Camelia, the Perl 6 bug

IRC log for #bioclipse, 2010-02-01

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All times shown according to UTC.

Time Nick Message
06:19 sneumann__ joined #bioclipse
07:12 annzi joined #bioclipse
07:59 sneumann__ joined #bioclipse
08:09 Gpox joined #bioclipse
08:16 egonw joined #bioclipse
08:24 egonw moin
08:24 egonw @tell masak what about 13WAAAOVA ?
08:35 mgerlich joined #bioclipse
08:54 sneumann joined #bioclipse
09:08 olass joined #bioclipse
09:14 egonw hi olass
09:15 olass hi egonw
09:15 jonalv joined #bioclipse
09:15 egonw hi jonalv
09:16 egonw hi all others too
09:21 olass hi
09:23 jonalv hi all
09:33 * jonalv rebbots
09:33 jonalv |reboots
09:47 jonalv joined #bioclipse
09:47 egonw olass: ping
09:47 olass pong
09:47 egonw quick question
09:48 egonw how much work is involved in writing a text editor with error reporting?
09:48 egonw in rcp
09:49 egonw (or wrt to that paper you just send around... a OWL browser, but that's a different question :)
09:49 olass I have never done error reporting, but is hould be pretty simple. My problem was that I tried error reporting in an editor not backed up by a Resource, and that was much more problematic. a text editor should be straightforward
09:49 jonalv Gpox: http://www.doodle.com/ee5g5panbe6dk6n9
09:49 olass so I'd say quite easy
09:49 jonalv zarah: tell masak http://www.doodle.com/ee5g5panbe6dk6n9
09:49 egonw olass: please read my blog of this weekend
09:50 egonw olass: I have the CDK code to do this for text based files...
09:50 jonalv zarah: ping
09:50 olass @gg egon willighagen blog
09:50 egonw olass: and this would show the power of RCP nicely, and actually have something novel
09:50 egonw http://chem-bla-ics.blogspot.com/2010/01​/validating-mdl-sd-files-and-symyx.html
09:50 egonw 13WAAAOVA: ping
09:50 jonalv Zarah!!!
09:50 jonalv :(
09:50 egonw jonalv: 13WAAAOVA is zarah
09:50 jonalv @ping
09:50 egonw well, too...
09:51 egonw jonalv: btw, please read that blog too...
09:51 jonalv egonw: sry what blog?
09:51 egonw I just gave the link of
09:51 jonalv egonw: cdk 1.2.5 changes?
09:52 egonw [02/01/10 10:50] <egonw> http://chem-bla-ics.blogspot.com/2010/01​/validating-mdl-sd-files-and-symyx.html
09:52 jonalv egonw: ah sry I am blind
09:52 egonw indeed :)
09:52 egonw np :)
09:52 olass egonw: reg your blog, this was what I propsed last year ;)
09:52 egonw excellent
09:52 olass glad you have the code
09:52 egonw CDK can now do it :)
09:52 olass error reporting in a file-based text editor is quite easy
09:52 olass I did some preliminary study
09:52 egonw OK, let's make that a 2.4 goal then
09:53 olass might be aböe tp dig up the code...
09:53 olass yes
09:53 olass I think this is very important in Bioclipse
09:53 olass since chemical file formats are so messed up...
09:53 egonw quite so
09:54 * olass will try to dig up the error reporting code he wrote last year
09:54 * jonalv what he said
09:54 olass FYI I added the ErrorView to Bioclipse :)
09:54 egonw cool :)
09:55 olass but I think no one has used it yet..
09:55 jonalv olass: do we have a policy on how that should be used?
09:55 olass no
09:57 jonalv olass: so basically no one knows how it should be used... :(
09:58 olass jonalv: have you felt an urgen pressing need for it?
09:58 jonalv olass: to use it? No
09:58 jonalv olass: for a policy? YEs just when you told me about it a couple of minutes ago
09:59 olass jonalv: file me a bug
10:00 * egonw will reboot zarah
10:00 egonw jonalv: don't you have reboot powers too?
10:01 zarah joined #bioclipse
10:01 egonw zarah: welcome back!
10:01 zarah egonw: I did not understand that
10:02 egonw @tell masak I rebooted zarah on your behalf
10:02 zarah Consider it noted.
10:07 jonalv egonw: I have reboots powers but not the skills I guess..
10:07 egonw :)
10:08 * egonw has skills to make coffee
10:08 jonalv zarah: tell masak http://www.doodle.com/ee5g5panbe6dk6n9
10:08 zarah jonalv's link is also http://tinyurl.com/ybkoj42
10:08 zarah Consider it noted.
11:19 egonw feels good to work on the CDK again :)
11:20 * egonw released CDK 1.2.5
11:20 egonw and is preparing CDK 1.3.2 for Bioclipse
11:21 sneumann still waiting for your coffee to arrive here ;-)
11:21 egonw :)
11:44 s_wolf joined #bioclipse
11:47 s_wolf hi there
11:48 s_wolf [12:42] <sneumann> [12:36] <sneumann> Just talked to Sebastian, he likes that idea
11:48 s_wolf [12:42] <sneumann> [12:42] <egonw> good... I'll set up a wiki page, where we can summarize functional goals...
11:48 s_wolf [12:42] <sneumann> [12:42] <egonw> please ask him to email ola spjuth for a wiki account
11:48 s_wolf [12:42] <sneumann> [12:42] <egonw> or ask on #bioclipse
11:48 sneumann Hm, how many indirections before IRC implodes ?!
11:48 s_wolf ;)
12:02 egonw joined #bioclipse
12:02 egonw olass: can you please provide s_wolf with a wiki account?
12:05 egonw http://it-republik.de/jaxenter/news/053649
12:05 zarah egonw's link is also http://tinyurl.com/yhks7hn
12:14 sneumann Bioclipse
12:14 sneumann This site is temporarily unavailable.
12:14 sneumann Please notify the System Administrator
12:14 sneumann i.e. sbd is working on it ? Or is it actually down ?
12:14 egonw www.bioclipse.net ?
12:14 sneumann si
12:14 egonw yeah, same here
12:14 egonw olass: ping
12:15 egonw well, it seems slow...
12:15 egonw I actually got some content
12:15 egonw but not all
12:19 sneumann Wiki has problems, too:
12:19 sneumann http://wiki.bioclipse.net/index.php?title​=Special:UserLogin&amp;returnto=Main_Page
12:19 zarah sneumann's link is also http://tinyurl.com/yb4myes
12:19 sneumann Sorry! This site is experiencing technical difficulties.
12:19 egonw yeah, same machine I think
12:20 sneumann Could be a database down ?
12:20 egonw yes, could be
12:20 egonw trying to reach olass
12:20 egonw olass: ping
12:21 egonw he's not at his cellular
12:21 egonw mobile
12:21 egonw Handy
12:21 sneumann you already did that. Maybe louder: olass: ping ping ping ping ping
12:21 egonw olass: ping
12:21 egonw olass: ping
12:21 egonw olass: ping
12:21 zarah olass: ping
12:21 egonw :)
12:22 sneumann @tell olass sneumann also wants an wiki account
12:22 zarah Consider it noted.
12:39 olass egonw: pong
12:39 zarah olass: You have new messages. Write '/msg zarah @messages' to read them.
12:40 olass @clear-msg
12:40 zarah olass: Messages cleared.
12:40 egonw ok, so you'r on it?
12:40 olass yup
12:40 egonw wiki accounts too?
12:40 egonw (just making sure)
12:41 olass egonw: I need full name and desired email for s_wolf and sneumann
12:41 olass s_wolf, sneumann: could you let me know?
12:50 egonw olass: see priv chat
13:00 jonalv olass: ping
13:01 olass pong
13:02 egonw s_wolf, sneumann: http://wiki.bioclipse.net/i​ndex.php?title=Metabolomics
13:02 zarah egonw's link is also http://tinyurl.com/yaxcrdz
13:06 olass s_wolf, sneumann: You should have received accounts by email
13:10 s_wolf olass: ok thx
13:11 * sneumann keeps checking his mail ...
13:13 * egonw is afk for coffee and homemade cake
13:25 egonw back
13:30 olass sneumann: did you get that wiki account?
13:30 olass if not , let me know
13:30 annzi joined #bioclipse
13:32 sneumann sorry, editing as you speak :-)
13:45 * sneumann just edited http://wiki.bioclipse.net/​index.php?title=Main_Page updating the Announcements
13:45 jonalv sneumann++
13:46 s_wolf i did not yet recieve an email
13:46 sneumann it is marked as "[SPAM_ipb] Account creation for BioclipseWiki", do you have a filter ?
13:46 egonw s_wolf: should have gone to your gmail account
13:47 s_wolf ah ok
13:47 s_wolf I didnt check this one
13:47 egonw which I got from your linkedin account :)
13:48 s_wolf :)
13:49 egonw sneumann: perhaps add IPB to http://wiki.bioclipse.net/index.​php?title=Category:BioclipseLabs ?
13:49 zarah egonw's link is also http://tinyurl.com/ye2xyno
14:03 sneumann egonw: Done.
14:05 egonw great, thanx!
14:15 jonalv egonw: ping
14:15 egonw pong
14:15 jonalv egonw: do you have a second + Bioclipse?
14:16 jonalv egonw: It's regarding the superimpose action
14:16 egonw what's up?
14:16 jonalv egonw: in sample data 3D structures
14:16 jonalv select the two pentan* molecuels and choose superimpose
14:17 jonalv egonw: ready?
14:17 egonw you want me to do that?
14:17 jonalv egonw: please
14:17 egonw that's not a second...
14:17 egonw mom, firing up bc2.2
14:17 jonalv egonw: almost
14:18 jonalv :)
14:18 egonw and installing the sample from the update site
14:18 jonalv egonw: you don't need to grab them from the update site. These samples are shipped...
14:18 egonw ah, that saves some time
14:18 egonw crap
14:18 egonw my bioclipse2.2 does not boot
14:19 egonw it did after download, but now just stopped working :(
14:19 jonalv egonw: huh?
14:19 egonw not error, no nothing
14:19 jonalv egonw: just run it from Eclipse then...
14:19 egonw master version also fine?
14:19 jonalv egonw: yea
14:19 jonalv this hasn't changed for a while...
14:20 egonw well, master has a new Jmol...
14:20 egonw anyway, let's short cut this
14:20 egonw instead of letting me try to reproduce it now
14:20 egonw what's the bug?
14:20 jonalv egonw: that is what I want your help figuring out...
14:21 jonalv egonw: but the superimpose seems rater bad for those two...
14:21 egonw for what?
14:22 jonalv pentanal-1-ol and pentanal
14:22 egonw oh, that might very well be...
14:22 egonw check the MCS
14:22 egonw I'm sure there are some degrees of freedom
14:22 egonw soon, we'll discuss the SMSD paper
14:22 egonw for better alternatives
14:23 jonalv egonw: okey, then it was the jmol problem of course...
14:23 egonw why jmol?
14:23 jonalv but that is sort of out of the point right now
14:23 egonw jmol is not doing the overlapping
14:23 jonalv it doesn't show both m,olecules when we do superimpose
14:23 jonalv not by default...
14:23 egonw no, you'd select them in the outline
14:23 jonalv yea...
14:23 egonw once we have a IJmolMolecule
14:24 egonw or similar, we have more power
14:24 * jonalv is preparing his jmol talk..
14:24 egonw ic :)
14:24 egonw file a bug report, if you like, and add the IJmolMolecule as blocker
14:25 egonw OK, going offline for the rest of the afternoon
14:25 jonalv I might, right now jmol is a mess though...
14:25 egonw jonalv: what's new?
14:25 egonw bbl tonite
14:25 jonalv egonw: I am suprised at how bad your superimpose worked
14:25 egonw yeah, one has to do with whatever is available
14:26 egonw and you picked bad examples
14:26 egonw try aligning protein sequences of 1CRN with a HIV protein
14:26 jonalv egonw: I didn\t pcik em. These are the examples Bioclispe ships with
14:26 egonw that's not the point
14:26 egonw we can try to align apples and oranges...
14:26 jonalv okey then I missed the point
14:26 egonw that will more or less work too
14:26 egonw but not very well
14:27 egonw you picked two molecules with not too much in common
14:27 jonalv egonw: they are very much alike
14:27 egonw and are now suprised that it doesn't align a hydroxyl with a carbonyl well
14:27 egonw too many degrees of freedom
14:27 egonw that's all
14:28 egonw jonalv: are you doing the pharmbio course now?
14:28 jonalv hm I just expected some atoms to be on top of eachother...
14:28 egonw OK, got to run now?
14:28 jonalv egonw: no I am not
14:28 jonalv egonw: oki cya
14:28 * egonw : yeah, you really should!
14:28 egonw (that was an internal note :)
14:28 egonw bye
15:35 sneumann chmod +x bioclipse.gtk2.18.sh
15:39 sneumann Bioclipse 2.2 welcome screen still says "2.0"
15:52 * jonalv mumbles something about us really needing that script for setting a new version...
15:53 jonalv sneumann: could you file a but report?
15:53 jonalv |bug
16:01 sneumann yup, done
16:17 sneumann cu
16:22 jonalv ah sneumann++
16:38 jonalv :w
16:38 jonalv OSX--
18:32 egonw joined #bioclipse
19:18 sneumann joined #bioclipse
19:59 egonw_ joined #bioclipse
20:14 egonw joined #bioclipse
20:25 egonw cool to see Bioclipse all over the German media news channels
20:25 zarah egonw: You have new messages. Write '/msg zarah @messages' to read them.
20:25 egonw http://www.heise.de/newsticker/meldung​/Bioclipse-2-2-ist-fertig-919641.html
20:25 zarah egonw's link is also http://tinyurl.com/y8hfj2j
20:26 egonw lovely comments :)
20:26 egonw http://www.heise.de/open/news/foren/S-Re-Kl​ingt-erst-mal-spannend-was-genau-kann-man-d​amit-machen/forum-173578/msg-18032744/read/
20:26 zarah egonw's link is also http://tinyurl.com/yd6hf7m
20:43 sneumann_ joined #bioclipse
21:39 olass joined #bioclipse
21:39 olass egonw: ping
22:44 sneumann_ hi olass,
22:45 sneumann_ tried the http://gist.github.com/170410 this afternoon,
22:46 sneumann_ is there an easy way to put the result
22:46 sneumann_ res=metaprint2d.calculate(mollist);
22:46 sneumann_ into my workspace instead of the console ?

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