June 2010 - binari@psb.ugent.be - maillist.psb.ugent.be

[Binari] system.gc() is a bitch!
by Sofie Van Landeghem 11 Jun '10

11 Jun '10

Does anybody ever use it? I thought it'd speed up my program... instead it turned a 5 minute job into a 100 hour one :s Sofie -- Sofie Van Landeghem PhD Student VIB Department of Plant Systems Biology, Ghent University Bioinformatics and Evolutionary Genomics Technologiepark 927, 9052 Gent, BELGIUM Tel: +32 (0)9 331 36 95 fax:+32 (0)9 3313809 Website: http://bioinformatics.psb.ugent.be

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[Binari] [Fwd: density]
by Lieven Sterck 11 Jun '10

11 Jun '10

'total loss' vrees ik ... ;-) -------- Original Message -------- Subject: density Date: Fri, 11 Jun 2010 12:15:49 +0200 From: Stephane Rombauts <strom(a)psb.vib-ugent.be> To: research(a)psb.ugent.be Dear all, I'm looking for away to measure the density of a biopolymer lighter than 0.00001g. I could of course collect enough of this polymer to get a mass > 0.0001g, and submerge it then in water to measure the volume via water displacement... But then I would need a LOT of material. And given it is not necessarily easy to get the pure material in large quantities, any other way would be welcome. One option could be a CsCl column and centrifuge it with the biopolymer as was done some time ago to purify DNA (isopycnic centrifugation <http://en.wikipedia.org/wiki/Isopycnic_centrifugation>). The problem there is that I have no way of labeling the polymer to be able to see where in the column the polymer ends up and as I will need a density ladder, the measurement will remain approximative. Alternatively, if you know a (UGent/VIB) department that has a machine that does it all and is sensitive enough, let me know. best regards Stephane -- ============================================================== 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.vib-ugent.be Website: http://bioinformatics.psb.ugent.be ============================================================== "You tried your best and you failed miserably. The lesson is: never try!" - H. Simpson

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[Binari] doea anyone
by Lieven Sterck 11 Jun '10

11 Jun '10

already use the module system to load software on 'login' (eg perl, ...) 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.vib-ugent.be Website: http://bioinformatics.psb.ugent.be ============================================================== "You tried your best and you failed miserably. The lesson is: never try!" - H. Simpson

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[Binari] first !
by Frederik Delaere 11 Jun '10

11 Jun '10

finish foto van de race naar de ardennen ik zou zeggen: het was spannend, maar dan zou ik liegen ! :p -- ================================================================== Frederik Delaere Tel:+32 (0)9 331 38 14 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM frlae(a)psb.vib-ugent.be http://www.psb.vib-ugent.be ==================================================================

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[Binari] automatic download script
by Sofie Van Landeghem 11 Jun '10

11 Jun '10

Does anybody happen to know how you can easily/best download -say- 600 files (I have the URL for each)? Cheers, Sofie -- Sofie Van Landeghem PhD Student VIB Department of Plant Systems Biology, Ghent University Bioinformatics and Evolutionary Genomics Technologiepark 927, 9052 Gent, BELGIUM Tel: +32 (0)9 331 36 95 fax:+32 (0)9 3313809 Website: http://bioinformatics.psb.ugent.be

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[Binari] tar question
by Michiel Van Bel 10 Jun '10

10 Jun '10

ok, don't want to spend half an hour googling and reading man-pages: I have a directory with 25 subdirectories (each containing from 200MB to 3 GB of data) I want to have each subdirectory archived in a separate archive file. Any idea on how to do this in 1 command? 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.vib-ugent.be http://www.psb.vib-ugent.be http://bioinformatics.psb.ugent.be ==================================================================

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[Binari] DB backup
by Sofie Van Landeghem 10 Jun '10

10 Jun '10

Right, I'm by no means developing a new database today :p Can somebody remind me again about the DB backup policy here? Which brings me to the next idea - maybe the BEG-IT-policy mailinglist needs to accept questions etc. from people not on the list? Then I would send it there. And you guys could advertise the mailinglist to BEG. BSB I mean. Sigh. Cheers, Sofie -- Sofie Van Landeghem PhD Student VIB Department of Plant Systems Biology, Ghent University Bioinformatics and Evolutionary Genomics Technologiepark 927, 9052 Gent, BELGIUM Tel: +32 (0)9 331 36 95 fax:+32 (0)9 3313809 Website: http://bioinformatics.psb.ugent.be

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[Binari] DB's
by Sofie Van Landeghem 10 Jun '10

10 Jun '10

Is het eigenlijk mogelijk om hier een MySQL DB op te zetten die toegankelijk is van buiten? Nee zeker? :-) Sofie -- Sofie Van Landeghem PhD Student VIB Department of Plant Systems Biology, Ghent University Bioinformatics and Evolutionary Genomics Technologiepark 927, 9052 Gent, BELGIUM Tel: +32 (0)9 331 36 95 fax:+32 (0)9 3313809 Website: http://bioinformatics.psb.ugent.be

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[Binari] Googling 'VIB' gets you to weird places
by Thomas Van Parys 08 Jun '10

08 Jun '10

http://www.latenightwithjimmyfallon.com/blogs/2009/04/we-get-stuff-vacation… -- ================================================================== Thomas Van Parys 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 thomas.vanparys(a)psb.vib-ugent.be http://bioinformatics.psb.ugent.be ==================================================================

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[Binari] In de gazet
by Thomas Van Parys 08 Jun '10

08 Jun '10

http://www.demorgen.be/dm/nl/992/Wetenschap/article/detail/1115245/2010/06/… -- ================================================================== Thomas Van Parys 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 thomas.vanparys(a)psb.vib-ugent.be http://bioinformatics.psb.ugent.be ==================================================================

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