Postdoctoral positions and PhD studentships on the ERC project "Skye: A programming language bridging theory and practice for scientific data curation"

Project: Skye: A programming language bridging theory and practice for scientific data curation
Supervisor:James Cheney
Deadline: Match 17, 2017 (PhD studentship)
An additional postdoctoral position will be advertised in 2017.

We seek strong candidates for PhD and postdoctoral positions on the project "Skye: A programming langauge bridging theory and practice for scientific data curation". The project will be supervised by Dr. James Cheney, Reader in the Laboratory for Foundations of Computer Science, School of Informatics, University of Edinburgh. Funding is provided by a five-year, €1.99M Consolidator Grant from the European Research Council.

Project description

Science is increasingly data-driven. Scientific research funders now routinely mandate open publication of publicly-funded research data. Safely reusing such data currently requires labour-intensive curation. Provenance recording the history and derivation of the data is critical to reaping the benefits and avoiding the pitfalls of data sharing. There are hundreds of curated scientific databases in biomedicine that need fine-grained provenance; one important example is the IUPHAR/BPS Guide to Pharmacology database (GtoPdb), a pharmacological database developed in Edinburgh.

Currently there are no reusable methodologies or practical tools that support provenance for curated databases, forcing each project to start from scratch. Research on provenance for scientific databases is still at an early stage, and prototypes have so far proven challenging to deploy or evaluate in the field. Also, most techniques to date focus on provenance within a single database, but this is only part of the problem: real solutions will have to integrate database provenance with the multiple tiers of web applications, and no-one has begun to address this challenge.

The Skye project will build support for curation into the programming language itself, building on recent research on the Links Web programming language, including advances in language-integrated query, and on provenance and data curation. Links is a strongly-typed language that provides state-of-the-art support for language-integrated query and Web programming. This project will build on Links and other recent language designs for heterogeneous meta-programming to develop a new language, called Skye, that can express modular, reusable curation and provenance techniques. To keep focus on the real needs of scientific databases, Skye will be evaluated in the context of GtoPdb and other scientific database projects. Bridging the gap between curation research and the practices of scientific database curators will catalyse a virtuous cycle that will increase the pace of breakthrough results from data-driven science.

Skye will draw on the best ideas developed in cutting-edge research on language-integrated query, Web programming, and heterogeneous meta-programming. Skye will provide dialects, or first-class client language definitions, along with translations that map programs written in one dialect to another, or (as a special case) that perform source-to-source translation on a single dialect, for optimisation or to add functionality such as provenance- tracking. These translations will be available as libraries that can change the behaviour of already-written applications by rewriting code, so scientific database developers using Skye will be able to reuse these features instead of having to reimplement them from scratch or make wholesale changes to existing applications.

The Skye project will support a group of PhD students and postdoctoral researchers under the leadership of Dr. Cheney to pursue research on programming language design for integrating Web programming and databases, in aid of scientific data management. Topics for research could include:

  • Language design: How can we program with first-class client languages (dialects) and translations flexibly and safely?
  • Expressing and optimising client languages: How can existing client languages be embedded as dialects and translated to efficient client language code?
  • Defining modular curation techniques: How can existing (or new) curation techniques be defined using type-safe translations among dialects?
  • Case studies: What are the benefits and costs of using Skye to develop curated scientific databases?

For additional information about the project background, please consult our recent publications on this subject here and here.

PhD studentships

One studentship is available to start in the 2017 academic year, covering full fees and a stipend of approximately £14,000 per year for a student of any nationality.

Background required

We are currently seeking applicants with a strong background and research interests in functional programming, typed language design and implementation, metaprogramming, or Web/database programming. Candidates with demonstrated research ability in programming languages, and with at least some familiarity with databases or bioinformatics, would be especially suitable for this project. Outstanding candidates with a database-centric background and some familiarity with programming languages research will also be considered.

About the position

This PhD studentship provides a total of 4 years funding for full-time research (with no required teaching obligations). This can be structured as a 4-year PhD (for candidates who already have research experience e.g. a suitable Master's project) or as a 1-year Master's by Research followed by 3 years of PhD research, hosted in one of the School's two EPSRC Centres for Doctoral Training, in Data Science or Pervasive Parallelism. Prospective applicants are encouraged to discuss these alternatives with the supervisor before applying.

Application information

To apply, please follow the instructions here. Alternatively, you may apply directly to one of the Centres for Doctoral Training (or to both programs). In any case, make sure to indicate interest in this project as part of the application.

Important: A research proposal is required as part of the PhD application, for either the regular LFCS PhD program or a CDT program. The research proposal is used to assess applicants' understanding of what research involves and capability to generate research ideas. Your research proposal should address a topic relevant to this project; it should not simply be a restatement of the advertisement. Applications with a research proposal that is simply copied verbatim from this advertisement will not be considered. If applying to multiple programs, the same proposal may be used, or different proposals.

Postdoctoral positions

An additional postdoctoral research position will be advertised during 2017. If you are potentially interested in working on this project, please get in touch.

The Team

These positions will be under the supervision of the Skye project PI, Dr. James Cheney, whose group currently includes four postdoctoral researchers and four PhD students, working on topics including provenance, programming languages, security, and databases. The current team is supported by funding from AFOSR, DARPA, Microsoft Research, Google, and the European Union. The Skye project will also benefit from strong collaborative links with other world-leading experts in LFCS, particularly in the Edinburgh Database Group and the Programming Languages and Foundations group.

Environment

The University of Edinburgh School of Informatics brings together world-class research groups in theoretical computer science, artificial intelligence and cognitive science. The School led the UK 2014 REF rankings in volume of internationally recognized or internationally excellent research. In 2013, the School of Informatics received an Athena Swan Silver Award, in recognition of its commitment to advancing the careers of women in science, technology, engineering, mathematics and medicine (STEMM) employment in higher education and research. Overall the University of Edinburgh has achieved a Silver Award.

The Laboratory for Foundations of Computer Science (LFCS) established by Burstall, Milner and Plotkin in 1986, is recognized worldwide for groundbreaking research on topics in programming languages, semantics, type theory, proof theory, algorithms and complexity, databases, security, and systems biology. Formal aspects of databases, XML and provenance (Libkin, Fan, Buneman), language-based security (Aspinall, Stark, Gordon), and Web programming languages (Wadler) are active areas of investigation in LFCS complementary to this project.

The Edinburgh Database Group is part of the Laboratory for the Foundations of Computer Science and includes six faculty members, five postdoctoral researchers, and six PhD students. Interests of the group span all aspects of database systems and theory. Topics of current interest include graph databases, XML, data integration, novel approaches to query processing and storage, data provenance, archiving and annotation. Many of these topics are relevant to scientific data management, an area in which Edinburgh has unique strengths.

Programming Languages and Foundations is one of the largest research activities in LFCS, including 15 academic staff, 8 postdoctoral researchers, and 10 current PhD students, working on functional programming, types, verification, semantics, software engineering, language-based security and new programming models. We participate in a thriving PL research community across Scotland, with Scottish Programming Languages Seminars hosted every 3-4 months by PL groups at Glasgow, Strathclyde, Heriot-Watt, St. Andrews, Dundee and Edinburgh.

For more information about study in Edinburgh and the School of Informatics, see these pages:


Last modified: Thu Dec 1 11:26:19 GMT 2016