Camelia, the Perl 6 bug

IRC log for #bioclipse, 2010-07-21

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All times shown according to UTC.

Time Nick Message
04:35 egonw joined #bioclipse
04:46 egonw moin
04:46 zarah saluton egonw
05:35 swolfswolf__ joined #bioclipse
07:37 sneumann_ joined #bioclipse
07:39 egonw ok, one hotel reservation done: Oxford
07:39 egonw next up: Boston
08:36 sneumann_ joined #bioclipse
10:00 olass joined #bioclipse
10:00 olass moin
10:00 zarah hello olass, you fantastic person you
10:00 * olass blushes
10:18 egonw hi olass
10:18 olass hi egonw
12:04 CIA-71 bioclipse.ds: Ola Spjuth master * r7de2b5f / (59 files in 29 dirs):
12:04 CIA-71 bioclipse.ds: * Refactored out ames.sign and cpdb.sign into parent plugins.
12:04 CIA-71 bioclipse.ds: * Refactored out base classes for DS-LibSVM, SignaturesClassification2Classes, and SignaturesRegression
12:04 CIA-71 bioclipse.ds: * Read all models from files specified in plugin.xml
12:04 CIA-71 bioclipse.ds: * Impute (0,0) from range files if missing
12:04 CIA-71 bioclipse.ds: * Updated to latest CPDB and AMES QSAR models with aromatic signatures - http://bit.ly/9uKMWS
12:33 olass egonw: ping
12:33 olass in SmilesParser line 257, it does not use logger byt a system.out.println
12:33 olass not so nice
12:33 olass just a remark
12:34 olass (this is cdk reo, in bioclipse2.4 branch btw)
12:41 egonw please file a bug report
12:41 egonw otherwise I'll forget
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15:47 samuell Gaggle has the stuff I'd like to see in Bioclipse :/ ... http://gaggle.systemsbiology.org/docs/
15:47 zarah samuell's link is also http://tinyurl.com/33vktee
15:47 samuell ( Paper: http://www.biomedcentral.com/1471-2105/7/176 )
15:47 zarah samuell's link is also http://tinyurl.com/378cql5
15:47 samuell (Java based, open source)
15:48 samuell (LGPL)
15:48 samuell Too bad everyone is working on their own framework :/
15:58 egonw_ joined #bioclipse
16:48 olass samuell: what is the stuff you like to see in bioclipse?
16:49 olass what does gaggle have that we don't?
16:49 samuell Systems biology stuff :)
16:49 olass like..?
16:49 olass SBML?
16:50 olass pathways?
16:50 olass networks?
16:50 samuell Yes ...
16:50 olass more specific?
16:51 samuell But I mean ... I of course don't have a specific need of it at the moment ... it's just that I think Bioclipse would be a good framework for this kind of functionality
16:51 samuell And as it is gaining popularity (systems biology) that would be beneficial to Bioclipse
16:53 samuell But see it more as wishful thinking :)
16:55 samuell But I think a marriage of the cheminf functionality of Bioclipse with systems biology functionality would enable very interesting workflows
16:56 samuell (Like, look up and visualize all the pathways where a given chemical occurs etc)
17:01 olass samuell: you got a good point there
17:02 * olass would love to see pathways in Bioclipse
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