Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-01-21

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All times shown according to UTC.

Time Nick Message
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09:18 steinbeck moin
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10:51 edrin hi
10:52 jonalv hi edrin
10:53 edrin hi jonalv
10:55 olas hi edrin
10:55 edrin hi ola
10:57 * jonalv @ lunch
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11:27 edrin egonw: i think i found a simple way to give w3c DOM objects to the client lib for sending them as a payload. i think that should be sufficient, what do you think?
11:36 egonw edrin: need more input...
11:40 edrin egonw: when invoking a function like: function.invokeSync(input) the input must be some input DOM. i thought about allowing the input DOM to be a w3c java DOM and not only the StreamElement DOM of the JSO XMPP library. on the other hand I do not know if sun's Java also has functionality to validate XML DOMs against a XML Schema...
11:41 edrin egonw: do you think it is a must that input and output can be JDOM, too?
11:43 edrin egonw: ah, and the validation just means a "pre"-check befor submission. of course the service can check it again and still say, "no, input is not valide"...
11:44 CIA-14 bioclipse: ospjuth * r4732 /branches/bioclipse2/bioinformatic​s/plugins/net.bioclipse.jalview/: Initial import.
11:47 CIA-14 bioclipse: ospjuth * r4733 /branches/bioclipse2/bioinformati​cs/plugins/net.bioclipse.jalview/ (33 files in 9 dirs): Initial import. This plugin is for visualizing and editing multiple sequence alignments by wrapping Jalview (http://www.jalview.org).
11:48 olas 'blog coming up
11:48 edrin olas: blog about sequence editing
11:48 edrin ?
11:50 olas blog about Jalview in Bioclipse
11:50 * olas is away for lunch
11:55 egonw edrin: sorry... someone needed to talk with me
11:55 egonw olas: met with Harm Nijveen this morning, and chatted about Bioclipse...
12:05 olas egonw: yes
12:05 olas what did he say?
12:06 olas I remember talking to him about EMBOSS in Bioclipse
12:08 egonw right...
12:08 egonw not sure...
12:08 egonw but I had enough time to demo...
12:08 egonw Andreas is a bit put off by the heavy weight...
12:08 egonw but I think they liked the features I showed...
12:08 egonw and
12:09 egonw I convinced them that having a C/C++ program is no problem
12:09 egonw edrin: yes, please do blog about sequence editing...
12:10 egonw better visibility will attract sequence people
12:10 egonw edrin: no, whatever DOM is fine with me...
12:10 egonw edrin: the input can not be something serialized?
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13:14 olas http://bioclipse.blogspot.com/2008/01/​multiple-alignments-in-bioclipse.html
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13:25 egonw ha, there are those announced maintenance thingies... :)
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13:25 olas annoying
13:25 egonw well, you only had to pick the right server this morning
13:25 egonw not one which would see this happening :)
13:26 CIA-14 bioclipse: ospjuth * r4734 /branches/bioclipse2/bioinformati​cs/plugins/net.bioclipse.jalview/ (4 files in 3 dirs): Cleaned up code, icon, and set editor name set to filename.
13:26 olas haha
13:26 olas egonw: did you like my blog about jalview?
13:26 egonw no idea
13:26 egonw did not read it yet
13:27 egonw very nice
13:27 egonw will relay this to Harm and Andreas
13:29 egonw jalview does DNA/RNA too?
13:29 CIA-14 bioclipse: jonalv * r4735 /trunk/playground/plugins/net.biocli​pse.expression/META-INF/MANIFEST.MF: new version number on expression
13:30 egonw olas: and, are there other ongoing development projects for sequence (prot/dna/rna) for bioclipse?
13:30 olas egonw: yes
13:30 olas egonw: yes
13:30 olas quite some focus actually
13:31 olas alignments are important
13:31 olas but the big missing piece is a good alignment editor
13:32 olas I don't know if it even exists
13:32 olas at all :-)
13:32 egonw got a wiki page with plans?
13:32 olas no
13:32 egonw they demoed a Primer utility
13:32 egonw ack
13:32 olas we will set up a plan together with viklund
13:32 olas have a few use cases
13:33 olas http://wiki.bioclipse.net/index.p​hp?title=Bioinformatics_use_cases
13:33 egonw this jalview is not good enough a sequence alignment editor?
13:34 olas yes, I think so
13:34 olas but it's not a sequence editor
13:34 egonw ack
13:57 CIA-14 bioclipse: ospjuth * r4736 /branches/bioclipse2/misc/net​.bioclipse.data.sampledata/: Initial import of plugin to install sample data using a NewProjectWizard.
13:57 egonw olas: oh... that reminds me...
13:57 egonw the Install Sample Data was missing from the Operations menu...
13:57 egonw even though the plugin was installed for 1.2.0 from the update site...
13:57 olas please file a bug
13:58 olas in wrong place to fix now
14:00 egonw ack
14:01 olas egonw: what does the net.bioclipse.data contain in the folders 2DStructures, 3DStructures and reactions?
14:01 olas not BODR?
14:01 olas 3D structures seems very similar to BODR...
14:02 egonw not sure...
14:02 olas egonw: if you can confirm that I will remove them from net.bioclipse.data
14:02 egonw don't remember those dirs...
14:02 egonw file a bug report
14:02 egonw in the wrong time-space to fix now
14:02 olas working on it now
14:02 olas yea, sure
14:03 * egonw is working on setting up biomoby services
14:03 olas cool
14:03 olas hope you get it working
14:03 egonw I hope so too :)
14:03 olas then you can help me with the BioMoby client in Bioclipse
14:03 olas I have spent so many hours on it...
14:03 egonw :)
14:03 egonw yeah, would be fun
14:04 olas it is now partially working
14:04 olas but the problem is really for how a user should know what to provide
14:04 olas and design the GUI for that
14:05 edrin egonw: in what way is biomoby different to soap?
14:05 egonw indeed
14:05 egonw edrin: it adds semantics
14:05 edrin in example?
14:05 egonw biomoby services work on a certain object type
14:05 egonw for example, on sequences
14:05 edrin ok
14:06 edrin but it is synchronous?
14:06 edrin is it using soap?
14:06 egonw and there is a central registry for looking up services... (sounds familiar, not?)
14:06 egonw yes, uses SOAP
14:06 * egonw is getting coffee now...
14:06 egonw bbl
14:06 edrin ok
14:36 CIA-14 bioclipse: carl_masak * r4737 /trunk/playground/plugins/net.bioclipse.base2/ (10 files in 6 dirs):
14:36 CIA-14 bioclipse: [net.bioclipse.base2]
14:36 CIA-14 bioclipse: * now connects to database and pulls down things
14:36 CIA-14 bioclipse: * so, no more mocking here
14:36 CIA-14 bioclipse: [net.bioclipse.base2.model]
14:36 CIA-14 bioclipse: * mostly API interaction code to accomplish the above
14:40 CIA-14 bioclipse: carl_masak * r4738 /trunk/playground/plugins/net.bioclipse.base2​/src/net/bioclipse/base2/views/TreeView.java:
14:40 CIA-14 bioclipse: [TreeView.java]
14:40 CIA-14 bioclipse: * whitespace
14:40 CIA-14 bioclipse: * removed unused imports
14:42 edrin olas: will you port your biomoby plugin to bc2?
14:46 olas yes
14:46 CIA-14 bioclipse: ospjuth * r4739 /branches/bioclipse2/misc/ne​t.bioclipse.data.sampledata/ (56 files in 14 dirs): Added wizard and data to be installed. No installation yet.
14:46 olas I will later
14:46 edrin olas: :D
14:47 olas And even more
14:47 olas I want the object model to be compatible
14:47 edrin what = more?
14:47 olas so you can select an ISequence in Bioclispe and run BioMoby services on it directly
14:47 olas so will try to get a toMoby() method in the API
14:47 edrin yes, would be cool to not loose all the plugins
14:47 olas sure
14:48 edrin ah
14:48 edrin ok
14:48 olas the aim is that most should work with minor modifications
14:49 edrin olas: The development plans of Bioclipse sometimes appear to me a bit cryptic... it's hard to know what is happening and planned.
14:49 edrin Just in case someone wants to contribute code it's a little bit cryptic i fear right now
14:49 egonw [2008-01-21 15:50:59] <egonw> oi, things are going really fast...
14:49 egonw [2008-01-21 15:51:03] <egonw> cheers Ola!
14:50 egonw olas: what would be really nice...
14:50 egonw is an online IRC chat session
14:50 egonw on how resource navigating works in BC2
14:50 edrin egonw: within bioclipse?
14:50 edrin ah ok
14:50 edrin ;)
14:50 masak edrin: I understand that feeling. some things are really difficult to communicate to outside of the Uppsala team
14:50 egonw becuase that's the major thing changed
14:51 masak edrin: however, nudge us and we will keep trying :)
14:52 edrin in example it would be great if it is more clearified who is doing what right now. And what - finally - is the set of plugins that are named "core"
14:52 edrin together
14:52 masak good idea
14:53 egonw edrin: we'd really need a deverlopers meeting :)
14:53 masak edrin: our main focus now -- since the working prototype of the recorder -- is fleshing out the data model, i.e. ISequence et al
14:53 edrin if everything is only ONE plugin it is hard to develop it by multiple persons.
14:54 edrin ok
14:54 edrin have students now, have to go again :)
14:54 masak among the three of us (olas, jonalv, masak), olas is working on GUI and editors, jonalv is working on connections downward towards Spring and OSGi, and I'm tending the scripting capabilities
14:54 edrin ok
14:55 edrin bye
14:55 masak bye
14:55 CIA-14 bioclipse: ospjuth * r4740 /branches/bioclipse2/misc/net.b​ioclipse.data.sampledata/data/: Updated installable data.
14:59 CIA-14 bioclipse: ospjuth * r4741 /branches/bioclipse2/misc/net.b​ioclipse.data.sampledata/data/ (285 files in 26 dirs): Updated installable data.
15:16 * jonalv is going for databases as soon as possible :)
15:24 CIA-14 bioclipse: carl_masak * r4742 /trunk/playground/plugins/net.bioclip​se.expression.tests/src/net/bioclipse​/expression/tests/FunctionsTest.java:
15:24 CIA-14 bioclipse: [FunctionsTest.java]
15:24 CIA-14 bioclipse: * character '%' now allowed in function names
15:24 CIA-14 bioclipse: * 1 failing test
15:25 masak jonalv: because of special demands like this, it might be difficult ever to re-use the expression parser
15:27 egonw '%' in function names???
15:27 egonw what language is that?
15:27 jonalv yes I know but what's your point?
15:28 masak egonw: it's a math expression evaluator
15:28 masak but it's used in a plugin that jonalv is developing
15:28 jonalv we wanted a function name to si%
15:28 masak I don't condone it, I just follow orders
15:29 masak jonalv: if you ask me, I think it's a bit of a mistake, actually
15:29 jonalv what do you want to use % for?
15:29 masak we should change it back while we can
15:29 masak it's not a question of that
15:29 masak it's a question of Least Surprise
15:29 masak there are so many languages where % is not a legal character in identifiers
15:30 masak there's an almost universal standard of how an identifier looks
15:30 jonalv I don't think you should dissalove things for no good reason. At least not when I want to the thing you are trying to dissalove for no good reason...
15:31 masak the good reason being the expectations of 99% of everyone who'll ever use the program
15:31 jonalv But you explain for my user why she can't name her functions after what they actually are..
15:31 masak but ultimately, it's your decision
15:31 masak jonalv: yes, I might, if you want
15:31 jonalv you are of course wrong in those statistics...
15:32 masak of course
15:32 jonalv 100% of my users want the feature...
15:32 jonalv =)
15:32 masak true.
15:32 masak so we should just go ahead and allow %
15:32 jonalv I don't see who it's gonna hurt
15:33 masak me neither
15:33 jonalv besides I predict that most of these sort of things will be done with javascript in bioclipse 2 anyway...
15:33 masak yes
15:33 masak thinking short-term can be very relieving :)
16:03 CIA-14 bioclipse: jonalv * r4743 /trunk/playground/plugins/net.bioclipse.expressi​on/src/net/bioclipse/expression/Calculator.java: % is now a legal character in functions in the expression parser
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