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

[Binari] games (fwd)
by Kenny Billiau 19 Aug '08

19 Aug '08

:/ -- ---------- Forwarded message ---------- Date: Tue, 19 Aug 2008 11:34:13 +0200 From: Luc Van Wiemeersch <luc.vanwiemeersch(a)psb.ugent.be> To: Kenny Billiau <kebil(a)psb.ugent.be> Cc: Dany Cuyt <dacuy(a)psb.ugent.be> Subject: games Hi Kenny, Is het wel verstandig om games te organizeren in het lab? Weet Yves hiervan? Het gaat niet om de werkuren, wel om misbruik PSB netwerk met mogelijke security risico's. We vertrouwen op jullie gezond verstand en verantwoordelijkheidsgevoel. Ik zou dit niet doen als ik van jou was, ik ken Dirk Inzé zijn reacties hierop en dit kan gevolgen hebben. By the way, we hebben zelf een game specialist in de groep. Kan je dit niet buiten het lab? thanks voor begrip, Luc -- ================================================================== Luc Van Wiemeersch IT management Tel:+32 (0)9 331 38 12 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM luc.vanwiemeersch(a)psb.ugent.be http://www.psb.ugent.be ==================================================================

1 0

[Binari] Its SQL-time again
by Michiel Van Bel 19 Aug '08

19 Aug '08

Hey people, I've some problems (execution-time related) with some of my queries, involving go-labels. For those not familiar with go-labels: these labels form a directed graph (which can be cyclic), so we have child-parent relationships between the various go-labels. Now, we already have an extra table parents_go (with 2 columns: child_go, parent_go). For each parent_go, all the children (and grandchildren, and great-grandchildren,...) are included as child_go, so we do not have to travel in the graph anymore. In this case, GO:0004402 has 6 children go-labels. This query attempts to find the count of genes (with a certain go-label, in this case GO:0004402), sorted by their evidence tags. Now this is my query: SELECT COUNT(DISTINCT(`gene_go`.`gene_id`)) as 'count',`gene_go`.`evidence` FROM `gene_go` WHERE (`gene_go`.`go`='GO:0004402' OR `gene_go`.`go` IN (SELECT `child_go` FROM `go_parents` WHERE `parent_go`='GO:0004402')) GROUP BY `gene_go`.`evidence` Problem is that it takes a while friggin 27 seconds to perform (which is pretty lame for a website, even with ajax). Okay I thought, lets be smart and first get all the child_go labels from GO:0004402, then loop over them and execute a query each time, counting the genes per evidence tag only for that specific child_go label. This results in a whooping 17 ms execution time... but the results are not the same (apparently some idiots annotated some genes with both the label of a child_go and of a parent_go label). So my questions are: a) Why is the execution time for the first query so goddamn slow compared to the php-loop solution. b) Any idea how to fix the problem? I'd rather not retrieve all the genes and start manually sorting and counting them. Michiel -- ================================================================== Michiel Van Bel PhD student 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 mibel(a)psb.ugent.be http://www.psb.ugent.be ==================================================================

2 2

[Binari] what is the funniest code?
by Kenny Billiau 19 Aug '08

19 Aug '08

http://www.reddit.com/comments/6wx6a/ask_reddit_whats_the_funniest_code_you… SayBro CheckItOut -- ================================================================== 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 ==================================================================

1 0

[Binari] my first real question
by lieven sterck 18 Aug '08

18 Aug '08

does anybody knows whether perl can deal with leading zero in number context? eg. 0012 > 11 , will this work? thx, L. PS. is the binari exclusively dutch?? -- ============================================================== 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 -------------------------------------------------------------- Algal Genetics Group UMR 7139 CNRS-UPMC Végétaux Marins et Biomolécules (Marine Plants and Biomolecules) Station Biologique Place Georges Teissier, BP74 29682 Roscoff Cedex, France Website: http://www.sb-roscoff.fr/UMR7139/en/genetics.html ============================================================== "Facts are meaningless. You could use facts to prove anything that's even remotely true!" H. Simpson

5 5

[Binari] voor windoos gebruikers van ET
by Thomas Abeel 18 Aug '08

18 Aug '08

http://www.psb.ugent.be/~thabe/personal/et.zip Gewoon extracten en het zou moeten werken. 157.193.202.167 is still up and running

3 3

[Binari] extra patch
by Michiel Van Bel 18 Aug '08

18 Aug '08

http://www.wolfenstein.nl/downloads/essential/ Lees ff wat hier op site staat. -- ================================================================== Michiel Van Bel PhD student 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 mibel(a)psb.ugent.be http://www.psb.ugent.be ==================================================================

1 0

[Binari] Lanparty stuff
by Michiel Van Bel 18 Aug '08

18 Aug '08

`mkay, enkel zaken die we nog moeten regelen (daarna zenden we wel een mail naar alle genodigden). * food : brengt iedereen zijn eigen ding mee ? * timetable? Ik zou zeggen iets als dit: * 17u tot 17u30 : installatie van games (tot nu toe zijn enkel wolfenstein ET en quake 3 zeker (al weet ik niet of er hiervan hier een linux-versie van ligt)). * 17u30 tot 18u00: testen van games/servers/... * 18u00 tot ... : w00t! game on! * Ik zou het wel niet *al* te laat maken, de volgende dag moet er weer gewerkt worden :( Ik zou (zeker in het begin) enkele (korte) testrondes spelen. Misschien ook om de "nieuwe" spelers een beetje te helpen leren spelen (geoefend dit weekend Sofie?)... Enfin, we zien wel. Volgens mij zijn dit de genodigden: 1. Sofie 2. Thomas VP 3. Kenny 4. Michiel 5. Thomas A 6. Lieven 7. Stephane 8. Nathalie (van onze groep, niet de secretaresse :) 9. Tine B 10. Jonathan 11. Greg 12. Seppe Informatie over wolfenstein ET vind je (na installatie) in een html-file in de doc-dir van wolfenstein ET. Quake 3 is een heel stuk meer basic (loop, neem wapen, schiet op alles wat beweegt)... Ik heb ook UT liggen, maar de installatie van cd duurt nog wel vrij lang. Linux-support weet ik ook niet. bruikbare pc's: 1. Sofie 2. Kenny 3. Michiel 4. Thomas A 5. Yvan (voor Thomas VP). 6. Lieven 7. Stephane 8. Jeffrey (tenzij hij meedoet zou ik daar dan ook iemand zetten). 9. Nathalie 10. Cindy (voor ?) 11. Seppe 12. Tine 13. ... Anyway, ik zou de mensen toch wat proberen te "clusteren". Nog zaken? Michiel -- ================================================================== Michiel Van Bel PhD student 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 mibel(a)psb.ugent.be http://www.psb.ugent.be ==================================================================

4 5

[Binari] allo
by lieven sterck 14 Aug '08

14 Aug '08

happy to be part of the binari-list! millennium falcon is the best! L. -- ============================================================== 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 -------------------------------------------------------------- Algal Genetics Group UMR 7139 CNRS-UPMC Végétaux Marins et Biomolécules (Marine Plants and Biomolecules) Station Biologique Place Georges Teissier, BP74 29682 Roscoff Cedex, France Website: http://www.sb-roscoff.fr/UMR7139/en/genetics.html ============================================================== "Facts are meaningless. You could use facts to prove anything that's even remotely true!" H. Simpson

6 9

[Binari] Lieven
by Kenny Billiau 14 Aug '08

14 Aug '08

Hi, Lieven aked me yesterday to join in binari. His main reason for this was that he could ask development related questions to the binari people (we are all hax0rz). So my question to you all is: - do we allow this post doc to enter in our exclusive group? - now that we can print colored DIY TUXes again, do we let him make one before he joins if he is allowed to join? -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 ==================================================================

4 4

[Binari] russia - georgia
by Sofie Van Landeghem 14 Aug '08

14 Aug '08

http://answers.yahoo.com/question/index?qid=20080811122917AAmOaHy

1 0