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Modules at EPSRC & BBSRC Centre for Doctoral Training in Synthetic Biology Jan - April 2017

EPSRC & BBSRC Centre for Doctoral Training would like to open a limited number of spaces on courses in Synthetic Biology for any students that might be interested.
The EPSRC & BBSRC Centre for Doctoral Training has now been running for almost three years; two cohorts have completed successfully the taught training phase, and the third cohort has nearly completed one term of "introductory" training in Synthetic Biology. Next term (from January - April 2017) students will be following more advanced courses in Synthetic Biology.

As in previous years, the EPSRC & BBSRC Centre for Doctoral Training would like to open these courses for any students that might be interested in the courses below. There is limited availability, so please get in touch early, by getting in contact with Sophie Tarry, the SynBioCDT administrator, at sophie.tarry@dtc.ox.ac.uk. The typical weekly pattern of modules is Monday (all day), Tuesday (morning), Thursday (morning) and Friday (all day) and we use lectures and pen and paper or computer exercises to deliver it. All students are expected to complete the whole week as well as the module assessment.
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SYNTHETIC CIRCUIT DESIGN
This course will cover modelling and analysis of synthetic genetic circuits. Topics covered will include logic circuits, standardization and registry of standard biological parts, libraries and chassis and the engineering design test cycle. Tools including CAD tools, Eugene, Clotho, BioFAB, GEC Compilers, Snapgene will be covered as well as best implementation of designs. In the second week information will be provided on promoter engineering and promoter interference/inducible expression, translation and RNA secondary structure, RBS and codon usage, CRISPR/RNA silencing, RNA circuits/riboswitches and ultimately protein engineering, maturation and degradation. Wetlab practical sessions will be spread throughout the 2 weeks. 

Course Leaders: Robert Carlisle and Orkun Soyer
Contact Email Address: Robert.carlisle@eng.ox.ac.uk and
o.soyer@warwick.ac.uk
Dates : 03.1.17 – 06.1.16 and 09.1.17 – 13.1.17

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CELLULAR DESIGN I

This module will introduce some of the concepts, technologies and techniques, which can allow the design and engineering of novel cellular functionality. The week will begin with lectures on flux in metabolic networks, describing the process of going from analysis to manipulation and engineering metabolism. This will be followed by Gene Cluster Discovery and Combinatorial Engineering of Metabolism. Lectures on Directed Evolution as a tool will introduce the basic notions and the use of evolution as a design tool in synthetic biology.. Lastly, this module will cover genome minimization and advanced genome editing.

Course Leaders: Thomas Gorochowski and Claire Grierson
Contact email Address: thomas.gorochowski@bristol.ac.uk and
claire.grierson@bristol.ac.uk
Dates: 30.1.17 – 3.2.17

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BIOMIMETIC CONSTRUCTION I

The basic concepts behind the natural production, synthesis, modification of polypeptides and nucleic acids will be explained in addition to nanostructures and assemblies and protein engineering and design. In particular, topics to be explored will include Protocells, Functional complexes in membranes, Natural protein production and modification, Applications of modified nucleic acids and Making Prokaryotic and Eukaryotic Cell Division Machines.


Course Leaders: Andrew Turberfield and Dek Woolfson
Contact email Address: andrew.turberfield@physics.ox.ac.uk and
d.n.woolfson@bristol.ac.uk
Dates: 20.2.17 - 24.2.17

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CELLULAR DESIGN II

This module will build on Cellular Design I, developing concepts and applications from use in situations where engineering of single cells is undertaken to examples where impact is made at a multi-cellular level. Topics covered will include Multicellular computing, Biofilms and mathematical modelling of microbial communities, Synchronisation/Quorum sensing and Synthetic communities.


Course Leaders: Sabine Hauert and Claire Grierson
Contact email Address: sabine.hauert@bristol.ac.uk and
claire.grierson@bristol.ac.uk
Dates: 27.2.17 – 03.3.17

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BIOMIMETIC CONSTRUCTION II

This module will build on Biomimetic Construction I. After information regarding the rules for Biopolymer folding/ assembly are explained, these rules will be applied to the synthesis of DNA and RNA nanostructures and materials and developed further for more complex Peptide nanostructures and materials and even Enzymes and pathways. Finally, Antibodies and mimics, _de novo_ proteins, natural motors, synthetic mimics will be discussed


Course Leaders: Andrew Turberfield and Dek Woolfson
Contact email Address: andrew.turberfield@physics.ox.ac.uk and
d.n.woolfson@bristol.ac.uk
Dates: 06.3.17 – 10.3.17

 

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CURRENT RESEARCH TOPICS IN SYNTHETIC BIOLOGY I

This module will build on concepts discussed throughout the course. Lectures on Systems and Control, Retroactivity and Scalability, Noise and Stochasticity will build to describe how Synthetic Circuits can be built in mammalian cells and the insights we can garner from evolution regarding system design will be discussed. Delivery will be by conventional lectures, discussion sessions, reference to the literature and MATLAB/pen and paper exercises. (_Duration: one week_)

Course Leader: Declan Bates
Contact e-mail address: d.bates@warwick.ac.uk
Dates: 13.3.17 – 17.3.17

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CURRENT RESEARCH TOPICS IN SYNTHETIC BIOLOGY II

This module will re-evaluate the engineering mantra in the biological domain and its expansion to organisational levels beyond cellular circuits. In the former domain, the focus will be on the relation between evolutionary dynamics and engineering. In the latter domain, we will discuss engineering at the level of microbial communities, tissues, and plants. Delivery will be by conventional lectures, discussion sessions, reference to the literature and MATLAB/pen and paper exercises.

Course Leader: Orkun Soyer
Contact e-mail Address: o.soyer@warwick.ac.uk
Dates: 20.3.17 – 24.3.17

 

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ELSA/RESPONSIBLE RESEARCH AND INNOVATION

This module introduces the core concepts and approaches adopted in ethical, legal and social aspects (ELSA) of synthetic biology. It will enable students to reflect critically on their own and others assumptions about synthetic biology and to articulate the relevance of ELSA for the present and next stages of their careers. It is designed to give students a basis on which to discuss synthetic biology with a range of publics and to act as ambassadors for synthetic biology. Topics include ethics, justice, dual effect, the nature of 'humanity', public understanding of synthetic biology, biosecurity, synthetic biology as an interdisciplinary research community, futures, expectations and values.


Course Leader: Robert Carlisle
Contact e-mail Address: robert.carlisle@eng.ox.ac.uk
Dates :27.3.17 – 31.3.17

 

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