Recent Projects at the Image Bioinformatics Research Group in Oxford

Posted: 3 August 2011 by Alistair Miles in Uncategorized
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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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  1. […] worked in our research group, spent yesterday afternoon catching up with us, and has written a nice blog post on the MalariaGen Informatics Blog describing our current activities, including our work on the […]

  2. […] worked in our research group, spent yesterday afternoon catching up with us, and has written a nice blog post on the MalariaGEN Informatics Blog describing our current activities, including our work on the […]

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