Camelia, the Perl 6 bug

IRC log for #bioclipse, 2007-11-16

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All times shown according to UTC.

Time Nick Message
00:17 drzz joined #bioclipse
02:20 yangming_ joined #bioclipse
03:25 Deanne joined #bioclipse
03:26 Deanne Hey...
03:26 Deanne Anyone awake?
03:41 pohyg hi
03:41 Deanne Hi...
03:42 pohyg i don't think the rest are awake
03:42 Deanne Must be earky there
03:42 Deanne er
03:42 Deanne early :)
03:42 pohyg Deane: are u a bioclipse user?
03:43 Deanne Hopefully a bioclipse developer soon. :)
03:43 pohyg oic
03:43 Deanne we are in Boston MA and have been mailing Ola and others...we want to add to Bioclipse
03:45 Deanne I haven't used IRC in about 10 years now.
03:46 Deanne Interesting how I can remember some commands.
03:46 Deanne what about you?
03:51 pohyg I am new on irc
03:51 pohyg I am currently looking for a framework to support routine analysis
03:52 pohyg I am from Kuala Lumpur
03:52 Deanne What kind of analysis are you doing?
03:52 pohyg various
03:53 pohyg gene finding, gene mapping, translation etc
03:53 pohyg commercial tools are expensive
03:53 pohyg currently i m dependent of emboss, and blast
03:53 pohyg i m not sure if bioclipse can be the right framework or not
03:57 pohyg in which aspect are you looking into contributing to bioclipse?
04:10 pohyg I do find bioclipse is somewhat slow
04:10 Deanne left #bioclipse
06:38 rojasm joined #bioclipse
06:54 rojasm left #bioclipse
06:54 rojasm joined #bioclipse
07:48 yangming joined #bioclipse
08:05 egonw joined #bioclipse
08:39 egonw joined #bioclipse
09:16 yangming egonw?
09:16 egonw hi yangming
09:16 yangming hi!
09:16 egonw welcome at #bioclipse :)
09:17 yangming thank you
09:17 yangming I would like to ask if bioclipse support drawing of plasmids/vectors in SVG?
09:18 egonw ah, sounds interesting...
09:18 egonw not sure...
09:18 egonw must of the Bioclipse functionality is provided by plugins...
09:18 yangming oic
09:18 egonw must -> much
09:19 egonw but I am currently not aware of a pluging supporting plasmids/vectors SVG drawing...
09:24 yangming in your opinion, how does BioClipse compare to BioEdit?
09:24 egonw which bioedit is that?
09:24 yangming It seems a world apart yet share some common features
09:25 yangming http://www.mbio.ncsu.edu/BioEdit/bioedit.html <- this one
09:25 yangming Bioedit is a good tool, it helps me alot
09:25 yangming but it is not open source
09:26 egonw another important difference is that Bioclipse is really a platform...
09:26 egonw it's not targeted at one particular type of (bio)chemical data...
09:26 egonw instead, it is aimed at integrating different data types
09:26 egonw e.g. Bioclipse will allow you to view the 3D structures for the protein sequences... (using Jmol)
09:27 egonw using Bioclipse scripting, you may even color code the residues in Jmol with alignment scores...
09:27 egonw etc
09:27 egonw to indicate one possible integration of data types
09:27 yangming hmm...
09:28 yangming so I have to install all the plugin I need before I can use it, right?
09:29 egonw typically, just the plugins relevant for your type of research
09:29 egonw this is organized in 'features'
09:29 egonw but the sequence feature is a bit underdeveloped...
09:30 yangming oic. thanks.
10:21 jonalv joined #bioclipse
10:26 Deanne joined #bioclipse
10:59 egonw hi Deanne
10:59 egonw very nice meeting you
11:01 egonw Deanne: going for lunch time, but will be back later
11:01 egonw the others around her (jonalv, kaskelot) are from the Uppsala team
11:01 egonw rojasm and me are from the former Cologne team
11:02 egonw bbl
11:47 Deanne Hi, Egonw
11:47 Deanne Sorry I was silent -- was in the shower
11:47 egonw hi
11:47 Deanne just waking up now. :)
11:48 Deanne and eating a bagel...
11:48 egonw :)
11:48 Deanne I guess there's 6 hours difference or so between us.
11:48 egonw east cost, yes...
11:48 egonw assuming both winter time
11:48 Deanne Did you already go to lunch?
11:49 Deanne <- just got back to screen
11:49 egonw yes, back from lunch
11:49 Deanne I used to use IRC a lot back in the mid-1990s, not for 10 years, though. :)
11:50 egonw yes, IRC indeed goes back a long time...
11:50 egonw but I still like it much more than other chat environments...
11:50 egonw better functionality/glamour ratio
11:51 Deanne I prefer a high ratio, too. :)
11:51 Deanne <-- geek too
11:51 egonw that were two impressive emails
11:52 egonw did Ola respond yet? or have you been in contact with him earlier
11:52 egonw ?
11:54 Deanne He's responded a lot in various emails.
11:54 Deanne Did he tell you about James Galagan?
11:54 egonw no
11:54 Deanne There'a group at the Broad Institute that might be also interested in developing modules.
11:54 egonw he said yesterday to write up something...
11:54 egonw but he has not done that yet
11:55 Deanne well, I just sent an email yesterday.
11:55 Deanne so not so long ago. :)
11:56 egonw indeed
11:57 Deanne They have a team of developers on the Broad Institute's TB website -- they have a lot of Java apps that could be developed as plugins for genome browsers and the like.
11:57 egonw URL?
11:57 egonw yeah, sounds good
11:57 egonw one of the big pluses for Bioclipse is the ease with which things can be integrated
11:58 Deanne http://www.broad.mit.edu/annota​tion/genome/tbdb/MultiHome.html
11:58 Deanne Yea, it was fun to watch James' face light up like the sun when he realized the potential in the platform. :)
11:58 egonw "The TB Genomes DB does not support your combination of browser and OS"
11:58 egonw lovely
11:58 Deanne I had to take a few minutes to show him the paper, but I'm no expert in Bioclipse 2. :)
11:59 Deanne Huh...weird.
11:59 Deanne Try just tbdb
11:59 Deanne cut off the multihome
11:59 egonw well, no one is expert in Bioclipse2 yet...
11:59 egonw still under heavy design I think :)
11:59 egonw website seems to work fine...
12:00 Deanne They said they were having problems with browser interfaces.
12:00 Deanne They're moving to Flash for that reason.
12:00 Deanne So when he considered distributed Bioclipse with remote DB connections, he got happy. :)
12:00 egonw :)
12:01 Deanne Means they don't have to work within limitations of a browser and everyone would have the same views(mostly)
12:01 egonw indeed
12:01 Deanne except for the look-and-feel adaptations of eclipse, they could realize their vision for the interfaces.
12:01 Deanne I also am talking to a medical/bioinformatics colleague.
12:02 Deanne ...they have problems trying to link statistics applications used in clinics to the databases for bioinformatics analysis (no good front end)
12:02 Deanne which ties back to our original desire to build a part of bioclipse to handle population genomics and systems biology connections.
12:03 Deanne This is James:
12:03 Deanne http://www.broad.mit.edu/a​bout/bios/bio-galagan.html
12:03 Deanne Do you know where the R integration is in the development stages?
12:04 egonw one of Ola's student is working on that...
12:04 Deanne OK.
12:04 Deanne Thank you...
12:04 egonw but I expect that to be operational before end of March
12:04 egonw likely even earlier...
12:05 Deanne I'd like to help get Bioconductor working within Eclipse
12:05 Deanne er, Bioclipse.
12:05 egonw about the same :)
12:05 Deanne yup.
12:05 Deanne should be no different if the R connection is good.
12:05 egonw yes, R integration is important
12:06 egonw there is prior art:
12:06 egonw http://www.walware.de/goto/statet
12:06 Deanne Oh, lovely.
12:07 Deanne I didn't see that, thank you.
12:07 egonw jonalv: who was doing the R things again? Bjarne, right?
12:07 egonw neither did I...
12:07 egonw it's new to me...
12:07 egonw will have to try it this afternoon...
12:07 egonw OK, some other things that will likely happen in terms of compatibility...
12:07 Deanne All the interesting programming projects are in northern Europe. Maybe I should move. :)
12:07 egonw Ola has been working on BioMoby integration...
12:07 egonw and BioMart support will hopefully be implemented too
12:08 egonw yeah, the grass is always greener ...
12:09 Deanne Excellent...
12:10 Deanne How difficult will it be, you think, for us to build a module that can pass data among modules within Bioclipse? I mean, is there a model there for that already in B2?
12:11 egonw that is basically done via the ISelectionEvent mechanism of Eclipse
12:14 Deanne If I'm a novice, please forgive me. I'm going to ask stupid questions for a little while yet. :)
12:14 * jonalv back from lunch
12:14 * Deanne waves to jonalv
12:15 egonw Deanne: no problem
12:16 egonw Deanne: that's what this channel is for
12:17 masak joined #bioclipse
12:17 masak jonalv asked be to say that he'll be right back
12:17 egonw ack
12:17 masak his laptop battery died
12:17 egonw masak: who is doing the R integration again?
12:17 masak egonw: kaskelot++
12:17 egonw good
12:17 egonw kaskelot: around?
12:18 egonw kaskelot: are you aware of that Eclipse R plugin mentioned earlier?
12:18 masak egonw: he is
12:18 egonw good
12:18 jonalv joined #bioclipse
12:18 masak Statet something
12:18 kaskelot egonw: tell me
12:18 kaskelot oh that
12:18 kaskelot I am aware of that, and it appears to be trivial
12:18 jonalv egonw: Yes bjarni == kaskelot from now on is working with R
12:18 Deanne egonw: one of the things we'd like to build is a front-end to put together an analysis pipeline.
12:19 Deanne kind of like the commercial Pipeline Pilot.
12:19 Deanne drag-and-drop assembly of a work flow.
12:19 egonw Deanne: running Taverna workflows in Bioclipse is on the agenda
12:19 masak Deanne: also, we're looking at other similar technologies
12:19 egonw Deanne: there is also knime.org, but that is not 100% Open, not like Taverna
12:20 * jonalv 's computer died because of no power left in battery
12:20 egonw but KNIME is written using the Eclipse RCP, just like Bioclipse
12:20 Deanne Saw the note about Taverna...
12:20 masak there's something called BPL that we reviewed the other day
12:20 egonw BPL?
12:20 masak ...or something similar
12:20 Deanne Would probably like to have something inside Bioclipse native, though. Maybe that won't be needed if Taverna is embedded, but there will be a lot of connections to make to Taverna?
12:20 jonalv I am not sure about the name but it was pronunced "bippel" anyway
12:21 masak BLP (or whatever) a flowchart standard designed parallel to Taverna
12:21 masak it seems saner/cleaner in many ways
12:21 Deanne Taverna seemed more complicated than I could talk a desktop computer-savvy biologist into using...but I don't have a lot of experience with it.
12:22 Deanne So I was biased by ignorance. :)
12:22 edrin joined #bioclipse
12:22 masak hi edrin
12:22 * Deanne waves to edrin
12:24 edrin hi masak
12:24 masak Deanne: some kind of macro capability is planned for Bioclipse 2
12:24 Deanne We were hoping to make a flowchart to individual modules recognizable to Bioclipse, say, Affy Chip data -> Bioconductor's affy routine's normalization -> stats analysis of gene enrichment -> clustering
12:24 edrin Deanne: so
12:24 masak Deanne: yes. exactly that.
12:25 Deanne cool. :)
12:25 edrin you finally found your way in here
12:25 Deanne I did.
12:25 masak ...but even the design is in its early stages
12:25 Deanne I know IRC pretty well -- or used to.
12:25 Deanne I have a doctor's appt this morning so can't stay much longer.
12:25 Deanne but i'll be back this afternoon -- probably when you're all eating dinner, though.
12:26 Deanne I'm not writing up a grant yet, but I  wrote the list because I need to propose to my dept. how much money we will need for development -- so just in case we don't get a grant, I might be able to ask for some money from Harvard itself.
12:27 egonw OK
12:27 Deanne so I'm still exploring the wiki and figuring out what needs to be done, so as I said earlier here -- I'm still very ignorant.
12:27 egonw seems time to set up a more modular development process
12:27 egonw that is, more organized sub projects
12:27 Deanne Is there a project management plugin for Eclipse?
12:28 Deanne I seem to remember something like that.
12:28 egonw I use taskjuggler which is KDE-based
12:28 Deanne we could do CVS on project management docs. :)
12:28 Deanne Whatever works --
12:28 Deanne just let me know...
12:28 * jonalv @meeting...
12:28 Deanne @doctor now -- thank you for talking with me.
12:29 * Deanne goes *poof*
12:29 egonw :)
13:24 jonalv egonw: I think Ola was talking about jfeature. Do you know it?
13:24 egonw no
13:24 jonalv <https://jfeature.dev.java.net/>
13:25 egonw mom, busy...
13:25 egonw will look at that later, sorry
13:25 jonalv np
13:30 clarezoe joined #bioclipse
14:00 pohyg joined #bioclipse
14:36 olas joined #bioclipse
14:36 egonw jonalv: looks interesting...
14:36 egonw hi olas
14:36 olas hi
14:36 egonw olas: Deanne was here earlier today
14:36 olas oh, sorry to have missed her
14:36 olas Answering her mail to bioclipse-devel right now :-)
14:37 egonw she said to try to join IRC later today...
14:37 olas ack
14:38 olas jonalv: what's so interesting for egonw?
14:38 egonw jfeature...
14:38 egonw well, the idea really...
14:38 olas yup
14:38 egonw not sure about the being-based-on-junit
14:38 olas why not?
14:38 egonw was hoping it was more like based on inline tags in the source code
14:38 jonalv inline tags in the source code?
14:38 egonw because I do not intend to write up the full requirement analysis as junit tests before I start hacking...
14:38 jonalv Who would want that?
14:38 egonw jonalv: yeah, like @TODO
14:39 jonalv ah
14:39 jonalv but isn't it cleaner to ahve it seperate?
14:39 egonw maybe
14:39 egonw yes, it is
14:52 jonalv But question is what is needed. Do you think jfeature does what you had in mind?
15:10 steinbeck joined #bioclipse
15:11 CIA-18 bioclipse: carl_masak * r4253 /trunk/playground/plugins/net.bioclipse.base2/: Initial import.
15:12 olas great!
15:12 egonw what is base2?
15:13 olas microarray LIMS
15:13 egonw really?
15:13 egonw how is it integrated?
15:13 olas http://base.thep.lu.se/
15:13 CIA-18 bioclipse: carl_masak * r4254 /trunk/playground/plugins/net.bioclipse.base2/ (19 files in 9 dirs): Initial import.
15:13 masak olas: very early work so far though
15:13 olas it will be integrated via Web services
15:13 jonalv masak is working on a plugin able to connect to a base2 server. right?
15:13 masak what I committed is essentially an empty view :)
15:13 olas the thought is to be able to get access to microarray data inside of Bioclipse
15:14 masak jonalv: right
15:15 egonw http://www.thep.lu.se/~jari/svndigest/base/
15:15 egonw olas: maybe install that for Bioclipse too?
15:16 egonw never mind
15:27 steinbeck left #bioclipse
16:28 CIA-18 bioclipse: jonalv * r4255 /trunk/playground/plugins/net.biocl​ipse.base2/src/net/bioclipse/base2/ (6 files in 2 dirs): Made mock implementation of tree view.
16:30 masak jonalv: thanks!
16:30 jonalv :)
16:33 edrin left #bioclipse
16:44 CIA-18 bioclipse: ospjuth * r4256 /branches/bioclipse2/core/​plugins/net.bioclipse.ui/ (8 files in 2 dirs): Updated intro page a little...
16:45 CIA-18 bioclipse: ospjuth * r4257 /branches/bioclipse2/core/​plugins/net.bioclipse.ui/ (4 files in 3 dirs): Completed refactoring to net.bioclipse.ui
18:14 olas left #bioclipse
18:40 egonw joined #bioclipse
18:59 Deanne joined #bioclipse
18:59 * Deanne waves.
18:59 egonw hi Deanne
19:59 Deanne left #bioclipse
21:51 Deanne joined #bioclipse
21:51 Deanne Yikes.
21:53 Deanne I found BPEL
22:13 * egonw thinks he likes KNIME more
22:28 Deanne KNIME?
22:29 * Deanne goes to look
22:45 egonw knime.org
22:46 egonw Deanne: enter my nick, and I will get notified that someone on IRC has something directly aimed at me
22:46 egonw am doing many things at the same time :)
22:50 Deanne egonw
22:50 egonw yes?
22:51 Deanne Heh -- sorry, was just following what you said.
22:51 egonw :)
22:51 Deanne <-- low attention span
22:51 Deanne Am reading Fark.com
22:51 Deanne Someone is doing a serious study of the Flying Spaghetti Monster.
22:51 Deanne religious study.
22:52 Deanne <-- low attention span because they gave us beer in the school again today
22:52 Deanne every other friday is beer & pizza day here.
22:52 Deanne Add that on top of how tired I am today...
22:53 egonw :)

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