Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-05-28

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Time Nick Message
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08:24 edrin joined #bioclipse
08:30 edrin hi
08:33 olas hi edrin
08:34 edrin hey ola
08:40 jonalv hi
08:41 edrin hi jonalv
08:42 egonw joined #bioclipse
08:43 edrin hi egonw
08:43 edrin i still did not fix the thing ;)
08:43 egonw hi edrin
08:52 malick left #bioclipse
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10:05 CIA-46 bioclipse: jonalv * r5716 /bioclipse2/trunk/plugins/net.bioclipse.str​ucturedb.tests/tests/net/bioclipse/structur​edb/persistency/dao/StructureDaoTest.java: rewrote a test to make sure fingerprints survives a trip to the database. I probably tested it somewhere but I wanted to make sure...
10:06 CIA-46 bioclipse: jonalv * r5717 /bioclipse2/trunk/plugins/ne​t.bioclipse.structuredb/src/ (5 files in 3 dirs): Work on select statement performing a bitwise AND for the fingerprint substructure search. For the moment it's not going great... :(
10:07 * jonalv -> lunch
10:47 egonw joined #bioclipse
11:10 jonalv ping egonw
11:13 egonw pong
11:15 jonalv I wonder
11:15 jonalv the fingerprint is a 1024 long bitset right?
11:15 masak joined #bioclipse
11:15 egonw yes
11:15 egonw make sure to use the extended fingerprint
11:15 jonalv it seems that hsqldb persists it in a hava inetger
11:15 jonalv java integer
11:15 egonw :(
11:16 egonw that would not be good
11:16 jonalv or rather it seems as if binary in hsqldb is a java integer
11:16 jonalv the strange thing is that it seems to work...
11:16 jonalv what's the extended fingerprint?
11:16 egonw well, any bit string can be represented as an integer
11:16 egonw the normal fingerprint + some extra fields
11:16 masak I think the main issue is which operator to use for ANDing together two bitsets
11:16 egonw (but still 1024 length)
11:16 egonw masak: yes, think so too
11:16 jonalv you lost me
11:17 masak this needs to be done in the db layer, right?
11:17 egonw yes
11:17 masak otherwise searches will be slow
11:17 * masak peruses the SQL92 standard
11:17 jonalv I am trying to move it there to speed up searches yea
11:18 jonalv but how can a 1024 long bitset be stored in an integer?
11:19 masak jonalv: not all ints are Java ints
11:19 egonw because something like 01011 = eleven
11:19 jonalv masak: I don't understand
11:19 masak egonw: let's not go there :)
11:19 jonalv egonw,  I don't understand..
11:19 masak jonalv: 'int' here simply means 'integer'
11:20 masak not '32-bit integer'
11:20 jonalv why not?
11:20 masak because.
11:20 masak otherwise 1024 bit would not fit
11:20 jonalv hsqldb uses a java integer
11:20 masak maybe it uses several, then
11:21 jonalv masak: http://hsqldb.org/doc/guide/​ch09.html#datatypes-section
11:21 jonalv um hang on
11:21 jonalv range: as Integer.MAXVALUE
11:21 jonalv that might be the number of bits...
11:22 jonalv still means troubkle since there binaryAnd takes two inegers
11:22 masak jonalv: I don't see bitsets in the table
11:22 jonalv binary
11:22 masak ok
11:23 masak ah, it's a byte[]
11:23 egonw jonalv: what about using BinSet instead of byte[] ?
11:23 jonalv http://hsqldb.svn.sourceforge.net/viewvc/hsqldb/b​ase/trunk/src/org/hsqldb/Library.java?view=markup
11:23 jonalv row 502
11:24 jonalv binset?
11:24 jonalv egonw, sure, how?
11:24 egonw BitSet
11:24 masak jonalv: yeah, that method doesn't help you
11:24 egonw http://java.sun.com/j2se/1.4.2/​docs/api/java/util/BitSet.html
11:24 masak it just ANDs two native ints, ju
11:24 egonw that should map to OBJECT on the hsqldb side
11:24 jonalv yea well I do use that in the domain objects
11:25 jonalv but persisting those is abit trixy, better to use the sql type binary
11:25 egonw but it does not have an subbitset map in the lib... ok
11:25 jonalv and binary happens to be a byte[] in hsqldb
11:25 egonw stefan wrote custom C code for MySQL for the bitset type
11:25 masak still the question remains: can a bitwise AND be performed on two 1024-bit bitsets in the db layer?
11:26 masak egonw: maybe that's the way to go here too, then
11:26 * jonalv thinks he needs to write custom java code for the bitwise and for the hsqldb
11:26 masak jonalv: I think you should
11:27 jonalv write a byte[] bitwiseAnd([byte[] a, byte[] b)
11:27 egonw remains the question if one can plugin custom compare methods into hsqldb
11:27 masak jonalv: yes
11:27 masak three line implementation
11:27 jonalv egonw, that you can. sry I didn't say that :)
11:27 jonalv masak: thrree lline? won't I need a loop an stuff?
11:27 masak problem solved, then.
11:27 masak jonalv: yes
11:28 masak it's just that I don't use braces for that
11:28 masak so I get one line less than you :)
11:28 jonalv the problem is that when I get to mysql I will need to do it all over again. But I guess I could ask Stefan for help then :)
11:28 masak ah, maybe four lines. need to declare the result as well
11:28 egonw this is what chemdb.sf.net is for
11:28 jonalv it's using mysql?
11:29 egonw there is such code for mysql, oracle at least...
11:29 egonw but other dbs too, I think...
11:29 masak you cdk people already solved everything! :)
11:29 jonalv good then I can borow that code that day :)
11:29 egonw no, chemdb is getting different chem db projects to use the same APIs
11:29 egonw masak: well, cdk has been aroud for a while already :)
11:29 masak true
11:39 olas joined #bioclipse
11:52 olas egonw: have you worked against PUG?
11:52 olas Pubchem Power User Gateway?
11:52 egonw yes
11:52 egonw but not the SOAP yet...
11:53 egonw but hope to do that soon too
11:53 olas is it in cdk?
11:53 egonw no, in bioclipse1
11:53 olas why use the soap?
11:53 olas I like better the REST
11:53 egonw well, depends on the input
11:53 egonw request by CID is easy
11:53 olas what you mean?
11:53 egonw but request by substructure?
11:53 egonw if via SMILES it should work
11:54 egonw SMARTS, that is
11:54 olas but?
11:54 egonw but if it becomes more complex
11:54 egonw e.g. SMARTS *and* some other criterium...
11:55 egonw well, can't think of a good example, given the current services...
11:55 olas ok
11:57 olas I was thinking of implementing the following: http://pubchem.ncbi.nlm.nih.gov/pug_s​oap/examples/java_axis/java_axis.html
11:57 olas all these example services
11:57 olas egonw: do we have all that in bc1?
11:57 egonw no
11:57 egonw ummm
11:57 egonw why not the Java way...
11:57 egonw check this code for SOAP services:
11:58 egonw ... mom ...
11:58 olas egonw: that is the Java way, using axix1.4
11:58 olas what is not java with that?
11:58 olas or do you mean via HTTP instead of SOAP?
11:58 egonw sorry, I meant with the default libs that come with your JVM
11:59 olas so not axis you mean?
11:59 egonw right
11:59 olas give me a url to a tutorial
11:59 egonw http://metware.svn.sourceforge.net/viewv​c/metware/MetDriver/trunk/src/main/net/s​f/metware/masslookup/drivers/ChemSpiderD​river.java?revision=373&view=markup
12:00 egonw bbl
12:00 olas please explain this
12:00 olas or I will use axis :-)
12:14 egonw lines 140 ff
12:14 egonw that creates a HTTP connection
12:15 egonw which requires a SOAPMEssage
12:15 egonw line 143
12:15 egonw for which the method at line 105 is used
12:15 egonw which creates the necessary XML for the message
12:16 egonw by using regular XML DOM calls, like addChildElement
12:16 egonw each SOAPMessage has a body, where the fun stuff is
12:16 egonw e.g. a CML document
12:16 egonw (not that that applies to the PUG SOAP)
12:17 egonw the ChemSpider SOAP expects two elements for the SearchByMass port: <mass> and <range>
12:17 egonw so, those are created there...
12:17 egonw need to relocate...
12:17 egonw bbl
12:30 CIA-46 bioclipse: jonalv * r5718 /bioclipse2/trunk/plugins/ (6 files in 5 dirs): My tests pass. I think I have moved the fingerprint check down into the database layer correctly but it went way too easy so there is probably some problem left...
12:33 * olas likes jonalvs commits
12:34 jonalv someone should test to see if ot does it what it is supposed to do and not just something random... :)
12:36 egonw joined #bioclipse
12:37 egonw olas: did that help?
12:37 jonalv I got cdk trouble...
12:37 egonw name it
12:38 jonalv stack trace comming...
12:38 jonalv http://paste2.org/p/32630
12:39 egonw jonalv: you're on OS/X too?
12:39 masak he is soon
12:39 egonw but not yet?
12:40 egonw jonalv: did you update the cdk today?
12:40 egonw I did upload the xercesImpl...
12:40 egonw should be in the classpath now
12:40 jonalv right, I might not have updated cdk
12:40 egonw not that this exception should be happening at all...
12:40 * jonalv is still getting used to not having cdk in bioclipse repo...
12:41 egonw it will pay off later...
12:41 * jonalv hinks that checking out complete cdk repo might not have been a brilliant idea...
12:41 egonw but any transition is difficult
12:41 egonw :)
12:41 egonw correct
12:41 egonw just do cdk/trunk
12:41 jonalv egonw, couldn't we have a svn:externals for the plugin?
12:41 egonw directly in svn:externals...
12:41 jonalv I don't have energi to redo it just now
12:41 egonw yes, good idea
12:41 jonalv I am swiching computer soon...
12:41 egonw did not think of that
12:42 egonw ok, hang on
12:42 jonalv then I will do cdk/trunk but external would be even nicer :)
12:42 * egonw is setting up that svn:externals
12:45 olas egonw: one question reagrding cdk10
12:45 olas there are some classes that are excluded from build path
12:45 olas why is that so?
12:46 olas that breaks my export in Eclipse
12:46 olas what to do?
12:46 egonw because they require certain .jars not in the CDK SVN repos
12:46 egonw how does that break export?
12:46 olas export tries to build ALL
12:46 egonw oh crap... :(
12:46 olas yes
12:47 olas I've taken tha habit NOT to have excluded classes in my eclipse plugins
12:47 olas maybe there's some way around, but no easy solution
12:47 egonw that habit has not reached Nijmegen yet
12:47 olas but it IS cdk10
12:47 egonw will need to think about that
12:47 olas ok
12:47 olas for me, I will just remove them
12:47 olas since they are not used in Bioclipse at all
12:48 egonw yes, but since it's svn:externals... :(
12:48 olas I know
12:48 olas will not commit
12:48 olas but need to test export
12:48 olas of cdk10
12:48 egonw yes, I understand
12:51 jonalv brb
12:51 CIA-46 bioclipse: egonw * r5719 /bioclipse2/trunk/plugins/: Set up svn:externals for org.opscience.cdk
12:54 egonw jonalv: added note on SVN checkout of the plugins/ dir, which should now auto:svn:externals:checkout org.openscience.cdk
12:54 egonw added that to the wiki
12:54 olas egonw: so what now?
12:54 olas we don't check out from cdk?
12:54 egonw yes, you do
12:54 olas but?
12:54 egonw no but
12:54 olas please explain the change
12:54 egonw just, there are two ways of doing it
12:55 olas can I get it from bioclipse as before?
12:55 egonw yes, you can do that now
12:55 egonw I added an svn:externals on the plugins/ dir
12:55 egonw so, doing
12:55 egonw svn update plugins/
12:55 egonw will now also download/update org.openscience.cdk
12:56 egonw but a separate checkout is fine too
12:56 egonw both will still show up as org.openscience.cdk project in Eclipse
13:00 olas egonw: can we not have tests in a different plugin called cdk.tests?
13:00 olas why all in same?
13:00 egonw because that's what CDK devels like
13:00 olas :-(
13:00 egonw mmm... me is starting to feel this was not so good idea
13:01 olas maybe not
13:01 olas but on the other hand
13:01 olas we can filter packages in the build.properties
13:01 olas it's just hard to keep up2date
13:01 egonw won't help
13:01 egonw can you filter for classes too?
13:01 egonw *Test.java ?
13:02 egonw because the tests are in the same package as the tested classes itself
13:02 olas NO
13:02 olas that's really discouraged
13:02 egonw by who?
13:02 olas and not true
13:02 egonw it's the Maven way
13:02 olas theres a test package
13:02 jonalv egonw, why was what not such a good idea?
13:02 egonw in cdk10 there is a cdk.test package, yes
13:02 egonw not in CDK trunk
13:03 olas org.openscience.cdk.test
13:03 egonw yes, for cdk10
13:03 olas :-(
13:03 olas :-(
13:03 olas :-(
13:03 jonalv olas: having tests in the same package is not discouraged it's a good idea because it makes you able to see packe protected things...
13:03 egonw jonalv: right
13:03 jonalv olas: what you shouldn't do is having the tsts in the same folder
13:04 jonalv you should have a parallell folder structrue with the same names
13:04 jonalv thus having the tests in the same package but not in the same folder if you see what I mean :)
13:04 masak jonalv: I've only seen that working within Eclipse, though
13:05 masak no, wait, maybe we did get javac to accept it using $CLASSPATH
13:05 jonalv masak: we did it for effortless java didn't we? :)
13:05 jonalv masak: yea
13:05 masak yes, but I was unsure about whether we got it to work
13:05 masak in the end we did, I think
13:06 jonalv yea it worked great if you gave the right paramaters to jsavac
13:06 jonalv but, egonw, why was what not such a good idea?
13:07 egonw export seems to conflict with the full cdk dir from CDK SVN
13:07 egonw for cdk10 at least
13:08 olas yes
13:08 jonalv ah that's related to the complete switch in cdk ways right?
13:08 olas I have deleted all tests, and all excluded java files
13:08 egonw olas: ack
13:08 * egonw wonders if there is no cleaner way of doing this... :(
13:11 CIA-46 bioclipse: ospjuth * r5720 /bioclipse2/trunk/plugins/net.bioclip​se.cdk10.sdfeditor/build.properties: Updated build.properties for export.
13:12 CIA-46 bioclipse: ospjuth * r5721 /bioclipse2/trunk/plugins/net.bi​oclipse.cdk10/build.properties: Updated build.properties for export.
13:16 CIA-46 bioclipse: ospjuth * r5722 /bioclipse2/trunk/plugins/net.bioclip​se.cdk10.jchempaint/build.properties: Added build.properties.
13:16 CIA-46 bioclipse: ospjuth * r5723 /bioclipse2/trunk/plugins/net.bioclipse.cdk10.jche​mpaint/src/net/bioclipse/cdk10/jchempaint/outline/ (BioPolymerContentProvider.java ChemTreeView.java): Removed excluded files for export to work.
13:20 olas egonw: you can write bin.excludes in the build.properties
13:20 olas that would resolve a lot of problems
13:20 egonw ah, good
13:20 egonw please commit a bug report fo that in CDK's BTS
13:20 olas ok
13:38 egonw olas: you may commit such changes yourself too, of course
13:40 CIA-46 bioclipse: ospjuth * r5724 /bioclipse2/trunk/plugins/ (3 files in 2 dirs): Updated build.properties.
13:40 CIA-46 bioclipse: ospjuth * r5725 /bioclipse2/trunk/plugins/net.bioc​lipse.scripting/build.properties: Updated build.properties.
13:44 CIA-46 bioclipse: ospjuth * r5726 /bioclipse2/trunk/plugins/net.bi​oclipse.logger/build.properties: Updated build.properties.
13:44 CIA-46 bioclipse: ospjuth * r5727 /bioclipse2/trunk/plugins/net.bio​clipse.cdk10.ui/build.properties: Updated build.properties for export.
13:51 CIA-46 bioclipse: ospjuth * r5728 /bioclipse2/trunk/plugins/net.bioclipse.cdk10/ (META-INF/MANIFEST.MF build.properties): Getting really frustrated tracking down errors in build.properties...
13:52 CIA-46 bioclipse: ospjuth * r5729 /bioclipse2/trunk/plugins/net.bioclip​se.cdk10.jchempaint/build.properties: Yup, another error in build.properties. Never forget the dot '.'. Grr.
13:52 jonalv olas, you are doing a gret job!
13:53 EskilA joined #bioclipse
13:53 olas YES
13:53 olas FINALLY managed to export JCP
13:53 olas :-)
13:53 egonw excellent !
13:53 * egonw feels a prerelease comming...
13:53 olas still cannot edit on mac though, but that never was the case
13:54 olas SDFEditor seems fine too :-)
13:54 * olas is smelling a first alpha-releaee coming along
13:55 jonalv olas++
13:55 CIA-46 bioclipse: Annzi * r5730 /bioclipse2/trunk/plugins/net.bioclipse.cdk10.​jchempaint/src/net/bioclipse/cdk10/jchempaint/ (3 files in 2 dirs): Some small changes to get editing working in SDFEditor JCPPage. One step closer.
13:55 olas go Annzi!
13:55 EskilA hon har lämnat oss, men hennes anda lever kvar!
13:55 olas Annzi=Gpox in this case
13:55 olas english here please
13:55 olas Gpox++
13:56 EskilA Translation for the swedish impaired: Annzi may have left us, but her spirit lives on!
13:56 olas we should remove her credentials from that windows computer
13:57 masak indeed
13:59 CIA-46 bioclipse: ospjuth * r5731 /bioclipse2/trunk/plugins/net.bioclipse.c​dk10.sdfeditor/src/net/bioclipse/cdk10/sd​feditor/editor/StructureTableEntry.java: Allow for custom colorer in SDFEditor.
14:00 CIA-46 bioclipse: ospjuth * r5732 /bioclipse2/trunk/plugins/net.b​ioclipse.core/build.properties: You guessed right: another updated build.properties. The last perhaps? Now it runs properly (or so it seems).
14:00 CIA-46 bioclipse: ospjuth * r5733 /bioclipse2/trunk/plugins/net.b​ioclipse.ui/bioclipse.product: Oh crap, forgot that the product was updated as well.
14:00 egonw :)
14:01 olas egonw: about that SDFWriter...
14:01 olas ETA?
14:02 egonw umm...
14:02 egonw what's wrong with the one I added to BC2 SVN?
14:02 olas did you add one?
14:02 olas where?
14:02 egonw yes, directly...
14:02 egonw well, after some 20mins
14:02 egonw mom, let me chek
14:02 egonw +c
14:02 * olas must have missed that commit
14:02 olas what pkg and plugin?
14:03 egonw cdk10.sdf I think
14:03 olas oh, found it
14:03 egonw hang on
14:03 olas great
14:03 egonw ok, good
14:03 olas will test it now
14:03 egonw ok
14:03 * jonalv is performing substructuresearch in a 700k big sdf file looking for benzene
14:03 jonalv I should prpbably do some test with a timer and see if things are quicker now...
14:03 masak gotta find that benzene...
14:03 masak jonalv: yes, please do
14:04 jonalv wo wI got very strange output
14:05 jonalv ah now I know. :)
14:05 jonalv I am pretty sure it's faster :)
14:06 jonalv but I somewhat broke the statusbar i nthe process.. :)
14:06 masak never mind that, if it's fast! :)
14:06 jonalv olas: I am also having loggin trouble after you got things running on Windows. Not that it doesn't work but I get alot of angry error messages on the output...
14:07 olas egonw: grr
14:07 olas Cannot writer anything other than IMoleculeSet.
14:07 olas ok, I need to change some
14:07 olas no problem
14:07 olas oh, that was an easy change
14:09 egonw ummm... writing IMoleculeSet SDF seemed to make sense ... :)
14:09 olas hmm, does not work out of the box...
14:09 * olas will debug
14:09 olas egonw: are you somehow using some new features that the reader in cdk10 cannot read?
14:09 olas just a question...
14:10 olas oh
14:10 olas what has ahappened here?
14:10 CIA-46 bioclipse: jonalv * r5734 /bioclipse2/trunk/plugins/ (2 files in 2 dirs):
14:10 CIA-46 bioclipse: Moved the bitwiseAdd code from the structuredb plugin to the hsqldb plugin. Eclipse dependencies can be a bit troublesome. I really wanted that code in structredb but circular dependencies isn't the way to go...
14:10 CIA-46 bioclipse: Anyway now substructreSearch can be performed from th JS-console again
14:10 olas hmm
14:11 olas the last MDLfile in the SDfile got only halfways
14:11 * olas suspects a buffer full or such
14:12 olas will do a wc
14:12 egonw mom
14:12 * egonw is doing some dbdesigner hacking...
14:12 olas what for?
14:12 egonw http://metware.sf.net/
14:13 egonw what features are you thinking of?
14:13 olas egonw: it only wrote 8192 chars
14:13 egonw mmm...
14:13 egonw ok, add a writer.flush() after each molecule to the SDFWriter ?
14:13 olas ok
14:14 olas that solved it
14:14 olas :-)
14:14 olas hmm
14:14 olas it is writing props in another order now
14:14 olas that is annoying
14:15 olas maybe we should have them sorted by header string?
14:15 egonw ah, because Map does not have an order
14:15 egonw possible
14:15 olas Probably Map is not the best way
14:15 olas but I guess there's no obvious order of props in an SDFile
14:16 egonw guess not
14:17 egonw alternatively, you could impose this ordering in the table?
14:17 olas sure
14:17 olas if need be
14:17 olas gotta run now
14:22 egonw ack, bye
14:46 jonalv Moving the fingerprintsearch down to the database layer made the substructuresearch 3.36 times faster for my test files :)
14:47 masak jonalv++
15:46 CIA-46 bioclipse: jonalv * r5735 /bioclipse2/trunk/plugins/ne​t.bioclipse.structuredb/src/ (6 files in 4 dirs): Updated the progress monitor for substructure search to show the correct info after having moved the fingerprint matching to the database layer
16:45 olas joined #bioclipse
16:45 olas hi
16:46 edrin hi :)
17:17 egonw olas: thanx!
17:17 CIA-46 bioclipse: ospjuth * r5736 /bioclipse2/trunk/plugins/net.biocli​pse.cdk10.sdfeditor/src/net/bioclips​e/cdk10/sdfeditor/io/SDFWriter.java: Added flush after each MDLMolfile to solve buffer overflow bug.
17:17 CIA-46 bioclipse: ospjuth * r5737 /bioclipse2/trunk/plugins/net.biocli​pse.cdk10.sdfeditor/src/net/bioclips​e/cdk10/sdfeditor/CDK10Manager.java: Use new SDFWriter instead of MDLWriter.
17:18 olas bye for now
17:18 olas egonw: Gpox solved JCP on Mac!
17:18 olas did you hear that?
17:18 egonw cool!
17:18 egonw Gpox+++++
17:18 olas and the grey box thingy
17:18 egonw that too?
17:19 egonw who is this guy?
17:19 egonw (or girl?)
17:19 olas our new IT-hero in the Bioclipse project
17:19 olas started last week
17:19 egonw :)
17:19 egonw excellent
17:19 egonw will try that tonite
17:19 olas We're builing a strong team
17:19 egonw enough metware for today
17:19 olas building
17:19 egonw yes, indeed
17:19 olas same here
17:19 olas will build kitchen now
17:20 egonw build??
17:20 egonw not just dinner?
17:20 olas renovating
17:20 egonw you do that every day?
17:20 egonw you cook that badly?
17:20 olas :-)
17:20 olas not really
17:20 egonw ok, me will go home too
17:20 olas bis morgen
17:20 olas hmm
17:20 olas tomoroow I'll only drop in occasionally
17:20 egonw I'd wish I could reply in Swedish ...
17:20 egonw already bought books :)
17:20 olas vi ses imorgon
17:21 olas eller
17:21 egonw ok, will remember that
17:21 olas vi hörs imorgon
17:21 olas see or hear
17:21 egonw and 'vi' ?
17:21 egonw we?
17:21 olas we
17:21 olas we see tomorrow
17:21 egonw not future tense?
17:21 olas meaning see you tomorrow
17:21 olas we'll see each other tomorrow
17:22 olas vi ses imorgon
17:22 egonw ses == future tense?
17:22 olas no
17:22 egonw ok, never mind...
17:22 olas expression
17:22 egonw will read up on linguistics :)
17:22 olas but used a lot so good to know
17:22 egonw ok, tot morgen
17:22 olas ok, bye
17:22 olas thcüss
17:22 olas left #bioclipse
18:12 ilogger2 joined #bioclipse
19:37 rojasm joined #bioclipse

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