O'Really?

December 10, 2008

Congratulations Carole Goble, e-Scientist

Filed under: awards — Duncan Hull @ 5:20 pm
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Carole Goble wins first Jim Gray e-Science awardAt the Microsoft e-Science workshop in Indianapolis, earlier this week Carole Goble was awarded with the first Jim Gray 2008 e-Science award, pictured here collecting the prize from Tony Hey of Microsoft Research. You can read all about it in the Seattle Tech Report which says:

“As director of the U.K.’s myGrid project, Goble helped create Taverna, open source software that allows scientists to analyse complex data sets with a standard computer.”

It is very inspiring when colleagues win prizes and awards. Personally, I would not be here doing what I’m doing if it wasn’t for Carole and myGrid, and neither would many other people who work on (or have worked on) myGrid and related projects.

Carole, you are an inspiration to us all, congratulations! To celebrate your success, I’m off to commit some more of the seven deadly sins of bioinformatics [1]…

References

  1. Carole Goble The Seven Deadly Sins of Bioinformatics
  2. e-Science in Indianapolis: Carole Goble wins the 1st Jim Gray eScience Award
  3. Joseph Tartakoff British professor given first Jim Gray Award, Seattle Post-Intelligencer, Tech Report
  4. Todd Bishop UK prof receives Jim Gray award Tech Flash
  5. Savas Parastatidis Carole Goble as the first recipient of the “Jim Gray eScience Award”
  6. Microsoft Recognise Manchester e-Science Contribution
  7. Deborah Gage Microsoft creates award in the name of Jim Gray San Francisco Chronicle, The Tech Chronicles
  8. Microsoft New tools for Discovery on Display at e-Science workshop

March 5, 2008

Science 2.0

Filed under: web of science — Duncan Hull @ 5:43 pm
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I’ve often wondered how all the ridiculous fluffy Web 2.0 marketing hype (see Tim O’Reilly’s principles of Web 2.0) maps into the world of Science. In a talk yesterday, Dave DeRoure argued there is a massive gap between scientists and infrastructure on the Web of Science, most people would agree with this. He points out that there is nothing in the middle to bridge between the two disparate worlds of people and technology. He also claims that Web 2.0 can bridge the gap, and also explains how Web 2.0 “design patterns” maps onto Science. You can see the original slides for yourself, here is my summary. (more…)

May 26, 2006

BioGrids: From Tim Bray to Jim Gray (via Seymour Cray)

Filed under: biotech — Duncan Hull @ 11:30 pm
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Recycle or Globus Toolkit?Grid Computing already plays an important role in the life sciences, and will probably continue doing so for the forseeable future. BioGrid (Japan), myGrid (UK) and CoreGrid (Europe) are just three current examples, there are many more Grid and Super Duper Computer projects in the life sciences. So, is there an accessible Hitch Hikers Guide to the Grid for newbies, especially bioinformaticians?

Unfortunately much of the literature of Grid Computing is esoteric and inaccessible, liberally sprinkled with abstract and wooly concepts like “Virtual Organisations” with a large side-order of acronym soup. This makes it difficult or impossible for the everyday bioinformatican to understand or care about. Thankfully, Tim Bray from Sun Microsystems has a written an accessible review of the area, “Grids for dummies”, if you like. Its worth a read if you’re a bioinformatician with a need for more heavyweight distributed computing than the web currently provides, but you find Grid-speak is usually impenetrable nonsense.

One of the things Tims discusses in his review is Microsoftie Jim Gray, who is partly responsible for the 2020 computing initiative mentioned on nodalpoint earlier. Tim describes Jim’s article Distributed Computing Economics. In this, Jim uses wide variety of examples to illustrate the current economics of grids, from “Megaservices” like Google, Yahoo! and Hotmail to the bioinformaticians favourites, BLAST and FASTA. So how might Grids affect the average bioinformatician? There are many different applications of Grid computing, but two areas spring to mind:

  1. Running your in silico experiments (genome annotation, sequence analysis, protein interactions etc), using someone elses memory, disk space, processors on the Grid. This could mean you will be able to do your experiments more quickly and reliably than you can using the plain ol’ Web.
  2. Executing high-throughput and long-running experiments, e.g. you’ve got a ton of microarray data and it takes hours or possibly days to analyse computationally.

So if you deal with microarray data daily, you probably know all this stuff already, but Tims overview and Jims commentary are both accessible pieces to pass on to your colleagues in the lab. If this kind of stuff pushes your button, you might also be interested in the eProtein Scientific Meeting and Workshop Proceedings.

[This post was originally published on nodalpoint with comments.]

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