O'Really?

January 8, 2009

Data Integration in the Life Sciences (DILS 2009), Manchester

Cristiano Ronaldo by vuhlserData Integration in the Life Sciences (DILS 2009) is the sixth in an international workshop series that aims at fostering discussion, exchange, and innovation in research and development in the areas of data integration and data management for the life sciences. DILS 2004 in Leipzig, DILS 2005 in San Diego, DILS 2006 in Cambridge, DILS 2007 in Philadelphia, and DILS 2008 near Paris each attracted around 100 researchers from all over the world [1]. This year, DILS 2009 is being held in the People’s Republic of Manchester, UK.

Although the workshop isn’t until the 20th July,  the deadline for paper abstracts is the 13th February, so if you’re planning on coming, better hurry up (see picture, top right) with those submissions. As with last year, the workshop proceedings will be published by Lecture Notes in Computer Science (LNCS) from Springer.

References

  1. Fifth International Workshop, DILS 2008, Evry, France, June 25-27, 2008. Proceedings 10.1007/978-3-540-69828-9

[Gratuitous creative commons licensed picture of Manchester United Football Club player Cristiano Ronaldo by vuhlser. Must be time to buy a new Ferrari.]

December 17, 2008

Happy Christmas Lectures 2008

Machines that learn by Kaustav BhattacharyaOne of the most important Christmas traditions in Europe, aside from drinking too much, excessive eating and generally conspicuous over-consumption, are the Royal Institution Christmas lectures. This year, they are being given by Professor Christopher Bishop (pictured right), Chief Scientist at Microsoft Research and are on the subject of the Quest for the Ultimate Computer. This hi-tech trek includes subjects such as machine learning, microchip design, artificial intelligence and Web technology. Here is the blurb from the one of the lectures to give you a flavour:

“Computers are extraordinary machines, able to perform feats of arithmetic that far exceed the capabilities of any human. They can store a huge quantity of data, and recall it perfectly in the blink of an eye. They can even beat the world champion at chess. So why do computers struggle to solve apparently simple tasks such as understanding speech, or translating text between languages? Why is a 3 year old toddler better at recognising everyday objects than the world’s most powerful supercomputer? In the last of this year’s Christmas Lectures, Chris Bishop will look at one of the great frontiers of computer science. We’ll see how some of the toughest computational problems are now being tackled by giving computers the ability to learn solutions for themselves, in much the same way as people learn by example. This has led to impressive progress with problems such as recognising handwriting and finding information on the web. But we are only beginning to explore the power of computation, and there are many challenges ahead in our quest for the ultimate computer.”

Broadcast on Channel 5 (starting Monday 29th December, consult your UK TV guide for details), these lectures are aimed at children, but can be enjoyed by kids of all ages (including grown ups). The lectures will also be available as a webcast from rigb.org and probably youtube as well. Whatever you’re doing over the coming holidays have a very happy Christmas, pagan solstice festival, winterval. Wherever you are, don’t forget to enjoy an intellectually nourishing side-portion of Computer Science with your festive feasting!

References

  1. http://www.rigb.org/christmaslectures08/
  2. Watch this: Royal Institution Christmas Lectures 2008, The Guardian 2008-12-29
  3. Review of Last Night’s TV: Christmas Lectures, The Independent 2008-12-30
  4. John Benyon Christmas Lectures: Untangling the Web
  5. Rich from Bechtle Christmas Lectures 2008, much better!

[Picture of Chris Bishop by Kaustav Bhattacharya]

December 10, 2008

Congratulations Carole Goble, e-Scientist

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

December 2, 2008

SWAT4LS: The Semantic Web in Scotland

James Clerk MaxwellLast Friday, the UK National e-Science Centre in Edinburgh hosted a workhop, Semantic Web Applications and Tools for the Life Sciences (see SWAT4LS.org for the full details). Here are some incomplete and abbreviated notes from the workshop where there were some interesting people, paperware and software.

People and Paperware

70 people registered to attend SWAT4LS in total, many familiar names and faces, plus some new people I’ve never met before: (more…)

November 27, 2008

Blogging Professors: Douglas Kell at the BBSRC

Filed under: web of science — Duncan Hull @ 12:53 pm
Tags: ,

Biotechnology and Biological Sciences Research CouncilTo add to the growing list of big boffins with blogs, Professor Douglas Kell has launched his BBSRC hosted blog. So has blogging finally gone from an innovative underground movement to grown-up mainstream everyday technology, as recently suggested in The Economist? How many more senior scientists might we see blogging in the future? Take a look at blogs.bbsrc.ac.uk to find out..

I asked Doug if he would consider blogging, for the Science blogging challenge posed by Nature Publishing Group, so thanks Doug for being open minded and willing to experiment, you’ve also been entered for the Open Laboratory 2008 competition too. It will be interesting to see what the result of this project will be…

References

  1. Zoe Corbyn (2008). New BBSRC chief executive enters blogosphere, Times Higher Education, 11th December 2008.

November 24, 2008

Embracing Registries of Web Services

Filed under: informatics,web of science — Duncan Hull @ 2:00 pm
Tags: , , , , , , , , ,

Embracing by tanakwhoIf you travel back in time, to around 2002, it isn’t difficult to find people claiming that Web services were going to be the new silver bullet technology to create world peace, eradicate global poverty and finally make some sense of all the data produced by the human genome project. Over hyped? Just a bit. One of the many reasons none of these things happened, is it turned out to be much harder than anticipated to build centralised registries, where people could go to find Web services to perform a given task. Can service registries ever be built? Critics like Tim Bray at Sun Microsystems for example, have suggested that (quote) “registries are a fantasy”, but some already exist and there are more in the pipeline. This article briefly introduces some of them: Seekda, BioMOBY, the Embrace service registry and the Biocatalogue project. (more…)

November 17, 2008

Science blog meme: Why do we blog?

Keep Calm and Carry On via AJC1I have been virally infected by Martin Fenner’s “why do we blog” meme.

1. What is your blog about?

Science and technology, especially bioinformatics, systems biology and the Web. It is a personal laboratory notebook-cum-diary, with a few facts and many opinions that would be difficult to publish conventionally [1].

2. What will you never write about?

Banal personal trivia (“I went shopping today”), confidential work, collaborative projects before they have been published. If in doubt, I try to ask people, “is it OK if I blog this?”

3. Have you ever considered leaving science?

Already did, I left science after my undergraduate degree to work in industry, but came back after six years to do a PhD. I don’t think Science ever really leaves you, once a scientist, always a scientist. Can’t see myself “leaving” again, but you never know.

4. What would you do instead?

Tend olive trees in Greece. Sequence 10,000 + Olive tree genomes, do some olive tree systems biology [2]. Subsidise scientific research with money from olive oil export business.

5. What do you think will science blogging be like in 5 years?

Pretty much the same as it is now I reckon, maybe more senior scientists will start blogging, see big boffins with blogs.

6. What is the most extraordinary thing that happened to you because of blogging?

I’m pretty sure blogging was a significant factor in being invited to Science Foo Camp (scifoo)

7. Did you write a blog post or comment you later regretted?

Non, rien de rien. Non, je ne regrette rien. Some of the posts about semantic web and molecular biology I might come to regret in the future though, but life is too short. There is an ever present temptation to write controversial blog posts (that might be regretted later) to get more visitors to your blog. Sometimes I can’t resist. Also, there is no safety net of peer-review, so you can make mistakes very quickly, even faster than by drinking tequila. I often wonder what prospective employers and/or funding bodies would make of it all – by the time I find out, it might be too late 🙂

8. When did you first learn about science blogging?

Via nodalpoint which is run by Greg Tyrelle.

9. What do your colleagues at work say about your blogging?

So far, there have been five basic responses to my blog among colleagues.

a) Great idea, carry on (see picture, top right). Can you blog this for me?

b) Bad idea, why do you waste so much time blogging? When are you going to do some “real” work?

c) Teasing: “I’m drinking a coffee, are you blogging this?”

d) Head-in-the-sand, no acknowledgment, denial, look the other way.

e) Ignorance is bliss. What is a blog? Do you have one of those interweb things on your computer?

References

  1. Michael R. Seringhaus and Mark B. Gerstein (2007). Publishing perishing? towards tomorrow’s information architecture. BMC Bioinformatics 8, 17+. DOI:10.1186/1471-2105-8-17, pmid:17239245
  2. Royston Goodacre, Douglas B Kell, Giorgio Bianchi (1992). Neural networks and olive oil. Nature 359 (6396), 594. DOI:10.1038/359594a0

[Keep Calm and Carry On via AJC1]

October 31, 2008

Defrosting the Digital Library

Bibliographic Tools for the Next Generation Web

Sunset Ice Sculptures by Mark K.We started writing this paper [1] over a year ago, so it’s great to see it finally published today. Here is the abstract:

“Many scientists now manage the bulk of their bibliographic information electronically, thereby organizing their publications and citation material from digital libraries. However, a library has been described as “thought in cold storage,” and unfortunately many digital libraries can be cold, impersonal, isolated, and inaccessible places. In this Review, we discuss the current chilly state of digital libraries for the computational biologist, including PubMed, IEEE Xplore, the ACM digital library, ISI Web of Knowledge, Scopus, Citeseer, arXiv, DBLP, and Google Scholar. We illustrate the current process of using these libraries with a typical workflow, and highlight problems with managing data and metadata using URIs. We then examine a range of new applications such as Zotero, Mendeley, Mekentosj Papers, MyNCBI, CiteULike, Connotea, and HubMed that exploit the Web to make these digital libraries more personal, sociable, integrated, and accessible places. We conclude with how these applications may begin to help achieve a digital defrost, and discuss some of the issues that will help or hinder this in terms of making libraries on the Web warmer places in the future, becoming resources that are considerably more useful to both humans and machines.”

Biotechnology and Biological Sciences Research CouncilThanks to Kevin Emamy, Richard Cameron, Martin Flack, and Ian Mulvany for answering questions on the CiteULike and Connotea mailing lists; and Greg Tyrelle for ongoing discussion about metadata and the semantic Web nodalpoint.org. Also thanks to Timo Hannay and Tim O’Reilly for an invitation to scifoo, where some of the issues described in this publication were discussed. Last but not least, thanks to Douglas Kell and Steve Pettifer for helping me write it and the BBSRC for funding it (grant code BB/E004431/1 REFINE project). We hope it is a useful review, and that you enjoy reading it as much as we enjoyed writing it.

References

  1. Duncan Hull, Steve Pettifer and Douglas B. Kell (2008). Defrosting the digital library: Bibliographic tools for the next generation web. PLoS Computational Biology, 4(10):e1000204+. DOI:10.1371/journal.pcbi.1000204, pmid:18974831, pmcid:2568856, citeulike:3467077
  2. Also mentioned (in no particular order) by NCESS, Wowter, Twine, Stephen Abram, Rod Page, Digital Koans, Twitter, Bora Zivkovic, Digg, reddit, Library Intelligencer, OpenHelix, Delicious, friendfeed, Dr. Shock, GribbleLab, Nature Blogs, Ben Good, Rafael Sidi, Scholarship 2.0, Subio, up2date, SecondBrain, Hubmed, BusinessExchange, CiteGeist, Connotea and Google

[Sunrise Ice Sculptures picture from Mark K.]

October 30, 2008

Congratulations Matthew Horridge!

George Best Genius by sahmeepeeSo, congratulations are due to Matthew Horridge, Bijan Parsia and Ulrike Sattler from The University of Manchester for winning the keenly fought best paper prize at the International Semantic Web Conference [ISWC 2008] in Karlsruhe for their paper “Laconic and Precise Justifications in OWL”. An abstract of the paper is reproduced below:

“A justification for an entailment in an OWL ontology is a minimal subset of the ontology that is sufficient for that entailment to hold. Since justifications respect the syntactic form of axioms in an ontology, they are usually neither syntactically nor semantically minimal. This paper presents two new subclasses of justifications—laconic justifications and precise justifications. Laconic justifications only consist of axioms that do not contain any superfluous “parts”. Precise justifications can be derived from laconic justifications and are characterised by the fact that they consist of flat, small axioms, which facilitate the generation of semantically minimal repairs. Formal definitions for both types of justification are presented. In contrast to previous work in this area, these definitions make it clear as to what exactly “parts of axioms” are. In order to demonstrate the practicability of computing laconic, and hence precise justifications, an algorithm is provided and results from an empirical evaluation carried out on several published ontologies are presented. The evaluation showed that laconic/precise justifications can be computed in a reasonable time for entailments in a range of ontologies that vary in size and complexity. It was found that in half of the ontologies sampled there were entailments that had more laconic/precise justifications than regular justifications. More surprisingly it was observed that for some ontologies there were fewer laconic justifications than regular justifications.”

But what does it all mean? One of the results of this research project has been an explanations plug-in for the Protégé ontology editor, see explanation in OWL at http://owl.cs.manchester.ac.uk. This helps users to understand when and why the reasoning goes all pear-shaped through better explanations than has previously been possible. So this is another step toward making building better ontologies with the Web Ontology Language (OWL) easier and less confusing. Yay!

References

And the winner is... by guitarfish

  1. Matthew Horridge, Bijan Parsia and Ulrike Sattler (2008). Laconic and Precise Justifications in OWL Lecture Notes in Computer Science, LNCS Volume 5318/-1 The Semantic Web – ISWC 2008 DOI:10.1007/978-3-540-88564-1_21

[Picture of Manchester United player George Best by Sammy, Best paper prize picture by guitarfish]

October 27, 2008

OWL Experiences and Directions (OWLED) 2008

Great Grey Owl by Brian ScottThe Web Ontology Language (OWL) is a language for creating ontologies on the Web. It does exactly what it says on the tin. But what is an ontology? One way to think of it is as a better way of storing data and knowledge. Instead of just capturing and describing data in a databases, ontology languages like OWL provide ways to capture and describe knowledge in a knowledge base. Ontologies can allow more intelligent querying, integration and understanding of data than is possible using a plain old relational database.

Since 2003 developers and users of the Web Ontology Language, abbreviated to OWL (not WOL), have been gathering at a two-day workshop called OWLED (OWL Experiences and Directions). This year the workshop is in Karlsruhe in Germany. The full list of accepted papers is available, as with previous years, this years workshop has a distinctly biological flavour to the proceedings: (more…)

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