Camelia, the Perl 6 bug

IRC log for #cdk, 2008-04-07

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All times shown according to UTC.

Time Nick Message
05:06 jbrefort joined #cdk
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07:30 tjeerd joined #cdk
07:54 de_maas joined #CDK
08:13 jonalv joined #cdk
08:24 CIA-30 bioclipse: ospjuth * r5363 /bioclipse2/trunk/plugins/net.bioclipse.bioja​va.ui.test/src/net/bioclipse/biojava/ui/test/ (3 files in 2 dirs): Another attempt to create a test to catch bug 1934611.
08:29 masak joined #cdk
08:30 jonalv no egonw here...
08:40 thomas_ku joined #cdk
08:40 thomas_ku moin
08:47 rojasm joined #cdk
08:51 egonw joined #cdk
08:51 egonw moin
08:52 jonalv hi egonw, I am wondering a bit about how fingerptin search could work....
08:54 egonw browse the cdk-user ML
08:54 egonw or ask Stefan Kuhn or jpansanel
08:54 jonalv what ML stand for?
08:54 egonw Mailing List
08:55 jonalv where can I browse that?
08:57 egonw sourceforge.net/projects/cdk
08:57 egonw or google for something like 'cdk mysql fingerprint' or so
09:01 egonw meeting, bbl
09:26 jpansanel hi
09:27 jpansanel the computation of Tanimoto with mychem is pretty fast
09:28 jpansanel less than 0.5 seconds for more than 72,000 entries
09:34 thomas_ku joined #cdk
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11:35 CIA-30 bioclipse: ospjuth * r5364 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.business/src/net/bioclipse/cdk/business/ (CDKManager.java ICDKManager.java): Implemented trivial getSmiles as already on IMolecule. Fixed some warnings.
11:35 CIA-30 bioclipse: ospjuth * r5365 /bioclipse2/trunk/plugins/net.bioclipse.c​dk.business/src/net/bioclipse/cdk/domain/ (CDKMolecule.java ICDKMolecule.java): Implemented CDKMolecule.
11:36 sneumann__ joined #cdk
11:36 egonw hi sneumann__
11:37 sneumann__ Hi, so answer #1 is: report to the frontdesk, since we'll be in the lecture room just next to the main entrance
11:37 sneumann__ You'll take a taxi or tram from the station ?
11:38 egonw which is faster?
11:38 sneumann__ Taxi is faster, should be around 15€
11:38 sneumann__ tram is without changing, and 2*500m to walk
11:38 sneumann__ around 4€ for you both
11:39 egonw which line?
11:39 egonw and direction?
11:39 sneumann__ I'll send directions vai mail
11:39 egonw thanx
11:40 CIA-30 bioclipse: ospjuth * r5366 /bioclipse2/trunk/plugins/net.bioclipse.cdk.​business.test/src/net/bioclipse/cdk/domain/ (. tests/ tests/TestCDKMolecule.java): Tests for CDKMolecule.
11:40 sneumann__ Roeland is going by car or train ?
11:40 egonw car, i think
11:42 CIA-30 bioclipse: ospjuth * r5367 /bioclipse2/trunk/plugins/net.biocl​ipse.biomoby/src/net/bioclipse/biom​oby/business/BiomobyManager.java: Refactored out section for parsing molecule into List of BiojavaSequence.
11:51 egonw sneumann__: still around?
11:52 sneumann__ yup
11:53 egonw tjeerd: waht about you?
11:53 egonw sneumann__: tjeerd is a scientific programmer for the Netherlands Metabolomics Center
11:53 egonw ummm
11:54 egonw he's working for BioAssist, which is developing a metabolomics support platform for the NMC
11:54 egonw and this BioAssist project has shown high interest in MetWare...
11:54 egonw using MetWare in the area of clinical metabolomics studies...
11:54 sneumann__ I like several places cooperating together
11:55 egonw tjeerd: sneumann__ is Steffen Neumann from Halle
11:55 sneumann__ We have just officially entered the www.massbank.jp consortium for tandem-MS spectra
11:55 egonw the support platform will include both data management *and* workflow stuff (Taverna-like)
11:55 sneumann__ sorry to interrupt you
11:55 egonw ah, interesting...
11:55 egonw no worries
11:55 egonw MS^2 that is?
11:56 sneumann__ mostly. They have IonTrap, CE-MS and GC-MS  as well
11:56 egonw within NMC, MS^n work will happen (spectral trees)
11:56 sneumann__ MassBank (MB) is currently adding support for this as well.
11:56 egonw right, you mentioned something like that
11:56 sneumann__ I visited them back in January, and I have seen some mockups
11:57 sneumann__ Their record format is plain text and uhm, how to say it polite ...
11:57 sneumann__ but the most important bit is getting the data and labs together
11:57 egonw could make advantage of some semantics?
11:57 sneumann__ I also proposed to work out some XML format, so far there was no reaction.
11:58 sneumann__ I don't know enough about semantics here, we'll probably have that onb wednesday ;-)
11:58 egonw right
11:58 jpansanel sneumann__ : are you working on Proteomics ?
11:58 egonw Peter MR was at my defense last Wednesday... and we discussed CMLSpect for metabolomics...
11:59 sneumann__ Proteomics: Not really. We have proteomics in-house (Gel, Maldi, LC-IonTrap)
11:59 sneumann__ but people are just setting up protocols. Second problem is manpower
12:00 sneumann__ in my group, so we need some staff for the proteomics side.
12:02 * egonw needs to focus hard for the next 60 mins on a project proposal... bbl
12:06 jpansanel ok
12:16 CIA-30 bioclipse: jonalv * r5368 /bioclipse2/trunk/plugins/ (10 files in 7 dirs): Wrote tests for structuredb internal managers
12:27 CIA-30 bioclipse: jonalv * r5369 /bioclipse2/trunk/plugins/net.bioclipse.core/​src/net/bioclipse/core/domain/IMolecule.java: added throws to has3dcoordinates
12:28 thomas_ku joined #cdk
12:42 CIA-30 bioclipse: ospjuth * r5370 /bioclipse2/trunk/plugins/net.biocl​ipse.biomoby/src/net/bioclipse/biom​oby/business/BiomobyManager.java: Code cleanup.
12:43 CIA-30 bioclipse: ospjuth * r5371 /bioclipse2/trunk/plugins/n​et.bioclipse.biomoby.tests/ (5 files in 3 dirs): Managed to create a failing test for bug 1934611.
12:43 malick joined #cdk
12:43 egonw hi malick
12:43 * egonw wonders if a #metware should be started
12:43 malick hi egon im sitting here with miguel
12:43 rojasm joined #cdk
12:44 tjeer1 joined #cdk
12:45 tjeer1 believe an old session is still active
12:45 egonw tjeer1: did you see my earlier messages?
12:46 tjeer1 nope
12:48 egonw tjeer1: http://irclog.perlgeek.de/cdk/today
12:49 egonw see http://irclog.perlgeek.de/cdk/2008-04-07#i_253769
12:49 egonw and onwards...
12:49 egonw tjeer1: please meet sneumann__, the MetWare group leader in Halle
12:55 sneumann__ Yes, google spot is close enough. You're in the green there ;-)
12:56 CIA-30 bioclipse: ospjuth * r5372 /bioclipse2/trunk/plugins/net.bioclipse.biomoby.​tests/src/net/bioclipse/biomoby/tests/services/ (TestBiolistFromMoby.java TestDBServices.java): Refactored out failing test into its own class.
12:56 egonw sneumann__: ack
12:57 egonw sneumann__: join #metware ?
12:57 tjeer1 hello sneumann
12:58 tjeer1 you are from Halle I saw
12:58 sneumann__ Yup.
13:00 tjeer1 may I ask what is your background?
13:00 tjeer1 or current affiliation
13:01 sneumann__ What exactly ? We're the bioinformatics group at the IPB, supporting the LC-MS metabolomics people
13:01 sneumann__ with signal processing, metabolite identification, databases, statistics ...
13:01 sneumann__ Anything in particular ?
13:02 tjeer1 no, that sounds good :)
13:02 egonw tjeer1: http://www.ipb-halle.de/de/forschung/stress​-und-entwicklungsbiologie/alle-mitarbeiter/
13:03 tjeer1 bookmarked
13:03 sneumann__ web presentation is not all the best ...
13:04 tjeer1 i recognize your face/picture, i've looked you up before (possibly because I heard your name)
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14:58 CIA-30 bioclipse: jonalv * r5373 /bioclipse2/trunk/plugins/net.bioclipse.​biomoby.tests/src/net/bioclipse/biomoby/​tests/services/TestBiolistFromMoby.java: read (and refactored) testParseItoBiolistOSGI. The problem seems to be with the biojava plugin.
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15:13 CIA-30 bioclipse: ospjuth * r5374 /bioclipse2/trunk/plugins/net.bioclipse.services/ (3 files in 2 dirs):
15:13 CIA-30 bioclipse: Added Drop support for ServiceView. Demonstrates the dropping of IBioObjects on
15:13 CIA-30 bioclipse: IServiceObjects. If an IFile is dropped, the ContentProvider of the Bioclipse
15:13 CIA-30 bioclipse: Navigator is used to parse the file into an array of IBioObjects that is
15:13 CIA-30 bioclipse: subsequently handed to the IServiceObject.
15:34 rojasm joined #cdk
15:40 CIA-30 bioclipse: jonalv * r5375 /bioclipse2/trunk/plugins/net.bioclipse.core/src​/net/bioclipse/recording/WrapInProxyAdvice.java:
15:40 CIA-30 bioclipse: Fix to bug #1934611
15:40 CIA-30 bioclipse: I wrongly thought that I could cache a proxyfactory in the wrap in proxy advice. Now it creates a new factory each time instead and that seems to work.
15:46 CIA-30 bioclipse: jonalv * r5376 /bioclipse2/trunk/plugins/net.bioclipse.​core.tests/net.bioclipse.recording/net/b​ioclipse/core/domain/BioListTest.java: removed testBug1934611 since it had absolutely nothing to to with the bug and turned out to test things that are more or less trivially true
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16:45 CIA-30 bioclipse: jonalv * r5377 /bioclipse2/trunk/plugins/ (15 files in 6 dirs): Implemented internal business methods. 0 tests passes for this at the moment because foreign key constraints forces me to get at least a mocked auditservice working before any tests will start to pass.
16:48 CIA-30 bioclipse: jonalv * r5378 /bioclipse2/trunk/plugins/net.bioclipse.core​/src/net/bioclipse/core/domain/BioList.java: Added constructor for Biolist taking a list and using a defensively copied copy as the internal list representation.
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22:49 CIA-30 cdk: rajarshi * r10585 /cdk/trunk/build.xml: Updted to include cdk-dict.jar in the big jar

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