Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-04-29

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Time Nick Message
06:34 rojasm joined #bioclipse
07:11 malick joined #bioclipse
07:40 jonalv joined #bioclipse
08:43 thomas_ku joined #bioclipse
08:53 masak joined #bioclipse
08:53 masak what's the difference between cdk and cdk10?
08:54 CIA-44 bioclipse: carl_masak * r5530 /bioclipse2/trunk/plugins/net.biocli​pse.cdk10.jchempaint/src/net/bioclip​se/cdk10/jchempaint/Activator.java:
08:54 CIA-44 bioclipse: [Activator.java]
08:54 CIA-44 bioclipse: * typo
09:01 egonw joined #bioclipse
09:07 CIA-44 bioclipse: jonalv * r5531 /bioclipse2/trunk/plugins/ (3 files in 3 dirs):
09:07 CIA-44 bioclipse: Fixed the last DAO test. All DAO tests and all internal manager tests now
09:07 CIA-44 bioclipse: passes. Problem left is with running multiple local database instances which
09:07 CIA-44 bioclipse: might not be worth it. Also no SDF file parsing done yet. And will also need
09:07 CIA-44 bioclipse: some sort of lazy loading of huge amounts of structures from the database
09:09 egonw "Also no SDF file parsing done yet."?
09:09 egonw jonalv: anything I can do?
09:09 egonw btw, the editor is now looking like an editor...
09:09 jonalv hm for structuredb?
09:10 egonw except that the data model is not updated...
09:10 egonw about SDF parsing
09:10 masak egonw: what's the difference between cdk and cdk10?
09:10 jonalv not unless you are good with hsqldb :)
09:10 egonw masak: version
09:10 egonw cdk10 is CDK 1.0.x
09:10 egonw cdk is trunk/
09:10 masak ah
09:10 egonw the latter is generally better, but does not have a ported JCP yet
09:10 jonalv I think you did the troublesome part of SDF parsing. I just need to use it somehow :)
09:10 egonw jonalv: ack
09:11 jonalv brb
09:17 EskilA joined #bioclipse
09:26 egonw masak: what was channel for the logger again?
09:27 masak egonw: #irclogger
11:12 CIA-44 bioclipse: ospjuth * r5532 /bioclipse2/trunk/plugins/net.bioclipse.ui/src/​net/bioclipse/ui/views/ActionHistoryView.java: Remove listener on dispose.
11:12 olas joined #bioclipse
11:13 olas hi all
11:14 olas left #bioclipse
12:00 olas joined #bioclipse
12:23 CIA-44 bioclipse: ospjuth * r5533 /bioclipse2/trunk/plugins/net.bioclipse.ser​vices/src/net/bioclipse/services/business/ (3 files): Services are run with generic Object as input, not List<Object>. Resource extraction pushed to manager instead of in DropAdapter.
12:23 CIA-44 bioclipse: ospjuth * r5534 /bioclipse2/trunk/plugins/net.bioclip​se.services/src/net/bioclipse/service​s/views/ServiceViewDropAdapter.java: Updated the dropAdapter accordingly.
12:31 masak joined #bioclipse
13:46 egonw hi all
13:47 egonw who is using subclipse and who subversion?
13:47 egonw subversive, I meant
13:47 masak subclipse
13:47 masak I don't think I ever used subversive
13:48 egonw I used to use subclipse too...
13:48 egonw but we installed subversive earlier...
13:48 egonw looked really nice...
13:48 masak this all sounds like a commercial :)
13:48 egonw allowed detection of trunk/branches/tags...
13:48 egonw yeah, sorry about that :)
13:48 masak np
13:51 * jonalv is using commandline subversion and subclipse
13:51 masak I'll have a look at subversive
14:22 CIA-44 bioclipse: ospjuth * r5535 /bioclipse2/trunk/plugins/net.bioclipse.ser​vices/src/net/bioclipse/services/business/ (ServiceManager.java ServiceManagerHelper.java): Fixed unwrapping lists and selections + parsing of Files in drag and drop depending on accepted inputs in service.
14:24 de_maas joined #bioclipse
14:27 egonw olas: around?
14:28 olas yes
14:28 egonw I got somewhat further last nite...
14:29 egonw mouse events are now passed to JCP
14:29 egonw and there are JCP icons in the global toolbar
14:29 egonw it even sees the model is dirty, when I do an edit action...
14:29 egonw but that's about it...
14:29 egonw need some clean up, but reasonable progress...
14:29 olas great
14:30 olas good job
14:30 egonw tried to figure out where it failed to update the data model, but without success so far...
14:30 olas right
14:30 olas file a bug?
14:30 egonw yeah, possible...
14:30 egonw I'll try to find some time to summarize on the ML
14:37 jonalv Eclipse crached again :(
14:37 egonw use Java 1.5
14:37 jonalv is that the trick?
14:37 egonw for me it was
14:37 egonw nasty interaction bug with some lib for java 1.6 upwards...
14:38 egonw but that was on linux
14:38 jonalv hm maybe I should download that then
14:38 jonalv I am on linux
14:38 jonalv ubuntu
14:38 egonw right
14:38 jonalv I get Permspace exceptions all the time
14:39 egonw sudo aptitude install sun-java5-jdk or so
14:39 jonalv that works?
14:39 jonalv apt has sun stuff?
14:40 egonw yes
14:40 jonalv seems so. where does it put it then?
14:40 EskilA joined #bioclipse
14:40 egonw /usr/lib/jvm
14:41 jonalv thanks!
14:41 egonw de_maas: thanx for you comment
14:41 egonw +r
14:41 egonw if you don't edit SDF files, BC2 already works fine with Ola's code
14:41 de_maas Gee your fast
14:42 egonw I get an email warning :)
14:42 de_maas Well the editing is not the most important part but also very usefull to get rit of error entries.
14:42 egonw yes indeed
14:43 egonw this is being worked on... that is, porting the JCP editor...
14:43 egonw compared to my blog item, I made some progress....
14:43 olas we'll need to sort that out, such as removing entries from an SDFile
14:43 olas that is the SDFileEditors concern
14:43 olas also making JCP accept a part of an SDFile is a concern
14:44 de_maas Is there a limit to the number of entries it can process?
14:44 olas egonw?
14:44 egonw the SDF?
14:44 de_maas Yep
14:45 CIA-44 bioclipse: ospjuth * r5536 /bioclipse2/trunk/plugins/net.bioclipse.ser​vices/src/net/bioclipse/services/business/ (IServiceManager.java ServiceManager.java): Added scriptable version of services.run(String name, Object input).
14:45 egonw I heard some mentioning of 6MB working fine...
14:45 egonw olas: how large was your largest SD file again?
14:45 jonalv I tested with 6MB
14:45 de_maas Hmmm
14:45 egonw de_maas: but, work is ongoing for SDF import into the structuredb
14:45 jonalv and that didn't work great...
14:45 egonw that will solve that issue once and for all
14:46 de_maas That will even be better.
14:46 de_maas 6MB is considered very small over here.
14:47 de_maas What format would the structuredb be?
14:47 jonalv how do you mean what format?
14:48 de_maas The sdf import into the structure db. Is the structure db a new format or is it using an existing database format?
14:48 jonalv the database is just a few tables but yes it's a new database format
14:49 jonalv It's more or less a persisting of CDK molecules
14:50 de_maas So you do not rely on an other package.
14:50 jonalv no just cdk
14:51 jonalv there is some information here: <http://wiki.bioclipse.net/i​ndex.php?title=Structure_DB>
14:51 jonalv not very updated though I just reaslied... :)
14:52 de_maas Thanks
14:52 de_maas but it did not went very good?
14:52 jonalv I have problems yea. But they are related to hsqldb
14:52 de_maas doesn't ring a bell
14:53 jonalv hsqldb is the databasemanager I am using
14:53 de_maas So you are using an existing database engine?
14:54 jonalv uhm yea I wouldn't write that by myself then we wouldn't have system before ten years from now or something :)
14:56 de_maas Sure , but then we misunderstood each other a few rows ago ;-)
14:56 jonalv okey I see, I thought you where talking about formats like biomart (not sure what that is either)
14:59 de_maas I don't know to much about hsqldb , would someone be able to exchange a hsqldb to somebody else like an acces database?
14:59 egonw no without some conversion
14:59 jonalv we are planning on supporting MySQL later on too
15:00 de_maas It's more widely use I think.
15:00 CIA-44 bioclipse: jonalv * r5537 /bioclipse2/trunk/plugins/ (5 files in 3 dirs): Added test.sdf file to the structuredb tests and more fighting with hsqldb. No sucess yet on tht front though...
15:00 jonalv hsqldb is going to be used for local database instances and MySQL is gonna be used for public databases shared among many but that's a bit in the future...
15:01 egonw jonalv: jerome pansanel has mychem
15:01 egonw but that's really targeted as molecules...
15:01 egonw where the bioclipse2 db stuff aims at a more general framework
15:01 egonw to support any 'bioresource'...
15:01 * jonalv has no idea about what mychem is.
15:01 olas egonw: not really
15:01 egonw http://mychem.sourceforge.net/
15:01 jonalv the structuredb is VERY much targeted at molecules
15:02 egonw ask jpansanel on #cdk
15:02 olas only I'd say
15:02 egonw sure, structuredb is...
15:02 egonw but the choice for hsqldb is not, I assume?
15:02 olas there is no other
15:02 egonw oh, no sequencedb anymore?
15:02 olas mysql will also be supported
15:02 olas not yet
15:02 olas but will be
15:02 olas might bi BioSQL though
15:03 jonalv egonw, no sequencdb yet no
15:03 olas not yet, but will be, yes
15:03 olas after structuredb
15:03 olas but no "general" db for IBioObjects, no
15:03 olas (that's impossible)
15:04 jonalv at lest it wouldn't make any sence
15:05 egonw then drop hsqldb?
15:05 egonw and make a custom general interface?
15:05 jonalv egonw, how do you mean?
15:06 * jonalv is looking at mychem but not really understanding. Is it Perl based?
15:06 egonw well, I'd rather see something easy to maintain/develop, than using a off-the-shelf tool which does not really add extra features
15:06 egonw [17:02] <egonw> ask jpansanel on #cdk
15:07 egonw though he seems a sleep...
15:07 jonalv are you saying that you don't think there should be a relational database engine running it?
15:07 * jonalv is lost thne...
15:07 egonw no, there should!
15:08 egonw mychem uses mysql as RDBS
15:08 jonalv egonw, what are you trying to say?
15:08 egonw ummm...
15:08 egonw that I feel sorry for your struggle with hsqldb
15:08 jonalv yea what I can't do with it for the moment is the following.
15:08 jonalv after I ahve started a database server
15:08 jonalv stop it
15:09 jonalv and created another database instance
15:09 jonalv and restart it
15:09 jonalv with two database instances running
15:10 jonalv but most of the structuredb is java code and iBatis mappigns
15:10 de_maas Why do you want multiple instances? Isn't there something like mutiple scheme's?
15:15 jonalv multipple schemes?
15:15 * jonalv has never heard about that
15:16 de_maas Well I'm an oracle user.
15:16 jonalv oh might be something oracle specific perhaps?
15:16 de_maas within oracle running multiple instances is take up a lot of memory.
15:16 jonalv okey
15:16 de_maas But within oracle you create users which can hold a set of tables and sources.
15:17 jonalv MAybee I haven't thougth this through wnough....
15:17 de_maas Usually you create a user which holds an application.
15:17 jonalv ANyway we wan't to be able to do both sequencedaabases and structuredatabses
15:18 jonalv so anyway I need to be able to have multiple databses running but maybe I could start them all at once?
15:18 de_maas In one go, I guess you will be unique in creating an application focussed on both.
15:18 jonalv well you know Bioclipse is targeting all of it... :)
15:18 de_maas Hear hear!
15:19 jonalv huh?
15:20 de_maas just saying I'm please with your comment, targetting all of it
15:20 CIA-44 bioclipse: ospjuth * r5538 /bioclipse2/trunk/plugins/net.bioclipse.ser​vices/src/net/bioclipse/services/business/ (ServiceManager.java ServiceManagerHelper.java): Tried to parse String inputs as IResource if accepted input is IResource.
15:21 jonalv well I spend 50% of my time with a high troughput cell screening LIS for Bioclipse and sits in an office with a guy working on a multiple sequence alignment editor :)
15:25 de_maas Just looked at hsqldb, it uses the same concept as Oracle with user and roles. So why not create an user for every application?
15:26 olas SF is REALLY slow today
15:26 CIA-44 bioclipse: ospjuth * r5539 /bioclipse2/trunk/plugins/net.bioclips​e.services/src/net/bioclipse/services/ (2 files in 2 dirs): Deprecated service.run() that did not take service name as input. All for better recording. Also made DropAdapter use new run(String servicename, Object input).
15:26 jonalv de_maas, I have no idea what that means... :(
15:27 de_maas OK , you want me to explain?
15:27 jonalv sure
15:28 jonalv that would be great
15:28 de_maas Let;'s say you want an application which does chemistry and you have one for biology. You can create 2 users: chemy and bioot
15:29 de_maas Any of them can create tables without seeing each others tables.
15:29 de_maas Of course you should be able to grant rights too each other.
15:29 jonalv running on the same database instance...
15:29 de_maas YES!
15:30 jonalv what's the benefit (except that I don't neeed to restart the server)
15:30 de_maas So when you connect using jdbc you will provide the database name , username and password you will see one application or the other .
15:30 de_maas Advantage is in adminstration. 1 database to maintain.
15:30 de_maas and memory on you computer.
15:31 jonalv hm interesting, maybe I should go with that aprroach
15:31 de_maas But also, you can use each others tables and source
15:31 jonalv No I don't want that  Ietink
15:31 jonalv but say that I want multiple instances of the structure database?
15:32 de_maas OK , you can you do not have to.
15:32 de_maas Be creative and give them several names.
15:32 jonalv yea
15:32 de_maas You can copy the tables , load different structures but use the same code!
15:33 jonalv yea I use java and iBatis and stuff for all that
15:33 jonalv I am not that great with databases though. I wanna do as little as possible with them :)
15:33 de_maas For instance, we are hosting our one database on www.specs.net  but the same database is also used for hosting the journal of heterocyclic chemistry.
15:33 de_maas on www.jhetchem.com
15:34 jonalv okey
15:34 jonalv I didn't know hasldb supported thios
15:34 de_maas OK, but some basics is never bad right?
15:35 jonalv but how do you create new users?
15:35 jonalv you need some sort of admin user to the databse able to do such things?
15:36 de_maas usually you do but as I said, I do not know hsqldb.
15:36 jonalv hm I know MySQL works like this but I have never done it yet
15:36 de_maas http://hsqldb.org/doc/guide/c​h09.html#create_user-section
15:37 jonalv The thing about hsqldb is that it's 100% java and can just come with Bioclipse and run without alot of configuration
15:37 jonalv I have only used it for testing my java persisting and retrieving yet though. (that works great btw) :)
15:38 de_maas Well there you go.
15:38 de_maas Keep i mind that jdbc is not know for best performance.
15:38 de_maas But I guess you're not targetting to get the biggest database out.
15:39 olas hsqldb is mainly for smaller local databases
15:39 jonalv I am using java so I sort of don't get best perforamcne by default :)
15:39 olas if working on something larger, mySQL is probably a better solution
15:39 olas (or similar)
15:40 jonalv we would still be using jdbc...
15:40 jonalv but that's the only way as far as I see
15:40 egonw you'll always use jdbc
15:40 egonw what ever database, whatever wrapper lib
15:40 de_maas Check, OK.
15:42 de_maas Egonw: about the sd-file editor. Will it catch to disk or will it try to read every thing to memory?
15:42 egonw olas? memory, not?
15:42 egonw or does RCP some caching by default?
15:43 jonalv so I shouldn't have multiple databaseinstances but multiple users of one databseinstance... Hm I wonder how to make this work but it should be possible :)
15:43 olas Would that create different files?
15:44 jonalv we where talking about using that iterator I think and load to memory as you scroll. right?
15:44 de_maas For instance, I read some big sd-files (> 40.000) into Knime and it keeps working with a reasonable performance.
15:44 egonw yeah, KNIME has db caching...
15:44 egonw that's what this structuredb will basically do too for SD files
15:44 olas hsqldb?
15:44 egonw olas: the current SDF editor does not cache anything, does it?
15:44 olas in KNIME?
15:44 egonw in bioclipse
15:45 olas does KNIME use hsqldb?
15:45 egonw olas: not sure hwat db KNIME is using...
15:45 olas current SDFEditor reads all SDFile
15:45 olas does not use iterator
15:45 olas egonw: would it be OK to omit the TextEditor tab from the SDFileEditor?
15:46 jonalv but it instantiates the guio stuff lazily at least right?
15:46 egonw olas: yes
15:46 de_maas knime is using file system on disk. Every node you create makes a directory containing meta data and real data.
15:46 egonw olas: was thinking of doing the same for MDLMolfileEditor...
15:46 olas yes
15:46 olas but for SDFiles it really does not make sense to show texteditor
15:47 egonw yes
15:47 egonw and for MDLMofiles, it would just make my life easier
15:47 egonw which I find important too :)
15:48 olas ok
15:50 olas egonw: how should we handle SDFiles where mols have 3D coordinates?
15:51 egonw good point
15:51 egonw well... isn't there a Jmol SWT widget?
15:51 olas no
15:51 olas and that would not be feasible
15:51 egonw how so?
15:51 olas for large SDFiles
15:51 egonw why not?
15:51 olas why so?
15:52 olas why would you want interactivity in a list?
15:52 egonw well, Jmol is more performant than JCP, I think
15:52 olas if you double-click on individual mols, yes you can get it in Jmol
15:52 egonw no, but one would like 3D, not?
15:52 olas JCP just generates an image
15:52 olas which is cached
15:52 egonw you could use the CDK SDG...
15:52 olas hence quite performant
15:52 egonw ah, nice
15:52 olas is that OK?
15:53 olas is there no 3D renderer in CDK?
15:53 olas which is fast?
15:53 olas I think rendering images with Jmol would be slow
15:53 olas but hey, I don't know
15:53 olas what do you think, egonw?
15:54 olas SDG doesn't feel right
15:54 olas what do other software do in this case?
15:54 olas anyone?
15:54 olas I can ask on bioclipse-devel if you have no good suggestion
15:55 egonw don't know a better solution...
15:55 olas than?
15:55 olas what is your best shot?
15:55 de_maas Well I can tell you what isis does.
15:55 olas please
15:56 de_maas It shows you a flattend (so not so nice) 2d structure. If you want to play with it you can take it too rasmol!
15:57 de_maas Or too isis draw, but that's not really a good 3d viewer.
15:57 olas ok
15:57 olas so they generate 2D
15:57 olas thx
15:57 de_maas Chemaxon , makes up it's mind during rendering
15:58 olas so sometimes 2D and sometimes 3D?
15:58 de_maas So if there are 3D coordinates they give you a 3D editor otherwise a 2D editor.
15:58 olas Maybe let users decide?
15:58 olas hmm
15:58 olas yes, but for the list
15:58 de_maas Hmmm the biggest problem is always between the keyboard and the chair.
15:58 olas if you hav 40.000 mols in a list, do thsy open up a 3D-representation for all or just a static image in2D or 3D?
15:58 * egonw got to catch a train
15:59 olas gye egonw!
15:59 olas bye!
15:59 egonw gye to you too :)
15:59 de_maas Later
15:59 de_maas Hmm there is my problem.
16:00 de_maas MDL does not have an sd file viewer. You alway have to convert to a database (local or host)
16:00 de_maas Maybe take a look at accelrys ds viewer.
16:01 de_maas They show first an spreadsheet.  they give you 2d structures but you can add a 3D window
16:02 olas but there is never 3D in a large list of mols?
16:02 olas that you can rotate individually?
16:03 de_maas No never seen it like that.
16:03 olas ok
16:03 olas so only 2D in list
16:03 de_maas Maybe not that usefull.
16:03 olas true
16:03 olas ok, I'll go for generating 2D
16:03 de_maas 2D like the diagrammer or just a projection?
16:03 olas thanks
16:03 olas ?
16:04 olas hmm
16:04 olas fastest would be just to omit Z-values
16:04 olas but using a SDG would be better visualization
16:04 de_maas You could project the initial 3D to the flat screen with out doing calculation of the SDG I think
16:04 olas yes
16:04 olas but that would not look too good
16:05 olas on the other hand
16:05 olas maybe enough
16:05 de_maas SDG would be way to slow I guess.
16:05 olas right
16:05 olas probably true
16:05 olas ok
16:05 olas will just omit Z-values
16:05 olas thanks for the help!
16:05 de_maas You welcome
16:06 de_maas Looking forward to version 2.0
16:09 de_maas Just check DS Visualizer with a list. The do a full 2D rencering on 3d coordinates (and yes, it's slow).
16:10 de_maas Initially it seems they have some catch for them because you can run through them faster later on.
16:10 de_maas It's free so you might give it a quick shot.
16:12 olas right
16:15 de_maas OK, I'm off . Have a nice evening.
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