e-Science blog
Posted by peanutbutter in bioinformatics, CARMEN, microsoft on October 25, 2007
A new blog has appeared over the last month entitled e-science ramblings. This blog is edited by Hugo Hiden who is the technical director of the North Eastern Regional e-Science centre which is based at Newcastle University.
As described in his first post:
The reason for this blog is, primarily, to document my experiences with writing a prototype e-Science research platform using Microsoft tools instead of the more traditional approach of fighting with Open Source. This way is easier, supposedly. The task I have set myself is to recreate, at a basic level, the software being developed by the CARMEN project.
I think this should be an interesting read both on the technical aspects and the usability of Microsoft products compared to open source software for e-science.
Windows and ubuntu Synergy
Posted by peanutbutter in howto, ubuntu on October 18, 2007
I have just installed Synergy on my Gutsy Ubuntu machine. This allows me to switch seamlessly between my ubuntu desktop and my windows laptop using the same keyboard and mouse. It was very easy to install, via apt. I followed the ubuntu synergy how to and it worked perfectly first time.
How to install Java on ubuntu
Posted by peanutbutter in howto, java, ubuntu on September 18, 2007
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
AHM day 2
Posted by peanutbutter in conference report on September 12, 2007
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.
All Hands meeting Day 1
Posted by peanutbutter in conference report on September 12, 2007
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?
Conferences
Posted by peanutbutter in Uncategorized on September 11, 2007
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.
I see science
Posted by peanutbutter in bioinformatics, Journals Publishing, open data, open science, Social Media, Uncategorized, video on August 20, 2007
It is interesting to see new developments in the dissemination of scientific discourse, such as scientific blogging and paradigms such as open science, come on-line with developments in web-based social media. The latest medium to receive the Science 2.0 treatment (poor pun on applying Web 2.0 technologies for science) is the video.
YouTube is probably the granddaddy, or at least the most prominent of the video upload and broadcast services. Although YouTube doesn’t not have a defined science category, it is easy to find science related videos and lectures, mixed in with the general population. However, several specialist sites have appeared dealing specifically with science research, all have been labeled as “YouTube for science”. The most recent site is SciVee, which is a collaboration of the Public Library of Science (PLoS), the National Science Foundation (NSF) and the San Diego Supercomputer Center (SDSC). The fact the a publishing house (PLoS) has got involved in this effort is encouraging, and maybe an admittance that a paper, in isolation of public commentary, the data used to produce the paper, and a sensible presentation mechanism, is no longer sufficient in the web-based publishing era (or maybe I have got over excited and read to much into it). The most interesting feature on SciVee, and probably the most powerful compared to some of the other broadcasters, is the ability to link to an Open Access publication, setting the context and relevance of the video. The flip side could also be true, where a video provides evidence of the experiment, such as the methods or the displays the result.
Another scientific video broadcaster is the Journal of Visualized Experiments (JOVE). As the name suggests, JOVE focuses on capturing the experiment performed within the laboratory, rather than a presentation, or general scientific discourse. As a result JOVE can be though of as a visual protocol or methods journal and is stylaised as a traditional journal, already on Issue 6; a focus on Neuroscience.
If JOVE is a visual journal for life-science experiments then Bioscreencast could be thought of as a visual journal of Bioinformatics. Bioscreencast focusses on screencasts of software, providing a visual “How-to” on scientific software, presentations and demonstrations.
No doubt these three may not be the last scientific video publishers, but they have an opportunity to become well established ahead of the others. Now, where is my webcam, I need to video myself writing code and submit it to JOVE, produce a demo and submit it to Bioscreencast. Then I have to write a paper on it, submit the pre-prints to Nature Preccedings get it published in an Open Access Journal, then video myself giving a presentation on the paper, submit it to SciVee and link them all together.
SciFoo
Posted by peanutbutter in Uncategorized on August 6, 2007
There is lots of blogging activity at the minute around Scifoo. I am excited, just reading the posts and looking at the range of people there, not to mention the range topics on discussion. The most comprehensive one I have found is Duncan’s on Nodalpoint, and bbgm although there are other people which you can probably track via the scifoo Technorati tag
I wish I was there, oh well maybe next year……….
RSS readers
Posted by peanutbutter in bioinformatics, cloud, Google, Social Bookmarking, Social Media on July 2, 2007
I have outlined my growing tendency at the minute to handing over applications to the “Internet cloud” in an earlier post.
I prefer using web-based applications because I tend to jump from several machines throughout the day at work and then use a different machine at home. Having applications, floating in the ether cloud, means moving around is considerably easier. I have been using bloglines for quite a while now for my RSS feeds. I did have a early look at Google reader when it first launched, but I felt then it was not quite what I wanted and definitely not as good as bloglines at the time. However a re-visiting of Google reader over the last week or so has dramatically changed my perception. Re-vamped with a new interface (similar to bloglines) has made reading posts alot easier. All the post from your subscribed feeds are actually saved, by default and don’t disappear once read, unlike in bloglines (unless you check the “keep new” box). I think the biggest feature for me is the ability to tag posts, combined with the saved posts facility, this should prove to be a very handy source of reference rather that just an “recent-post viewer”.
A new feature that has just been added to Google reader is the offline mode. Working in conjunction with Google Gears this provides the ability to read the last 2000 recent items, a feature I am looking forward to testing during the flight to ISMB in a few weeks.
If you use another RSS reader or have an opinion on Google reader then let me know.
With using gmail, and calendar, with trying out Google reader (and probably switching from bloglines), using google docs and spreadsheets more everyday, there is every danger that my cloud is going to be raining google. With the added prospect of Google presentations round the corner will it be long before I am floating off to the Google OS cloud?
More on Open science
Posted by peanutbutter in open science on July 2, 2007
Thanks to everybody that commented on my post Do scientists really believe in open science? and to Open access news and Nautilus for picking up on it. It has definately stimulated some discussions
James keep us posted on the outcomes of the theft of your colleagues work.
This is just a note to say that Michael Barton of Bioinformatics Zen has started an open science wiki page at Nodalpoint, I think, for a special edition of Bio::blogs so feel free to comment.
License
This work by Frank Gibson is licensed under a Creative Commons Attribution 3.0 Unported License.
fgibson.com 