Recent Projects at the Image Bioinformatics Research Group in Oxford

I just spent a very pleasant afternoon catching up with colleagues at the Image Bioinformatics Research Group, based in the department of Zoology here in Oxford. Here’s a few tidbits I picked up …

Tanya Gray is working on the MIIDI standard (Minimum Information for an Infections Disease Investigation) and associate tools. She’s done some very nice work on a MIIDI metadata editor, using eXist and Orbeon forms, with her own additions to generate XForms from an annotated XML Schema. Tanya’s also working on the DryadUK project, which is a data repository supporting publication of data associated with journal articles.

Stephen Wan (visiting from CSIRO) has developed a cool extension for Firefox (and now Chrome) called IBES (In-Browser Elaborative Summariser). If you point it at Wikipedia, for each link you hover over it shows a summary of the page at that link, built intelligently from the link’s context. Then if you navigate to the link, it tells you where you came from. Very handy if (like me) each visit to Wikipedia is a rambling journey, and you often forget why you went there in the first place. He’s also done some related work to help navigate citations in scholarly articles, called CSIBS (The Citation-Sensitive In-Browser Summarizer).

Alex Dutton is working on the JISC Open Citations project. He has some nice visualisations of citation networks (although one of the articles in that graph looks like it cites itself – if only that were possible :). The graphs are generated using dot from RDF representation of metadata from the PubMedCentral Open-Access journal articles. All of the usual dot options are available, so you can play with how the networks get rendered. The whole site is driven by SPARQL, and the bottom of each page shows the SPARQL queries used to generate the page content, so you can see what’s going on under the hood.

Bhavana Ananda is working on the JISC DataFlow project, the DataStage component of which is a follow-on from previous work by Graham Klyne on the Admiral project. I think the philosophy of simple tools to help research groups manage and share their data with each other has a lot of traction, and I think it’s great they’ve got funding to turn the Admiral prototypes into something more.

Graham Klyne is embroiled in the Workflow 4Ever project, and we had a great chat about possible connections with managing our Plasmodium SNP discovery and genotyping pipelines for MalariaGEN. I’m now expecting Graham to solve all my problems.

And David Shotton (group head) is, as always, making it all happen. It was great to raise my head above the trenches for a few hours, I need to do that more often.

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Intro to AtomBeat

This post is by way of a brief introduction to AtomBeat, which is a piece of software I’ve been coding on-and-off for the past year or so. AtomBeat is a web application that you can use as a generic content and data repository. It implements the Atom Publishing Protocol, which is a standard for data-centric web services, and which is also the basis for things like GData, OData, CMIS and SWORD. AtomBeat also implements a number of more-or-less standard extensions to Atom, including support for fine-grained access control policies, and support for versioning of data resources. The idea was that we had several applications which had similar underlying needs w.r.t. managing data and content and exposing functionality to other applications via web services – so AtomBeat is an attempt to factor out some of those common capabilities into a generic piece of software.

AtomBeat is coded almost entirely in XQuery – about 14,000 lines of it at last count – which, you might think, makes me totally mad. But AtomBeat uses the eXist XML database as the underlying persistence engine, and because Atom is an XML-based protocol, using XQuery to work with XML both at the protocol level and the persistence level is actually very convenient, once you’ve established a few patterns. I’d hate to think how many lines of code it would have taken if I’d done it all in Java using DOM and SAX APIs.

Anyway, I’ll leave it there for now, but if you’d like to know more check out the AtomBeat wiki and the release notes.