Archive for September, 2007

How to install Java on ubuntu

I am writing this post because I keep forgetting how to do it and end up trawling the web trying to find it. The Unbuntu starter guide should be the first port of call to install whatever flavour of java you want via apt.

Then this comes from [1]

If you want to use Sun’s Java instead of the open source GIJ (GNU Java bytecode interpreter) you need to set it as default. To list installed JVMs:

update-java-alternatives -l

To select, for example, Sun’s JVM as provided in Ubuntu 6.06, run:

sudo update-java-alternatives -s java-1.5.0-sun

You should also edit /etc/jvm and move /usr/lib/jvm/java-1.5.0-sun to the top of JVMs offered.

To set the JAVA_HOME environment variable I followed this [2]

export JAVA_HOME=/usr/lib/jvm/java-1.5.0-sun-1.5.0.08

You can find your JAVA_HOME using the locate command for a file belonging to the JDK.

locate /rt.jar
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AHM day 2

This was a busy day on the booth for me so did not get to attend many talks. I did however attend the Keynote by Professor Tom Kirkwood entitled The Grand Challenge of Population Ageing: e-Science to the Rescue. It was a very interesting talk by a good speaker on the science behind ageing. However the e-Science to the Rescue was very thin. As this was an e-science conference I would have liked to have seen a more emphasis on the e-science. I am familiar with this project and the excellent work on an omics data portal called symba. Unfortunately symba was restricted to a slide or two that were quickly flashed up near the end of the presentation, which I found a bit of a let down.

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All Hands meeting Day 1

I’m a bit late in my posting, just been to busy going to talks and discussing things, anyway. My first session at this years AHM was a workshop on “Issues is Ontology Development and Use. The welcome and workshop overview was presented by Alan Rector. I only caught the end of this introduction, as I was getting my fix of caffeine after travelling all day. The full program for the workshop and the full meeting can be found here. However there were a few presentations that stood out for me. The first one for all the wrong reasons. A talk entitled Ontology building as Practical work:Lessons from CSCW was a talk given on an overhead projector. No chance of power point poisoning tonight. Apparently he has had to step in at
the last minute to give the talk so they are not his slides, and it is starting to show. Oh dear he has given up on some of the slides and is just reading them out, disappointing.

Another talk entitled “A Socio-technical Perspective on Ontology Development in HealthGrids” by Jenny Ure, was interesting and CARMEN got a mention to which is always good. The talk described the alignment of the development of ontologies within similar e-Science projects and the BIRN project for Neuroimaging

Another talk that stood out for me was by Alistair Miles entitled “Collaboration in the value Grid for Semantic Technologies”. Within this talk I heard alot of new terms such as “Value Grids” in collaborating and building ontologies, all which is relevant for my work, and now apparently I am a “Collaborative engineer”. At the end of the talk he also gave a purl for his blog which I though was a nice touch. His post on the workshop which can be found here.

The final session of the workshop was an open discussion session on the main themes of the workshop, some of the discussion points are listed below. Unfortunately due to time there were no definitive answers to these points. However the slant was different from what I have been used to in other ontology workshops in the past where the application and use drives ontology development. However this discussion was more concerned with the computing science development rather than ontology application.

  • How are ontologies developed in practice and why?
  • Who should be involved and how should they work together?
  • How would we deal with disagreement and conflict?
  • What is the right strategy for encouraging adoption?
  • What is the right technical strategy?
  • Do we have the right languages tools, development environments?

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Conferences

I am currently at the All Hands meeting 2007 in Nottingham, so more posts to follow with some notes on the events and presentations. In addition, a couple of people from my lab are also at the Integrative Bioinformatics conference in Ghent Belgium so you can follow Allyson’s and Matt’s comments on that event.

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