Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-09-23

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All times shown according to UTC.

Time Nick Message
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07:01 olass moin
07:01 zarah privet olass
07:02 olass zarah: dobra dan
07:02 zarah olass: excuse me?
07:05 masak o/
07:10 egonw moin
07:10 zarah oh hai egonw
07:12 masak oh hai egonw
07:17 Gpox oh hai egonw
07:17 zarah oh hai egonw
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08:39 egonw ha, the eclipse community picked up our Bioclipse SDK: http://feedproxy.google.com/~r/MetaBeta/~3/5FlNjn​uyB7c/creating-plugin-project-plugin-project.html
08:39 zarah egonw's link is also http://tinyurl.com/myq428
08:39 egonw and seriously responding!
09:24 egonw olass: ping
09:24 olass egonw: pong
09:26 olass egonw: pong
09:26 egonw right
09:26 egonw pong
09:27 egonw sorry... was distracted by a naste headache...
09:27 egonw ummm
09:27 egonw I implemented a second ui.newFile()
09:27 egonw the current one creates an empty file
09:27 egonw my addition takes a second String with file content
09:27 egonw can I commit
09:27 egonw ?
09:28 olass sure
09:29 olass egonw: I was sort of wondering if you could have a look at running the CDK plugin junit-tests
09:29 egonw yes
09:29 olass they fail for me with some complaints about logging
09:29 egonw damn nasty thing of grant applications is...
09:29 egonw your body rejects being ill
09:29 olass hum, is that a bad thing?
09:29 egonw but only the deadline
09:30 egonw and then it makes up for the days not being ill
09:31 CIA-52 bioclipse.core: Egon Willighagen master * rfb04598 / (2 files): Added newFile() that takes a String with file content - http://bit.ly/3Z7fst
09:34 egonw olass: I also want to commit the code for the xml manager...
09:34 olass what is that?
09:34 egonw it's still being worked on, but like to start making commits (to have a back up)
09:35 egonw helper stuff for XML validation and introspection
09:35 olass a new plugin?
09:35 egonw yes
09:35 olass what are the deps?
09:35 egonw net.bioclipse.xom
09:35 egonw only that
09:35 egonw no eclipse featuers
09:35 olass sounds fine
09:41 CIA-52 bioclipse.core: Egon Willighagen master * r1790c56 / (26 files in 8 dirs): Added stubs for the XML helper manager for validation and introspection - http://bit.ly/uKvDv
09:56 samuell joined #bioclipse
10:47 egonw hi samuell
10:50 samuell hi egon
10:52 * samuell just got started for today
10:52 samuell egonw: Do you have good tip for a paper on OWL?
10:53 egonw as in tutorial ?
10:53 egonw http://www.w3schools.com/RDF/rdf_owl.asp
10:53 zarah egonw's link is also http://tinyurl.com/bc287q
10:53 egonw http://www.w3.org/TR/2009/PR​-owl2-new-features-20090922/
10:53 zarah egonw's link is also http://tinyurl.com/mt2u57
10:54 samuell egonw: Thanks!
10:56 samuell egonw: Yeah, well tutorials are always good. Also still looking for sth which gives a good overview of how it fits in with other technologies.
10:57 samuell but probably I'll find it in the tutorials, and the Pellet paper
11:00 egonw no jonalv?
11:02 samuell w3schools++
11:03 samuell http://www.w3schools.com/RDF/rdf_owl.asp was exactly the kind of summary I was looking for :)
11:03 zarah samuell's link is also http://tinyurl.com/bc287q
11:04 samuell egonw++
11:04 samuell as well.
11:04 samuell (Don't really understand this ...++ system though :| )
11:06 egonw @karma egonw
11:06 zarah egonw has a karma of 134
11:11 egonw @karma samuell
11:11 zarah samuell has a karma of 2
11:11 samuell :o
11:12 samuell :|
11:13 masak samuell++
11:13 samuell Thanks :)
11:13 masak pleasure. :)
11:25 samuell egonw: "Pellet is coupled with a Datalog reasoner" (Pellet paper)
11:25 egonw ah, ack
11:26 samuell Datalog = subset of Prolog, right...
11:27 egonw oh :)
11:44 samuell btw, which citation style is most common in bioinformatics?
11:44 samuell Or, which is best to use, in general?
11:46 egonw I don't care much
11:46 egonw are you into latex?
11:46 egonw if so, just use the default
11:46 egonw if not, please do consider it :)
11:46 egonw btw, there are nice latex presentation styles
11:46 egonw for Uppsala University
11:52 CIA-52 bioclipse.core: Egon Willighagen master * r97598ca / plugins/net.bioclipse.xml/src/net/bio​clipse/xml/business/IXmlManager.java : isMethods should return true/false - http://bit.ly/4fp6XL
11:52 CIA-52 bioclipse.core: Egon Willighagen master * r713cfa6 / (2 files in 2 dirs): Implemented isWellFormed() - http://bit.ly/11GL8l
12:11 samuell egonw: Ok! Have tried a little bit of latex, but didn't get into it too much.
12:11 egonw I will send a presentation of mine
12:11 samuell Ok!
12:30 egonw samuell: email on its way
12:31 samuell Ok, thanks!
12:31 masak egonw++ # knows "its" from "it's"
12:36 samuell :)
12:36 samuell The tar seems broken though, can't extract it
12:37 samuell Get an unrecoverable error
12:37 masak is it a .tar or a .tar.gz?
12:37 samuell .tar.gz
12:37 egonw tar zxvf fr...tar.gz
12:37 samuell yep
12:37 masak samuell: and you didn't forget the 'z'?
12:37 samuell no
12:37 masak hm.
12:37 samuell evn tried both
12:37 samuell (even)
12:38 egonw works here
12:38 masak try 'md5 fr...tar.gz'
12:38 egonw $ md5sum frankfurt2009.tex.tar.gz
12:38 egonw 5e78e69366b4b7153d750530b62e20ef  frankfurt2009.tex.tar.gz
12:38 masak and compare against egonw's.
12:38 samuell Hmm, succeeded now
12:38 masak o.O
12:38 samuell Probably the problem was saving the file to an NTFS disk
12:39 masak huh.
12:39 samuell Worked when saving to dekstop (/home folder is ext3)
12:41 samuell Indeed, the md5sum was different, on the NTFS disk
13:10 masak NTFS--
13:10 masak google ntfs different md5sum
13:10 zarah masak: http://www.knoppix.net/foru​m/viewtopic.php%3Ft%3D28912
13:15 egonw and once more my bioclipse does not boot... :(
13:17 samuell masak: Thanks!
13:18 masak um, that URL didn't resolve for me. YMMV.
13:18 samuell No, but googled it up myself :)
13:18 masak heh :)
13:18 masak zarah: google it up yourself!
13:18 zarah masak: http://www.urbandictionary.com/define​.php%3Fterm%3Dbig%2520up%2520yourself
13:19 masak 'big up yourself' isn't defined yet... :)
13:21 samuell IRC needs an 'url_decode()' function
13:24 masak seeing as knowing what is and what isn't a URL is a difficult problem in itself...
13:25 samuell Yep, and different url representations (w/wo escape chars) + different charsets = big mess
13:25 samuell (different charsets generating different url escape codes et.c.)
13:28 * samuell goes for lunch
13:48 masak already?
13:52 samuell :)
13:52 shk3 joined #bioclipse
13:53 samuell argh... can't retract my away status (in X-Chat Gnome)
13:54 samuell (Never mind. Just succeded. Seems they've fixed the bug.)
14:03 egonw olass: ping
14:17 olass egonw: in tel
14:17 egonw no worries
14:22 olass egonw: pong
14:22 CIA-52 bioclipse.core: Egon Willighagen master * r6421f0e / plugins/net.bioclipse.core.tests/src​/net/bioclipse/managers/tests/Abstra​ctManagerMethodDispatcherTest.java : Removed unused import - http://bit.ly/3AMLAw
14:22 CIA-52 bioclipse.core: Egon Willighagen master * r49b6e8c / features/net.bioclipse.core_feature/feature.xml : Deps required by org.apache.xml - http://bit.ly/4lPUm2
14:22 CIA-52 bioclipse.core: Egon Willighagen master * r3437b11 / (5 files in 3 dirs): Implemented validate() using Apache's Xerces and XOM - http://bit.ly/zaAJG
14:22 CIA-52 bioclipse.core: Egon Willighagen master * r584ed07 / (4 files):
14:23 CIA-52 bioclipse.core: Reworked how errors are passed.
14:23 CIA-52 bioclipse.core: * removed the Validation.Event enumeration
14:23 CIA-52 bioclipse.core: * added XMLError to hold an arbitrary error message - http://bit.ly/2petXE
14:23 egonw to validate, I seem to need apache xerces
14:23 egonw which pulls in a few extra plugins
14:23 egonw (but still no special features)
14:23 olass are they in core feature?
14:23 egonw see commit: [09/23/09 16:23] <CIA-52> bioclipse.core: Egon Willighagen master * r49b6e8c / features/net.bioclipse.core_feature/feature.xml : Deps required by org.apache.xml - http://bit.ly/4lPUm2
14:23 egonw they were not, but are now
14:24 olass ok
14:24 olass sounds logical that they are there IMO
14:27 egonw ok, good
14:45 CIA-52 bioclipse.core: Egon Willighagen master * rb6ece03 / (2 files): Fixed the testing for well-formedness; no longer fails on validity issues - http://bit.ly/VlLwl
15:01 egonw wow... eclipse 3.5 can even undo file renames...
15:36 samuell egonw: What do you have to say about SWRL? (In one line)
15:37 samuell In relation to other stuff. Does is seem to be much work done with SWRL et.c.?
15:40 egonw samuell: no experience with that yet
15:41 samuell egonw: Ok
16:26 egonw and I love the fact that 3.5 can copy imported projects directly into a working set!
16:26 egonw eclipse 3.5 rules
16:26 egonw with Prolog, Pellet and whatever ;)
16:27 samuell :)
16:33 samuell SWRL btw, seems to be an alternative project to integrate OWL with rules (RuleML in this case) - alternative to the OWL DL / Datalog combination that is used in reasoners like Pellet.
16:34 samuell SWRL is getting some critique though, in this article: http://www.cs.uwaterloo.ca/~gwed​dell/cs848/SWRL_Parsia_et_al.pdf
16:34 zarah samuell's link is also http://tinyurl.com/lgqza4
16:34 egonw parsia?
16:35 egonw parsia has a link to Pellet
16:35 egonw pellet is by parsia, if not mistaken
16:36 samuell Parsia?
16:36 egonw right
16:37 samuell Just to continue: In the article it seems they think SWRL has too much expressivity, so it does too much outside OWL... or something like this...
16:37 samuell Trying to get some idea about all this.
16:37 egonw yeah, it's a rather large field
16:37 egonw don't dwell too much
16:37 egonw you do not have enough time for that in your project :)
16:37 samuell Seems true :)
16:38 egonw that is, keep a good focus on your goals...
16:38 samuell SWRL is suggested for W3C though, so that's why...
16:38 samuell But it seems there are quite a bit of overlapping technologies out there.
16:39 egonw bbl
16:46 samuell Ah, now I see why you asked about "Parsia"! :) Didn't realize that the paper was by the authors of Pellet.
16:46 samuell (Didn't look at the URL or file name either)
17:24 samuell brb
17:38 samuell egonw: Will try to send you some slides at least before lunch tomorrow.
17:38 samuell bbl
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