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

[Binari] Stupid regexp
by Michiel Van Bel 31 Oct '08

31 Oct '08

K, my brain hurts a bit... I have a plain-file(blast-output) that's already been formatted. Of course, when I just read it in php and send it to html, the layout is totally gone (newlines, spaces, tabs, ...). Anyone has an idea how to easily fix it? $data = str_replace("\n","<br/>",$data); //fixes newlines I'd say that replacing every multiple (2+) occurrence of a space should be replaced by the same multiple of ( &nbsp ), but I can't figure it out exactly (brain is still hurting): $data = preg_replace("/(\s)(\s+)", ... ,$data); // -->how do you get the count of \s+ ???, so i can replace it by the same count of &nbsp's ? anyone? -- ================================================================== 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 ==================================================================

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[Binari] Did you know...
by Thomas Van Parys 31 Oct '08

31 Oct '08

The newly released Ubuntu is called 'Intrepid Ibex' ... Seems like each release they have a harder time coming up with an alliterating animal. This is an ibex: http://en.wikipedia.org/wiki/Image:Capra_ibex_ibex_%E2%80%93_03.jpg And 'intrepid' means 'fearless'. So we have a fearless goat with ridiculously large horns. Thought I'd share this with you. T. -- ================================================================== 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.ugent.be http://bioinformatics.psb.ugent.be ==================================================================

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[Binari] triple f
by Kenny Billiau 31 Oct '08

31 Oct '08

Hi, are going for fries today? I don't have a sandwich, so my hunger for fries will be excruciating by noon. We're still going, aren't we? -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] wth
by Michiel Van Bel 30 Oct '08

30 Oct '08

Anyone has any idea why cdparanoia (ripping software for audio-cd's) is installed on midas? Can you actually access you cd-drive from midas? -- ================================================================== 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 ==================================================================

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[Binari] Rules of the lab (pun intented on research@)
by Kenny Billiau 29 Oct '08

29 Oct '08

1. When you don't know what you're doing, do it neatly and sterile. 2. Experiments must be reproduceable, they should fail the same way each time. 3. First draw your curves, then plot your data. 4. If your data are skewed due to inaccuracy, there must be a problem with the equipment. 5. A record of data is essential, it shows you were working. 6. Prefer your colleages equipment above yours, that way you don't break or contaminate your own labstuff. 7. To do an experiment really well, write down your results in advance. 8. If you can't get the answer in the usual manner, start at the answer and derive the question. 9. If that doesn't work, start at both ends and try to find a common middle. 10. If you don't like doing a particular experiment, put your undergraduate student on that! 11. Do not believe in miracles---rely on them. 12. Team work is essential. It allows you to blame someone else. 13. Always put your name on everything, especially when it is not yours. 14. Any delicate and expensive piece of glassware will break before any use can be made of it. (Law of Spontaneous Fission) 15. If you don't succeed, destroy all evidence that you have tried. 16. Never replicate a successful experiment, just copy-paste the previous data. 17. An undergraduate student is the perfect excuse for all failures! 18. Never fall asleep in the lab, unless you are looking through a microscope (no one will notice). 19. Never cough or sneeze on your own sterile lab bench, but use your colleage's bench for that. 20. A couple of months in the laboratory can often save a couple of hours in the library. bron: http://aardbeiwormpje.spaces.live.com/ (aardbeiworpje bij god!) -- ================================================================== 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] biomart download
by Tine Blomme 29 Oct '08

29 Oct '08

Hi, I'm trying to download large fasta files from Ensembl using the biomart tool, but I never succeed in obtaining the entire file. It looks like the query is stopped after a period of time with the message that the download it is complete. However, it is not complete at all! Has this something to do with time out settings? Any suggestions to solve this? Tine

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[Binari] clustering
by Esther-Kristin Lather 27 Oct '08

27 Oct '08

Hi! I have to cluster the whole Arabidopsis proteome (~30.000 proteins), tested under 940 and 85 different conditions. I tried to do the 85*30000 set with Genesis (to find among the Network Programs) and after 20 minutes or so it runs out of memory. Has anyone a script with which I can do the clustering (well, I only know Perl and a bit of R)? Who from our group works on this? Thanks! Esther.

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[Binari] We've got a new winner
by Kenny Billiau 27 Oct '08

27 Oct '08

https://bioinformatics.psb.ugent.be/knowledge/wiki-bioinformatics/Hall_of_s… -- ================================================================== 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] no discussion about fries today?
by Esther-Kristin Lather 24 Oct '08

24 Oct '08

To summarize: solan: small one (& mayonaise) WITH a cheeseburger kebil: small met stoofvleessaus en een sate thpar: small one with mayonnaise sepro: large one with stoofvlees saus and 'n viandel

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[Binari] no discussion about fries today?
by Esther-Kristin Lather 24 Oct '08

24 Oct '08

I don't want any (except your leftovers which will not be much because by now all of you know which size is the best for you ), but I would volunteer for fetching them. Any orders or someone joining me? Esther.

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