Camelia, the Perl 6 bug

IRC log for #bioclipse, 2010-07-22

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All times shown according to UTC.

Time Nick Message
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17:38 abereles egonw hi
17:38 abereles i am looking at clustering and here is a question
17:38 abereles do you think a reasonable approach is to make Cluster an object?
17:41 egonw sure
17:41 egonw in the Java world everything is an object :)
17:41 abereles i am looking at java code that looks like fortran
17:41 egonw :)
17:42 abereles and i don't think we should go that way
17:42 abereles i am hoping we get something elegant -- i will report back later, thanks for the confirmation
17:43 egonw make sure to also check if there is not a library you can reuse...
17:43 egonw Weka might be useful, but is GPL-licensed
17:43 abereles i did an initial search, nothing free showed up
17:44 abereles i will spend some time seeing about what I mentioned, i don't see at this point why it won't work
17:44 egonw why is it so important to have it in Bioclipse as Java code?
17:44 abereles but i have been wrong before
17:45 egonw I asked Ola about earlier... why not use R from Bioclipse?
17:45 abereles oh, not important
17:45 abereles if there is a library i would use it
17:45 abereles what is R?
17:47 egonw r-project.org
17:47 egonw there is a Bioclipse plugin already
17:47 egonw but moving data back and forth between R and Bioclipse needs a bit of polishing...
17:48 egonw possible, but not yet tightly integrated...
17:48 egonw but you'd have all the types of clustering there you like...
17:48 egonw and then you can test what the best clustering method is for your data / problem
17:49 abereles well, that seems to be the way to go, doesn't it
17:49 egonw dunno
17:49 abereles i will look at it
17:49 egonw I know too little about your use case to decide
17:50 abereles trying to compare a collection of molecules using single linkage
17:52 abereles the r-project site looks promising
17:52 egonw yeah, the R software is well established
17:52 egonw it's the Linux for statistics
17:53 abereles if there is a plugin, it sounds like a nobrainer
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17:55 egonw last time I tried it, it work really nice
17:55 egonw but haven't recently checked if the plugin runs with 2.4
17:55 egonw I think it should
17:55 abereles i will find out
18:06 egonw ok, somewhere in the bug tracker there is a bug report about the path passed to R
18:06 egonw and somewhere I have a script to highlight how to run R scripts from inside Bioclipse
18:06 egonw but neither I can find
18:08 abereles i am still trying to find the plugin and also it looks like R has to be installed on the machine for the plugin to work?
18:08 egonw yes, think so
18:08 egonw what OS are you running?
18:08 abereles windows
18:09 egonw there should be an installer for Win
18:09 egonw http://wiki.bioclipse.net/index.p​hp?title=Integrate_R_in_Bioclipse
18:09 zarah egonw's link is also http://tinyurl.com/3a4u2ej
18:11 egonw OK, I found the plugin
18:11 abereles it seems like you have used the R scripting but not calls from Java? or i am not understanding?
18:11 egonw it's in the bioclipse.experimental repository
18:12 egonw if I understood correctly...
18:12 egonw the fire up an R session in the JavaScript console
18:13 dsurdyk joined #bioclipse
18:13 abereles ?
18:13 dsurdyk hey - does anyone have experience with creating an eclipse Job() and then linking its output to the console inside bioclipse?
18:14 egonw abereles: I did not write the plugin... not sure how it works internally
18:14 egonw dsurdyk: I don't
18:15 egonw dsurdyk: jonalv would have know... but he's on holiday right now
18:15 dsurdyk egonw: do you know what plugin jonalv wrote that uses the console?
18:16 dsurdyk maybe I can look up his code
18:16 dsurdyk all examples i've seen use the jsconsole
18:18 abereles net.bioclipse.scripting?
18:18 dsurdyk yea - they all use the jsconsole
18:18 dsurdyk but my plugin will be contributing a significant amount of console output - so I don't want to clutter the jsconsole with it
18:19 egonw btw, 2.4 uses the Java API for scripting... and I played with a GroovyConsole, which worked quite well... only one bug
18:19 egonw dsurdyk: use the logger ?
18:19 abereles egonw: i will see if there is a way that R is supposed to be callable from Java in Eclipse, but if not, I have to find something else
18:19 egonw yeah, you can call R from Java...
18:20 egonw no need to use the console for this, I think
18:20 egonw a good r manager would be nice, to run simple scripts, without firing up a full R session
18:24 dsurdyk possibly - but this will be all teh CLI output from programs such as clustal, phylip, and muscle
18:25 dsurdyk so i dont want to overwhelm the logger
18:29 dsurdyk thanks for the ideas - g2g
18:35 abereles i am so far reading things that make me pessimistic about calling R from Java but I am continuing to search
18:36 abereles maybe i found something
19:24 olass egonw: I disagree about using R for simple statistics, since we don't have a proper R connection
19:24 olass I don't mind having java-implementations of basic stuff, but more advanced stuff should probably use R
19:25 olass if we want a plot where we can click on dots and get selection events, then we cannot rely on R
19:25 olass so for simple stuff (like a clustering algorithm) we can have a java implementation
19:26 olass this is my opinion
19:26 olass you might have another
19:39 abereles joined #bioclipse
19:41 abereles egonw: I installed R on my machine and got bioclipse.experimental which indeed has something that looks like R in it but I cannot yet invoke R from Bioclipse
19:43 abereles and i mean in the js console
19:48 abereles joined #bioclipse
19:49 abereles any thoughts?
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19:57 egonw abereles: put the experimental feature in the bioclipse.product
19:58 egonw away from keyboard again
19:58 egonw js> R
19:58 egonw to boot a R env, I think
20:00 abereles that it shows up as a plugin in Bioclipse is not enough?
20:01 abereles i did try R in js
20:06 abereles i added experimental feature as a dependency -- is that what you meant?
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20:30 egonw hi samuell
20:30 samuell hello egonw
20:30 egonw samuell: was wondering... can you access the SPARQL of SWMW from Bioclipse too?
20:30 egonw I have had time to try that yet
20:30 egonw I have had not time to try that yet
20:30 samuell It should be possible yes
20:30 egonw I have not had time to try that yet
20:31 samuell I even started to think, that I'm now in the position that I could possibly write something up based on this, for the second thesis project
20:32 samuell But that's just an idea
20:37 samuell Anyway ... should also be nice to be able to paste RDF/XML to SMW from Bioclipse
20:37 egonw indeed :)
20:37 samuell But maybe Jena can convert RDF/XML to SPARQL Update syntax?
20:37 egonw a sw mediawiki plugin for Bioclipse
20:37 egonw cool !
20:37 samuell Yeah, was thinking a bit of that
20:37 egonw since it's all over HTTP, it should not be overly difficult...
20:37 egonw how about a IRDFStore backed by a mediawiki ?
20:37 samuell No ...
20:38 egonw oh goodies...
20:38 samuell :)
20:38 egonw rdf.createMediaWikiStore("http://wiki.bioclipse.net/")
20:38 samuell :)
20:38 egonw actually... pretty cool
20:38 egonw and quite doable I guess
20:39 egonw anyway... back to work :)
20:39 samuell Heh, yes :)
20:41 edrin joined #bioclipse
20:41 edrin hi
20:41 zarah hi edrin
20:42 egonw hi edrin
20:43 egonw olass: ping
20:43 olass pong
20:43 edrin egonw: what is the current recommended eclipse download ? classic 3.6.0?
20:43 egonw olass: do we have amino acide descriptors in bioclipse yet?
20:43 egonw 3.5 and 3.6 should both work for development
20:43 edrin or the Eclipse for RCP and RAP Developers, 191 MB ?
20:43 egonw eclipse rcp
20:43 edrin not classic?
20:43 egonw for the current platform description, it will download the 3.5 plugins
20:43 edrin i think in the past i always got classic
20:44 egonw isn't class aimed as IDE for java developers?
20:44 egonw edrin: yeah, you can install any feature later too
20:44 egonw it's a bit artifical, those flavors...
20:44 edrin Eclipse IDE for Java Developers, 99 MB
20:44 egonw it's like Ubuntu versus Kubuntu
20:44 edrin Eclipse Classic 3.6.0, 170 MB
20:44 edrin yeah
20:44 egonw ah, bigger...
20:44 edrin extremely confusing
20:44 egonw dunno really...
20:44 egonw not sure which one I downloaded...
20:44 edrin Eclipse for RCP and RAP Developers, 191 MB
20:45 egonw have not even booted it yet :)
20:45 olass egonw:  >> aa descr: nope, not in Bioclipse
20:45 edrin oh you got a new one?
20:45 edrin i will get classic
20:45 edrin classic sounds good
20:45 olass edrin: I suggest RCP devel
20:45 olass if you plan on writing plugins
20:46 edrin A complete set of tools for developers who want to create Eclipse plug-ins, Rich Client or Rich Ajax Applications (RCP+RAP), plus Mylyn, and an XML editor.
20:47 egonw that sounds appropriate
20:48 egonw you want mylyn anyway
20:48 egonw a good xml editor is a plus too
20:48 egonw olass: ack, tack
20:49 edrin http://www.eclipse.org/downloads/compare.php
20:49 zarah edrin's link is also http://tinyurl.com/2b278w4
20:49 edrin aha!
20:51 edrin olass: indeed!
20:51 edrin a good suggestion
20:57 edrin did you try 64 bit versions?
20:57 egonw I am running 64bit for a long time now
20:57 egonw on Linux that is
21:22 egonw olass: do all those nicks here on this channel make you so happy too?
21:22 egonw it's 11pm and there are 10+ people here :)
21:22 olass :)
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21:37 egonw hi maclean
21:37 maclean hi egonw
21:37 olass hi maclean
21:37 maclean hi olass
21:38 maclean egonw: amino acid descriptors? (yes I browse the logs :)
21:38 egonw and nucleotide descriptors in particular
21:38 egonw for proteochemometrics like work
21:39 maclean What kind of things are described upon nucleotides?
21:39 maclean Sorry, that's some ridiculous english I just typed. "Described upon" == "what descriptiors are there"
21:41 egonw indeed, that's the question
21:41 maclean Ah, right :)
21:41 egonw rajarshi was asking about it
21:42 maclean It's just that I'm working on a kind of descriptor engine for biomolecules, so wondered what they might be.
21:42 maclean I'll google it...
21:43 egonw post a question on the Blue Obelisk eXchange, and I'll answer this weekend
21:43 maclean hmmm. doi:10.1016/j.jtbi.2009.02.02
21:43 maclean egonw : ack
21:44 egonw the pharmbio.org course has info on amino acid descriptors at least
21:45 maclean gah. there should be an option in google searches to exclude dictionary pages :(
21:45 maclean they make it difficult to search for rare combinations of words from the same domain
21:58 maclean anyway, bye
22:09 olass egonw: Z-scales is easy AA-descriptors
22:09 olass just a simple lookup in a table
22:09 olass been used a lot in PCM
22:09 egonw indeed...
22:09 egonw do u know the equiv for nucleotides?
22:09 olass you looking for something more elaborate?
22:09 olass nope
22:10 egonw neither do I
22:10 egonw that's what Rajarshi was primarily asking about...
22:10 olass what do you need it for?
22:10 olass ah
22:10 egonw I think he needs to invent them :)
22:10 olass he should
22:10 egonw someone actually has a trademark on "Science 2.0"
22:10 olass but really, it depends on what he is aiming for
22:10 olass stupid, isn't it?
22:10 egonw DCM work
22:11 egonw dnamometrics I think
22:11 olass TM means _nothing_
22:11 olass anyone can place a (TM) on anything
22:11 olass has no legal meaning
22:11 egonw this is (R)
22:11 olass (R) on the other hand...
22:11 olass ah
22:11 egonw sorry for my sloppy termo
22:14 egonw crap...
22:14 egonw it's friday
22:14 egonw got to go now
22:14 egonw got a plane to catch today
23:47 CIA-71 bioclipse.core: Ola Spjuth master * ra3cd4d2 / plugins/net.bioclipse.core/src/net/​bioclipse/core/util/ImageUtils.java : Added a method to translate SWT Image to AWT. - http://bit.ly/9teBdU
23:47 CIA-71 bioclipse.core: Ola Spjuth master * r72ebe8b / (40 files in 9 dirs): Added a JasperReports plugin to core. - http://bit.ly/aOfQD9

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