ERC project "Skye: A programming language bridging theory and practice for scientific data curation"
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.
An additional postdoctoral research position will be advertised during 2019. If you are potentially interested in working on this project, please get in touch.
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:
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.
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: