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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
Research associate position(s) available (deadline September 21, 2020)

The project is 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.

Positions available

Research associate in programming language design

This postdoctoral research position is on programming language design in the Skye project. This project builds on the Links web programming language to add built-in support for scientific data management needs, based on Links's already strong support for language-integrated query/update (ICFP 2013, SIGMOD 2014, ICFP 2018), type inference with first-class polymorphism (PLDI 2020), and Elm-style model-view-update programming (ECOOP 2020). Links also has support for distributed programming with session types (POPL 2019) and algebraic effects and handlers (JFP 2020), which may find further applications to the project.

A broad range of programming language design topics potentially within the scope of this project. The successful candidate will work on extending the Links web programming language with stronger support for database programming (e.g. language-integrated query), client/server web programming, programming with effects (e.g. graded monads, algebraic effects/handlers), heterogeneous meta-programming/staging, modular language extensibility, or concurrent/distributed programming, and develop applications of these capabilities.

Background required

The ideal candidate will have a strong background in programming languages or databases. Familiarity with programming language foundations is also desirable, as is experience with functional programming (e.g. Scala, OCaml, Haskell). Candidates with a strong background in either database or programming language research will be considered as long as there is clear evidence of ability to learn the complementary background.

About the position

The position is available for 18 months, starting as soon as possible and before March 21, 2021. A second position may become available for this post depending on future funding.

Prospective applicants are encouraged to contact James Cheney (jcheney@inf.ed.ac.uk) before applying to discuss these positions.

Application process and deadlines

A complete application consists of a CV and a 1-3 page research statement summarizing your background, previous research experience, and how they relate to this position.

Applications must be submitted by 5pm UK time on September 21, 2020, through the University of Edinburgh recruitment site, directly using the following link:

Applicants must apply using the University jobs website above. This requires creating an account, and applicants are recommended to complete this process well before the deadline. Applications submitted after the deadline may not be considered.

Interviews will likely be held (via Skype) in late September.

Due to the ongoing COVID-19 pandemic, remote working is possible and encouraged until limitations on travel and social distancing requirements are lifted. Successful candidates who are eligible to work in the UK without a visa (= UK or EEA nationals) will be able to take up the post and work remotely prior to arrival in Edinburgh. Candidates currently in the UK on Tier 4 student visas will also be able to begin work while waiting for a Tier 2 visa. Candidates in other situations may be able to start work remotely but this depends on UKVI guidelines which are in flux; such candidates are advised to contact us to discuss the situation.

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.

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:


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