Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-01-14

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All times shown according to UTC.

Time Nick Message
07:35 egonw joined #bioclipse
07:51 rojasm joined #bioclipse
08:50 jonalv joined #bioclipse
09:22 Annzi joined #bioclipse
09:26 thomas_ku joined #bioclipse
09:36 thomas_ku_ joined #bioclipse
09:46 viklund joined #bioclipse
09:47 jonalv hi viklund
09:47 viklund helo
09:47 jonalv what's news?
09:47 viklund sry, ehlo
09:48 viklund umm, "Boten anna" är listetta i storbrittanien!!
09:48 jonalv right
09:48 viklund As "Now Your're Gone"
09:48 jonalv what's news with your bioclipse project?
09:48 viklund http://www.youtube.com/watch?v=IgFwiCApH7E
09:48 viklund so good song!!
09:49 jonalv you are working on something right?
09:49 viklund I thought I restart it right after I parsed a blast file into a db
09:49 viklund didn't really start with it, and now seems like a good time to jump in again.
09:49 jonalv yes what was it again?
09:49 viklund could you please point me to a good tutorial for making webservices with eclipse?
09:49 viklund dnds calculation
09:50 jonalv no I havent' made any webbservices...
09:50 viklund (or ka/ks)
09:50 viklund "Now you're gone, I realize that my love for you was strong..."
09:50 jonalv stop me if I am wrong but that sounds like a rather small little computation so why do you want it as a webbservice?
09:50 viklund go Eurodisco!!
09:50 jonalv =)
09:51 viklund oh, that was hmm, whots-his-name, idea...
09:52 jonalv but it's like a proof of concept thing or?
09:52 viklund "Vi sitter här i venten och spelar lite dota!": http://www.youtube.com/watch?v=kQ-TZk4gPKM
09:52 viklund yep
09:52 jonalv so later on you want to do fancier webbservices as well?
09:52 viklund yep
09:52 viklund need to start somewhere right?
09:52 jonalv then it seems reasonable
09:52 viklund basically it's just a frontend to the program yn00
09:53 jonalv you should talk to Carl he is also working with webb services in some way...
09:53 viklund he's not here though
09:53 viklund well, well, I'll be back after lunch when my blast is in my db..
09:53 jonalv no he is probably stiill asleep
09:54 viklund (the lazy bastard ;))
09:54 jonalv yes...
09:59 egonw viklund: is your code in Java?
09:59 egonw and you're happy with SOAP?
09:59 egonw well, sure... nothing else provided by Eclipse...
09:59 viklund no code yet and yes
09:59 egonw stupid question...
10:00 egonw anyway... have a look at the SOAP/WDSL stuff in Java6
10:00 egonw *really* easy
10:00 jonalv and works great on mac OS X *NOT*
10:00 egonw oh... really?
10:01 egonw stupid OS/X
10:01 * jonalv grumbles about java 6 not existing for mac os x...
10:01 egonw don't even have a decent JVM
10:01 jonalv or wait a minut it might be that the latest version has it btw...
10:01 egonw seriously... I'm really disappointed in Apple...
10:02 jonalv but I now that masak is having problems with that
10:26 EskilA joined #bioclipse
10:26 jonalv hi EskilA
10:26 EskilA hello
10:53 viklund ok, now i'm ready (the blast report will be in my db in 4.6 days...)
10:55 viklund took 25 days to run it...
10:59 viklund what eclipse version are you at?
10:59 viklund jonalv?
10:59 viklund (dont remember this since last time=
10:59 viklund )
11:00 viklund 3.3?
11:26 viklund got it...
11:43 * jonalv is back from lunch @ New India
11:43 jonalv I'm full...
11:43 masak joined #bioclipse
11:49 masak viklund: ping
12:05 viklund pong
12:06 * viklund is back from lunch @ lunch corner (mm, pasta salad)
12:06 masak viklund: I hear you are descending into the web services inferno
12:07 viklund yep
12:08 masak nice to see you around, btw
12:08 masak jonalv and me have had semi-plans to come and visit you and discuss more use cases
12:09 viklund mhmm
12:17 Annzi left #bioclipse
12:34 olas joined #bioclipse
13:35 CIA-20 bioclipse: carl_masak * r4668 /trunk/playground/plugins/net.bioclipse.expressio​n/src/net/bioclipse/expression/FunctionBody.java:
13:35 CIA-20 bioclipse: [FunctionBody.java]
13:35 CIA-20 bioclipse: * further clarification of the implications of cloning
13:41 CIA-20 bioclipse: carl_masak * r4669 /trunk/playground/plugins/net.bioclipse.base2​/src/net/bioclipse/base2/views/TreeView.java:
13:41 CIA-20 bioclipse: [TreeView.java]
13:41 CIA-20 bioclipse: * respacing
13:41 CIA-20 bioclipse: * more realistic names for the mocked objects
13:45 thomas_ku joined #bioclipse
14:08 egonw jonalv: and, is J6 available for OS/X?
14:08 egonw Taverna wants to switch to J6...
14:08 egonw not sure if there are many Taverna users using OS/X
14:08 masak egonw: olas says it's avail for OS X 10.5
14:09 CIA-20 bioclipse: updatebjarni * r4670 /branches/bioclipse2/core/plugins/net.​bioclipse.r/src/net/bioclipse/r/pty.c: Made pty controlling terminal so R dies right.
14:09 jonalv egonw, I have no idea just knows taht masak had problems...
14:10 CIA-20 bioclipse: jonalv * r4671 /trunk/playground/plugins/net.bioclip​se.keyring/src/net/bioclipse/dialogs/ (EditSuperUserDialog.java ValueInputDialog.java): Added dialog reachable from context menu since SWT for windows is borken
14:10 CIA-20 bioclipse: updatebjarni * r4672 /branches/bioclipse2/core/plugins/net.​bioclipse.r/native-bin/pty-linux-i386: Recompiled from latest source.
14:14 CIA-20 bioclipse: carl_masak * r4673 /branches/bioclipse2/core/plugins/​net.bioclipse.r/native-bin/pty-mac os x-i386:
14:14 CIA-20 bioclipse: [pty-mac os x-i386]
14:14 CIA-20 bioclipse: * recompiled from latest source
14:18 CIA-20 bioclipse: carl_masak * r4674 /trunk/plugins/net.bioclipse.rhino/src/net/biocli​pse/plugins/bc_rhino/views/RhinoConsoleView.java:
14:18 CIA-20 bioclipse: [RhinoConsoleView.java]
14:18 CIA-20 bioclipse: * renamed method
14:18 egonw http://www.molegro.com/mvd-tutorials.php
14:20 thomas_ku joined #bioclipse
14:20 olas joined #bioclipse
14:20 kaskelot joined #bioclipse
14:20 masak egonw: looks impressive
15:08 EskilA joined #bioclipse
15:40 rojasm left #bioclipse
16:20 CIA-20 bioclipse: carl_masak * r4675 /branches/bioclipse2/core/plugins/n​et.bioclipse.ui/src/net/bioclipse/u​i/views/ScriptingConsoleView.java:
16:20 CIA-20 bioclipse: [ScriptingConsoleView.java]
16:20 CIA-20 bioclipse: * disabled updating when scrolling down to prompt
16:20 CIA-20 bioclipse: * this is a test to see if X behaves better
16:58 * jonalv summons shk3
17:03 masak jonalv: not working too well, is it? :>
17:03 jonalv gumble
17:05 * jonalv wonders which timezone he is in...
18:23 jonalv he=shk3
18:27 masak simplifying, e = sk3
18:27 edrin joined #bioclipse
18:28 masak hi edrin
18:28 jonalv hi edrin
18:28 edrin hi masak
18:28 edrin hi jonalv
18:28 jonalv edrin, you know where shk3 is?
18:28 edrin no, do you?
18:28 jonalv no :(
18:29 jonalv do you know where in the world he is? Or more exactly which timezone?
18:30 edrin isn't shk3 Stefan Kuhn? so he is in germany i guess
18:30 jonalv so 6 pm would have been for 1.5 hour ago for him?
18:30 * jonalv has been waiting a while... :)
18:31 edrin yup
18:32 jonalv edrin,  do you know how Tobias database project is supposed to work?
18:32 edrin no, sorry
18:33 jonalv k np
18:33 edrin i never worked in their group, so i am not familiar with the stuff they did
18:37 jonalv okey
18:38 jonalv edrin, have you read our "short" mail to the list?
18:41 edrin yep, I did
18:42 masak edrin: was it digestible?
18:42 jonalv no comments?
18:42 edrin i think so. it was very big
18:44 masak :)
18:45 masak the design for bc2 is a bit ambitious
18:48 jonalv edrin: you can try calling biojava.loadsequence("") in the javascript console in bc2 now and see the history view update itself :)
18:48 edrin i think your plans are a bit too overdesigned.
18:48 masak jonalv: maybe we should have provided that as an example
18:49 jonalv yea
18:49 masak edrin: that's exactly the kind of thing we need to hear early on, I think
18:49 edrin jonalv: I am currently not at a bc capable machine
18:49 jonalv Okey in what way?
18:50 edrin the console thing?
18:50 jonalv yes you think it's to ambitious?
18:51 edrin no, i mean the project is a bit too overdesigned
18:51 jonalv overdesigned? In what way?
18:51 masak in the sense of 'thinking too much before starting'?
18:52 jonalv We have started you know...
18:52 jonalv We have a proof of concept implementation
18:52 masak or in the sense of 'wanting one program to do too many things'?
18:52 edrin there are big plans but i assume it is a little bit too much to do it without having hundred program developers
18:52 masak :)
18:52 masak as always
18:53 masak actually, right now it feels good being a fairly small core team
18:53 masak with layers of interested fringe developers further out
18:53 masak in my opinion, it's working surprisingly well
18:54 edrin i like the concept of having bioclipse to represent data in bio objects that will be handeled with a certain interface by bioclipse itself.
18:54 jonalv yes this is the part I am probably the most nervous about
18:55 jonalv The domain objects will wrap around things like atomcontainer but he question is how much we can do on the say molecule interface and how much will actuall be on the atomvontainer
18:56 edrin jonalv: it's ok like this. you need bioclipse resource manager to handle/move/copy the data and plugins to handle them
18:57 jonalv yes the manager will handle them
18:57 jonalv managers
18:57 jonalv and they will of course unwrap and work on the say Atomcontainer if taht is needed
18:58 edrin the "record GUI actions and make a script" thing is - in my opinion - a little bit too much. i am not sure if it's worth doing this.
18:59 edrin consider, most of the users are academic persons as well
18:59 jonalv The thing is that it isn't very much more work when we already ahve this structure
19:00 jonalv The structure of on bioclipse api in Spring managed managers acceible both from the gui and the scripting tools makes it an easy thing to add
19:00 jonalv That is also what I am thinking about
19:00 masak edrin: the goal is still to provide simplicity to people who only need simplicity
19:00 jonalv Most people working with sequences do so by first learn how to program Perl
19:01 jonalv But the biggest think is that the managers should be seaprate units and thus easy to test
19:01 jonalv And tests are something that we seriously lack
19:02 edrin if spring would make it that easy, ok, but are you sure the work invested in other things would not be more convincing?
19:02 masak no, of course not
19:02 masak no-one has ever done this before
19:03 jonalv I am planning to invest my time in a blast database real soon now. But I would have to say no
19:03 jonalv If you ask me
19:03 masak but as for myself, I'm pretty intrigued with where this is going
19:03 jonalv you probably should ask olas though
19:03 edrin are you talkin to me?
19:03 jonalv I must pioint out that the most part of finding out how to this is already tdoen what reminds is to actually do it...
19:05 jonalv Waht reminds is what has been there all the time. Figure out what Bioclipse should do and how and write methods doing that in the managers
19:05 jonalv hm s/reminds/remains
19:05 jonalv more or less anyway...
19:05 edrin jonalv: did you know, Microsoft Word/Office supports recording "visual basic scripts" exactly like we want to have it in bc. However I can not remember a case where i ever used it.
19:05 jonalv There will probably be a few more problems along the way... :)
19:05 masak edrin: I have used them
19:06 masak it's called VBA
19:06 masak point taken, scripting is not for everyone
19:06 masak but nobody here claims that either
19:06 jonalv That is because when you use Word you don't work with wast amounts of sequences say all known bacterial DNA or so...
19:09 edrin on the other hand if you are someone who has to work with wast amount of sequences, i would hope that this guy/girl would know how to handle all these data anyway - (or at least be willing to learn javascript)
19:09 jonalv But I think it's great that you are skeptical taht keeps us on our toes :)
19:10 jonalv yes, but to have visualisation possibilities at your finger tips as you would in bioclipse, that I think would be a great extra feature
19:11 jonalv But once again look at it this way
19:11 jonalv We need to do testing
19:11 jonalv Taht means that we need a seaprate layer for testable logic
19:11 jonalv That would be the managers
19:12 jonalv You have my word that spring is worth the learning time for this
19:12 jonalv It helps and it will be great when we start working with databases through ORM's and such
19:13 jonalv When we all this the script recording is just around the corner...
19:13 jonalv That's at least how I see it...
19:16 jonalv time to go home
19:16 jonalv sort of past time to go home... :)
19:17 jonalv cya
20:03 edrin left #bioclipse
22:10 edrin joined #bioclipse
22:11 edrin hello EskilA, who are you?

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