Research Associate on Theory of approximation in experimental biochemical protocols

Department of Computer Science, Parks Road, Oxford.

Research Associate on Theory of approximation in experimental biochemical protocols

Full Time and Fixed Term until 31 August 2023

Grade 7: Salary £34,308 - £36,386 p.a. (Post may be under-filled at Grade 6: £30,502 - £36,386 p.a.)

We are looking for motivated Research Associate to play key roles in the application of Logic and Stochastic methods to Molecular Programming (a branch of nanotechnology that often uses DNA as a computational material). You will be a member of the collaborative project team working at the cutting edge of Computer Science. Reporting directly to Professor Luca Cardelli (Oxford) and Professor Radu Mardare (Strathclyde), you will be contributing to the development of theories, models and algorithms for the comparison and approximation of automated laboratory protocols. Based within an internationally leading research group, you will benefit from working in Oxford University’s acclaimed Computer Science Department, located in the heart of Oxford’s Scientific Keble Triangle.

Research Project: Theory of approximation in experimental biochemical protocols. Biochemical laboratories are moving towards more precise and reproduceable experiments via laboratory protocols supported by full automation, and towards higher throughput investigation via automated hypothesis generation supported by data analysis and model inference. To achieve these goals, we need to integrate lab protocols, which define the steps carried out during an experiment, with mathematical models that describe physical processes and guide future experiments. This integration has not yet been achieved to the levels of rigour needed, and in particular it requires accounting for approximations that arise in experimental procedures, and approximations that arise from uncertain knowledge of model parameters. In a recent paper we have proposed a language for modelling and optimizing biological protocols, which has been implemented in the Kaemika chemical simulator app. Significant challenges remain in characterizing the reliability of these formalized protocols in terms of uncertainty in their outcomes, in model refinement driven by data, and in the attribution of fault to either the model or the equipment when an experiment fails. Mardare’s quantitative Barycentric algebra naturally handles the core operation of the proportionate mixing of reagents during experiments, and formally models tolerances in model parameters, equipment operations, and data collection, including handling iterative and recursive protocols and other high-level features necessary for a fully expressive protocol language. We aim to extend our understanding of the interactions between models and protocols, to support a fully automated scientific discovery cycle. The proposed research is interdisciplinary, aiming to apply Logic and Computer Science to Biology and Physics, with concrete foundations in Nanotechnology that helps miniaturize and automate laboratory procedures.

You will carry out research on the above project. This may involve discrete, probabilistic, stochastic, and continuous approaches to the behaviour of dynamical systems, drawing from Logic and Theoretical Computer Science. Suitably qualified candidates will have an opportunity to implement algorithms and employ or develop software analysis tools.

You will be expected to write research articles for leading conferences and journals, complete clear task objectives, organise your workload, and proactively contribute towards the research group’s objectives.

You should hold a PhD (or be close to completion) in computer science, mathematics or related discipline, possess sufficient specialist knowledge across some/all areas of discrete, probabilistic, stochastic, and continuous mathematics, as well as have proven experience of software development and use of tools in relevant areas. Prior familiarity with logic and stochastic systems is desirable.

The closing date for applications is 12 noon on 28 November 2022. Interviews are expected to be held in December.

We are a Stonewall Top 100 Employer, Living Wage and Mindful Employer, holding an Athena Swan Bronze Award, HR excellence in Research and Race Equality Charter Bronze Award.

Our staff and students come from all over the world and we proudly promote a friendly and inclusive culture. Diversity is positively encouraged, through diversity groups and champions, for example http://www.cs.ox.ac.uk/aboutus/women-cs-oxford/index.html , as well as a number of family-friendly policies, such as the right to apply for flexible working and support for staff returning from periods of extended absence, for example shared parental leave.

Demonstrating a commitment to provide equality of opportunity. We would particularly welcome applications from women and black and minority ethnic applicants who are currently under-represented within the Computer Science Department. All applicants will be judged on merit, according to the selection criteria.

For further details and to apply please visit:

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