O'Really?

November 24, 2009

Semantic Web Applications and Tools for the Life Sciences (SWAT4LS) 2009, Amsterdam

Snow in Amsterdam by Bas van GaalenLast Friday, the Centrum Wiskunde & Informatica (CWI) in Amsterdam hosted a workshop called Semantic Web Applications and Tools for the Life Sciences (SWAT4LS) 2009.

Following on from last year [1], the workshop proceedings will be published at ceur-ws.org and in a special issue of the Journal of Biomedical Semantics, but if you want to find out what happened in the meantime, take a look at the #swat4ls2009 hashtag on twitter. Twitter makes bloggers lazy (they blog less but tweet more), but thankfully Nico Adams has studiously blogged the workshop very extensively.

Disruptive Technologies Director (cool job title!) Anita de Waard from Elsevier was asking what were the conclusions of the workshop. So here is an incomplete summary: Roughly speaking, people agreed to disagree (again). Keynote speaker Barend Mons argued that redundant data should be eliminated through the use of “nano-publications” and micro-attribution in his entertaining but controversial keynote. Some people in the audience disagreed with this. Greg Tyrelle thinks that redundancy is a feature, not a bug, in the Web and we have to deal with it. Alan Ruttenberg argued that semantic web reasoners  are required to clean up and sanity check all the messy and noisy biological data but emphasised the importance of Computer Scientists learning to speak Biologists language.

The good thing about this workshop is its size: small, friendly but internationally attended. Thanks to M. Scott Marshall, Albert Burger, Adrian Paschke, Paolo Romano and Andrea Splendiani for organising another good workshop, hope to see you again next year (if not before).

References

  1. Burger, A., Romano, P., Paschke, A., & Splendiani, A. (2009). Semantic Web Applications and Tools for Life Sciences, 2008 – Introduction BMC Bioinformatics, 10 (Suppl 10) DOI: 10.1186/1471-2105-10-S10-S1 part of the special issue on SWAT4LS 2008

[CC-licensed picture of Amsterdam in the snow by Bas van Gaalen]

September 4, 2009

XML training in Oxford

XML Summer School 2009The XML Summer School returns this year at St. Edmund Hall, Oxford from 20th-25th September 2009. As always, it’s packed with high quality technical training for every level of expertise, from the Hands-on Introduction for beginners through to special classes devoted to XQuery and XSLT, Semantic Technologies, Open Source Applications, Web 2.0, Web Services and Identity. The Summer School is also a rare opportunity to experience what life is like as a student in one of the world’s oldest university cities while enjoying a range of social events that are a part of the unique summer school experience.

This year, classes and sessions are taught and chaired by:

W3C XML 10th anniversaryThe Extensible Markup Language (XML) has been around for just over ten years, quickly and quietly finding its niche in many different areas of science and technology. It has been used in everything from modelling biochemical networks in systems biology [1], to electronic health records [2], scientific publishing, the provision of the PubMed service (which talks XML) [3] and many other areas. As a crude measure of its importance in biomedical science, PubMed currently has no fewer than 800 peer-reviewed publications on XML. It’s hard to imagine life without it. So whether you’re a complete novice looking to learn more about XML or a seasoned veteran wanting to improve your knowledge, register your place and find out more by visiting xmlsummerschool.com. I hope to see you there…

References

  1. Hucka, M. (2003). The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models Bioinformatics, 19 (4), 524-531 DOI: 10.1093/bioinformatics/btg015
  2. Bunduchi R, Williams R, Graham I, & Smart A (2006). XML-based clinical data standardisation in the National Health Service Scotland. Informatics in primary care, 14 (4) PMID: 17504574
  3. Sayers, E., Barrett, T., Benson, D., Bryant, S., Canese, K., Chetvernin, V., Church, D., DiCuccio, M., Edgar, R., Federhen, S., Feolo, M., Geer, L., Helmberg, W., Kapustin, Y., Landsman, D., Lipman, D., Madden, T., Maglott, D., Miller, V., Mizrachi, I., Ostell, J., Pruitt, K., Schuler, G., Sequeira, E., Sherry, S., Shumway, M., Sirotkin, K., Souvorov, A., Starchenko, G., Tatusova, T., Wagner, L., Yaschenko, E., & Ye, J. (2009). Database resources of the National Center for Biotechnology Information Nucleic Acids Research, 37 (Database) DOI: 10.1093/nar/gkn741

February 26, 2008

So, no-one told you life was going to be this way

Filed under: semweb — Duncan Hull @ 1:29 pm
Tags: , , , , , , , ,

Friends via Hot Rod HomepageSo, no-one told you life was going to be this way
Your job is a joke, you are broke, your love life is DOA.
It is like you are always stuck in second gear
Well, it has not been your day, your week, your month, or even your year…

OWL be there for you, when the rain starts to pour. Software engineer Leigh Dodds explains how: (more…)

July 19, 2006

May 5, 2006

The Rubric Theme. Blog at WordPress.com.

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