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Research

Biological systems - including the simplest cells - exhibit a broad range of functions to thrive in their environment. Research in the Imperial College Centre for Synthetic Biology is focused on the possibility of engineering the underlying biochemical processes to solve many of the challenges facing society, from healthcare to sustainable energy. In particular, we model, analyse, design and build biological and biochemical systems in living cells and/or in cell extracts, both exploring and enhancing the engineering potential of biology.

As part of our research we develop novel methods to accelerate the celebrated Design-Build-Test-Learn synthetic biology cycle. As such research in the Centre for Synthetic Biology highly multi- and interdisciplinary covering computational modelling and machine learning approaches; automated platform development and genetic circuit engineering ; multi-cellular and multi-organismal interactions, including gene drive and genome engineering; metabolic engineering; in vitro/cell-free synthetic biology; engineered phages and directed evolution; and biomimetics, biomaterials and biological engineering.

Publications

Citation

BibTex format

@article{Exley:2019:10.1186/s13036-019-0141-z,
author = {Exley, K and Reynolds, C and Suckling, L and Chee, SM and Tsipa, A and Freemont, P and McClymont, D and Kitney, R},
doi = {10.1186/s13036-019-0141-z},
journal = {Journal of Biological Engineering},
title = {Utilising datasheets for the informed automated design and build of a synthetic metabolic pathway},
url = {http://dx.doi.org/10.1186/s13036-019-0141-z},
volume = {13},
year = {2019}
}

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RIS format (EndNote, RefMan)

TY - JOUR
AB - BackgroundThe automation of modular cloning methodologies permits the assembly of many genetic designs. Utilising characterised biological parts aids in the design and redesign of genetic pathways. The characterisation information held on datasheets can be used to determine whether a biological part meets the design requirements. To manage the design of genetic pathways, researchers have turned to modelling-based computer aided design software tools.ResultAn automated workflow has been developed for the design and build of heterologous metabolic pathways. In addition, to demonstrate the powers of electronic datasheets we have developed software which can transfer part information from a datasheet to the Design of Experiment software JMP. To this end we were able to use Design of Experiment software to rationally design and test randomised samples from the design space of a lycopene pathway in E. coli. This pathway was optimised by individually modulating the promoter strength, RBS strength, and gene order targets.ConclusionThe use of standardised and characterised biological parts will empower a design-oriented synthetic biology for the forward engineering of heterologous expression systems. A Design of Experiment approach streamlines the design-build-test cycle to achieve optimised solutions in biodesign. Developed automated workflows provide effective transfer of information between characterised information (in the form of datasheets) and DoE software.
AU - Exley,K
AU - Reynolds,C
AU - Suckling,L
AU - Chee,SM
AU - Tsipa,A
AU - Freemont,P
AU - McClymont,D
AU - Kitney,R
DO - 10.1186/s13036-019-0141-z
PY - 2019///
SN - 1754-1611
TI - Utilising datasheets for the informed automated design and build of a synthetic metabolic pathway
T2 - Journal of Biological Engineering
UR - http://dx.doi.org/10.1186/s13036-019-0141-z
UR - http://hdl.handle.net/10044/1/66973
VL - 13
ER -