Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-09-08

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All times shown according to UTC.

Time Nick Message
03:28 ilogger2_ joined #bioclipse
06:52 ilogger2 joined #bioclipse
07:01 Gpox joined #bioclipse
07:09 olas joined #bioclipse
07:10 olas moin
07:10 zarah hi olas
07:26 malick joined #bioclipse
07:58 jonalv joined #bioclipse
07:58 jonalv hi
07:58 zarah hi jonalv
07:58 olas hi jonalv
07:59 jonalv hi olas, what's up?
08:03 jonalv nothing?
08:03 maclean joined #bioclipse
08:04 shk3 joined #bioclipse
08:06 olas not much
08:06 olas much monday though :-)
08:07 maclean There is a whole lot of Monday today, it's true.
08:08 jonalv very much moday...
08:08 jonalv I sort of overslept. Don't know what happend... :/
08:09 maclean :(
08:12 olas maclean: http://wiki.bioclipse.net/index.php?​title=Run_Workflows_inside_Bioclipse
08:12 olas and http://wiki.bioclipse.net/index.php?title=Projects in general
08:13 maclean :) Thanks.
08:13 olas (regarding your blog post)
08:13 maclean I know.
08:13 olas I never got it to work with taverna in Bioclipse
08:13 maclean I was thinking about the opposite today.
08:13 olas but was close
08:13 olas aha?
08:13 jonalv I didn't know there was a working prototype for Taverna in bc1
08:13 maclean Exporting workflows from Bioclipse to Taverna.
08:14 olas yes
08:14 olas we have considered doing a Bioclispe-node
08:14 jonalv oh, there wasn't? But that scrren dump looked promising...
08:14 olas which could run arbitrary Bioclipse-script
08:14 olas jonalv: it was close
08:14 olas but maven/runtime problems
08:14 maclean Although, for non-trivial workflows, there's a danger of re-implementing taverna's interface in a wizard.
08:15 olas could only execute workflow in awt-headless or something
08:15 maclean Ahhh. Headless. I remember that.
08:15 olas taverna has improved a lot lot since
08:15 olas it might be time to take up this thread again
08:15 * olas has no time however
08:15 maclean It is nice, but I do sneakily prefer the look of Knime.
08:16 jonalv this projects siste needs an update...
08:16 * olas too
08:17 maclean I do see a nice use-case for bioclipse to test out taverna workflows to make sure they are doing the right thing.
08:17 maclean Anywaaay. Back to work.
08:25 thomas_ku joined #bioclipse
09:54 CIA-30 bioclipse: ospjuth * r6906 /bioclipse2/trunk/plugins/net.bioclipse.q​sar.ui/src/net/bioclipse/qsar/ui/editors/ (4 files): Updated QsarEditor to use EMF model as model for selected descriptors.
09:57 olas damn, that broke a lot :-(
09:57 * olas needs to fix things now
10:01 CIA-30 bioclipse: jonalv * r6907 /bioclipse2/trunk/plugins/ (4 files in 3 dirs): Hacked in (it's a bit ugly) support for opening a structuredb annotation in the sdfeditor by doubleclicking it in the services view.
10:14 egonw joined #bioclipse
10:15 maclean hi egon : sorry; stefan just explained it.
10:16 maclean I did try to consider package-level dependencies, I didn't really realise about the module-level ones.
10:23 egonw maclean: no worries
10:23 egonw this kind of things happen to me all the time
10:23 egonw s/si/ese/
10:24 egonw umm... s/is/ese/
10:24 maclean hmmm. maybe I need to make a module-to-package diagram...
10:24 maclean (for me, at least)
10:24 egonw maybe...
10:25 egonw maclean: last week we discussed POM and Eclipse support for CDK...
10:25 egonw and I am writing patches to do this...
10:25 maclean Yup. how's that going?
10:25 egonw which will actually need to involve some sort of registry of CDK module info...
10:25 egonw so, working on a backend for that...
10:25 egonw making progress...
10:25 egonw with all the house moving not too much time...
10:25 maclean registry?
10:26 egonw yeah, in lack of a better term
10:26 egonw not like windows registry...
10:26 egonw but a central API for module info...
10:26 egonw let's move this to #cdk
10:26 maclean Right.
11:55 CIA-30 bioclipse: ospjuth * r6908 /bioclipse2/trunk/plugins/net.bioclipse.qsar/ (6 files in 4 dirs): Removed DescriptorInstance in favor of DescriptorType.
11:55 CIA-30 bioclipse: ospjuth * r6909 /bioclipse2/trunk/plugins/net.bioclipse.qsar.test/ (3 files in 3 dirs): Updated tests to reflect descriptorInstance removal.
11:56 CIA-30 bioclipse: ospjuth * r6910 /bioclipse2/trunk/plugins/net.bioclipse.q​sar.ui/src/net/bioclipse/qsar/ui/editors/ (DescriptorLabelProvider.java DescriptorsPage.java): Removed references to DescriptorInstance.
12:04 jonalv_ joined #bioclipse
12:25 shk3 hi all
12:25 zarah hi shk3
12:26 shk3 jonalv: can you tell me once more where the example code for child resources is to be found?
12:26 shk3 somewhere in sdfeditor?
12:26 malick joined #bioclipse
12:30 Gpox shk3: check the navigatorContent extentionpoint in net.bioclipse.cdk.ui/plugin.xml
12:30 shk3 thanks
12:40 jonalv Is there a way in Bioclipse to concatenate for example mol files and make an sdf file?
12:41 maclean are you concatenating them in memory, or creating a new .sdf file?
12:42 maclean (I don't know the answer either way, I'm just trying to work out what you are doing :)
12:42 jonalv I want to create an example sdf file containing both molecules with 3d coordinates and only 2d coordinates...
12:43 jonalv I just wondered if we have any tools that can do that yet or if it is still in the pipe?
12:43 maclean oh.
12:44 maclean I'm still confused : can't you just cut'n'paste? Or am I getting the wrong end of the stick?
12:44 shk3 don't think we have got it
12:44 shk3 but would be nice
12:45 shk3 like highlight several molecule resources,
12:45 CIA-30 bioclipse: shk3 * r6911 /bioclipse2/trunk/plugins/net.bioclip​se.specmol/src/net/bioclipse/specmol/ (16 files in 7 dirs): code cleanups
12:45 shk3 right click and say "concatenate" or so
12:45 jonalv cut an paste? (remember I am a bioinformatician not a chemoinforamtician, I don't know all these chemical file formats on the back of my hand...)
12:46 maclean Oh, right, right.
12:46 jonalv shk3: yea soimething like that. And drag and drop into open sdf editor....
12:46 shk3 drag and drop in sdf editor would even be better
12:46 * maclean is a bioinformatician too.
12:46 jonalv I know sdf is a concatenation of something but what??
12:46 jonalv I guess it's not cml...
12:47 maclean http://en.wikipedia.org/wiki/Chemical_table_file
12:47 jonalv thank you
12:48 maclean n/p
12:48 jonalv Gpox: remind me top show you strange bug with jmol view listening on new sdf editor
12:49 jonalv brb
13:28 CIA-30 bioclipse: ospjuth * r6912 /bioclipse2/trunk/plugins/ (3 files in 3 dirs): Adapted cdk.qsar and cdk.qsar.test to operate without descriptorInstance.
13:29 CIA-30 bioclipse: ospjuth * r6913 /bioclipse2/trunk/plugins/net.bioclipse​.qsar/src/net/bioclipse/qsar/business/ (IQsarManager.java QsarManager.java): Made some methods public.
13:59 CIA-30 bioclipse: goglepox * r6914 /bioclipse2/trunk/plugins/ (4 files in 3 dirs): Made the outline a little more responsive by adding DeferredTreeContentManager to MoleculesEditorContentProvider
14:32 malick left #bioclipse
14:39 CIA-30 bioclipse: goglepox * r6915 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.ui.sdfeditor/src/net/bioclipse/cdk/u​i/sdfeditor/MoleculesOutlinePage.java: Added icon from net.bioclipse.core
14:48 CIA-30 bioclipse: goglepox * r6916 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.ui.sdfeditor/src/net/bioclipse/cdk/u​i/sdfeditor/MoleculesOutlinePage.java: Changed icon to one from net.bioclipse.ui
15:06 CIA-30 bioclipse: ospjuth * r6917 /bioclipse2/trunk/plugins/net.bioclipse.qsar.ui/ (9 files in 3 dirs): Replaced editor models with EMF model. Don't know why I didn't do this from the beginning.
16:09 CIA-30 bioclipse: ospjuth * r6918 /bioclipse2/trunk/plugins/net.bioclipse.q​sar.ui/src/net/bioclipse/qsar/ui/editors/ (DescriptorsPage.java MoleculesPage.java): Some code cleanup. Undo/redo still not working.
16:16 olas left #bioclipse
20:25 m4r1in joined #bioclipse

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