PhD Studentship in Computing Science - Verification of Portable Synthetic Biocircuits EPSRC Portabolomics

Newcastle University

Value of award

100% of UK/EU tuition fees and an annual stipend of £14,553  full award

Number of awards: 1

Start date and duration: October 2017 for three years

Overview

The vision of the Portabolomics project is to bring forth a breakthrough in Synthetic Biology that will enable the development of portable biocircuits across chassis. For example, a novel antibiotic pathway engineered in a laboratory strain e.g., E. coli , could be ported to a proprietary industrial strain for mass production e.g., Bacillus spp without substantial re-engineering. In Information Technology, the Java virtual machine has enabled the reuse and portability of software across different operating systems and hardware platforms. Likewise, our approach represents a true breakthrough in practical biological circuit reuse and portability for living organisms.

Our vision is centred on the development of a new in vivo middleware architecture, called a ‘bio-adaptor’, that will provide a standardised interface to the cell’s essential biological services e.g., replication, transcription, and translation . A biocircuit engineered within a chassis that implements the Portabolomics bio-adaptor will run as-it-is on another chassis that adheres to the same interface. This vision requires substantial innovation in formal verification of biocircuits before they are actually built in the laboratory.

This PhD project will advance our world-leading model checking technologies for both verifying and designing biocircuits that are certifiably compliant with the bio-adaptor. This challenge includes the following research strands:

  • Property description formalisms for specifying design requirements for the bio-adaptor and more generally for Synthetic Biology.
  • Model checking and partial order reduction techniques for combating state-explosion in formal verification of bio-engineered designs.
  • Formal parameter synthesis protocols and design exploration for hybrid network models for hybrid abstract-concrete network models.
  • This studentship provides a unique opportunity to perform interdisciplinary, high-impact research within a well-funded group of researchers. The successful candidate will join the ICOS group, which consists of 50 individuals conducting cutting-edge research at the interface of computing science and complex biological systems.

Sponsor

School of Computing Science, Newcastle University

Name of supervisor s

Dr Paolo Zuliani, School of Computing Science

Eligibility Criteria

Eligible for UK/EU candidates only

The successful candidate should have an excellent first degree in, e.g., computer science, mathematics, or physics. Knowledge of biology is not a prerequisite, since the ICOS group offers plentiful learning opportunities via their own MSc modules, weekly research seminars, etc.

How to apply

You must apply through the University's online postgraduate application form. Only mandatory fields need to be completed.  However, you will need to include the following information:

  • Insert the programme code 8050F in the programme of study section
  • select 'PhD Computer Science Computing Science ', as the programme of study
  • insert reference CS062 in the studentship/partnership reference field
  • attach covering letter, CV and if English is not your first language a copy of English language qualifications. The covering letter must state title of studentship, quote reference CS062 and describe how your research interests fit with the topic of research project outlined in the advertisement maximum of two pages .
  • please send your covering letter and CV by e-mail to cs.pg@ncl.ac.uk.  

Contact

For further details, please email Dr Paolo Zuliani.

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Type / Role:

PhD

Location(s):

Northern England