Camelia, the Perl 6 bug

IRC log for #bioclipse, 2007-11-20

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All times shown according to UTC.

Time Nick Message
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11:03 * olas is on lunch
11:21 egonw better than on drugs :)
11:53 egonw is the Uppsala team back from lunch?
11:53 egonw those bloody long swedish lunches :)
11:54 egonw should be forbidden to have a sauna break during ones lunch
12:24 masak joined #bioclipse
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12:25 * olas is back from a short lunch-break
12:25 olas hi egonw
12:26 * olas is away for a coffee-break
12:26 jonalv LOL
12:26 * masak arrives out of the sauna
12:26 masak hi everybody
12:37 egonw has the Uppsala team experience with EMFT and/or JPOX with respect to database integration in Eclipse ?
12:38 egonw just wondering...
12:39 * olas is still on his short coffee-break and refuses to answer
12:39 egonw short, as in only one sauna?
12:40 olas :-)
12:40 olas to answer: not really
12:40 olas jonalv is the most experienced but we have worked with Hibernate and Ibatis, not JPOX (which is based on JDO AFAIK)
12:41 olas but we are looking into EMF
12:41 * olas bought a book for EMF 2.0 today
12:42 egonw I worked on the mzdata plugin yesterday...
12:42 egonw and is nicely working again...
12:42 egonw mostly that is...
12:42 olas cool :-)
12:42 egonw except that EMF needs to be upgraded to 2.3
12:42 jonalv I see my name mentioned (and it is not just wishfull thinking) so what are you talking about?
12:42 olas persisting EMF models
12:42 egonw the mzdata plugin uses EMF(T) and JPOX
12:42 egonw that's why I ask...
12:42 jonalv aouch that's like the holy grail
12:43 olas http://en.wikipedia.org/wiki/JPOX
12:43 egonw jonalv: the mzdata plugin for Biolcipse uses that...
12:43 jonalv to persist emf?
12:43 egonw jonalv: and I have contact with the author ... (the group where Stefan stayed after CUBIC)
12:43 jonalv to database?
12:43 egonw yes
12:43 jonalv cool
12:44 egonw not sure it the Bioclipse plugin actually uses that...
12:44 olas author of the EMF plugin that is
12:44 egonw but the mzdata plugin code itself can... and was written as Eclipse plugin first
12:44 olas the EMF-based mzData plugin
12:44 egonw Stefan reworked it to play nicely with Bioclipse1
12:44 olas for BC2 we can just use it out of the box
12:44 jonalv what is mzData?
12:45 egonw mom... have to meet with someone...
12:45 egonw will be back in 15 minutes... (+/- 60 minutes)
12:45 jonalv lol wgonw brings in the holy grail. and then dissaperas...
12:46 masak jonalv: : "I'm in ur Holy Grailz, having to meet with someone" :)
12:47 jonalv jpox seems to be compatible with spring: <http://en.wikipedia.org/wiki/JPOX>
12:48 jonalv hm wrong
12:48 jonalv <http://www.jpox.org/docs/1_1/t​utorials/springframework.html>
12:48 jonalv that's the one
12:50 olas mzData is a data format for Mass Spectrometry data exchange
12:50 olas data standard
12:50 olas (and format)
12:51 jonalv k
12:51 olas http://www.ipb-halle.de/en/research/st​ress-and-developmental-biology/researc​h/bioinformatics-mass-spectrometry/res​earch-projects/mzdata-eclipse-editor/
12:51 jonalv we need lambdabot
12:52 masak olas: http://tinyurl.com/2qnwzx
12:52 jonalv if just olas could get his broken mac to use the escape button we could run it on maradona...
12:52 jonalv :)
12:52 edrin joined #bioclipse
12:52 edrin hi
12:53 jonalv hi edrin
12:53 masak jonalv: it's like the Pettson book "Pannkakstårtan"
12:53 masak hi edring
12:53 masak s/g//
12:53 jonalv yep
12:57 olas hi edrin
13:01 egonw OK, back
13:01 jonalv did you bring the holy grail? :)
13:02 egonw no, I left it here... did someone steal it !?!? NOOO !!!!!
13:02 masak don't tell me you lost the Grail...
13:02 masak now you have to go on a Quest for it
13:03 masak before it gets all worn an holey
13:03 jonalv ah heley holy grail wouldn't be the same..
13:03 masak :)
13:03 olas a greeeiiijl?
13:03 jonalv pah the only word inte that sentence that it was important to spell correctly...
13:04 masak tought.
13:04 masak er, "tough" :)
13:04 olas thomas_ku got bored of us
13:04 masak figures.
13:05 jonalv I think I saw a carrier beside the battleship
13:16 olas egonw: did you solve the JmolAdapter problem I had?
13:16 egonw no...
13:17 egonw first thought was to chat with Bob...
13:17 egonw but on second though...
13:17 egonw since this is an Editor
13:17 egonw just look at Jmol.java
13:17 olas i'm stuck with editor oin BC2
13:17 olas you'll probably solve it in 2 mins
13:17 egonw no, don't think so...
13:17 olas I would need to start all over
13:18 egonw how so?
13:18 olas why does it work in BC2 but not BC1?
13:18 olas new CDK?
13:18 egonw visa versa I guess?
13:18 olas yes
13:18 olas sorry
13:18 egonw no, in BC2 CDK should not be involved at all
13:18 olas ??
13:18 olas why not?
13:18 olas I disagree
13:19 egonw because Jmol can now use its own data model
13:19 olas for what purpose?
13:19 olas that means we can't get CDK properties from the file
13:19 olas and we can't run any CDK Actions on it
13:20 olas Let's say I want to calculate descriptors from the file. I can only do that on an IChemFile
13:20 egonw OK, please explain me how the new architecture works...
13:20 olas hmm, maybe it is possible...
13:20 olas I don't know
13:20 olas hmm
13:20 olas ok, will use jmol API first
13:20 olas and no CDK
13:20 olas let's see how that works out
13:20 egonw mo, phone
13:25 egonw when you have time...
13:25 egonw let's talk about the data model...
13:25 egonw how that works in BC2
13:26 jonalv AAAh d*mn dependecies always broken!!!!
13:31 olas egonw: there's no data model yet
13:31 olas we are working towards it
13:31 olas so nothing to report yet
13:31 * olas is figuring things out as he proceeds
13:31 jonalv we might use EMF for datamodel ut we are not even sure about that yet..
13:33 egonw olas: I understood ... one editor, one data model
13:46 olas maybe
13:46 olas but then there's adapters
13:46 olas have not fully understood that yet
13:46 olas plugins can add functionality for specific classes
13:46 olas will get back on that
13:47 olas trying to figure out if I can give Jmol a Stream instead of a file
13:47 olas File should be banned
13:51 olas egonw: what version of Jmol do we want to use?
13:52 olas head?
13:52 olas or what branch?
13:52 egonw 11.3.x
13:52 egonw which might be trunk/
13:52 egonw this branch becomes stable next month
13:52 olas there's no 11_3 branch
13:53 olas will use trunk then
13:53 egonw then it's simply trunk/
13:53 egonw right
13:58 CIA-18 bioclipse: ospjuth * r4301 /branches/bioclipse2/chemoinf​ormatics/net.bioclipse.jmol/ (5 files in 5 dirs): Removed deps on CDK and prepared for Jmol API.
13:58 olas Was that the first commit of the day?
13:59 egonw OMG... they did not just steal the Grail, but also all of todays commits !?!?!?
13:59 olas bloody thieves
14:05 egonw FYI: http://metware.wiki.sourceforge.net/
14:06 egonw (it mentions BioClipse... aka Bioclipse :)
14:12 sneumann joined #bioclipse
14:18 egonw sneumann: olas is the head Bioclipse developer
14:18 egonw olas: sneumann is the developer of the mzdata plugin for Eclipse
14:21 olas hi sneumann
14:21 olas We'd be very interested in your opinion on EMF and JPOX for data model and persistence
14:31 CIA-18 bioclipse: ospjuth * r4302 /branches/bioclipse2/core/plugi​ns/net.bioclipse.ui/plugin.xml: Updated extension for PDBEditor to .pdb2 to be compatible with new JmolEditor.
14:33 egonw .pdb2 ?
14:33 egonw no default editors anymore?
14:42 olas haha, only temporary
14:42 olas will merge them
14:43 olas Weehow, got my first editor working for BC2!
14:43 olas Screenshot to follow
14:44 CIA-18 bioclipse: ospjuth * r4303 /branches/bioclipse2/chemoinf​ormatics/net.bioclipse.jmol/ (3 files in 3 dirs): Got the JmolEditor working for PDB files. Uses a String as model, and calls JmolViewer.openStringInline(content) to populate Jmol.
14:44 egonw :)
14:44 olas egonw: there is one problem though
14:45 egonw yeah, the grail is still missing, I know
14:45 olas I can't show the outline, as that needs CDK to be present to extract the relevant polymers/monomers/sheets etc
14:46 egonw yeah, so the Jmol plugin needs to register its own OutlineContributor
14:46 egonw makes sense
14:46 olas I still thinks we should have a IChemFile as model
14:46 olas so we can get the info from it
14:47 olas what do you think?
14:47 egonw I don't have time to keep the Adapter up to date all the time...
14:48 olas Can we not just use the latest Jmol and be OK with it?
14:48 olas I don't see any way around it
14:48 egonw be OK with what?
14:48 egonw that the Outline does not work yet?
14:48 egonw yeah, I'm happy with that
14:48 olas we use latest CDK and latest Jmol, you do the latest changes to the adapter, and then we don't update the Jmol
14:49 olas ok?
14:49 egonw ah, that's where the idea breaks down
14:49 egonw huh???
14:49 olas is it that big thing to update the adapter only once?
14:49 egonw "we use latest CDK and latest Jmol" versus "we don't update the Jmol" ??
14:49 egonw no, should be fairly easy to update that adapter...
14:49 egonw don't think bob changed that much...
14:49 egonw ok, ok
14:50 egonw will email him...
14:50 olas great
14:50 egonw but still, I think the Jmol editor should use the Jmol data model
14:50 egonw because then the Jmol script works properly...
14:50 olas I see
14:50 egonw the CDK PDB reader is not good enough
14:50 olas but can we get the info we need from the Jmol model to give to the outline?
14:51 egonw yeah, it is also possible to convert a Jmol data model into a CDK model...
14:51 egonw bit expensive, but possible
14:51 olas ok, then I'm happy
14:51 olas Let's get the outline from the jmol model then
14:52 olas and worry about CDK operating on the object later
14:52 olas so,
14:52 olas How do I get the strands/polymers/chains from the Jmol model?
14:54 egonw OK, you got a Jmol 'clientFile' somewhere? right?
14:54 egonw to pass to the JmolAdapter...
14:54 egonw now... from then on, you got:
14:54 egonw AtomIterator
14:54 egonw BondIterator
14:54 egonw StructureIterator
14:54 egonw see http://jmol.svn.sourceforge.net/viewvc/j​mol/trunk/Jmol/src/org/jmol/api/JmolAdap​ter.java?revision=8353&amp;view=markup
14:56 olas thx
14:56 olas no
14:56 olas did openStringInline
14:56 olas so got no clientFile
14:56 olas can I get it from the viewer?
14:56 egonw yeah, think so...
14:56 egonw mom
14:58 egonw http://jmol.svn.sourceforge.net/viewvc/​jmol/trunk/Jmol/src/org/jmol/api/JmolVi​ewer.java?revision=8480&amp;view=markup
15:02 olas Screenshot: http://wiki.bioclipse.net/​index.php?title=Bioclipse2
15:04 masak neat!
15:04 egonw yes, *very* nice!
15:04 jonalv looks good
15:05 edrin olas: the bioclipse explorer, is it == the eclipse file navigator?
15:07 edrin the js console, is it part of core or a plugin already?
15:07 masak edrin: re explorer: I think so, but it depends on the exact semantics of '=='
15:07 masak edrin: js console: core
15:07 masak at least, for now
15:07 edrin the js console, is it in its own thread or using main thread?
15:08 masak edrin: it's using the main thread
15:08 masak is that bad?
15:09 masak I could "borrow" your code for it using its own thread if you think it matters
15:09 edrin well, if you call a long lasting function maybe. but on the other hand you might get other problems when runing it in its own thread
15:10 masak yes.
15:10 edrin masak: for example if you call a function that "never ends", while(i){}; ... the bioclipse will be blocked and all data will get lost...
15:10 masak I've gotta try that :)
15:10 masak be right back
15:11 edrin but if you run it in its own thread... you will have problems accessing the main thread...
15:11 masak edrin: in what way?
15:12 * masak just hung bc2 with a simple while (1) ;
15:12 masak fascinating.
15:12 egonw hehehe
15:12 masak heh maybe we should defer infinite loops to their own threads, and do everything else in the main thread? :)
15:13 egonw hey, wait...
15:14 egonw maybe you can make the infinite loop multithreaded... then it will even be faster :)
15:14 masak good idea
15:14 masak I think we're really onto something here
15:15 masak edrin: please elaborate on the difficulties of running the js in a separate thread
15:16 masak maybe simply spawning a thread every time a cammond is to be executed
15:18 jonalv Isn't the js engine running an own thread?
15:19 thomas_ku joined #bioclipse
15:20 edrin masak: please take a look at http://wiki.bioclipse.net/index.p​hp?title=Bc_rhino#Sample_script_4
15:20 masak jonalv: no.
15:20 jonalv it probably should...
15:21 edrin masak: how is the console done? you have a rhino object where you pass console input with a function and you return the result of this function to the console?
15:22 masak edrin: as of now, a console view has a js session
15:22 masak communication is one way from the view to the session
15:22 masak this will need to be changed with the introduction of spring
15:22 edrin masak: it does not return something?
15:22 edrin spring? what do you mean?
15:22 masak edrin: yes, but apart from that, communication is one way
15:23 masak edrin: re spring: I wish I knew more what I mean by that
15:23 * jonalv thinks the introduction od Spring is far away in the future... :(
15:23 masak we're investigationg
15:23 edrin me is now confused
15:23 masak welcome to the club
15:23 edrin what is spring?
15:23 jonalv www.springframework.org
15:23 masak jonalv: thx
15:24 masak I was wondering what to write exactly
15:24 masak I got to "it's a framework..."
15:24 jonalv yes...
15:24 masak ...bla bla bla...
15:24 masak ...eject horizontally...
15:24 jonalv aop
15:25 masak yup
15:25 jonalv inversion od control
15:25 olas after winter comes...
15:25 masak separation of concerns
15:25 egonw bye all
15:25 masak egonw: bye
15:25 jonalv bye
15:25 olas bye
15:25 edrin ... bye
15:31 EskilA_ joined #bioclipse
15:55 edrin masak: the spring should replace eclipse in bioclipse?
15:57 masak edrin: no
15:57 masak but it's a justified question :)
16:01 Deanne joined #bioclipse
16:01 * Deanne waves
16:01 * Deanne needs some advice.
16:02 olas hi Deanne
16:02 * Deanne is on an apple, this time around, and on bioclipse 1.1.3 beta
16:02 olas cool
16:02 Deanne I can't see the molecular 3d structure when I double click on the pdb file.
16:03 olas have you installed Chemoinformatics feature?
16:03 Deanne Yup, installed everything.
16:03 Deanne Is it in the chemoinformatics perspective?
16:04 olas open Chemoinformatics perpsective
16:04 Deanne My perspective drop-down only says default not other...
16:04 olas hmm
16:04 Deanne Ah, wait..
16:04 Deanne here it is.
16:04 Deanne wrong drop down.
16:04 Deanne <-- should check twice. :)
16:04 olas :-)
16:04 Deanne Oh, thank you.
16:05 * olas is working on Bioclipse2
16:05 Deanne It was nearly automatic on the windows machine.
16:05 * Deanne nods.
16:05 olas posted a screenshot today: http://wiki.bioclipse.net/​index.php?title=Bioclipse2
16:05 Deanne Ola: One of the faculty here is saying I don't want Bioclipse, I want Taverna. :)
16:05 * Deanne goes to look.
16:05 olas yup, heard that before
16:05 olas well, Bioclispe will not replace Taverna
16:06 * Deanne said Taverna doesn't play well with direct manipulations.
16:06 * Deanne nods.
16:06 olas Taverna2 will be a great product, but will not solve everything
16:06 Deanne I don't want Taverna, anyway, mol biologists here want visual tools.
16:06 olas It is not a workbench
16:06 olas exactly
16:06 * Deanne nods, exactly.
16:07 olas So if we can run Taverna WF's, then we can use the results of the people who design in Taverna
16:07 olas Taverna is not easy to design in
16:07 Deanne Is that image able to be enlarged (the screen shot)?
16:07 olas click on it?
16:08 olas Deanne: Have you registered your nick on freenode?
16:09 * Deanne has yet to register her nick.
16:09 * Deanne will do so. :)
16:09 Deanne I click on that screenshot and get a blank w/a broken image.
16:09 olas click on the blank image again
16:09 jonalv Deanne: in the wiki?
16:09 olas it doesn't show up since it's so big
16:10 olas maybe I should reduce the siize a little
16:10 jonalv The wiki seems to lack tools for resising images..
16:10 olas yes, it does
16:10 Deanne warning: imagepng() [function.imagepng] Unable to open '/customers/bioclipse.net/bioclipse.net/httpd.www​/wiki/images/thumb/800px-Bioclipse2firstshot.png' for writing in /customer/bioclipse/ (etc)
16:10 olas it is in need of a MediaWiki update
16:10 Deanne Image still not working for me.
16:11 Deanne no big deal, tho.
16:11 olas http://wiki.bioclipse.net/im​ages/Bioclipse2firstshot.png
16:11 Deanne That works. :)
16:11 olas Well, it's not much yet
16:12 olas There are too many bugs in Bioclipse1 that we will not resolve but fix in Bioclipse2
16:12 olas But we will release Bioclipse1.1.5 some day soon
16:12 olas with the latest QSAR stuff, a rudimentary BioMoby plugin, and charting capabilities, and scripting functionality
16:13 olas deanne: jonalv is working on building a Spring-based core for Bioclipse2
16:14 deanne How's the R/Bioconductor work going?
16:14 olas We are working on a rewrite of JRI that is threaded
16:14 olas The problem is otherwise that you could only have one R running at a time, which would not be sufficient
16:14 * deanne nods.
16:15 olas That will take some time, but will be well worth the time spent
16:15 deanne Well, it runs single-threaded for apps like bioconductor.
16:15 * deanne uses bioconductor quite a bit...most of it is sit and wait.
16:22 CIA-18 bioclipse: ospjuth * r4304 /branches/bioclipse2/chemoinf​ormatics/net.bioclipse.jmol/ (6 files in 5 dirs): Updated to latest Jmol.jar, head on v20071120, towards 11.4 release. Also refactored methods in JmolPanel.
16:26 CIA-18 bioclipse: ospjuth * r4305 /branches/bioclipse2/chemoinformatic​s/net.bioclipse.jmol/jars/Jmol.jar: Updated to latest Jmol.jar, head on v20071120, towards 11.4 release.
16:36 sneumann Hi olas, sorry, still need to get used to IRC
16:36 sneumann Correction: StefanK did the mzData Plugin for Bioclipse.
16:37 sneumann What we did was using EMF to generate model, edit and editor plugin for mzData. Was kind of an exercise to get to know EMF.
16:38 sneumann What you can do then is to use EMFT Teneo (formerly known as www.elver.org, where still some documentation is hosted) to generate a mapping between your POJOS and JDO.
16:38 sneumann (Or alternatively hibernate)
16:39 sneumann We have used JPOX as JDO implementation. Afterwards you can point your EMF.editor at your postgresql and edit the stuff in the database.
16:41 olas did it work out nicely?
16:41 olas You were happy about the design process and the result?
16:41 sneumann Well, that were my first steps with java, so I had a very steep learning curve.
16:42 sneumann There are still many knobs to tune, such as JPOX startup time
16:42 olas sounds impressive for a first try with java :-)
16:42 olas jonalv: What do you think?
16:42 sneumann Since it checks table structure on startup and generates tables if neccessary
16:42 sneumann Overall I liked the idea, because I expected to follow a moving standard, where the XSD might change frequently.
16:43 CIA-18 bioclipse: ospjuth * r4306 /branches/bioclipse2/core/​plugins/net.bioclipse.ui/ (bioclipse.product plugin.xml): Moved progress bar down and changed msg color to one with better contrast.
16:45 jonalv olas, sneumann it sounds very impressive.
16:46 * olas has to go
16:46 olas See you all tomorrow
16:46 * deanne waves to ola.
16:46 olas bye
16:46 olas left #bioclipse
16:46 jonalv bye
16:46 jonalv :(
16:46 deanne Anyone know what proteomics applications are in Bioclipse or being planned?
16:48 CIA-18 bioclipse: carl_masak * r4307 /branches/bioclipse2/core/p​lugins/net.bioclipse.core/ (8 files in 4 dirs):
16:48 CIA-18 bioclipse: [net.bioclipse.core]
16:48 CIA-18 bioclipse: * groovy support
16:48 CIA-18 bioclipse: * groovy console
17:16 Deanne joined #bioclipse
17:18 deanne Connection is bad.
17:18 deanne did anyone answer the question about proteomics apps in bioclipse?
17:29 masak don't think so
17:29 masak olas could probably answer, but he's logged out for today
17:34 deanne Saw that....asked him in msg but he was leaving at that point.
17:34 deanne tx anyway.
17:35 * deanne wants to start porting the ucsc genome browser into bioclipse.
17:35 * deanne is going to do that for her next project.
17:35 deanne ..first project, even. :)
18:11 edrin deanne: what proteomic aim/thing do you mean?
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