Camelia, the Perl 6 bug

IRC log for #bioclipse, 2010-02-11

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All times shown according to UTC.

Time Nick Message
04:18 egonw joined #bioclipse
06:28 annzi joined #bioclipse
07:10 annzi joined #bioclipse
07:34 annzi joined #bioclipse
07:36 Gpox joined #bioclipse
07:36 egonw Gpox: are you aware that the Structure2D view is broken?
07:36 egonw at least in master
07:36 egonw not sure about 2.2.0
07:37 Gpox no
07:37 egonw wanted to make a nice screenshot here: http://chem-bla-ics.blogspot.com/2010/02/b​ioclipse-understands-ontologies-note.html
07:37 zarah egonw's link is also http://tinyurl.com/ylza7yv
07:37 egonw but had to do with just the Prop view, and not Structure2D :(
07:37 egonw it reacts...
07:38 egonw and I get to see the Generated warning
07:38 egonw but nothing shows up
07:47 sneumann joined #bioclipse
07:48 egonw Gpox: but now it is working again...
07:52 egonw mmm... sort of...
07:57 egonw joined #bioclipse
08:00 CIA-71 bioclipse.rdf: Egon Willighagen master * ra07e044 / (3 files in 3 dirs):
08:00 CIA-71 bioclipse.rdf: Enabled translation of RDF triples into cheminformatics interpretable IBioObjects. Unfinished:
08:00 CIA-71 bioclipse.rdf: * introduces an unwanted dependency: to be replaced by an extension point
08:00 CIA-71 bioclipse.rdf: * reacts on click; needs to open an editor upon double click - http://bit.ly/aItDPH
08:26 egonw oh, Bioclipse is bloody fucking cool !
08:26 Gpox yes it is
08:26 egonw Gpox: watch this commit:
08:27 * egonw is interactively staging...
08:28 egonw here it comes :)
08:28 CIA-71 bioclipse.rdf: Egon Willighagen master * r56ddddb / (2 files in 2 dirs): Enabled double clicking on a RDF resource in the Zest-based editor, which will open a JChemPaint editor - http://bit.ly/aQexrT
08:30 * Gpox fixed DS coloring support for the updated molecules editor
08:34 egonw ok, let's see where we are...
08:34 egonw Gpox: we need to talk about:
08:34 egonw 1. updating cdk-jchempaint
08:34 egonw 2. backporting patches still in bioclipse.cheminformatics but not in cdk-jchempaint (radical support)
08:35 egonw 3. doing the 4 org.openscience.cdk.swt  bundles
08:35 egonw annzi: we need to get the MoSS manager going
08:36 annzi i'm working on it
08:36 egonw 1. set up a properties class we can pass around in methods
08:36 egonw ok, good
08:36 annzi at the moment I'm able to run a mossfile with default value from moss manager
08:36 egonw please do commit often, with small commits
08:36 egonw ok, good... please commit that
08:37 annzi yes, I attend to forget the commiting part
08:37 egonw 2. I will repopulate the ChEMBL rdf node today, but that's just a FYI
08:37 annzi first time with git, first I write add right then commit
08:37 egonw yes
08:38 egonw first you *stage*, then you commit when happy
08:38 annzi ok
08:39 egonw sneumann: we need to talk about where we are now, and what is next
08:39 egonw and how we will organize those things...
08:39 sneumann yup
08:39 egonw e.g. talk about spectrum support
08:40 egonw I saw the dependency on net.bioclipse.spectrum...
08:40 egonw but we need to decide on what formats to support
08:40 egonw (of course CMLSpect 4 MB)
08:40 egonw and we need to talk about that too, I guess
08:40 egonw that's been lingering for much too long now
08:41 sneumann MetFrag is able to write out mzAnnotate (aka CML4Metabolomics)
08:41 sneumann and we have reader/writer code for mzAnnotate sitting in the SVN for metware.sf.net
08:42 sneumann a student is currently doing some hibernate work for CML / mzAnnotate
08:42 sneumann and we might have a MassBank in CMLSpect format in a couple of weeks
08:42 sneumann Regarding CMLSpect:
08:43 sneumann MetFrag happily takes any peaklist from such a spectrum
08:43 sneumann although current BC plugins consider Spectrum==NMR, this is not hard-wired
08:44 sneumann We have R / Bioconductor code to turn LC-MS/MS data into peaklists
08:44 sneumann so if there is a working RBioClipse (or BioclipseR ?) plugin, we don't have to worry about file formats
08:45 sneumann and I am not inclined to create large-scale Mass Spectrometry GUI and algorithms into BC
08:45 sneumann (But I am happy if somebody turns MZmine into a plugin :-)
08:45 sneumann So, I'd love to see a working R plugin (again)
08:46 sneumann and I'd be greate if Speclipse can be used to manually annotate a MS SpecMol object
08:46 egonw yes, the latter should be possible...
08:46 sneumann the latter would probably have to come from the EBI
08:46 egonw or Miguel in Leiden
08:47 egonw OK, so we focus on CMLSpect4MB as format (mzAnnotate and MassBank conventions)
08:47 egonw make sure that works in net.bioclipse.spectrum
08:48 egonw Bioclipse-R plugin is operational
08:48 sneumann location of BioclipseR ?
08:48 egonw but we may need to formalize a best-practices bit on how to move data between the BC workspace and R
08:52 olass joined #bioclipse
08:52 olass egonw: see my reply on http://saml.rilspace.com/content/bio​clipse-manager-method-to-take-arbitr​ary-number-of-arguments#comment-53
08:53 olass I seem to remember Groovy has some nice parameter acceptance features
08:53 egonw yeah, a full groovy console would be interesting...
08:54 annzi I been having some problem with bioclipse. Does any of you know why? http://pastebin.com/m5c442d4d
08:54 egonw there is one, but the BSL domain language is not yet injected
08:54 olass annzi: you have a dependency problem
08:54 annzi what to do?
08:54 olass probably missing a plugin or so I'd say
08:55 olass do you run from features?
08:55 olass if not, please do
08:55 olass start from theproduct
08:55 egonw olass: you know the repos to find the R plugin?
08:55 olass egonw: hold on
08:55 olass is it not in bioclipse.experimental?
08:55 annzi olass: I do
08:55 * olass will confirm
08:55 * olass has confirmed
08:56 olass annzi: then the feature is corrupt and need be fixed
08:56 olass this is of course if it has previously worked
08:56 olass if not, then it could be some other problem
08:56 egonw sneumann: http://wiki.bioclipse.net/index.​php?title=Bioclipse.experimental
08:57 annzi olass: the problem began yesterday, what do you recommend?
08:57 olass annzi: the problem is this line I'd guess: java.lang.ClassNotFoundException: net.bioclipse.drprolog.test.bu​siness.DrPrologManagerFactory
08:57 egonw annzi: remove the drprolog plugin from your workspace
08:57 egonw it's crapware
08:58 egonw samuell moved to blipkit
08:58 olass egonw: should not just running the feature solve the problem?
08:58 olass why is it still listed then?
08:58 egonw olass: yes, that would solve it too
08:58 olass ok
08:58 egonw dunno
08:58 olass problem solved
08:58 egonw I guess someone forgot to remove it ...
08:59 egonw sneumann: feel free to put additional files in the new net.bioclipse.data.metabolomics plugin's data/Metabolomics folder
08:59 egonw sneumann: make sub folders if you like
08:59 egonw sneumann: what about those PB* files (or so)
09:00 sneumann MassBank test data
09:00 egonw support?
09:00 sneumann ?
09:00 annzi but it didn't, now I tried to use only the required plugins..same problem
09:00 egonw sneumann: should the feature support reading those?
09:00 sneumann no
09:00 egonw sneumann: ack
09:01 sneumann ahm, thinking again, why not
09:01 egonw :)
09:01 sneumann you could create an ISPectrum from those
09:01 sneumann or even a specmol
09:01 egonw right
09:01 sneumann MassBank has both a BioMoby interface (from IPB)
09:02 sneumann and a plain SOAP Web Service, which only accesses a single site,
09:02 sneumann not the whole MassBank Network as the BioMoby does
09:02 egonw olass: is there a biomoby manager?
09:03 egonw olass: that supports calling biomoby services?
09:03 olass egonw: not migrated yet
09:03 olass It's on my todo list
09:03 olass but needs to sort out data types
09:03 egonw argh.... can't some rich dude give us a big grant, please? pretty please?
09:04 olass +1
09:04 olass +10
09:04 egonw (rich dude)++
09:04 olass (filthy rich dude)++
09:04 sneumann @karma (rich dude)
09:04 sneumann where is zarah ?
09:05 olass zarah: ping
09:05 sneumann just looked at the R plugin, it does an exec(R) and communicates via the stdin/stdout
09:05 olass sneumann: it is quite simple for the moment
09:05 olass but not overly easy to even solve this on win/linux/mac
09:05 olass sneumann: any ideas for improvements?
09:05 sneumann the alternative way would be JNI and/or RServe, both of which have better support for datatypes
09:06 olass sneumann: you should ping masak when he is here
09:06 olass I think he is looking at R and Bioclipse, but not sure what his attack plan is
09:06 * olass would be extremely happy if someone boosted R support in Bioclipse...
09:07 egonw olass: yes, if we can show that it works, we will be able to interest a new group of people
09:07 olass indeed
09:07 egonw right now it works, but passing around data is not simple
09:08 olass right, and that's what we want :)
09:08 olass but we CAN access JS data in R
09:08 olass that is quite cool actually
09:08 egonw indeed
09:08 olass but we lack an R editor and ability to execute that file in R
09:09 egonw so much to have done, so little money :(
09:09 sneumann http://rforge.net/JRI/
09:09 sneumann JRI is a Java/R Interface, which allows to run R inside Java applications as a single thread. Basically it loads R dynamic library into Java and provides a Java API to R functionality. It supports both simple calls to R functions and a full running REPL.
09:09 sneumann JRI uses native code, but it supports all platforms where Sun's Java (or compatible) is available, including Windows, Mac OS X, Sun and Linux (both 32-bit and 64-bit).
09:13 egonw would that require us to ship native R code?
09:13 sneumann no, it links to R.dll
09:13 sneumann which is then an external dependency
09:13 egonw so, you just pass possible locations?
09:14 sneumann See the FAQ
09:14 sneumann Q:I get the following error, what's wrong?
09:14 sneumann java.lang.UnsatisfiedLinkError: no jri in java.library.path
09:15 egonw yeah, let's talk to Carl...
09:18 sneumann A huge project in that direction is http://biocep-distrib.r-forge.r-project.org/
09:23 olass sneumann: yes, seen it
09:25 egonw annzi: loading the new ChEMBL RDF
09:25 egonw annzi: with activity/ and fixed owl:sameAs to Bio2RDF ...
09:35 annzi joined #bioclipse
09:43 Gpox egonw: for 2. see http://pele.farmbio.uu.se/cgi-bin/gitweb​.cgi?p=gpox_cdk-jchempaint.git;a=summary
09:43 egonw Gpox: the last three?
09:43 Gpox yes
09:44 egonw great, tack!
09:52 olass egonw: ping
09:52 egonw pong
09:52 olass egonw: what to do with page http://wiki.bioclipse.net/i​ndex.php?title=ProjectsNew, filed as bug 1831?
09:52 olass what should be ported there?
09:53 egonw http://wiki.bioclipse.net/index.php?title=Projects
09:53 egonw it needs to be checked if we like the 'New' variant
09:53 olass do you want me to check them all?
09:53 egonw and if so, port all plugins on the current Projects not using the template yet
09:53 olass that will take some time...
09:53 olass I have fixed all my projects
09:54 olass should we remove this page after this?
09:54 egonw yes, when done, New can replace the current one
09:54 egonw ok, please reassign to someone else to check... e.g. jonalv
09:54 olass ok
09:55 annzi olass: is there some way to clean or remove bioclipse-workspace directory. I still haven't managed to open bioclipse
09:56 egonw annzi: start with a fresh empty workspace?
09:57 annzi ok will try
09:58 egonw no, that was a question...
09:58 egonw is that what you want to do?
09:58 egonw I did not understand your question
09:58 annzi oh but I already emptied it. I need to fix the metadata
10:00 annzi I only have the core plugin now and still can't open, http://pastebin.com/m1559f59a
10:00 annzi I would like to restore the metadata somehow
10:02 egonw Project -> Clean...
10:03 egonw right click on the plugin, PDE Tools -> Update classpath...
10:03 egonw open target-platform.target -> Set as Target Platform
10:03 egonw refresh
10:03 egonw repeat until it works
10:04 annzi will try!
10:04 annzi thanx
10:04 egonw these are the nasty eclipse details no one wants to talk about
10:05 annzi oooh I see, but I'm frustrated I want to talk :)
10:19 egonw annzi: now loading back in the activities.n3
10:21 * egonw is now going to do something he has very long not done: define a new extension point
10:23 masak joined #bioclipse
10:25 * egonw grabs is Eclipse book
10:27 egonw and lunch
10:27 CIA-71 bioclipse.rdf: Egon Willighagen master * r4ce1623 / plugins/net.bioclipse.rdf.ui/src/net/b​ioclipse/rdf/ui/editors/RDFEditor.java : Hooked in double click action - http://bit.ly/9GeQOc
10:27 CIA-71 bioclipse.rdf: Egon Willighagen master * r376552e / (4 files in 3 dirs): Added a proper RDF icon - http://bit.ly/bMmpj7
10:27 CIA-71 bioclipse.rdf: Egon Willighagen master * r5438179 / plugins/net.bioclipse.rdf.ui/src/net/biocli​pse/rdf/ui/editors/RDFContentProvider.java : Removed output to STDOUT - http://bit.ly/arIMdw
10:27 CIA-71 bioclipse.rdf: Egon Willighagen master * reddc322 / plugins/net.bioclipse.rdf.ui/src/net/b​ioclipse/rdf/ui/editors/RDFEditor.java : Use the file name as editor title - http://bit.ly/bagYip
10:27 CIA-71 bioclipse.rdf: Egon Willighagen master * r0c39594 / (2 files): Now with proper NS prefix use - http://bit.ly/aSFod3
10:30 annzi egonw: what do you think about this http://dev.zhourenjian.com/blog/2007/​11/07/eclipse-freezing-on-start.html?
10:32 egonw what about it?
10:35 annzi trying to solve my problem but I have little  knowledge about this. Do you know what .indexes does?
10:35 egonw if you think your workspace is bad...
10:35 egonw just delete it form your hard drive
10:36 egonw not with eclipse, but with a file browser
10:36 egonw if you think your Eclipse is broken, you typically just reinstall
10:37 annzi well these things I've done, but will try agian
10:55 egonw olass: http://wiki.bioclipse.net/index.php?title=Molecule
10:56 egonw masak: might you edit this page for your bioinfo stuff:
10:56 egonw http://wiki.bioclipse.net/index.​php?title=Category:DomainObjects
10:56 egonw following title=Molecule ?
11:33 sneumann hi masak
11:33 masak hi sneumann
11:33 sneumann this morning we talked about R in BC
11:34 sneumann and you have the prototype, which execve(R) and communicates via stdin/out
11:34 sneumann one question was whether http://rforge.net/JRI/ (or rather rJava) wouldn't be a better interface
11:35 masak bjarni (the one who implemented the current solution) had a look at JRI, I know.
11:35 sneumann allowing more complex datatypes to be passed, and avoids any string parsing
11:35 masak for some reason, he didn't consider it viable.
11:35 masak but I'd be very happy if someone made that work.
11:36 sneumann find / -name "someone"
11:36 masak no hits yet...
11:36 sneumann major bonus:
11:37 sneumann 2009/06/14 - rJava 0.6-3 released. Recommended update (includes bugfix for signature overflow), includes JRI 0.4-3 which supports REngine API which is now compatible both with Rserve and rJava/JRI.
11:37 sneumann which means one client API, and either local or remote execution
11:37 masak ok.
12:18 egonw masak: ping
12:18 masak egonw: pong
12:18 egonw masak: might you add some wiki stuff for the bioinfo domain object(s) ?
12:18 egonw http://wiki.bioclipse.net/index.php​?title=Bioclipse2_core_object_model
12:18 masak I'll make sure to put it on my list of things to do today.
12:19 egonw thanx... makes good documentation...
12:19 egonw and I need some documentation on how to create a ISequence from a string, and how to open it in an editor :)
12:20 masak that should certainly be doable already, at least.
12:23 masak egonw: there's a method called biojava.sequencesFromString
12:23 egonw yeah, I think we should default on some sections on those pages...
12:23 egonw = Building Objects =
12:23 masak seems jonalv created that method, if I read the blame-blame-blame correctly.
12:24 egonw = Methods =
12:24 egonw = Building Objects = <- would also include a pointer on how to read a file into that object
12:24 masak the methods I had made before that were not for ISequence objects in general, but for DNA, RNA and proteins.
12:25 masak seems jonalv needed the former for something and created that method.
12:25 masak maybe there is a case for removing the specific ones.
12:25 egonw dunno
12:25 egonw I'm impartial to that
12:25 egonw we now have the wiki to easily browse what DOs there are :)
12:25 egonw (once we finished filling it)
12:26 masak yeah.
12:26 masak that information is going to grow stale very quickly... :/
12:26 egonw I'm really pleased with the Category/Template work introduced by Samuel
12:26 masak I prefer to generate such things.
12:26 masak I'm sure categorizing helps, yes.
12:26 egonw which we forget to do for each release...
12:27 masak forgetting to generate is still a lesser annoyance than forgetting to update manually.
12:27 sneumann masak
12:27 masak sneumann
12:27 egonw masak: that's why the templates have fields for last updated and bioclipse version
12:27 sneumann that was meant to be a yes :-)
12:27 masak sneumann: I see.
12:28 egonw and it being RDF, we can have Bioclipse validate the wiki content :)
12:28 egonw hahaha
12:28 masak egonw: just saying that I prefer the push of a button to a lot of manual synching of code and external docs.
12:30 masak I'll happily help update the wiki, but I'd much prefer making the code self-conatined and well-commented.
12:31 masak that information would be closer to the thing it's describing, and therefore slightly more likely to change along with the source when it changes.
12:31 masak plus, it's where a developer expects to find the information.
12:31 egonw masak: I'm looking forward to a Bioclipse SDK plugin to allow one to browse all BDOs
12:33 egonw seriously... it would be just lovely of these wiki pages can be autogenerated
12:34 egonw the thing is that potential Bioclipse developers, start with the wiki, before they even consider downloading eclipse to set up a developers environment
12:34 egonw then, 2.
12:34 egonw they have no clue what code to check out, so not have any inline docs in their workspace to start with
12:36 egonw information is scattered over many repositories and not easily aggregated
12:36 egonw this is where the wiki comes in
12:38 masak nod.
12:41 egonw but I'd love to see some Perl6 code to convert API into wiki page content ;)
12:41 masak I might get around to writing a sufficiently powerful Java parser some day.
12:42 sneumann hu ? where is masak, and what did you do to him ??
12:42 masak I hear that a lot lately...
12:42 masak maybe I have been replaced. :)
12:42 egonw yeah, what was that talk about all those new languages??
12:43 egonw there can only be ... 20?!?!
12:43 masak Java is hardly new.
12:47 egonw ah, so Perl6 is not new either... good, we settled that :)
12:48 egonw masak: btw, I see the wiki more as a requirement analysis
12:48 egonw a specification to which the implementation should conform
12:51 egonw masak: anyway... where I am getting at with the sequence domain topic stuff...
12:51 egonw is to open this RDF graph: http://rdf.farmbio.uu.se/chembl/snorql/?query=SEL​ECT+DISTINCT+%3Fproperty+%3FhasValue%0D%0AWHERE+{%0D%0A++{+%3Chttp://rdf.farmbio.uu.se/chembl/targe​t/t100001%3E+%3Fproperty+%3FhasValue+}%0D%0A}%0D%0AORDER+BY+%3Fproperty+%3FhasValue
12:52 egonw in the new RDF editor, and being able to double click the main resource here
12:52 egonw and open it in the sequence editor
12:59 CIA-71 bioclipse.core: Egon Willighagen master * rceac633 / plugins/net.bioclipse.core/src/net/b​ioclipse/core/domain/IBioObject.java : Added more elaborate JavaDoc - http://bit.ly/d04iwn
13:04 masak I see.
13:06 egonw too bad jonalv is not around...
13:07 egonw olass, masak: is it reasonable to assume a 1-to-1 relation between BDO and B manager?
13:07 olass what is BDO?
13:07 egonw no, it should be 1-to-many, right?
13:07 * masak was going to ask that
13:07 egonw Bioclipse Domain Object
13:07 masak what's that?
13:07 egonw oh, wow...
13:07 masak why do you keep making up new terms?
13:07 olass a manager has nothing to do with a domain object
13:07 egonw no, I did not make that up myself...
13:07 egonw that's inherited from you guys
13:08 * masak never used that term
13:08 * olass neither
13:08 egonw masak-- (for blaming the wrong guy here)
13:08 masak egonw: I have no idea what you're talking about.
13:08 masak seriously.
13:08 olass egonw: who is the right guy to blame?
13:08 * olass has never seen BDO either
13:08 olass masak++ //wrongly accused
13:09 egonw domain object is used at Plugins/Bioclipse 2.x
13:09 masak egonw: getting back to your question, there's no 1-to-1 relation inherent in anything.
13:09 egonw olass-- (for making an incorrect correction)
13:09 masak egonw: it's all convention.
13:09 masak egonw: 'domain object', yes.
13:09 egonw and Service infrastructure
13:09 masak egonw: not 'Bioclipse Domain Object' with capital letters.
13:09 egonw and not the least: IBioObject !
13:10 masak yes. so what?
13:10 egonw "Definitions of the basic functionality of all domain objects"
13:10 masak still confuses me when you say 'Bioclipse Domain Object' and 'BDO'.
13:10 egonw being the JavaDoc of IBioObject
13:10 egonw so, I read that as: something that implements this interface is a domain object
13:11 * masak has answered egonw's question. goes back to work instead of bickering.
13:11 egonw now, the B prefix, is much like a namespace
13:11 * egonw apologizes for unappreciated linguistic features
13:13 * masak feels alone in the important fight against evil three-letter acronyms
13:14 egonw yeah, tweeting and IRC has bad influence on people
13:14 egonw I will write a alias that expends to 'domain object that is defined withing the scope of bioclipse'
13:15 egonw (can I capatalize Bioclipse? ;)
13:15 egonw within
13:15 egonw no g
13:15 egonw an
13:15 * egonw always feels linguistically challenged with masak online
13:16 masak :P
13:16 masak egonw: this is #bioclipse, so we can usually figure out which domain objects you're talking about.
13:16 egonw yes, IMolecule is very specific
13:17 egonw </sarcasm>
13:17 masak sarcasm is only effective if the recipient knows what it reacts against. :)
13:17 egonw [02/11/10 14:16] <masak> egonw: this is #bioclipse, so we can usually figure out which domain objects you're talking about.
13:18 egonw *usually* in particular
13:18 masak right. you might be talking about the domain objects of MS Word, but that's not very likely.
13:18 masak that's what I meant.
13:18 egonw ah, but you had no clue I was talking about the CDK IMolecule, did you?
13:18 masak usually you're talking about the domain objects of Bioclipse.
13:18 egonw and I am not refering to ICDKMolecule
13:18 masak since this is #bioclipse.
13:19 egonw that's rather optimistic
13:19 * masak once again vows not to waste more time on this discussion
13:19 egonw anyway...
13:19 egonw back to 1-to-1 or n-to-n
13:19 masak I already answered that.
13:19 egonw we need proper documentation on how to get (create) a domain object
13:20 egonw and how to serialize that ...
13:20 egonw masak: yes, you did... so I am asking something else now... (aka hold your horses)
13:20 egonw and if not mistaken the #bioclipse way is to do that via managers
13:21 masak Bioclipse does everything via managers.
13:21 egonw so, we need to link in the documentation what those n-to-n relations are
13:21 egonw masak: theorically
13:21 masak it even does managers via managers.
13:22 egonw e.g. it does not do toCML() via the manager... or toSMILES()
13:22 egonw well, sometimes...
13:22 egonw sometimes not
13:22 masak nailing down what n-to-n relations are sounds like something jonalv would enjoy.
13:22 masak he likes making type hierarchy diagrams.
13:25 egonw Gpox:
13:25 egonw ping
13:25 Gpox egonw: pong
13:26 egonw your patch from radical-support requires AbstractEdit
13:26 egonw which does not seem present in the 8-control-impl-extra branch
13:34 Gpox Should radical support be in extra? AbstractEdit is pressent in 6-control-impl-basic
13:34 egonw yes, I think so...
13:34 egonw but -extra depends on -basic...
13:35 egonw or... it should...
13:35 egonw ah!
13:35 egonw it does not :(
13:35 egonw thanx
13:40 annzi joined #bioclipse
13:41 CIA-71 bioclipse.core: Egon Willighagen master * rb38f80d / (2 files): Added more elaborate JavaDoc for ISpectrum and IBiobliodata - http://bit.ly/9ARWVk
14:34 egonw olass: ping
14:34 olass pong
14:35 egonw ummm... I lost track of time...
14:35 egonw but was github-bioclipse set up next week?
14:35 olass it will be, hopefully
14:35 olass have not had time yet :(
14:35 olass soon soon
14:35 olass maybe tomorrow
14:36 * olass is teaching Lars and Peter git
14:36 olass priorities :)
14:36 egonw olass++
14:47 masak olass++ # teaching people git!
14:49 olass :)
14:49 olass ok, meeting for new Bioclipse website coming up next here in sthlm
14:49 olass will be online but might be afk from time to time
14:50 egonw www.bioclipse.net ?
14:51 masak sneumann: looking at JRI in rJava now. yes, we might be able to use this.
14:51 masak sneumann: thanks for the tip. :)
14:53 sneumann looking forward !
14:59 masak my favorite direction... :)
18:00 sneumann joined #bioclipse

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