Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-07-23

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All times shown according to UTC.

Time Nick Message
05:16 sneumann_ joined #bioclipse
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07:24 egonw joined #bioclipse
07:29 jonalv joined #bioclipse
07:33 olass joined #bioclipse
07:37 olass moin
07:37 zarah saluton olass
07:37 olass zzzZZZZ
07:38 edrin joined #bioclipse
07:39 egonw moin
07:39 zarah hi egonw
07:39 edrin hi egon
07:41 jonalv hi egonw
07:42 egonw hi edrin, jonalv
07:43 wins joined #bioclipse
07:43 egonw hi wins
07:46 egonw wow...
07:46 egonw it's just an application note
07:46 egonw nothing really more...
07:46 egonw so, those can go into bmc bioinformatics too...
07:47 jonalv egonw: what are you talking about?
07:47 egonw http://www.biomedcentral.co​m/1471-2105/10/229/abstract
07:47 zarah egonw's link is also http://tinyurl.com/ksmse9
07:47 egonw it's about the size of a '
07:47 egonw it's about the size of a 'Bioinformatics App note'
08:28 olass egonw: what are you talking about?
08:29 egonw that publishing a short application note is possible in BMC Bioinformatics too
08:29 olass yes, seems so
08:30 olass strange, since it is not termed app note
08:30 olass but that paper surely is not a full research paper
08:30 olass good to know
08:30 olass for the future
08:37 egonw btw, anyone following the tour de france?
08:38 egonw amazed that so many of the main characters twitter, like Lance: http://twitter.com/lancearmstrong
08:38 zarah egonw's link is also http://tinyurl.com/6o7b2l
08:38 egonw this is so much changing journalism
08:48 olass brb
08:55 olass joined #bioclipse
09:01 masak joined #bioclipse
09:28 CIA-65 bioclipse.qsar: Ola Spjuth master * re02f695 / (7 files in 5 dirs): Removed all code and references to BIRT in QSAR feature and plugins. - http://bit.ly/X9B2C
09:42 CIA-65 bioclipse.qsar: Ola Spjuth master * r2eed42e / plugins/net.bioclipse.qsar.ui/src/net/bioclipse/qs​ar/ui/wizards/MoleculePropertyContentProvider.java : Updated for changed API in ICDKManager; now catch all Exceptions. - http://bit.ly/d5GX2
10:01 jonalv do anyone know about some manager not in the latest world order?
10:08 olass jonalv: yes
10:08 olass DSManager for example
10:08 jonalv olass: okey can you name them?
10:08 jonalv hm okey intesting
10:09 olass wait, maybe not...
10:09 olass no, it is migrated
10:09 olass hmm
10:09 * jonalv is tracking down a bug in CreateJobAdvice which is used in old world order managers.
10:09 olass thw qsar manager?
10:09 jonalv I was sort of hoping only StructureDB was still using that one... :)
10:09 olass pretty sure QSARManager is old world order
10:10 olass chck
10:10 jonalv I might have to change it's behavior in order to fix my trouble. I mean I am going to get it working as it was meant to but that means that it probably will work differently...
10:11 olass as long as it works
10:11 olass you can't leave it not-working for your holiday
10:12 jonalv that's why I am asking for use cases to try...
10:16 masak people! if you ever want to submit a patch to anything I have ownership of, you MUST adhere to the following conventions:
10:16 masak (1) no tabs
10:17 masak (2) no commented-out code without an adjoining explanation for commenting out the code
10:17 masak thank you.
10:18 jonalv masak: who would do somthing like that? :)
10:19 * masak doesn't name names -- no need
10:25 masak oh, and (3) be wary of introducing warnings into files. I tent to want to keep my code warning-free.
10:39 maclean joined #bioclipse
10:39 olass hi maclean
10:39 maclean 'lo
10:39 maclean how's the thesis writing :)
10:40 olass a lot to do...
10:40 olass actually a lot to program too
10:40 olass which is troublesome
10:40 maclean :(
10:40 olass but mor fun than writing at least
10:40 maclean that's the danger!
10:41 maclean don't get sucked into the writing code trap.
10:42 egonw I think ola is doing fine...
10:42 egonw have one paper on my desk as we speak
10:43 * olass is getting there
10:43 olass but slowly
10:44 olass maclean: how are the Signatures working out? Did you extend the test cases?
10:45 maclean Well, I'm pretty confident that it reproduces the c-code now
10:45 olass ok
10:45 olass Lars said he needed to change things to get it working... :)
10:45 maclean but, yes, I do have to test it with a more comprehensive test set. I'm documenting the methods
10:45 olass he'll be a good tester
10:46 olass ok, brb
11:07 olass joined #bioclipse
11:25 egonw lunch time
11:25 egonw maclean: ping
11:25 maclean I don't have your lunch :)
11:25 egonw maclean: let me know if you would appreciate feedback on further CDK integration
11:25 egonw to make it  first class CDK patch
11:25 egonw now going for lunch
11:26 egonw bbl
11:26 maclean ok.
11:33 CIA-65 bioclipse.core: jonalv master * rbf91caf / plugins/net.bioclipse.ui/src/net/bio​clipse/ui/jobs/CreateJobAdvice.java :
11:33 CIA-65 bioclipse.core: Fixed CreateJobAdvice.
11:33 CIA-65 bioclipse.core: It did not handle the plain old situation IFile, String -> IFile, String,
11:34 CIA-65 bioclipse.core: IProgressMonitor correctly. It however seemed to handle BioclipseUIJobs and
11:34 CIA-65 bioclipse.core: stuff. Probably introduced that problem when adding that. - http://bit.ly/cyWZl
12:27 egonw olass: ping
12:27 egonw org.eclipse.datatools.enablement.oda.feature
12:27 olass pong
12:27 egonw and
12:27 egonw org.eclipse.datatools.connectivity.oda.feature
12:28 olass yes?
12:28 egonw those are BIRT thingies too, not?
12:28 olass yes
12:28 egonw but still in the qsar feature
12:28 olass oh
12:28 egonw and still fail here
12:28 olass ok, will remove
12:28 olass sry
12:28 egonw thanx
12:28 egonw no worries
12:31 CIA-65 bioclipse.qsar: Ola Spjuth master * rf9c971e / features/net.bioclipse.qsar_feature/feature.xml : Removed more BIRT deps from QSAR feature. - http://bit.ly/9zQaR
12:31 olass egonw: there
12:31 olass please try now
12:32 egonw yes, that helps
12:57 masak egonw: by the way, how's the Groovy scripting console coming along? need any help?
13:06 egonw masak: had no time yet... :(
13:06 egonw but it is pretty high up my wish list
13:06 masak oki. just checking.
13:06 egonw so, if you have some spare time, and eager to do it, and want to earn a example:bear
13:07 egonw hahaha
13:07 egonw umm...
13:07 egonw example:beer
15:21 miguelrojasch joined #bioclipse
16:05 jonalv CIA-65: waky paky!!
16:05 jonalv :(
16:05 CIA-65 bioclipse.structuredb: jonalv master * r8fe4660 / plugins/net.bioclipse.structuredb/src​/net/bioclipse/structuredb/Label.java : added toString method used by Databases view - http://bit.ly/HA74q
16:05 CIA-65 bioclipse.structuredb: jonalv master * r8172fa8 / (7 files in 4 dirs): decorator for Structuredb instances showing number of molcules in the database. - http://bit.ly/JJHJe
16:05 CIA-65 bioclipse.structuredb: jonalv master * rd0b4d69 / (5 files in 3 dirs): decorator for Structuredb instances showing number of molcules in Labels. - http://bit.ly/9Me3w
16:06 jonalv ah finally :)
16:06 egonw jonalv++
16:07 jonalv egonw: feel free to have a look at Structuredb when you want a break. Especially the datases view
16:07 egonw yes, will want to do that...
16:07 egonw but got several other things on my mind right now...
16:08 jonalv egonw: yea,, I am going to be afk now for about a weak
16:09 egonw ok
16:11 * jonalv tests to import the 1 GB sdf file into StructureDB :)
16:11 edrin left #bioclipse
16:11 egonw jonalv: got YourKit enabled?
16:11 jonalv egonw: no
16:11 jonalv I first want to see if it works at all
16:11 jonalv and how long it takes
16:11 jonalv and how it feels :)
16:12 egonw :)
16:12 jonalv but this is going to take a while...
16:13 jonalv about 2000/200000 done...
16:17 olass jonalv: you CAN extrapolate, you know
16:18 jonalv olass: do an educated guess on time estimations during run time?
16:18 jonalv olass: yes that is probably a good idea...
16:18 olass what is your guess?
16:18 jonalv olass: http://xkcd.com/612/
16:19 jonalv olass: six days?
16:19 olass lol
16:19 jonalv :)
16:28 * jonalv aborted the import
16:28 jonalv okey it takes forever to import 1GB
16:28 jonalv it seems to work
16:28 jonalv and aborting the process is instantanious
16:29 jonalv I got 22316 molecules...
16:29 egonw what about calculating FPs etc in the background?
16:29 egonw i.e. *after* the molecules is imported
16:29 jonalv egonw: I don't know
16:30 jonalv egonw: you can't really do very much without fingerprints...
16:30 jonalv if you just want to browse you can open the sdf editor I guess?
16:36 jonalv egonw: I am testing substructuresearch for a simple molecule with a ring on those molecules I managed to import. Taht also take a _LONG_ time :)
16:36 * jonalv wonder how fast this can be...
16:40 olass I think we need a feasability study for database sizes
16:40 olass people do large screenings on clusters
16:40 olass that is not our objective
16:41 olass so we need numbers for what Bioclipse and StructureDB can handle
16:41 olass in reasonable time
16:41 olass this calls for some investigations and optimizations...
16:41 olass but an interesting and important study!
16:42 olass we should also ask people for use cases; what they _want_ to do
16:43 olass maybe we should hook up a CUDA for screening large databases? Now that would be something...
16:43 olass "improved screening of large chemical libraries with CUDA"
16:43 egonw yeah, for example, processing that 970M structure data set
16:43 olass not a bad title :)
16:43 olass why not?
16:43 olass as long as it is not your desktop computer
16:44 olass more than overnight is never acceptable
16:44 olass so, how far to we get in 8-10 hours?
16:46 jonalv yea
16:46 jonalv I am soon at 50% of the substructure search now
16:55 egonw so, HSQLDB is slow?
16:56 jonalv egonw: it might be taht CDK is slow... :)
16:56 egonw :)
16:56 olass will be nice to see what MySql is capable of...
16:56 jonalv olass: one step at a time
16:56 olass jonalv: you should profile!
16:56 olass see what is the bottleneck
16:57 jonalv olass: yes I will run yourkit when I get back
16:57 * egonw is going offline for dinner now...
16:57 egonw tomorrow I'll be offline...
16:57 jonalv I am going home to get some food soon. I just have to see the results from this substructureSearch
16:57 olass jonalv: and you are gone next week?
16:57 jonalv olass: yes
16:57 olass right
16:58 jonalv olass: WE still can't browse molecules  from StructureDB you know
16:58 jonalv but things are comming along nicely with the Databases view I thnk
16:58 olass jonalv++
17:01 jonalv lol
17:01 jonalv what a anti climax
17:01 olass why?
17:01 jonalv http://pastebin.com/m7d190188
17:02 jonalv ...I really msut do something about DBMolecule.toString()
17:02 olass lol
17:05 egonw hahahah
17:05 egonw ok, gone now
17:05 olass bye egonw
17:06 jonalv I am off as well
17:06 jonalv cya
17:06 olass trevlig semester
17:06 olass as they say in sweden
17:06 * olass will get food too
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18:21 wins joined #bioclipse
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