Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-06-12

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All times shown according to UTC.

Time Nick Message
05:29 rojasm joined #bioclipse
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07:09 olas morning
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07:48 CIA-47 bioclipse: ospjuth * r5839 /bioclipse2/trunk/plugins/net.bioclipse.pcore/doc/ (. editor_persist.xml): Added sample for editor model persistence.
07:50 CIA-47 bioclipse: ospjuth * r5840 /bioclipse2/trunk/plugins/net.bioclipse​.pcore/src/net/bioclipse/pcore/editors/ (8 files): Added functionality to import molecule files and diplay in treeviewer.
07:50 CIA-47 bioclipse: ospjuth * r5841 /bioclipse2/trunk/plugins/​net.bioclipse.pcore/icons/ (db_16.gif molecule2D.gif molecule3D.gif): Added som icons.
08:10 edrin joined #bioclipse
08:10 edrin thank you stain, rojasm already could help me
08:16 CIA-47 bioclipse: carl_masak * r5842 /bioclipse2/trunk/plugins/net.bioclipse.ui/​src/net/bioclipse/ui/editors/Aligner.java:
08:16 CIA-47 bioclipse: [Aligner] implemented selection capabilities
08:16 CIA-47 bioclipse: some experimenting lead me to believe that one
08:16 CIA-47 bioclipse: has to use MouseListener combined with MouseMoveListener
08:16 CIA-47 bioclipse: to do this. if anyone knows a better way, do tell.
08:16 CIA-47 bioclipse: ospjuth * r5843 /bioclipse2/trunk/plugins/net.bioclipse​.pcore/src/net/bioclipse/pcore/editors/ (MoleculesContentProvider.java PcorePage.java): Implemented removal of moleculeFiles
08:21 CIA-47 bioclipse: ospjuth * r5844 /bioclipse2/trunk/plugins/net.bioclipse.ui/sr​c/net/bioclipse/ui/dialogs/WSFileDialog.java: DoubleClick in WSFileDIalog selects and closes dialog.
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14:13 CIA-47 bioclipse: jonalv * r5845 /bioclipse2/trunk/plugins/​net.bioclipse.structuredb/ (.classpath build.properties): Removed tests and MetaInf from source in net.bioclipse.structuredb
14:53 rojasm joined #bioclipse
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17:04 egonw hi berry_nl
17:04 berry_nl egonw: hiya
17:04 egonw what brings you to #bioclipse ?
17:10 jonalv egonw: you found a connection somewhere? :)
17:10 egonw yes
17:10 egonw in the hotel
17:10 jonalv aha
17:10 egonw only 50 SEK pro day
17:10 jonalv I haven't even left here yet :)
17:14 jonalv right, Windows doesn't come with a jvm :)
17:28 berry_nl egonw: I am studying bioinformatics at the moment so i started to look for irc channels related to the subject and see who i could find with the same interests
17:29 egonw ah, ic
17:29 egonw berry_nl: what university, or hbo?
17:30 berry_nl egonw: HS Leiden (HBO, Bachelor)
17:30 egonw ah, ok
17:31 egonw well, if you ever feel like learning to program java...
17:32 berry_nl Actually already working on that ;)
17:32 egonw you are in the building behind the railway station, passed the hospital?
17:32 berry_nl egonw: jep, you are well informed. Where to you study yourself?
17:32 egonw well, passed studies for a while now
17:32 egonw am post-doc in Wageningen
17:33 egonw and had a cooperation with leidenuniv the past year
17:33 egonw passed your building just this monday :)
17:33 berry_nl Ah okay, sounds good. Probably know Jack Leunissen then?
17:33 egonw yes
17:33 egonw but I am not in his group
17:34 berry_nl Working parttime as a assistant researcher / bioinformatician at the Erasmus. The crosslinks group. Know them?
17:35 berry_nl egonw: since we are having this talk now anyway. I am kind of stuck with something all day. I have this huge csv file and i need to replace all values smaller < 20 and bigger > 16000. Know any fast / small UNIX trick to help me out?
17:36 egonw no, does not ring a bell... me got a chemoinformatics background, more than bioinformatics
17:36 egonw yes, R
17:36 egonw how large is the file?
17:37 egonw R is not so much a UNIX shell script, but rather efficient for this...
17:37 * jonalv gtg, cya
17:37 egonw though you may need to cut things up in batches
17:37 egonw jonalv: cu later
17:37 egonw depending on the file sizes you are dealing with
17:41 berry_nl egonw: Hmm i was afraid i'd need to jump to R. At the moment (the last 20 hours) I have been going about with Python. But the file is just to big for that.
17:45 egonw you should do things line by line
17:46 egonw throw away each line, after you modified it, and outputed it to STDOUT
17:46 egonw that is, iterate over the input lines, instead of reading everything first
17:46 egonw R will not work in this case, either then
17:46 egonw because it will also read everything...
17:47 egonw well... actually...
17:47 egonw btw, learning R as bioinformatician in a very wise thing you can do
17:47 egonw more useful than learning python
17:59 berry_nl egonw: Well we already had a course in R (in great length even) its just that i spend the last few hours doing something that worked with a small dataset and now fails at the big one. I know what i need to do know. Its just very hard to find the motivation at the moment ;)
18:03 * egonw has to leave for dinner
18:03 egonw berry_nl: good luck with the debugging...
18:28 berry_nl Got nobody else to share my joy with,,, so here goes......
18:28 berry_nl I DID IT!!!!
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