Last 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 , 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).
- 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]
The 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:
- Tony Coates, Londata Ltd., blogs at kontrawize
- John Chelsom, City University and Eleven Informatics LLP.
- Neil Cowles, Tolven Inc.
- Leigh Dodds, Talis Information Ltd., blogs at Lost Boy.
- Paul Downey, Osmosoft (Open Source applications from British Telecom) blogs at whatfettle
- Bob DuCharme, TopQuadrant Inc., blogs at snee.com
- Peter Flynn, blogs at silmaril.ie
- Marc Hadley, Sun Microsystems, blogs at java.net
- Duncan Hull, yours truly, blogs here.
- Michael Kay, Saxonica Ltd., home of the Saxon XSLT and XQuery Processor blogs at blogharbor
- Debbie Lapeyre, Mulberry Technologies,
- Eve Maler, PayPal Inc., blogs at Pushing String.
- Simon Phipps, Sun Microsystems Inc., blogs at sun.com
- Adam Retter, blogs at adamretter.org.uk
- Rich Salz, IBM, blogs at developerWorks
- Andy Seaborne, Hewlett-Packard laboratories, blogs at ARQtick
- Michael Sperberg-McQueen, Black Mesa Technologies LLC., blogs at Messages in a Bottle
- Ron Summers, Loughborough University
- Jeni Tennison, Jeni Tennison Consulting Ltd., blogs at jenitennison.com
- Norm Walsh, Mark Logic, blogs at norman.walsh.name
- Priscilla Walmsley, Datypic consulting
- Lauren Wood blogs at laurenwood.org
The 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 , to electronic health records , scientific publishing, the provision of the PubMed service (which talks XML)  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…
- 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
- 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
- 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
So, 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…)