November 2008 - binari@psb.ugent.be - maillist.psb.ugent.be

[Binari] What if The Matrix was run by .. Windows :o
by Kenny Billiau 12 Nov '08

12 Nov '08

http://www.collegehumor.com/video:1886349 Neo "Cypher I want to learn Kungfu" Cypher "Our free version of Kungfu has expired!" On no! -- ================================================================== Kenny Billiau Web Developer Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM kenny.billiau(a)psb.ugent.be http://bioinformatics.psb.ugent.be ==================================================================

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[Binari] mysql, helpful as ever
by Thomas Abeel 12 Nov '08

12 Nov '08

Wed Nov 12 15:37:44 CET 2008 WARN: Invalid value {1} for server variable named {0}, falling back to sane default of {2}. Now I know what is wrong in my program...

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[Binari] FFF
by Elisabeth Wischnitzki 07 Nov '08

07 Nov '08

Who is willing to go today? -- ================================================================== Elisabeth Wischnitzki Tel:+32 (0)9 331 38 22 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM elwis(a)psb.ugent.be http://www.psb.ugent.be ==================================================================

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[Binari] Fwd: YouTube - CNN 1st Time on TV, Jessica Yellin Hologram - Star Wars
by Tine Blomme 07 Nov '08

07 Nov '08

Lieven, Maybe you should have sent your message to binari to get the respect you deserve for this remark? Tine Begin doorgestuurd bericht: > Van: lieven sterck <lieven.sterck(a)psb.ugent.be> > Datum: 7 november 2008 10:30:34 GMT+01:00 > Kopie: Bioinformatics & Evolutionary Genomics <beg(a)psb.ugent.be> > Onderwerp: Antw.: YouTube - CNN 1st Time on TV, Jessica Yellin > Hologram - Star Wars > > Here is my geeky side: > > "Presentator Wolf Blitzer moest spontaan denken aan prinses Leia uit > Star Wars," > I would say 'kinda like starwars', the connaisseurs will have > noticed that the message sent by princess Leila via R2-D2 to the > confederation forces was a recorded message and not a live > transmission. :-D > > voila, how many geeky points did I score? ;-) > > L. > > Yves Van de Peer wrote: >> http://www.youtube.com/watch?v=0SIS2ZwkWDg&eurl=http://www.gva.be/nieuws/bu… >> ?art={C35D44F5-FF4F-4BAF-AE16-81FE84034C77} >> > > -- > ============================================================== > Lieven Sterck, PhD > > Tel:+32 (0)9 3313821 Fax:+32 (0)9 3313809 > VIB Department of Plant Systems Biology, UGent > Bioinformatics and Evolutionary Genomics Division > Technologiepark 927, B-9052 Gent, Belgium > Email: lieven.sterck(a)psb.ugent.be > Website: http://bioinformatics.psb.ugent.be > > ============================================================== > "Facts are meaningless. You could use facts to prove anything that's > even remotely true!" H. Simpson >

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[Binari] MOBY, the long haul
by Kenny Billiau 06 Nov '08

06 Nov '08

Hi, I've finally found the several reasons why the parsing of a 250KB xml file takes about 27 minutes in MOBY. (And this was supposed to be a quick save ;)) The first main bottleneck is the way they cast perl types to a string: sub as_string { my $self = shift; my $dump_str; my $io = IO::Scalar->new (\$dump_str); my $oio = select ($io); $DUMPER->dumpValue (\$self); select ($oio); return $dump_str; } Here they temporary change STDOUT to print to a variable and then do a dump from it (this is only useful for complet structures like hashes, arrays and objects and not for simple types like int and string). So I simply removed it as it gave me the same results as before. I should actually check if the datatype is complex or not instead of dropping this function. The speed up is (hold on to your pantyhose): 5500%. (Actually it's larger, but I stopped profiling after this number was reached.) I think someone was really really wasted when coding that. Or I'm really missing something. The second bottleneck was their way of finding a file in the mOBY cache of datatypes, services, etc.. They look in a default place and then transverse the @INC array (perls equivalent for $PATH). But they don't cache the results. Everytime a file is requested, it is checked for _on disk_. My cache was on a share, so I moved it to a local disk, but, and this is for once good for IT, I had only an improvement of mere 5%! Now I cache the results. Speed up is another 50% compared with the result from the first improvement. The third one is the building up of the whole MOBY environment _everytime_ a start_element event is fired from the SAX parser. Me thinks me's gonna write me a MOBY Factory. What a fuckup, Kenny -- ================================================================== Kenny Billiau Web Developer Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM kenny.billiau(a)psb.ugent.be http://bioinformatics.psb.ugent.be ==================================================================

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[Binari] Jezus Christus!
by Kenny Billiau 05 Nov '08

05 Nov '08

http://i38.tinypic.com/dwz1xc.jpg wha .. what? -- ================================================================== Kenny Billiau Web Developer Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM kenny.billiau(a)psb.ugent.be http://bioinformatics.psb.ugent.be ==================================================================

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Re: [Binari] coffee break
by Sofie Van Landeghem 05 Nov '08

05 Nov '08

Ok, sounds good. Though not much later than 15.30, I'm going home early to have a little nap probably (feeling sick on your birthday is awesome!) :-) Sofie Esther-Kristin Lather wrote: > Sofie Van Landeghem wrote: >> Around what time do you guys usually take a coffee break? I brought >> some chocolats for my birthday, so I'll send a mail around at that >> time to eat them downstairs maybe... >> >> Sofie >> _______________________________________________ >> Binari Intellectuals Need And Require Insanity >> https://maillist.psb.ugent.be/mailman/listinfo/binari > between 15:00 and 15:30. Today would be a day to make it rather later > (because of the LM).

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[Binari] coffee break
by Sofie Van Landeghem 05 Nov '08

05 Nov '08

Around what time do you guys usually take a coffee break? I brought some chocolats for my birthday, so I'll send a mail around at that time to eat them downstairs maybe... Sofie

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[Binari] my program got scared
by Sofie Van Landeghem 05 Nov '08

05 Nov '08

"Couldn't parse B00"

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[Binari] Tenacious D, new rerelease
by Kenny Billiau 05 Nov '08

05 Nov '08

Just in case you missed the new master works from our all time favorite rock band! http://www.tenaciousd.com/ -Kenny -- ================================================================== Kenny Billiau Web Developer Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM kenny.billiau(a)psb.ugent.be http://bioinformatics.psb.ugent.be ==================================================================

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