Camelia, the Perl 6 bug

IRC log for #bioclipse, 2010-01-29

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All times shown according to UTC.

Time Nick Message
06:19 egonw joined #bioclipse
06:20 sneumann joined #bioclipse
06:23 egonw joined #bioclipse
06:45 egonw moin
06:45 zarah hi egonw
07:14 edrin joined #bioclipse
07:15 edrin moin
07:15 zarah saluton edrin
07:15 annzi joined #bioclipse
07:16 egonw hi edrin, annzi
07:17 annzi egonw: good morning
08:14 Gpox joined #bioclipse
08:20 sneumann joined #bioclipse
08:36 annzi egonw: how does the chembl.rdf plugin work?
08:41 egonw via a SPARQL end point
08:41 egonw so, via the rdf.remoteSPARQL() manager method
09:01 egonw @pz statistics
09:01 zarah [1791] MatrixResource does not have a... http://tinyurl.com/ya7pvf8
09:01 zarah [1789] Statistics editor/feature is n... http://tinyurl.com/yh82k3v
09:01 zarah [1790] MatrixResource is not only a I... http://tinyurl.com/y93lfgw
09:01 zarah Entire list at http://tinyurl.com/ycvw46b
09:03 jonalv joined #bioclipse
09:04 egonw hi jonalv
09:06 jonalv hi egonw
09:21 egonw @tell masak you might find this interesting: http://plindenbaum.blogspot.com/2010/01/e​lementary-school-for-bioinformatics.html
09:21 zarah egonw's link is also http://tinyurl.com/y89z2yq
09:21 zarah Consider it noted.
09:22 egonw what a lovely weather! sun and tons of snow!
09:24 * egonw is still going through his 2.4 workspace and checking his git checkouts ...
09:24 egonw edrin: how's your git progress?
09:25 edrin egonw: not activity this month, it was just theoretically preparing to do this
09:25 egonw so, you start next week?
09:34 CIA-59 bioclipse.social: Egon Willighagen master * r35e94c2 / (4 files in 3 dirs): Set version to 2.2.0.v20100127 - http://bit.ly/dxkQhr
09:34 CIA-59 bioclipse.social: Egon Willighagen master * r1cd7272 / features/net.bioclipse.social_feature/feature.xml : Also depend on the RDF feature - http://bit.ly/asUir2
09:34 CIA-59 bioclipse.social: Egon Willighagen master * r93cae36 / plugins/net.bioclipse.myexpe​riment/META-INF/MANIFEST.MF : Removed versions from dependencies - http://bit.ly/cy6Atr
09:34 CIA-59 bioclipse.social: Egon Willighagen master * r0da5bb4 / features/net.bioclipse.soc​ial_feature/social.product : Added the RDF feature - http://bit.ly/8ZTOv8
09:35 egonw edrin: did you do anything on the KNIME nodes for XMPP ?
09:38 egonw edrin: see email
09:42 CIA-59 bioclipse.joelib: Egon Willighagen master * r88217de / (57 files in 9 dirs): Deleted source that was previously excluded from the source .classpath; however, exporting is not happy about such excluded. - http://bit.ly/5VdiV9
09:42 CIA-59 bioclipse.joelib: Egon Willighagen master * r31cff71 / features/net.bioclipse.joelib_feature/feature.xml : Added full GPL text (fixes #1763) - http://bit.ly/5h0XOn
09:42 CIA-59 bioclipse.joelib: Egon Willighagen master * rf978261 / (4 files in 3 dirs): Bumped version to 2.2.0.RC3 - http://bit.ly/5ZY3JJ
09:42 zarah bug #1763 | http://tinyurl.com/yjs9p5b
09:42 CIA-59 bioclipse.joelib: Egon Willighagen master * rd76ac88 / (4 files in 3 dirs): Set version to 2.2.0.v20100127 - http://bit.ly/btHgZY
09:47 CIA-59 bioclipse.cheminformatics: Egon Willighagen master * rf99c5e1 / (16 files in 16 dirs): Set version to 2.2.0.v20100127 - http://bit.ly/8YcJUP
09:47 CIA-59 bioclipse.cheminformatics: Egon Willighagen master * r0ddc6cc / (16 files in 16 dirs): Merge branch '2.2.x' - http://bit.ly/9t1VQX
10:23 olass joined #bioclipse
10:23 egonw hi olass
10:23 olass egonw: ping
10:23 egonw pong
10:23 olass hi
10:23 zarah saluton olass
10:23 olass why is there a http://wiki.bioclipse.net/inde​x.php?title=Category:Projects and a http://wiki.bioclipse.net/index.php​?title=Category:Bioclipse_Projects page?
10:23 zarah olass's link is also http://tinyurl.com/yh7jqah
10:23 olass what is the difference?
10:24 egonw the first is autogenerated
10:24 egonw the second existed long before we started adding categories
10:24 egonw I guess they could be merged
10:24 egonw oops
10:24 egonw sorry
10:24 egonw they are both categories
10:24 egonw overlooked a few critical chars :)
10:25 egonw yes, those certainly should be merged
10:25 olass sounds good
10:26 olass right now it is very confusing
10:26 olass and the two overlap on many occasions, but not all
10:26 olass please email the list too
10:26 olass so we decide which one to retain
10:27 * olass suggests to keep "Project" and remove "Bioclispe Project"
10:27 olass egonw: ping
10:28 olass http://pele.farmbio.uu.se/b​ioclipse/help/2.2/index.jsp still is not working?
10:28 zarah olass's link is also http://tinyurl.com/y8g44bl
10:28 olass any problems?
10:31 egonw olass: it's either or...
10:31 egonw 1. http://pele.farmbio.uu.se/bi​oclipse/proxy/2.2/index.jsp
10:31 zarah egonw's link is also http://tinyurl.com/yewbfyn
10:31 egonw 2. http://pele.farmbio.uu.se/bioclipse/help/2.2/
10:31 zarah egonw's link is also http://tinyurl.com/y9eazve
10:32 olass egonw++
10:32 egonw I got it working within 10 mins after you left :)
10:33 egonw I updated the wiki page with all the details
10:33 olass did you set up a cron job?
10:33 egonw ah, nope, not yet
10:33 olass would that be hard?
10:33 egonw need to think of a clever way to see if the service is running...
10:33 olass pele tends to go down..
10:34 egonw indeed
10:34 egonw which reminds me...
10:34 egonw we should upgrade the OS
10:34 egonw it's two versions behind
10:34 olass is that problematic?
10:34 egonw I think EOL is this April
10:34 egonw ending security support
10:35 egonw and that is problematic
10:35 egonw we'd also benefit from upgrade bugzilla
10:35 egonw 2.2 instead of 2.0
10:35 egonw but having 2.0 is not problematic
10:35 olass how big effort is it to upgrade?
10:36 egonw no, likely not...
10:36 egonw should be done in a day, but I need physical access if reboot fails...
10:36 egonw so, I need to do that when I am at BMC
10:36 olass ah, I see
10:38 egonw what d'you think of: http://wiki.bioclipse.net/index.​php?title=Category:BioclipseLabs ?
10:38 zarah egonw's link is also http://tinyurl.com/ye2xyno
10:38 egonw all: BTW, please merge anything remaining in 2.2.x branches into master
10:50 olass right
10:50 egonw trying to figure out how to do maintainance for his uu.se email account
10:59 egonw OK, deleted a whole bunch of old mails...
10:59 egonw now back at 33% of ridiculously low quotum
11:07 masak joined #bioclipse
11:18 egonw hi masak
11:18 CIA-59 bioclipse.cheminformatics: Egon Willighagen master * rc5969da / plugins/net.bioclipse.jmol/jars/Jmol.jar : Updated to the bug fix release 11.8.17 - http://bit.ly/dwWwei
11:19 masak hi egonw
11:19 zarah masak: You have new messages. Write '/msg zarah @messages' to read them.
11:19 masak zarah: messages
11:19 zarah masak: 1 h 57 m 47 s ago, egonw said you might find this interesting: http://plindenbaum.blogspot.com/2010/01/e​lementary-school-for-bioinformatics.html
11:19 * masak clicks
11:20 masak egonw: indeed.
11:20 masak egonw: very reminiscent of suffix trees, actually.
11:20 masak those wondrous computer-theoretical beasts which speed up some searches beyond some people's wildest imagination.
11:23 masak ah, I see the former was developed from the latter. makes sense.
11:31 * egonw notes that 3D tvs will hit the Dutch market this year
11:31 egonw and I was thinking Avatar was the first commercial 3D thing...
11:32 egonw there's a whole dimension behind 2D tvs already!
11:32 egonw pun intended :)
11:32 * masak doesn't get it
11:32 masak (referring both to the hype and the pun)
11:33 egonw nah, you've been too long in the 1D sequence world
11:33 masak that must be it.
11:33 masak everything's reducible to 1D anyway, so why bother?
11:36 egonw yeah, those lazy 3D people
11:36 egonw just put in another dimension, and your problems are solved...
11:36 egonw who cares about 11D string space
11:37 egonw "give me another 7 dimensions, and I give you the world"
11:42 egonw no Gpox?
11:42 egonw mmm...
12:28 egonw http://friendfeed.com/bioclip​se/6153a34d/bioclipsecheminfo
12:28 zarah egonw's link is also http://tinyurl.com/ybgx9ee
12:29 sneumann joined #bioclipse
13:18 sneumann Hi,
13:18 sneumann what is a "compound class" ?
13:19 sneumann There're several sources for classification, e.g. PubChem has MeSH terms
13:19 sneumann which (sometimes/often) include a "Chemical Class",
13:19 sneumann and ChEBI classifies compounds in (multiple) classes.
13:20 sneumann Is ther "THE" source for chemical classification ? Are they RDF-available somewhere ?
13:20 sneumann Which is the "THE" source for chemical classification ? Are they RDF-available somewhere ?
13:21 egonw ChEBI has RDF
13:21 egonw via bio2rdf
13:21 egonw not sure if the classification is part of that
13:22 sneumann Hm. seems to be a vast field ...
13:23 egonw http://bio2rdf.org/chebi:50004
13:23 zarah egonw's link is also http://tinyurl.com/yaanfpd
13:23 egonw sneumann: yeah, finding a useful classification is laborsome and non-trivial
13:23 egonw check that URL
13:23 egonw and check the is_a predicate
13:23 egonw that should give you your classification
13:31 sneumann merci
14:18 annzi joined #bioclipse
14:19 jonalv http://translate.google.com/#ja|en|Bioclipse%E3%81%A3%E3%81%A6Cheminfo%E7​%9A%84%E3%83%84%E3%83%BC%E3%83%AB%E3%81%A8​%E3%81%97%E3%81%A6%E3%81%A9%E3%81%86%E3%81​%AA%E3%82%93%E3%81%A0%E3%82%8D%E3%80%82
14:25 jonalv zarah: seen Gpox?
14:25 zarah I have not seen Gpox
14:25 jonalv zarah: seen GPox?
14:25 zarah I have not seen GPox
14:25 jonalv zarah: seen me?
14:25 zarah I have not seen me
14:26 jonalv zarah: seen masak?
14:26 zarah masak was last seen 1 h 39 m 23 s ago in #farmbio saying 'http://tantrikblog.files.wordpress.co​m/2010/01/pp-sd.jpg?w=444&h=800'
14:26 masak zarah: seen masak?
14:26 zarah masak was last seen right now in #bioclipse saying 'zarah: seen masak?'
14:26 masak :)
14:31 jonalv do anyone know anything about gpox?
14:32 masak yes, I know he usually sits to my left. he's quite a nice guy. good at programming.
14:32 jonalv zarah: slap masak for being a funny guy
14:32 * zarah decomposes masak for being a funny guy into several parts using the Banach-Tarski theorem and reassembles them to get two copies of masak for being a funny guy!
14:33 masak jonalv: the correct term is 'wise-ass'.
14:33 jonalv masak: now you did it gain
14:33 jonalv |again
14:34 masak no shit, Sherlock? :P
14:34 masak .oO( this is more of a #farmbio conversation... )
14:34 jonalv zarah: ping gpox
14:34 zarah Consider it noted.
14:48 * egonw is pushing new cdk-jchempaint patches to pele
14:58 samuell joined #bioclipse
15:07 egonw http://hudson.ch.cam.ac.uk/
15:34 jonalv egonw: regarding bug 389
15:34 jonalv @pz 389
15:34 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=389
15:34 jonalv egonw: what does ChemTree mean?
15:35 egonw Outline
15:35 egonw that was called ChemTree in BC1
15:35 jonalv egonw: ah but that is totally different in jmo land in jchempaint
15:35 egonw quite so
15:36 egonw first thing we need to do is get a IJmolMolecule
15:36 jonalv egonw: should I turn that bug into just jmol?
15:36 egonw no, split up, I'd say
15:36 jonalv egonw: I am pretty sure this has ben implemetned for jchempaint
15:36 egonw bug tickets are cheap
15:36 jonalv hence only jmol elft, hence turn the bug into just jmol
15:37 egonw ok, got to fetch wood for the fire place now
15:37 * jonalv heard an 'ok' and foes the chagnes
15:38 egonw olass++ (for suggesting doodles)
15:40 Gpox joined #bioclipse
15:42 egonw hi Gpox!
15:42 egonw Gpox: we missed you :)
15:42 masak Gpox! \o/
15:43 Gpox I am getting an NPE when trying to build with hudson
15:44 jonalv :(
15:44 jonalv Gpox: what's the status of the new molecule table?
15:45 jonalv how far are we from merge into master?
15:51 Gpox Splitting the context menu and renderer for ds test results. Properties needs a redesing but it works with the old system, next week shoulb be doable
15:52 jonalv Gpox: looking forward to that! :)
16:01 egonw jonalv, masak: please merge your 2.2.x branches into master
16:01 egonw if not done so yet
16:01 egonw Gpox: I have updated cdk-jchempaint on pele
16:01 masak will do.
16:02 egonw and will make an export for Bioclipse early next week
16:02 * jonalv tries to think but fails to come up with any repo with a 2.2.x branch that he maintains
16:02 masak done. git++ git++ git++
16:56 egonw olass-- (for a typo in the release email Subject: header) :)
17:06 masak olass-- (for advocating passive voice and nominalisations in jonalv's text)
17:16 jonalv olass++ (for being olass++)
17:24 edrin left #bioclipse
17:48 jonalv joined #bioclipse
19:02 sneumann joined #bioclipse
19:47 egonw joined #bioclipse
20:43 sneumann_ joined #bioclipse

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