another important element of the system which has been developed is the ability to display data and information in terms of two dashboards (i.e. single screens which show the most important information). The two dashboards display clinical information (the point of care dashboard) and management information (the management dashboard). © Springer International Publishing Switzerland 2014.
Luboz V, Kyaw-Tun J, Sen S, et al., 2014, Real-time stent and balloon simulation for stenosis treatment, VISUAL COMPUTER, Vol: 30, Pages: 341-349, ISSN: 0178-2789
Tay D, Poh CL, Goh C, et al., 2014, A biological continuum based approach for efficient clinical classification, JOURNAL OF BIOMEDICAL INFORMATICS, Vol: 47, Pages: 28-38, ISSN: 1532-0464
Kelay T, Kesavan S, Collins RE, et al., 2013, Techniques to aid the implementation of novel clinical information systems: A systematic review, INTERNATIONAL JOURNAL OF SURGERY, Vol: 11, Pages: 783-791, ISSN: 1743-9191
Tay D, Poh CL, Kitney RI, 2013, An Evolutionary Data-Conscious Artificial Immune Recognition System, 15th Genetic and Evolutionary Computation Conference (GECCO), Publisher: ASSOC COMPUTING MACHINERY, Pages: 1101-1108
© 2012 by Imperial College Press. All rights reserved. Synthetic Biology — A Primer gives a broad overview of the emerging field of synthetic biology and the foundational concepts on which it is built. It will be of interest to final year undergraduates, postgraduates and established researchers who are interested in learning about this exciting new field. The book introduces readers to fundamental concepts in molecular biology and engineering and then explores the two major themes for synthetic biology, namely ‘bottom-up’ and ‘top-down’ engineering approaches. ‘Top-down’ engineering utilises a conceptual framework of engineering and systematic design to build new biological systems by integrating robustly characterised biological parts into an existing system through the use of extensive mathematical modelling. The ‘bottom-up’ approach involves the design and building of synthetic protocells using basic chemical and biochemical building blocks from scratch. Exemplars of cutting-edge applications designed using synthetic biology principles are presented, including the production of novel biofuels from renewable feedstocks, microbial synthesis of pharmaceuticals and fine chemicals, and the design and implementation of biosensors to detect infections and environmental waste. The book also uses the Internationally Genetically Engineered Machine (iGEM) competition to illustrate the power of synthetic biology as an innovative research and training science. Finally, the primer includes a chapter on the ethical, legal and societal issues surrounding synthetic biology, illustrating the integration of social sciences in synthetic biology research.
Kitney R, Freemont P, 2012, Synthetic biology - the state of play, FEBS LETTERS, Vol: 586, Pages: 2029-2036, ISSN: 1873-3468
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