Camelia, the Perl 6 bug

IRC log for #bioclipse, 2007-11-01

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All times shown according to UTC.

Time Nick Message
00:11 edrin left #bioclipse
07:35 rojasm joined #bioclipse
07:35 rojasm moin
07:53 masak joined #bioclipse
08:32 egonw joined #bioclipse
08:43 egonw we need this asap in bioclipse: http://depth-first.com/articles/2007/10​/31/jinchi-run-inchi-anywhere-java-runs
08:44 olas joined #bioclipse
08:44 egonw [2007-11-01 09:43:43] <egonw> we need this asap in bioclipse: http://depth-first.com/articles/2007/10​/31/jinchi-run-inchi-anywhere-java-runs
08:44 egonw hi olas
08:44 olas hi egon
08:44 * olas is off to a meeting with Ma and his group
08:45 egonw :)
08:51 egonw coffee
09:56 EskilA joined #bioclipse
10:01 CIA-18 bioclipse: ospjuth * r4111 /trunk/playground/plugins/net.bioclipse.​biomoby.ui/src/net/bioclipse/biomoby/ui/ (BioMobyConstants.java BioclipseMobyModel.java): Caching of ontologies now works.
10:01 CIA-18 bioclipse: ospjuth * r4112 /trunk/playground/plugins/net.bioclipse.bio​moby.ui/src/net/bioclipse/biomoby/ui/prefs/ (4 files): Started working on preference page for multiple BioMoby Registries
10:02 CIA-18 bioclipse: ospjuth * r4113 /trunk/playground/plugins/net.bioclipse.​biomoby.ui/src/net/bioclipse/biomoby/ui/ (3 files in 3 dirs): Adapted to use cached registry.
10:38 olas egonw: around?
10:38 olas Name:    Molecule Auth:    org.openscience.cdk Desc:    Concept of a chemical molecule, such a metabolite. The molecule is represented in Chemical Markup Language. Contact: egonw@users.sf.net LSID:    urn:lsid:biomoby.org:objectclas​s:Molecule:2007-09-21T16-43-52Z ID:      null Parents: Object
10:38 olas Found you in biomoby :-)
10:38 egonw cool :)
10:38 olas working on that darn client
10:38 olas autogenerating GUI is not trivial
10:42 egonw no it is indeed not trivial :)
13:35 olas joined #bioclipse
15:14 edrin joined #bioclipse
15:15 edrin hello aagain
15:15 masak edrin: hi
15:15 edrin hello masak
15:15 masak edrin: I've been thinking increasingly about rhino and scripting in Bioclipse
15:16 masak although right now I don't have any concrete questions for you
15:16 masak just wanted to know I'm giving it some thought
15:16 edrin ok, fine :)
15:17 masak edrin: one thing I have been thinking of is that it would be nice to accept some kind of parameters into scripts
15:17 edrin yes, i know this will be important in next release
15:17 masak it could perhaps be possible to accept input through a message box or something, but that's very clunky
15:18 edrin input objects, and maybe even output objects
15:18 masak I'm thinking that a user might perhaps select a file or molecule or something
15:18 masak and then run a script on it
15:18 edrin to do "cross scripting"
15:18 edrin exactly
15:19 masak edrin: in fact, I need it for my degree project :)
15:19 masak so it's a high priority for me too
15:19 edrin i will need this, too
15:19 edrin because i want to do some sequence analysation with bioclipse soon
15:19 masak oh, ok
15:20 masak so if I did some early planning on how to accomplish this, you wouldn't be terribly upset?
15:21 edrin i thought about using biojava embl/genbank file parser and load my aspergillus genomes into a tree view... and then i could rightclick an Open Reading Frame and run a script on it...
15:21 edrin no
15:21 masak good
15:21 edrin of course not
15:21 masak right clicking sounds like a good idea
15:21 edrin maybe we could have a wikipage for this...
15:21 masak definitely
15:21 * masak makes one
15:22 edrin but everything should start with passing objects from/to scripts...
15:22 edrin but i can do this within a few minutes i think...
15:23 masak edrin: you can? excellent
15:23 edrin it's quite easy in fact...
15:23 masak then maybe we don't need a separate wiki page for it
15:23 masak I thought it was a biggish project to make it work
15:23 edrin not really...
15:25 edrin you know, from within the script you can access any objects in the bioclipse instance... all you will need then is to add a specific object to the script execution action...
15:25 masak unh...
15:26 masak well...
15:26 masak yes, that might work, but...
15:26 edrin what is your degree project??
15:26 masak hold on, I'll get the exact title for you
15:27 masak "Integrating Microarray Data with Drug Activity Patterns for Cellular Pharmacology"
15:28 masak it concerns data both from a LIS system inside of Bioclipse and from a database outside of it, imported via a plugin
15:37 CIA-18 bioclipse: ospjuth * r4114 /trunk/playground/plugins/​net.bioclipse.biomoby/lib/ (jmoby-dashboard.jar jmoby-others.jar jmoby.jar): Updated to latest BioMoby: 2007-11-01
15:37 CIA-18 bioclipse: ospjuth * r4115 /trunk/playground/plugins/net.biocl​ipse.biomoby/src/net/bioclipse/biom​oby/tests/TestRegistryCache.java: The cache test passes now.
15:39 CIA-18 bioclipse: ospjuth * r4116 /trunk/playground/plugins/net.bioclipse.biomoby/ (.classpath META-INF/MANIFEST.MF build.properties): Updated for latest BioMoby: 2007-11-01
16:15 olas egonw: it was OK
16:15 olas never met Ma though
16:15 egonw :(
16:59 edrin left #bioclipse
20:44 egonw joined #bioclipse

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