May 15, 2009

Y.M.C.A. – Just a little bit of G.T.C.A.

OK, look I know that by posting the latest viral marketing video from Bio-Rad Laboratories, Inc. I’m just a pawn (or vector) in their advertising game. This particular video has been around for a couple of months now but it is probably poor internet hygiene to spread these pandemic viral videos. I should just catch it, kill it and bin it. However, I can’t resist this one any longer because, like the last one, it is pretty kitsch, pretty funny and in a strange way, it might just increase the public awareness of Science. Maybe.

And it’s Friday today too, so to the tune of Y.M.C.A. by the Village People, you are now infected with just a little bit of (altogether now…) G.T.C.A.!

The lyrics go a little something like this: (more…)

February 6, 2009

The Loneliness of the Long Distance Researcher

Nice Idea by Libby MillerDespite what some people think (see “the myth of the lone inventor” in [1]) most scientists are usually pretty sociable people. Science is an inherently social activity [2], just take a look around you. Most laboratories are full of like-minded people working on related problems, our lab is no exception. Outside the lab, there are all the conferences, workshops, seminars, trips to the pub, coffee breaks and other meetings where scientists meet and exchange ideas and results. Finally, note the peer in peer-review – another essentially social activity, even when it is anonymous.

But in between these gregarious social activities there is a long, lonely and pretty unsociable road where you need to spend lots of time thinking, reading, writing and experimenting. Essentially you are alone, like a modern day hermit, especially at the earlier stages of a career. Solitary confinement in your ivory tower of choice needs to be balanced with various kinds of socialising. Talking about and watching what other people are doing, as well as publicising your own work are an essential part of the mix. But you still need to put the hours in on the road. It isn’t always easy to get it right, so how do you strike a balance between the social and the solitary activities to establish yourself as an independent research scientist? (more…)

July 15, 2008

ChEBI, Oh ChEBI, Oh Baby!

Filed under: informatics — Duncan Hull @ 2:30 pm
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cherry oh baby With sincere apologies to Jamaican reggae singer-songwriter Eric Donaldson, “ChEBI, Oh ChEBI, Oh Baby, don’t you know I’m in need of thee”?

Chemical Entities of Biological Interest (ChEBI) is a dictionary, controlled vocabulary, database, ontology of small (low molecular-weight) chemical entities that are considered to be biologically interesting, (like amphetamine (CHEBI:2679) for example). After a couple of recent meetings, ChEBI is going through some serious revision, to make it more efficient to maintain and use. Here are some brief notes on the changes, for my own benefit mostly and to collate links, but perhaps others are interested too.

Janna Hastings has created a wiki for the New ChEBI Ontology project which includes links to the ChEBI ontology remediation notes and meeting notes from 9th July 2008.

June 12, 2008

The drugs don’t work, they just make you worse

Filed under: informatics — Duncan Hull @ 3:45 pm
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StampsWhat exactly is a drug? A project I’m currently working on requires a good solid definition, at the very least comprehensible to humans, and preferably understandable by more intelligent, semantically aware computers too. I would like to be able to take some scientific model and ask questions like, “show (or hide) all the drugs in this model”. Trouble is, the word “drug” is such a heavily overloaded term, with many alternative meanings, that it is practically meaningless. Just when you think you have a definition, you can find a case that breaks it. I’m not just being an anally-retentive pedant, well no more than usual anyway. It turns out to be much harder than you might think to define what a drug is. The term drug depends on all kinds of contextual information, dosage, species, legality, intent, social conventions and so on. Here are some broken definitions, warts and all. As you’ll see, the various definitions of drugs don’t work, they just make you worse. (more…)

May 9, 2008

I Still Haven’t Found What I’m Googling For

Filed under: lyrical — Duncan Hull @ 8:03 am
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Irish GoogleTwenty one years ago this month, in May 1987, Irish rockers U2 released their classic Joshua Tree single, I Still Haven’t Found What I’m Looking For. Those twenty one years have seen incredible technological change: the adoption of desktop computers, mobile phones, the birth of the Web and the widespread use of search engines like Google. So with sincere apologies to Bono, The Edge, Adam and Larry, it’s time we updated the lyrics for the 21st century. So, I give you “I Still Haven’t Found What I’m Googling For” (21st anniversary, 2008 webby edition)… (more…)

March 14, 2008

Semantic Web? Yeah, Whatever!

Filed under: semweb — Duncan Hull @ 11:59 am
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(To be spoken in the best SoCal Valley Speak you can muster)

I went down to the beach and saw Yahoo
She was, like, all “semantic web
And I was, like, “whatever!”


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