Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-07-08

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All times shown according to UTC.

Time Nick Message
05:04 egonw joined #bioclipse
06:15 edrin joined #bioclipse
06:19 olass joined #bioclipse
06:19 * olass is almost asleep
07:03 mgerlich joined #bioclipse
07:32 olass egonw: is the doc plugin and doc devel up to date in svn?
08:01 edrin joined #bioclipse
08:12 mgerlich joined #bioclipse
08:18 olass @tell egonw Please build net.bc.doc and commit to SVN. Can't run-the-whole-thing here :(
08:18 zarah Consider it noted.
08:18 maclean joined #bioclipse
08:22 olass hi maclean
08:22 maclean hi olass
08:22 olass thx for your email
08:22 maclean np
08:22 maclean was it understandable :)
08:22 maclean ?
08:22 olass yes
08:22 olass I am not into the details
08:23 olass but I think it would be valuable with a ajav impl
08:23 maclean definitely
08:23 olass Lars said he'd be happy to compare stuff with his impl whenever you want or help out if you run into problems
08:23 maclean okay, cool.
08:23 olass he's good at math and numerical analysis
08:23 olass that's his background
08:23 maclean I saw - I wish I was better at maths...
08:24 olass don't we all
08:24 olass :)
08:24 maclean what were you using signatures for in bioclipse?
08:24 olass in decision support
08:24 olass to predict toxicity using a QSAR approach
08:25 maclean right.
08:25 olass with the signature with the highest influence highlighted
08:25 maclean I see.
08:25 olass as the most toxic part of the compound
08:25 olass (well, sort of)
08:25 olass from a model perspective anyway
08:25 maclean hmmmm. I realise that disconnected parts of compounds might not be well described this way
08:26 olass maybe not, I think Lars mentioned this
08:26 maclean which seems possible, since long ligands might have significant groups attached to a scaffold.
08:26 maclean but, then other QSAR approaches would handle those, I suppose.
08:27 * olass is not into this that much and no chemist either
08:27 olass ask Lars if you want opinions
08:27 olass he has used Signatures a lot
08:27 olass and validated against MANY molecules
08:27 maclean :) okay, will do.
08:27 olass just wanted to wish you luck with the impl
08:27 olass let me know if I can help
08:28 maclean thanks.
08:28 olass (though I fear I cannot that much)
08:28 olass but anyways ;)
08:28 olass need to run off and do some shopping
08:28 olass we'll have a Bioclipse release party today
08:28 olass in my flat
08:28 olass today is (hopefully) the day
08:29 olass for 2.0
08:29 olass afk
09:10 mgerlich joined #bioclipse
09:25 egonw joined #bioclipse
09:27 egonw moin
09:27 zarah hello egonw, you fantastic person you
09:27 zarah egonw: You have new messages. Write '/msg zarah @messages' to read them.
09:27 egonw hi maclean
09:27 egonw @msg
09:27 zarah egonw: 1 h 8 m 38 s ago, olass said Please build net.bc.doc and commit to SVN. Can't run-the-whole-thing here :(
09:27 maclean hi egonw
09:27 egonw olass: will test masak's fixes
09:37 maclean egonw : is there a way to determine bond orders with the cdk for molecules that have no bond-order information?
09:37 egonw yes
09:37 maclean oh?
09:37 egonw deducebondordersomthing
09:37 maclean ahhh.
09:38 maclean takk, I'll take a loot.
09:38 maclean s/loot/look/
09:40 maclean it's just that the PDB format does not give bond orders for ligands, it seems.
09:43 egonw olass: ping
09:43 egonw olass: masak did not implement yet which managers are in the release
10:07 sneumann joined #bioclipse
10:17 egonw maclean: ping
10:18 egonw maclean: linguistic question...
10:18 egonw when to use that and when which
10:18 egonw which is for phrases, right?
10:26 masak joined #bioclipse
10:29 edrin egonw: can you come to xws ?
10:49 sneumann joined #bioclipse
10:51 shk3 joined #bioclipse
10:54 olass egonw: ping
10:54 olass I'm back
10:55 * olass has been shopping
10:59 olass egonw: ping
11:05 masak egonw: plugins/net.bioclipse.ui.busine​ss/META-INF/spring/context.xml, line 42
11:05 masak says 'value="net.bioclipse.ui.business.IUIManager"  />'
11:06 egonw what is wrong with that
11:06 egonw ?
11:06 masak hm, maybe nothing.
11:06 egonw oh... ic
11:06 masak you do? oh, good. :)
11:06 egonw ah, come down again
11:06 egonw call is over
11:06 masak :P
11:06 egonw :)
11:08 egonw olass: ping
11:08 egonw olass: what functionality is using the UIManager?
11:08 egonw from Java?
11:08 olass much
11:08 olass why do you ask?
11:08 olass well, not overly much
11:08 olass but at least some
11:08 masak olass: turns out the plumbing for the uimanager is wrong.
11:08 olass aha
11:09 masak olass: we discovered this when the docs generator had problems with it.
11:09 olass and the plumbing means?
11:09 egonw so, I need a test case to verify that calling the UIManager from JavaCode via the proxy is working
11:09 masak XML, inheritance...
11:09 olass do a "references" on the methods and see...
11:09 egonw no, can't
11:09 olass ok
11:10 egonw because eclipse does not know about the proxy
11:10 olass aah
11:10 egonw so, proxied calls don't show up
11:10 olass true
11:10 olass can you do a "references" on th IUIManager?
11:10 egonw yes, perhaps
11:10 egonw let's try that
11:11 egonw OK, found one
11:11 egonw NewMOleculeWizard
11:12 egonw OK, that still works
11:13 shk3 hi all
11:13 zarah hi shk3
11:13 masak hi shk3
11:13 shk3 anything I can do for the wiki/website overhaul?
11:14 egonw where does Balloon put the conformers?
11:14 egonw ah, found it...
11:14 egonw OK, no exceptions, things seem to work
11:15 egonw now, let's check that it also fixes the managers docs
11:15 egonw then  bob's our friend
11:15 * egonw is very hungry
11:15 egonw excellent
11:18 egonw OK, here comes
11:18 CIA-54 bioclipse: egonw * r11643 /bioclipse2/trunk/plugins/net.bioclipse.doc/ (5 files in 2 dirs): Fixes generation of manager documentation: only list docs for released managers in the platform_feature.
11:18 mgerlich joined #bioclipse
11:19 CIA-54 bioclipse: egonw * r11644 /bioclipse2/trunk/plugins/​net.bioclipse.ui.business/ (2 files in 2 dirs): Finished interfaces set up of NWO: added missing Java interface
11:34 shk3 does anybody know where to find the news in the new sf layout?
11:35 shk3 i want to add one, but can't even find the existing ones on the project page
11:36 shk3 (not for bioclipse, btw)
11:47 maclean egonw : "when to use that and when which" ?? :)
11:47 maclean Unfortunately that is one of the rules of my language that I do not know.
11:48 olass I talked to an english teacher about that recently
11:48 olass (she is brittish btw)
11:48 olass In formal: always 'which'
11:49 olass if you are unsure, use 'which'
11:49 olass I liked that rule :)
11:49 maclean http://www.grammarbook.com/grammar/whoVwhVt.asp
11:49 zarah maclean's link is also http://tinyurl.com/26vnd8
11:49 maclean it seems like a reasonable rule, yes.
11:50 egonw edrin: there's your answer
11:50 olass well, after a comma that is
11:51 maclean English is like perl. Only parsable by itself.
11:53 * maclean has just realised that he's left his power cord at home :( 11% battery will not last long...
11:53 olass maclean: steal someone else's
11:54 olass that's what I do
11:54 maclean tempting.
11:54 olass if they are nice, yu might even return it
11:55 olass "Let's go get a coffee"... "Oh, I just forgot something..." and sneak back to steal it
11:55 olass just a tip
11:56 egonw ah, that's why everyone here cannot find the power cords all the time...
11:57 olass egonw: you should be lucky you don't have a Mac!
11:58 olass well, you should be sorry you don't have one too
11:58 olass Mac++
11:58 olass ok, I will now build 2.0
11:58 olass release
11:58 olass sharp
11:59 maclean right, I should go offline to conserve power. ttfn.
11:59 olass this export will take a while...
12:01 egonw 2.0.0++
12:07 masak "The early bird gets the worm but the second mouse gets the cheese."
12:10 olass masak: what does the third dog get?
12:10 masak olass: cat food.
12:11 olass poor dog
12:11 masak aye. :/
12:11 olass not cat for food?
12:12 masak not unless it's raining cats and dogs.
12:12 olass then you can blame it on the rain
12:12 olass (or the boggie, if you like)
12:12 olass hmm
12:13 * olass had forgotten to remove logging to stdout
12:13 olass rebuild :(
12:16 CIA-54 bioclipse: ospjuth * r11645 /bioclipse2/trunk/plugins/net.biocli​pse.data/src/net/bioclipse/data/samp​les/ExtendedSampleDataAction.java: Updated hardcoded extended sample data. Solves 677.
12:19 CIA-54 bioclipse: ospjuth * r11646 /bioclipse2/trunk/plugins/net.bi​oclipse.logger/log4j.properties: Set bioclipse logger to WARN and send output to file only. Solves 363.
12:21 egonw OK, leaving
12:21 egonw masak: cu at Uppsala C in 40 minutes
12:21 egonw olass: see you at 16-ish
12:21 masak egonw: nod.
12:21 olass yes
12:21 masak egonw: do you know the way to olass' apartment?
12:21 olass you are welcome
12:22 egonw masak: yes
12:22 masak goodie.
12:30 CIA-54 bioclipse: ospjuth * r11647 /bioclipse2/trunk/features/ (3 files in 3 dirs): Set size of data features. Solves 951.
13:23 CIA-54 bioclipse: shk3 * r11648 /bioclipse2/trunk/plugins/net.biocli​pse.bibtex/src/net/bioclipse/bibtex/ (Activator.java business/IBibtexManager.java): fixes bug with nwo implementation
13:27 CIA-54 bioclipse: shk3 * r11649 /bioclipse2/trunk/plugins/n​et.bioclipse.bibtex.test/: Initial import.
13:28 CIA-54 bioclipse: shk3 * r11650 /bioclipse2/trunk/plugins/​net.bioclipse.bibtex.test/ (20 files in 8 dirs): Initial import.
14:53 egonw joined #bioclipse
14:55 egonw moin
14:55 zarah hi egonw
14:55 egonw live from the Bioclipse 2.0.0 release party in Stockholm
15:06 shk3 so the release has been done?
15:06 shk3 or are you doing it on the party?
15:08 egonw the release is at Ola's laptop right now
15:08 egonw likely to hit SF tomorrow
15:12 shk3 ok
15:12 shk3 so I prepare the speclipse stuff for going to the update site tomorrow
15:12 shk3 how is webpage/wiki rewrite going?
15:12 shk3 I think it's important to have that ready with announcments etc.
15:18 shk3 anyway, enjoy the party
15:32 CIA-54 bioclipse: shk3 * r11651 /bioclipse2/trunk/plugins/net.bioclipse.spect​rum.test/src/net/bioclipse/spectrum/business/​test/AbstractSpectrumManagerPluginTest.java: added a test
15:33 CIA-54 bioclipse: shk3 * r11652 /bioclipse2/trunk/plugins/net.bioclipse.sp​ectrum.test/src/testFiles/mzdiv-762_c.jdx: and the file for it
15:57 CIA-54 bioclipse: egonw * r11653 /bioclipse2/tags/2.0.0/: Tagged Bioclipse 2.0.0
21:08 sneumann joined #bioclipse

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