sphyg's Journal http://use.perl.org/~sphyg/journal/ sphyg's use Perl Journal en-us use Perl; is Copyright 1998-2006, Chris Nandor. Stories, comments, journals, and other submissions posted on use Perl; are Copyright their respective owners. 2012-01-25T02:15:42+00:00 pudge pudge@perl.org Technology hourly 1 1970-01-01T00:00+00:00 sphyg's Journal http://use.perl.org/images/topics/useperl.gif http://use.perl.org/~sphyg/journal/ Long time, no see http://use.perl.org/~sphyg/journal/15961?from=rss Someone remind me to go to the December london.pm social... sphyg 2003-11-23T17:33:16+00:00 journal Biomail http://use.perl.org/~sphyg/journal/9436?from=rss <a href="http://www.biomail.org/">BioMail</a> are going to replace Perl with Java and MySQL. Ugh. sphyg 2002-12-13T11:43:37+00:00 journal Tech meet http://use.perl.org/~sphyg/journal/9079?from=rss I am no longer a tech meet virgin. I wandered down to London last night and managed not to forget my props. I like lightning talks - if I don't understand the topic, something new comes along in 5 minutes. Most crack-fuelled award goes to 'How Bond would kill bugs'. Met some (more) Australians, drank some beer, followed acme round the Tube. Karma to 2shortplanks for cat herding. Hmm, I should now put my non-slides on my website. sphyg 2002-11-22T10:31:07+00:00 journal TPR http://use.perl.org/~sphyg/journal/8793?from=rss Coo, I got mentioned in <a href="http://www.theperlreview.com/">The Perl Review</a>. So I bought a subscription. <p>Incidentally, is it time for a new use.perl poll?</p> sphyg 2002-11-06T12:50:28+00:00 journal *ponders* http://use.perl.org/~sphyg/journal/8701?from=rss Yet Another Bioinformatics Conference. sphyg 2002-10-31T18:23:24+00:00 journal Glutton for punishment? http://use.perl.org/~sphyg/journal/8160?from=rss Tonight was my third trip to London within a week. <p>On Saturday, acme, hex and myself went to the BodyWorlds exhibition. It was full of very cool anatomy and was interesting to see the reactions of people who didn't cut up bodies for a degree. They had a horse, which means they should do a camel next, and I now have a postcard of a dead guy hacking on a Mac. After a Brick Lane curry we perusaded kake and richardc to join us in a Notting Hill pub and then I visited the new flat of richardc and 2shortplanks to watch 'Dude, where's my car?' (dude, sweet). </p><p>On Tuesday, tantrix, neko, 2shortplanks and myself braved the tube strike and took the visiting Geoffrey Avery to see the Complete History of America (Abridged) by the Reduced Shakespeare Company. Bloody funny. </p><p>Tonight was the london.pm social in the Calthorpe Arms. Nice beer, conversation about parties, sushi, the new PM leaders list, organising a cam.pm tech meet, repaying people money, singing happy birthday to space and meeting jerakeen in the flesh. Followed by the slooow train home. </p><p>I'm looking forward to a (relatively) quiet weekend. Where quiet equals hosting someone else's birthday party in my house.</p> sphyg 2002-10-04T01:23:52+00:00 journal YAPC::Europe http://use.perl.org/~sphyg/journal/7907?from=rss Monday. Panic. <br>Packing and last minute data analysis due to biologists changing their minds. Had to walk to the bus station at 3.30am, so didn't bother going to bed. <p>Tuesday. We're off to see the wizard. <br>Met up with london.pm-ers, did the airport thing without getting frisked (unusual), flew through the clouds (very Quantum Leap). Hotel nice and central - though lacking in decent pillows, minibar, and free brekkie. Headed to a beer garden to sample local delicacies - all in the name of science, of course. The evening saw a large google of geeks (like a gaggle of geese) crammed into a nice local. Managed to put zome faces to names, or irc nicks. Got to sleep about 1am. This was to be the earliest night of the entire week. </p><p>Wednesday. And so it begins. <br>Was late arriving at the venue, due to a very bad map. Caught the end of Red's talk on GTK and was amused by Schwern. Caught a train to the middle of nowhere and the speaker's dinner. Felt a little out of place but talked to lots of people and ate far too much. Returned to the hotel to find (surprise, surprise) london.pm still in the pub, so joined them for a round of schnapps. Or three. </p><p>Thursday. Busybusybusy. <br>Got up in time for the opening ceremony, which I'd vaguely promised Foley I'd go to. Saw a talk on Perl 5.8, which I'm considering moving to, and Nick Clark (enthusiastic, as always) talk about speeding things up, which I could do with. Gellyfish provided a contentless, but highly entertaining, talk on SOAP. Greg proved my point that rotating 3D graphics gets you scientific funding. Thanks to Thomas Klausner, I've been lured over to the dark side of obfuscation and might even try and find time to play some golf. Managed not to make a complete fool of myself in my lightening talk. I *did* warn people there wasn't going to be any code. Damian said the usual things about Perl 6. We had a mini bio bof, which made a nice change from the usual nargery. I seem to remember that the evening's entertainment involved a conveniently located pub, followed by brandy, cigars and music in Greg's room. </p><p>Friday. And then there were four. <br>I'm managed not to pay much attention in the morning. Damian's Quantum::Superpositions gave Dr Lush and I cunning ideas about Blast (DNA alignment). I'm very tempted to write something along the lines of Acme::Schnapps and Acme::Phylogenetics. I bought a book, failed to start a purple website faction in the auction and watched half-naked men arm wrestle. In the evening we got rained on, then found a (very orange) bar that wasn't full. Numbers dwindled until 3am, when the survivors headed back to the hotel to find london.pm had kidnapped a Bavarian folk singer from the party next door. </p><p>Saturday. Beer foamy. <br>This was my designated lying-in day. After managing to locate a select group of mongers, we wandered round Munich, ate icecream, found the river, skimmed stones, and saw a coffee flavoured duck. The Queen laser show at the planetarium just had to be done. Likewise, Oktoberfest, which was very large and very busy. Still we managed to dance on a table and sing along to 'I will survive'. </p><p>Sunday. Playing catchup. <br>A leisurely breakfast. Wireless in the airport. A long bus journey. An overflowing inbox. Noodles. Sleep very soon.</p> sphyg 2002-09-22T22:40:14+00:00 journal Les Miserables http://use.perl.org/~sphyg/journal/6187?from=rss <a href="http://news.bmn.com/news/story?day=020626&amp;story=1">This story</a> made me giggle. sphyg 2002-07-05T11:30:06+00:00 journal *crosses fingers* http://use.perl.org/~sphyg/journal/5098?from=rss Soooo, in the past 2 months I went to a social meet with lots of people and cider. I had a birthday and a party, but no cake. We had a Getting rid of Grue party, but have acquired another ornamental Australian. I gave a seminar at Darwin, I might win some money for an essay, and I am currently backing up our luverly data. sphyg 2002-05-20T19:34:50+00:00 journal Sex, flies and microarrays http://use.perl.org/~sphyg/journal/3690?from=rss I've spent the past week learning about the carnal habits of Drosophila. Randy little blighters. I've been whizzing back and forth between <a href="http://flybase.bio.indiana.edu/">FlyBase</a>, <a href="http://www.fruitfly.org/annot/">GadFly</a> (uses perl, rah!), <a href="http://www.geneontology.org/">Gene Ontology</a> and the <a href="http://http//sdb.bio.purdue.edu/fly/aimain/1aahome.htm">Interactive Fly</a>. Tomorrow I shall talk to the people in the know upstairs and go to the library. Incidentally, an hour after someone asked me about crazy gene names on IRC I found <a href="http://www.flynome.org/">FlyNome</a> (more perl!). Find out more at YAPC::Europe... sphyg 2002-03-21T00:06:58+00:00 journal Crazy week http://use.perl.org/~sphyg/journal/3168?from=rss So far I've done 2 all nighters, been amused by Brad's comments at the <a href="http://www.technophage.com/">biohackathon</a>, completely failed to go to the pub and just had my attempt to do some actual PhD thwarted by a gaggle of geeks arriving in my living room. sphyg 2002-02-28T00:21:02+00:00 journal Busy doing nothing... http://use.perl.org/~sphyg/journal/2709?from=rss I'm supposed to be in the pub in London with a bunch of debauched <a href="http://london.pm.org/">perlmongers</a>. Instead I'm eating yoghurt and hacking on a pile of backlog $this_big. Have been trying to stir up some traffic on the O'Reilly bioinformatics list. Saw <a href="http://www.yanntiersen.com/">Amelie sountrack composer</a> in concert. Must send a reminder to <a href="http://cam.pm.org/">Cam.pm</a> about next week's social. Must also get head around CVS. Must stop talking like Bridget Jones. sphyg 2002-02-07T23:38:04+00:00 journal Playing catchup... http://use.perl.org/~sphyg/journal/2558?from=rss I've been busy<nobr> <wbr></nobr>;-) <p>Clustering genes, reading articles, writing <a href="http://www.gen.cam.ac.uk/~flychip/">HTML</a>, organising <a href="http://cam.pm.org/">Cam.pm</a>, arranging trips to <a href="http://www.helicon.org.uk/">Helicon</a> and <a href="http://www.yapc.org/Europe/">Yapc::Europe</a>, wishing I was in <a href="http://www.oreillynet.com/biocon2002/">Arizona</a>, drinking <a href="http://www.camra.org.uk/">beer</a>, visiting people, watching <a href="http://www.theonering.net/">Lord of the Rings</a>, cleaning the house, sleeping, and so on. </p><p>While I remember, go see some <a href="http://www.csa.ru/flyex/">pretty piccies</a>...</p> sphyg 2002-01-31T18:26:05+00:00 journal CUSFS Science Symposium http://use.perl.org/~sphyg/journal/1251?from=rss On Sunday evening I gave a talk, entitled 'Bioinformatics and Microarrays', at the inaugural science symposium of the Cambridge University Science Fiction Society. OK, so it really boiled down to me waffling to a room of about 10 people for about 15 minutes, but I thought it was quite successful. We were an an antiquated college room without a data projector so I got to draw silly coloured cartoons on for the OHP. I might scan them in for a laugh. Of course, now I have to do some proper work... sphyg 2001-11-14T09:56:52+00:00 journal 'Ome sweet 'ome http://use.perl.org/~sphyg/journal/1115?from=rss <p>There are far too many odd words in biology. Genome (an organism's full complement of genetic information) and proteome (all the proteins prodeuced from the genes in the genome) I can cope with, even if people are still debating their exact definition. Things start getting silly when we get transcriptome, physiome, metabalome, morphome, phenome, interactome, glycome, secretome, ribonome, cellome, operome, transportome, pseudome, functome, translatome, foldome, unknome...</p><p>I think we need a new word - the omome - to describe the full collection of 'omes.</p><p>Despite the terrible pun in the title, see:<br>Greenbaum, et al. Interrelating the different types of genomic data, from proteome to secretome: 'oming in on function. Genome Research 2001;11:1463-1468</p> sphyg 2001-10-31T11:04:57+00:00 journal Testing, testing... http://use.perl.org/~sphyg/journal/849?from=rss So...I'm going to join in the fun and wibble about stuff. Mainly about bioinformatics because - as opposed to gnat - I actually do it. And especially about microarray technology. I'll try and find time to write properly, but the current plan is to post interesting links here, rather than fill my work logs with them. Let's start off with <a href="http://www.open-bio.org/">The Open Bioinformatics Foundation</a>, home of the bio* projects and one of the first sites you should visit if you're interested in open source in bioinformatics. sphyg 2001-10-02T14:33:18+00:00 journal