Camelia, the Perl 6 bug

IRC log for #bioclipse, 2010-03-24

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All times shown according to UTC.

Time Nick Message
05:35 egonw__ joined #bioclipse
06:08 sneumann joined #bioclipse
06:32 annzi joined #bioclipse
07:22 egonw__ moin
07:22 zarah privet egonw__
07:22 egonw annzi: ping
07:22 annzi egonw: pong
07:23 egonw I'm canceling tomorrows journal club
07:23 egonw only you could be there
07:23 annzi oh ok
07:23 egonw that would result in too little discussion
07:23 annzi true, do you know when we will have it instead?
07:24 egonw two weeks after that
07:24 egonw I'm sticking to the schedule
07:24 egonw easiest
07:24 annzi ok
07:25 annzi btw I leave next Wednesday, do you think that we should meet up before that or perhaps directly when I come back?
07:29 egonw or both
07:30 egonw let's meet tomorrow at 14?
07:31 annzi ok
07:42 sneumann joined #bioclipse
07:47 egonw @tell samuell interesting post... performance testing is indeed tricky. Can you do the computation in Fig 1 a second time (of more), and plot the average as well as the standard deviation instead?
07:47 zarah Consider it noted.
07:47 egonw @tell samuell posting here, as I was unable to find where I could leave a comment in the blog...
07:47 zarah Consider it noted.
07:54 Gpox joined #bioclipse
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08:53 annzi joined #bioclipse
09:09 jonalv joined #bioclipse
09:31 egonw @ask samuell if it is difficult to put a twitter search on #bioclipse as headlines on the homepage
09:31 zarah Consider it noted.
10:15 annzi joined #bioclipse
10:54 masak joined #bioclipse
11:50 sneumann hi annzi,
11:50 sneumann could you give me an idea which steps are required
11:50 sneumann to run MOSS on two lists of molecules,
11:50 sneumann to mine for common (sub-) structures between them ?
11:51 sneumann Would you need two lists of SMILES,
11:51 sneumann or would it have to be a full-blown SPARQL endpoint ?
11:57 annzi sneumann: moss requires a moss supported file in the format like( id, threshold, SMILES).
11:57 sneumann So I prepare (one ? two ?)  files with SMILES, one per line ?
11:58 annzi one file with all SMILES as input
11:58 annzi if you like to set some in focus or complement you adjust the threshold
11:58 sneumann ah, just found http://www.borgelt.net/moss.html
11:58 zarah sneumann's link is also http://tinyurl.com/ye7vrkn
11:59 annzi was just going to send you that link :)
11:59 sneumann thanks, I'll play and report back
11:59 annzi have fun ;)
12:01 sneumann annzi: "The version supporting these features is property of Tripos, Inc."
12:01 sneumann do you know if that thing has a special name != MOSS from Tripos ?
12:01 annzi not that I know of..
12:05 egonw joined #bioclipse
12:55 jpansanel moin
12:55 zarah oh hai jpansanel
13:29 jonalv I hate class paths
14:02 sneumann classpath--
14:47 miguelrojasch joined #bioclipse
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14:50 jonalv joined #bioclipse
14:52 * jonalv has spent the day failing to get Brunn to run on HQSLDB instead of on MySQL andfailing to install MySQL on his machine. I mean how hard should it be to install MySQL?
14:53 jonalv evil computers
15:13 egonw_ joined #bioclipse
15:27 CIA-64 bioclipse.core: Carl Masak master * r0943d2e / (315 files in 73 dirs): [plugins] de-Javadoc'd all copyright/license comments - http://bit.ly/asdEME
15:27 jonalv masak++
15:27 masak long time, no commit :)
15:28 masak (and CIA bots still refuse to show my .bioinformatics commits)
15:31 jonalv masak: yea they ahve to be magicly configured somewhow. I think egonw nows how to do it...
15:40 egonw joined #bioclipse
15:53 jonalv egonw: do you know how to get the CIA bot to report commits here?
15:55 egonw yes
15:55 egonw in conf call right now
16:36 samuell joined #bioclipse
18:07 olass joined #bioclipse
18:07 olass o/
18:07 olass moin
18:07 zarah oh hai olass
18:18 _ilbot2 joined #bioclipse
18:18 Topic for #bioclipseis now An open source workbench for chem- and bioinformatics - http://www.bioclipse.net/ | BioclipseWiki => http://wiki.bioclipse.net/ !! | logs => http://colabti.org/irclogge​r/irclogger_logs/bioclipse & http://moritz.faui2k3.org/irc​log/out.pl?channel=bioclipse || Bioclipse2 beta released! See http://bioclipse.blogspot.com/ || http://www.youtube.com/watch?v=ZUBQknWUEYU
18:18 olass joined #bioclipse
18:34 egonw hi olass!
18:34 egonw we heard the news :(
18:34 egonw how is it?
18:34 olass pretty good
18:34 olass yes, sad we didn't get the trophy
18:34 egonw coverage on planet eclipse looks indeed quite good
18:34 egonw tried tasktop
18:34 egonw it's actually quite nice
18:35 olass how are things at home?
18:35 egonw good
18:35 olass now that the RDF paper is submitted, are things slowing down?
18:35 egonw my paper is submitted
18:35 egonw no, no
18:36 edrin joined #bioclipse
18:36 edrin hi
18:36 zarah hello edrin, you fantastic person you
18:36 edrin hi egonw
18:36 olass hi rdrin
18:36 egonw hej edrin
18:36 olass edrin: are you in STHLM now?
18:37 egonw edrin: really enjoyed our meeting yesterday!
18:37 edrin i realized there is an open access wlan around here, connection is not good but ok
18:37 edrin olass: yes
18:37 edrin hej ola :)
18:37 olass hej edrin
18:37 edrin egonw: thank you. I enjoyed it, too
18:38 egonw :)
18:51 edrin olass: unfortunately, we have seen, you did not get the first price
18:52 edrin we will fly to Kiruna tomorrow morning
18:52 olass yes, sad
18:52 olass Kiruna might be a bit cold
18:52 olass still
18:52 olass I'm sure you'll enjoy it!
18:52 edrin We are prepared, got my skiing stuff with me
18:52 egonw edrin++
18:58 edrin olass: when will you return?
18:58 olass April 1st
18:59 olass so next week thursday I think
19:00 edrin left #bioclipse
19:00 edrin joined #bioclipse
19:01 edrin as I said, no stable connection
19:02 edrin olass: when will you return?
19:02 olass April 1st
19:02 egonw [03/24/10 19:58] <olass> April 1st
19:02 egonw [03/24/10 19:59] <olass> so next week thursday I think
19:02 olass so next week thursday I think
19:02 olass need to go for lunch now
19:03 olass see you all later
19:03 olass bye
19:03 edrin ok
19:03 edrin cu
19:07 edrin egonw: i will be back later
19:07 edrin goto go
19:07 egonw ack
19:08 egonw cu
19:08 edrin cu
19:08 edrin left #bioclipse
19:12 sneumann joined #bioclipse
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20:39 edrin joined #bioclipse
20:39 edrin hi again
20:39 edrin left #bioclipse
20:39 edrin joined #bioclipse
22:03 egonw joined #bioclipse
22:15 egonw samuell: no, was not aware of that yet
22:15 egonw thanx for the ping
22:21 edrin left #bioclipse
22:22 samuell you're welcome
22:22 zarah samuell: You have new messages. Write '/msg zarah @messages' to read them.
22:23 egonw samuell: type @msg
22:23 egonw @msg
22:23 zarah egonw: You have no new messages.
22:23 samuell @msg
22:23 zarah samuell: You have no new messages.
22:23 egonw huh??
22:23 samuell Yep, got something in a private chat with zarah now :)
22:23 egonw ah
22:24 samuell Thankx
22:25 samuell Regarding twitter search ... Don't know ...
22:25 samuell Can check sometime soon
22:29 egonw no need
22:29 samuell Ok
22:33 samuell Ah, comment posting links are hidden in the current Drupal skin on my blog (copied it from an earlier project for a company who had no use of that ^^ ...)
22:33 samuell Will fix
22:34 samuell Regarding performance testing ... maybe std dev is good, but in fact the results are quite similar time after time
22:35 samuell Quite strange peak for the 40 peak data file though
22:35 samuell But the most important thing now I guess is to test for some larger datasets
22:35 samuell The current dataset is so small that these tests don't really say much
22:36 samuell Other things seem to quite easily diffuse the picture
22:36 samuell For larger datasets any difference between Prolog and Jena should be clearer
22:37 samuell (I was sticking with the small datasets just because pellet was so extremely slow when used on the TDB store)
22:37 egonw yes, that they are similar is clear to you; the std dev makes it clear for others too
22:37 samuell Well, good point
22:37 samuell :)
22:38 egonw remember, trust no one
22:38 egonw just facts as proof
22:52 samuell But I should trust you regarding this?
23:01 egonw no
23:01 egonw btw, did you read this:
23:02 egonw http://www.russet.org.uk/blog​/2010/03/leaving-bfo-discuss/
23:02 zarah egonw's link is also http://tinyurl.com/yja5pal
23:02 egonw makes the point that 2000 years of philosophy is nice
23:02 egonw but certaintly does not mean it helps for the (natural, experimental) science we do today
23:03 egonw it seems there is a serious lack in modern natural science philosophers
23:05 miguelrojasch joined #bioclipse
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23:23 samuell egonw: Read it now. Interesting read. There's much empty philosophy out there. Being confronted with reality is healthy.
23:24 samuell @tell egonw Read it now. Interesting read. There's much empty philosophy out there. Being confronted with reality is healthy.
23:24 zarah Consider it noted.

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