Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-07-13

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All times shown according to UTC.

Time Nick Message
06:35 sneumann joined #bioclipse
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07:17 edrin1 joined #bioclipse
07:17 edrin1 hi
07:17 zarah hi edrin1
07:17 edrin1 hi mgerlich
07:17 edrin1 mgerlich: who are you?
07:19 edrin1 zarah: ping
07:19 zarah edrin1: pong
07:21 mgerlich hi - i'am a bioinformatics PhD working at the IPB in Halle
07:21 edrin1 ah
07:21 edrin1 :)
07:21 mgerlich :)
07:22 edrin1 mgerlich: do you have a web page that is describing your group
07:22 edrin1 and/or work interest?
07:23 mgerlich http://www.ipb-halle.de/en/forschung/stre​ss-und-entwicklungsbiologie/forschungsgru​ppen/bioinformatik-massenspektrometrie/
07:23 zarah mgerlich's link is also http://tinyurl.com/m2eyph
07:25 mgerlich we're currently working on 2 webapps, the first one, called MetFrag tries to generate all possible fragments from a sample spectrum and identifies/proposes possible chemical compounds
07:26 mgerlich which fit to these fragments
07:27 edrin1 ah
07:27 edrin1 mgerlich: did you already decide to use bc2 for this?
07:29 mgerlich well currently not - it relies mostly on cdk and uses JSF to provide the web app
07:30 mgerlich the second app, MetFlow can be seen as some sort of portable Taverna workflow player, it relies on the Taverna platform code and JSF for web rendering
07:35 jonalv joined #bioclipse
07:36 jonalv o/
07:38 olass joined #bioclipse
07:49 olass moin
07:49 zarah hi olass
07:54 rojasm joined #bioclipse
08:13 edrin joined #bioclipse
08:13 edrin hi agin
08:13 edrin zarah: hi
08:13 zarah hello edrin :)
08:20 egonw joined #bioclipse
08:21 egonw moin
08:21 zarah ni hao egonw
08:25 edrin hi egonw
08:25 edrin zarah: ping
08:25 zarah edrin: pong
08:25 egonw hi edrin
08:36 egonw has carl been spotten yet?
08:36 egonw if not, I suggest we start without him?
08:37 egonw he can catch up later, and we start with things like comitting anyway
08:37 jonalv egonw: I have not seen masak no...
08:44 shk3 joined #bioclipse
08:48 egonw olass, jonalv: let's relocate
08:58 egonw joined #bioclipse
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10:09 masak joined #bioclipse
10:09 masak olass: http://tom.preston-werner.com/2​009/05/19/the-git-parable.html
10:09 zarah masak's link is also http://tinyurl.com/pm3g8u
10:09 zarah masak: You have new messages. Write '/msg zarah @messages' to read them.
10:09 masak @messages
10:09 zarah masak: 2 d 12 h 36 m 13 s ago, egonw said please read this wiki page, and the "Create patches for individual plugins/features" in particular: http://wiki.bioclipse.net/index.php?title=Git_De​velopment#Create_patches_for_individual_plugins.2Ffeatures
10:11 egonw_ joined #bioclipse
10:18 egonw_ olass: can you come for a sec?
10:18 olass in tel with Lars
10:18 egonw_ ack
10:20 olass I have to prepare a doc before we leave
10:20 olass might mean 5 mins delay
10:20 olass bugt important
10:20 olass but
10:30 egonw_ olass: http://ktown.kde.org/~zrusin/​git/git-cheat-sheet-large.png
10:30 zarah egonw_'s link is also http://tinyurl.com/35g6e2
10:31 egonw_ http://wiki.bioclipse.net/ind​ex.php?title=Git_Development
10:31 zarah egonw_'s link is also http://tinyurl.com/mqpa8m
10:36 olass ok, done
10:37 olass lunch?
10:45 masak YA
10:48 maclean joined #bioclipse
12:33 edrin masak: did you get my mail?
12:33 edrin zarah: ping
12:33 zarah edrin: pong
12:42 * masak is back from lunch
12:42 * jonalv is back from lunch
12:42 masak edrin: yes. haven't read it yet, though.
12:44 masak ah. a screenshot. :)
12:45 masak edrin: thanks. I will have many more questions, since this isn't something I've been doing so far myself.
12:45 edrin yes, sure
13:33 jonalv masak: http://woss.name/2008/04/09/using-g​it-submodules-to-track-vendorrails/
13:33 zarah jonalv's link is also http://tinyurl.com/594of7
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14:08 masak jonalv: http://github.com/guides/providing-your-ssh-key
14:08 zarah masak's link is also http://tinyurl.com/3yepyr
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14:59 edrin zarah: ping
14:59 zarah edrin: pong
15:05 shk3 hi jonalv
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15:25 shla Hi, what is the status for Systems biology (SBML support, simulation et.c.) for BioClipse? (Was mailing Ola about it, but figured out I can post here as well).
15:31 shla I'm a biotech (+bioinformatics) student at Uppsala Uni
15:31 shla I'm a biotech (+bioinformatics) student at Uppsala Univ.
15:32 olass hi shla
15:32 olass sry, was in a meeting
15:32 olass learning to use git
15:32 olass shla: I will respond to your email
15:32 olass in short: no one is owrking on SBML in Bioclipse currently
15:32 shla Ok
15:32 olass there was a prototype for Bioclipse1
15:33 olass but it is not migrated
15:33 olass sadly, I actually never run it (I don't know SBML that much (yet!))
15:33 olass shla: would you be interested in SBML in Bioclipse?
15:33 shla Yeah, the background to my asking is that I'm looking for a suitable degree project
15:34 shla ...and thinking that doing something related to BioClipse would be nice.
15:34 olass oh, that would be a great project for Bioclipse!
15:34 shla Ok, good to hear. :)
15:34 olass you should come over one day and talk with us here at BMC
15:34 shla Yeah, sure!
15:35 olass do you have summer holidays now?
15:35 olass and when did you plan to start your thesis?
15:35 shla Well, I'm still studying, so just tell me a suitable time, and I'll probably manage to com.e
15:35 shla This autumn.
15:35 olass ok
15:36 olass how about next week some day?
15:36 shla I've talked to Mats Gustavsson already, but we didn't have any concrete plans.
15:36 jonalv gah github is down
15:36 shla That sounds good
15:36 shla regarding next week.
15:37 olass how about tuesday next week?
15:37 olass we are not so booked during the summer
15:37 shla Yeah, that should be fine.
15:37 shla Time?
15:37 olass hmm, on second thoughts, would be good if egonw would be here too
15:38 olass let me get back to you with a date, ok?
15:38 olass will ask egonw first
15:38 shla Yeah, sure
15:38 shla You got my mail-address.
15:40 olass yup
15:40 olass sounds interesting indeed
15:40 olass have you worked with SBML a lot?
15:41 shla Not really
15:41 shla The bottom line is that I'm much interested
15:41 shla And have studied a combination of biotech / bioinformatics, and is hacking some Java
15:43 shla So, I guess a meeting is good, in order to figure out what is realistic and not.
16:20 * olass is relocating
16:20 olass see you later
16:21 olass shla: will email you asap
16:21 olass bye
16:24 edrin shla: what kind of thesis is it you are going to do?
16:24 edrin is it a phd thesis?
16:24 shla It's masters thesis
16:25 edrin ah ok
16:25 shla Or comparable (The biotech engineering degree in Sweden)
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18:34 olass joined #bioclipse
18:34 olass hi
18:34 zarah hello olass, you fantastic person you
18:57 olass joined #bioclipse
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19:19 olass @seen egonw
19:19 zarah egonw was last seen 10 h 31 m 7 s ago in #bioclipse saying 'olass, jonalv: let's relocate'
19:20 edrin joined #bioclipse
19:20 edrin hi again
19:22 edrin olass: still available
19:22 olass hi edrin
19:22 olass sort of
19:23 edrin got my mail?
19:24 edrin olass: got my mail?
19:24 olass yes
19:24 olass replying as we speak :)
19:25 edrin ah k
19:31 olass ok, replied
19:33 edrin k
19:34 olass need to go offline now
19:34 olass cu tomorrow
19:34 olass bye
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