Camelia, the Perl 6 bug

IRC log for #bioclipse, 2007-11-12

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All times shown according to UTC.

Time Nick Message
06:24 egonw joined #bioclipse
06:35 egonw joined #bioclipse
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12:17 egonw who added the Connotea support?
12:20 jonalv egonw: svn blame? What's that btw?
12:20 egonw huh?
12:21 jonalv egonw> who added the Connotea support?
12:21 jonalv <jonalv> egonw: svn blame? What's that btw?
12:22 egonw where does the blame and the svn come in?
12:22 egonw 2. define 'that'...
12:22 jonalv lol
12:22 jonalv that = Connotea
12:22 jonalv well if Bioclipse suddenly supports it (whatever it now is) can't you use svn to giffure out who did it?
12:23 egonw connotea is a system to store bibliographics references
12:23 * jonalv has probably missundetstood eveything
12:23 egonw ah... sorry... correct... something made a change in the wiki...
12:26 olas egonw: connotea was me
12:26 olas wasn't I logged in?
12:26 egonw did not show up in the RSS headlines
12:26 egonw I could have followed the link :)(
12:27 olas anyway: I thought it interesting
12:27 olas And there are Java clients
12:27 olas but we would need better entrez tools first I suppose
12:28 olas egonw: how's the new JCP coming along?
12:28 egonw not so fast, I'm afraid...
12:29 olas :-(
12:36 pohyg joined #bioclipse
12:36 egonw hi pohyg
12:37 pohyg hi egonw
12:37 egonw pohyg: thanx for the #bioinformatics tip :)
12:37 egonw never was aware of that channel
12:37 egonw (via your 'whois')
12:38 pohyg do i know you in person egonw?
12:38 egonw pohyg: no idea :)
12:38 egonw I don't even know we know each other virtually...
12:39 egonw you're a blogger?
12:41 pohyg i hv ppl stalking me from time to time.. u got me worried for a moment
12:41 pohyg I am not a blogger
12:41 egonw pohyg: no, just trying to make you feel welcome on #bioclipse ;)
12:42 pohyg OK... phew.
12:42 pohyg i m interested in several things
12:42 jonalv egonw: sounds like you are doing a somewhat bad job if you make our guests feel stalked... :)
12:42 pohyg bioclipse included
12:42 egonw jonalv: :)
12:42 egonw pohyg: yeah, go ahead
12:44 pohyg it is programmed in java isn't it?
12:44 egonw yes
12:44 pohyg with java
12:45 egonw but C/C++ projects have been included as plugin in the past
12:45 pohyg why it was not done with wxwidget/wxwindows in C++?
12:45 egonw additionally... there is scripting support for JavaScript...
12:45 egonw because it is based on the Eclipse Rich Client Platform
12:45 pohyg oh yeha
12:45 pohyg yeah
12:48 egonw but, as said, there are various ways to use C++ code in Bioclipse
12:48 jonalv So pohyg what's your main field of interest?
12:49 pohyg bioinformatics in general... more towards system biology
12:50 pohyg i also look at various bioinformatics softwares
12:50 egonw aren't we all going towards SB?
12:51 jonalv so what do you think of Bioclipse? :)
12:52 pohyg i hv tried bioclipse sometime ago
12:52 pohyg found it interesting but not using in for my daily research work
12:52 pohyg thinking about it
12:52 olas pohyg: are you using SBML?
12:53 * olas would love to get the SBML plugin active again
12:53 pohyg e-cell, cytoscape mostly
12:53 pohyg yes, smbl is in
12:54 egonw pohyg: were you in Amsterdam last thursday?
12:54 pohyg no
12:54 olas http://wiki.bioclipse.net/index.​php?title=Systems_Biology_plugin
12:55 olas There was this guy, Sebastian Bauer, who started to workon that plugin
12:55 olas But it is not active anymore, I don't know what the status is
12:56 olas His email is: mail@sebastianbauer.info
12:56 olas (if you want to get in contact with him)
13:00 pohyg the code is distributed via SVN?
13:00 olas yes
13:00 olas only
13:00 olas We are designing Bioclipse2 currently
13:01 pohyg oic.. so no .src.tar.gz
13:01 olas http://wiki.bioclipse.net/​index.php?title=Bioclipse2
13:01 pohyg bioclipse 2?
13:01 olas well, the next version of Bioclipse
13:01 olas A rewrite of the core with full scripting capability
13:01 olas But all plugins will be re-used
13:01 olas for SVN info: see http://wiki.bioclipse.net/​index.php?title=Subversion
13:02 olas but please use trunk
13:02 olas we should make a new binary release from trunk VERY soon I hope
13:15 egonw olas: yes, we should schedule a hack session...
13:15 egonw to bug fix things...
13:27 olas test things at least :-)
13:28 pohyg i might some free time to help test things
13:28 pohyg i m getting the code now, will try to compile it
13:28 egonw pohyg: do you see use of a cytoscape plugin for bioclipse?
13:28 pohyg no
13:28 egonw good
13:28 pohyg they hv one?
13:28 egonw than I won't spent my free hours on that :)
13:28 pohyg oic
13:29 egonw no, don't think there are plugins either way
13:33 olas no, haven't heard of that (and I have looked a lot)
13:41 pohyg is bioclipse strictly developed on sun's jdk1.5.0?
13:45 egonw no, 1.6 is fine too :)
13:45 egonw but 1.4.2 is not
13:45 pohyg ok
13:46 egonw even Classpath/OpenJDK should get you quite far
13:48 pohyg how many of you developing bioclipse from a linux machine?
13:49 egonw I am...
13:50 pohyg ok
13:53 olas I am on Mac
13:53 olas jonalv is on linux
13:54 pohyg i work primarily in linux
13:54 pohyg Just read the bmc paper. Interesting indeed
13:55 pohyg was there any concern about the performance in response time of bioclipse on certain tasks?
13:58 egonw depends...
13:58 egonw not in general...
13:58 egonw the chemoinformatics plugin is not overly performent...
13:58 egonw and with webservices you have to wait anyway...
13:58 egonw the MD/QM code is fast
13:59 egonw conclusion: really depends on the algorithms and actual library used...
13:59 pohyg i certainly would move to multicore machine with in a year
13:59 egonw there have been some infrequent issues with too many messages send around...
14:00 egonw Bioclipse will very much benefit from that... being threaded java
14:00 pohyg oic
14:07 edrin joined #bioclipse
14:07 edrin hi
14:08 olas hi edrin
14:08 edrin hi olas
14:10 edrin back in a minute
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20:20 edrin joined #bioclipse
20:20 edrin hi
21:36 edrin joined #bioclipse
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