Camelia, the Perl 6 bug

IRC log for #bioclipse, 2007-08-06

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All times shown according to UTC.

Time Nick Message
07:12 rprins joined #bioclipse
07:13 olas joined #bioclipse
07:13 jonalv joined #bioclipse
07:14 olas goood mooorning!
07:15 jonalv good morning
07:16 jonalv This matrix plugin. Is it used by some plugin?
07:19 olas by the descriptor plugin I think
07:19 olas ask egonw
07:19 olas probably not heavily used for the moment
07:19 jonalv yep will do
07:19 olas why do you ask?
07:20 jonalv I thought u said that we should redo it somehow and that got me interested
07:20 olas please do
07:21 jonalv please do what exactly?
07:21 olas the descriptor plugin has a wizard which should be generating a matrix
07:21 olas please redo the matrix plugin :-)
07:21 olas did you manage to check out nebula?
07:21 jonalv I think the grid plugin looks more promising than KTable but it is a little early to say for sure
07:22 jonalv yes, finally
07:22 jonalv needed 3.3 to get it to  work...
07:46 egonw joined #bioclipse
07:46 Nout morning egonw
07:47 egonw hi Nout
07:47 egonw hi rprins
07:47 egonw hi others
07:48 Nout is there any molecule in the moleculefactory which has a wedgebond?
07:49 jonalv Hi egonw, Do you know which plugins uses the matrix plugin?
07:50 egonw Nout: no, don't think so, but would be easy to add one..
07:51 egonw jonalv: net.bioclipse.descriptor
07:51 jonalv egonw, oki and no other?
07:51 jonalv (that you know of)
07:52 egonw not that I am aware of
07:52 egonw any particular thing you are looking for?
07:53 jonalv Well olas thinks that I should add functionality to it and I think that maybe we should use the Nebula project grid widget instead of KTable
07:53 egonw rprins, Nout: have you heard anything about thursday yet?
07:53 Nout hm no, not at all
07:53 egonw jonalv: can you compare the two at the mailing list? I'll reply there then...
07:55 jonalv Yes that's a good idea. Didn't think about that. I am still looking into the Grid widget but I have a fairly good idea of how KTable works
08:08 rprins Hi egon
08:15 egonw hi rprins
08:15 * egonw is now away for coffee
08:17 egonw bck
08:31 EskilA joined #bioclipse
08:59 olas hi EskilA
09:08 EskilA hello
09:31 laszlof joined #bioclipse
09:36 laszlof hi olas, EskilA
10:05 Nout egonw, i've been trying to create a molecule with a wedge to test some code, but http://rafb.net/p/BA3gCV63.html doesn't seem to get a very good result, anything obviously wrong?
10:06 lambdabot2 Title: Nopaste - code to create some molecule
10:06 Nout or if you'd have some molecule ready to test it on that would be fine aswell :)
10:09 Nout if you think 'what the heck is this', I was trying to build the molecule on http://courses.chem.psu.edu/chem210/tutor​ials/stereo-drawings/stereo-tutorial.html
10:09 lambdabot2 Title: Organic Chemistry at Penn State: Designation of Stereochemistry, http://tinyurl.com/23y7wp
10:31 Nout nvm, got it already, something is just a little different then I expected :)
10:34 edrin joined #bioclipse
10:34 edrin U
10:34 Nout hi edrin
10:34 edrin hi
10:42 egonw Nout: the code looked OK... at least the had the proper way of indicating the wedgyness
10:44 Nout yeh, distanceCalculator wasn't doing what I expected it to do so I got kinda confused at first hand by that
11:10 laszlof joined #bioclipse
11:15 sara joined #bioclipse
11:22 CIA-32 bioclipse: ospjuth * r3632 /trunk/playground/plugins/net.biocli​pse.biomoby/src/net/bioclipse/biomob​y/wizards/BioMobyInputsWizard.java: Replaced BioMoby dialog with a wizard
11:22 CIA-32 bioclipse: ospjuth * r3633 /trunk/playground/plugins/net.biocli​pse.biomoby/src/net/bioclipse/biomob​y/wizards/PrimaryArticlesPage.java: Added page for primary articles
11:22 CIA-32 bioclipse: ospjuth * r3634 /trunk/playground/plugins/net.bioclip​se.biomoby/src/net/bioclipse/biomoby/​wizards/SecondaryArticlesPage.java: Added page for secondary articles
11:22 CIA-32 bioclipse: ospjuth * r3635 /trunk/playground/plugins/net.biocl​ipse.biomoby/src/net/bioclipse/acti​ons/ExecuteMobyServiceAction.java: Adapted action to use wizard instead of dialog
11:27 CIA-32 bioclipse: ospjuth * r3636 /trunk/playground/plugins/net.bioclipse.b​iomoby/src/net/bioclipse/biomoby/wizards/ (BioMobyResultWizard.java PrimaryArticlesPage.java): Updated to use retrieved name for output
11:27 laszlof joined #bioclipse
11:27 CIA-32 bioclipse: ospjuth * r3637 /trunk/playground/plugins/net.bioclip​se.biomoby/src/net/bioclipse/biomoby/​wizards/SecondaryArticlesPage.java: Updated javadoc
11:31 sara olas, jag skulle kanske behšva mer ramminne. Elipse behšver 1024 och jag har 1,5 i ram nu sŒ det gŒr lite lŒngsamt.
11:32 egonw yes, that's a serious issue...
11:33 egonw the CDK/JCP stuff does not make it better either
11:33 olas sara: please only english here
11:33 olas and no private messages
11:33 egonw I'm running with 1GB now, and having trouble getting many OutOfMemory crashes
11:33 olas is that so?
11:34 egonw yes, but is I think a platform problem too...
11:34 egonw not sure what is oging on... at home I do not have this problem, and also 1GB
11:34 olas strange
11:34 jonalv outofmemory can be because you don't give the jvm permision to use all of the memory. But you don't do that wrong do you?
11:34 egonw but 512 is the very lower limit to get Bioclipse going...
11:34 egonw jonalv: using -Xmxbla
11:35 * olas will be back in half an hour or so
11:35 olas left #bioclipse
11:35 jonalv yes just checking...
11:36 sara left #bioclipse
11:44 CIA-32 bioclipse: ospjuth * r3638 /trunk/playground/plugins/net.bioclipse.biomoby/ (15 files in 4 dirs): Moved model to new package and started on PropertySources
11:44 olas joined #bioclipse
12:19 laszlof left #bioclipse
12:41 edrin welcome back olas
12:54 edrin left #bioclipse
12:55 edrin joined #bioclipse
12:56 edrin test
13:07 edrin olas: i am not sure if it will be possible to run axis 1.2 and 1.3 in parallel
13:08 edrin i guess axis 1 and 2 will run in parallel but not sure about different versions of the same lib at the same time
15:36 edrin hm

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