| Time |
S |
Nick |
Message |
| 05:21 |
|
|
ilbot2 joined #bioclipse |
| 05:21 |
|
|
Topic for #bioclipseis now An open source workbench for chem- and bioinformatics - http://www.bioclipse.net/ | BioclipseWiki => http://wiki.bioclipse.net/ !! | logs => http://colabti.org/irclogger/i[…]er_logs/bioclipse & http://moritz.faui2k3.org/ircl[…]channel=bioclipse || Bioclipse2 beta released! See http://bioclipse.blogspot.com/ |
| 05:31 |
|
|
ChanServ joined #bioclipse |
| 05:31 |
|
|
ilbot2 joined #bioclipse |
| 05:31 |
|
|
Topic for #bioclipseis now An open source workbench for chem- and bioinformatics - http://www.bioclipse.net/ | BioclipseWiki => http://wiki.bioclipse.net/ !! | logs => http://colabti.org/irclogger/i[…]er_logs/bioclipse & http://moritz.faui2k3.org/ircl[…]channel=bioclipse || Bioclipse2 beta released! See http://bioclipse.blogspot.com/ |
| 05:37 |
|
|
ilogger2 joined #bioclipse |
| 05:38 |
|
|
stain joined #bioclipse |
| 05:43 |
|
|
CIA-55 joined #bioclipse |
| 07:40 |
|
|
ilbot2 joined #bioclipse |
| 07:40 |
|
|
Topic for #bioclipseis now An open source workbench for chem- and bioinformatics - http://www.bioclipse.net/ | BioclipseWiki => http://wiki.bioclipse.net/ !! | logs => http://colabti.org/irclogger/i[…]er_logs/bioclipse & http://moritz.faui2k3.org/ircl[…]channel=bioclipse || Bioclipse2 beta released! See http://bioclipse.blogspot.com/ |
| 07:58 |
|
|
Gpox joined #bioclipse |
| 08:13 |
|
|
Gpox joined #bioclipse |
| 09:00 |
|
|
charlgren joined #bioclipse |
| 09:07 |
|
|
sneumann joined #bioclipse |
| 09:33 |
|
|
masak joined #bioclipse |
| 09:36 |
|
|
zarah joined #bioclipse |
| 09:38 |
|
|
edrin joined #bioclipse |
| 09:39 |
|
edrin |
@ping |
| 09:39 |
|
zarah |
edrin: pong |
| 09:46 |
|
CIA-55 |
bioclipse: carl_masak * r8500 /bot/trunk/zarah.pl: [zarah] now reports the official pelezilla url |
| 09:51 |
|
|
thomas_ku joined #bioclipse |
| 09:51 |
|
edrin |
hi# |
| 09:51 |
|
masak |
yallo |
| 10:19 |
|
|
sneumann joined #bioclipse |
| 10:35 |
|
|
olass joined #bioclipse |
| 10:35 |
|
olass |
moin |
| 10:35 |
|
zarah |
privet olass |
| 10:35 |
|
zarah |
olass: You have new messages. Write '/msg zarah @messages' to read them. |
| 10:35 |
|
olass |
@msg |
| 10:35 |
|
zarah |
olass: 43 m 17 s ago, masak said http://www.artima.com/weblogs/[…]jsp?thread=203994 |
| 10:36 |
|
olass |
yummy |
| 10:54 |
|
|
shk3 joined #bioclipse |
| 11:01 |
|
|
egonw joined #bioclipse |
| 11:01 |
|
egonw |
moin |
| 11:01 |
|
zarah |
hi egonw |
| 11:13 |
|
egonw |
sneumann: hi! where are you know? |
| 11:13 |
|
* egonw |
is with Stefan @ EBI |
| 11:17 |
|
egonw |
shk3: http://dx.doi.org/10.1021/ci8002123 |
| 11:17 |
|
zarah |
egonw's link is also http://tinyurl.com/cozx3v |
| 11:47 |
|
egonw |
leaving for lunch |
| 12:32 |
|
|
de__maas joined #bioclipse |
| 12:34 |
|
de__maas |
Hi All, just a very question about bioclipse 2 (great work) . Is it true that most of the CDK features (like qsar) are only accessible via the javascript console? |
| 12:50 |
|
olass |
de__maas: not really |
| 12:50 |
|
olass |
qsar for example is not added yet |
| 12:50 |
|
olass |
but the general idea is |
| 12:50 |
|
olass |
all functionality should be available from scripting |
| 12:51 |
|
olass |
and then guild nice GUIs on top of it |
| 12:51 |
|
olass |
naturally, having it as scripting is the first step |
| 12:51 |
|
olass |
but there will also be cases when the GUI will preceed the scripting |
| 12:51 |
|
olass |
qsar is one such example |
| 12:52 |
|
olass |
but generally I'd say that actions are first available from console, and then it is straightforward to build a GUI upon it |
| 12:52 |
|
olass |
de__maas: hope this sheds some light on the development procedure |
| 12:52 |
|
olass |
all important funct SHOULD have a GUI |
| 12:52 |
|
olass |
that is the objective |
| 12:58 |
|
de__maas |
olass: thanks that explains it :) |
| 12:58 |
|
de__maas |
Actually I was looking for the qsar stuff but indeed I could not find it. |
| 12:59 |
|
olass |
sorry, I have not yet put it up |
| 12:59 |
|
olass |
so many tasks, so little time :-) |
| 12:59 |
|
olass |
really focusing on Bioclipse 2.0 now |
| 12:59 |
|
de__maas |
Noworries, you sound like Rajarshi now. |
| 12:59 |
|
olass |
haha |
| 13:00 |
|
olass |
after 2.0, it will be QSAR and pharmacophores in bioclipse |
| 13:00 |
|
de__maas |
BTW, I like the reading of big SF-files , I used it on mine which are about 300,000 records |
| 13:00 |
|
olass |
did it work? |
| 13:00 |
|
de__maas |
Yes, pretty fast as well. |
| 13:00 |
|
olass |
we now process 200 at a time |
| 13:00 |
|
olass |
could be changed for best user experience |
| 13:01 |
|
olass |
we are experimenting with this |
| 13:01 |
|
de__maas |
Well if you need big files I can help you :-D |
| 13:01 |
|
olass |
haha, good to know |
| 13:01 |
|
olass |
well |
| 13:01 |
|
de__maas |
Would be nice if there is a way to see the additional fields. |
| 13:01 |
|
olass |
how big do you generally work with? |
| 13:01 |
|
olass |
yes |
| 13:01 |
|
olass |
in the pipe |
| 13:02 |
|
olass |
(a high prio bug) |
| 13:02 |
|
olass |
I know people work with bug sdfiles, but in what magnitude are we talking? |
| 13:02 |
|
olass |
>1Gb? |
| 13:02 |
|
de__maas |
good to know, our stock database is about 300.000 |
| 13:02 |
|
olass |
~500Mb? |
| 13:02 |
|
de__maas |
Oh, in size . give me a second. |
| 13:03 |
|
olass |
do you use it as an SDF generally? |
| 13:04 |
|
de__maas |
No, i try to get in a database (symyx) as fast as possible. |
| 13:04 |
|
de__maas |
Our last release to customers is 610Mb |
| 13:05 |
|
de__maas |
Not all our customers have tools to access databases or have chemical software at all. Mostly they request excell files :P |
| 13:06 |
|
de__maas |
So I like to point them to a non-commercial package which can handle that and BioClipse could be it. |
| 13:20 |
|
de__maas |
olass: is there any docs on the js or just the help which is included in js? |
| 13:20 |
|
olass |
hmm |
| 13:20 |
|
olass |
good question |
| 13:21 |
|
olass |
we are generating the inline help as HTML, but I donät think this is up yet |
| 13:21 |
|
olass |
masak: can you confirm this? |
| 13:21 |
|
olass |
the thing is, we generate HTML from all manager methods (lik a simple API documentation) |
| 13:22 |
|
olass |
to be used as a basis for a scripting documnetation |
| 13:22 |
|
olass |
(or at least a reference) |
| 13:23 |
|
masak |
olass: how do I confirm it? |
| 13:23 |
|
olass |
the HTML is not up? |
| 13:23 |
|
olass |
as we talked about earlier |
| 13:23 |
|
olass |
generated HTML not on pele? |
| 13:24 |
|
masak |
oh, that HTML. |
| 13:24 |
|
masak |
I'll have a look. |
| 13:24 |
|
olass |
great |
| 13:27 |
|
masak |
no, it's not up on pele. |
| 13:27 |
|
masak |
seems I put a version here: http://masak.org/carl/managers.html |
| 13:27 |
|
zarah |
masak's link is also http://tinyurl.com/5887bk |
| 13:28 |
|
masak |
I'll put one on pele instead. |
| 13:32 |
|
de__maas |
masak: what's pele? |
| 13:32 |
|
masak |
de__maas: it's our development server. |
| 13:32 |
|
masak |
@pz |
| 13:32 |
|
zarah |
masak: Pelezilla is at http://pele.farmbio.uu.se/cgi-[…]ugzilla/index.cgi |
| 13:32 |
|
olass |
masak++ //I like the generated manager doc a lot! |
| 13:33 |
|
de__maas |
Cool, thanks. |
| 13:33 |
|
masak |
olass: thank you :) made it while you were on vacation. |
| 13:33 |
|
masak |
it was a breeze to make with Perl. |
| 13:33 |
|
olass |
Perl++ |
| 13:33 |
|
masak |
the source is in bioclipse/managerdocs/ |
| 13:33 |
|
olass |
edrin: around? |
| 13:33 |
|
edrin |
yes |
| 13:34 |
|
olass |
I am setting up the xmpp/xws wiki on pele |
| 13:34 |
|
edrin |
ok :) |
| 13:34 |
|
olass |
for suppl info and docu etc |
| 13:34 |
|
edrin |
yes |
| 13:34 |
|
olass |
what should we call it? |
| 13:34 |
|
olass |
xmpp? |
| 13:34 |
|
olass |
xws? |
| 13:34 |
|
olass |
XMPP-XWS? |
| 13:34 |
|
olass |
cloudcomp |
| 13:34 |
|
edrin |
xmpp services |
| 13:34 |
|
edrin |
? |
| 13:34 |
|
masak |
sorry, bioclipse2/manager-apidocs/ |
| 13:40 |
|
masak |
hm, I'm not really sure where to put it on pele so that it'll be publicly visible. |
| 13:42 |
|
de__maas |
Aha, I thought it was just me |
| 13:47 |
|
olass |
masak: put it under /var/www/ |
| 13:48 |
|
olass |
well, a subdir |
| 13:48 |
|
olass |
placed there |
| 13:50 |
|
masak |
oki |
| 13:56 |
|
masak |
hm, running through tidy, I see I'm not quite done yet. :) |
| 13:56 |
|
masak |
@plan old bc2 |
| 13:56 |
|
zarah |
masak: bc2/console-egonw-single-line-refactor: 2 h planned, 21 h 53 m elapsed |
| 13:56 |
|
zarah |
masak: bc2/managerdocs-finder: 1 h 30 m planned, 1 h 37 m elapsed |
| 13:56 |
|
zarah |
masak: bc2/managerdocs-finder-html-skin: 1 h 15 m planned, 1 h 10 m elapsed |
| 13:56 |
|
zarah |
masak: bc2/scriptconsole-backspace-bug: 30 m planned, 2 m elapsed |
| 13:56 |
|
zarah |
masak: bc2/scriptconsole-literal-tab-bug: 30 m planned, 15 m elapsed |
| 13:57 |
|
masak |
@start managerdocs-finder-html.. |
| 13:57 |
|
zarah |
masak: Starting task 'bc2/managerdocs-finder-html-skin'. |
| 14:02 |
|
masak |
@stop |
| 14:02 |
|
zarah |
masak: Stopping task 'bc2/managerdocs-finder-html-skin' after 5 m at 1 h 15 m out of 1 h 15 m (100%). |
| 14:02 |
|
masak |
phew. |
| 14:07 |
|
CIA-55 |
bioclipse: carl_masak * r8501 /bioclipse2/trunk/manager-apidocs/render-as-html: [managerdocs] added HTML escaping to handle rogue characters |
| 14:21 |
|
CIA-55 |
bioclipse: carl_masak * r8502 /bioclipse2/trunk/manager-apidocs/render-as-html: [managerdocs] added an empty-string default to silence warnings |
| 14:21 |
|
CIA-55 |
bioclipse: carl_masak * r8503 /bioclipse2/trunk/manager-apidocs/run-the-whole-thing: [managerdocs] run-the-whole-thing now also runs tidy as a last step |
| 14:26 |
|
olass |
masak: please write to bioclispe-devel when the new manager-apidocs is up on pele |
| 14:26 |
|
masak |
olass: aye. |
| 14:40 |
|
|
grandm44 joined #bioclipse |
| 14:40 |
|
grandm44 |
hello |
| 14:40 |
|
zarah |
privet grandm44 |
| 14:40 |
|
olass |
hi grandm44 |
| 14:41 |
|
grandm44 |
i prepared something, but it's a bit long to paste it in the channel, do you have some mailing list I can send it to ? |
| 14:43 |
|
olass |
bioclipse-devel is fine |
| 14:43 |
|
olass |
@gg bioclipse-devel |
| 14:43 |
|
zarah |
olass: http://sourceforge.net/mail/%3Fgroup_id%3D150681 |
| 14:43 |
|
olass |
hmm |
| 14:43 |
|
olass |
nope |
| 14:44 |
|
grandm44 |
http://sourceforge.net/mailarc[…]e=bioclipse-users ? |
| 14:44 |
|
zarah |
grandm44's link is also http://tinyurl.com/akuus2 |
| 14:44 |
|
olass |
bioclipse-devel is better |
| 14:44 |
|
grandm44 |
ok |
| 14:44 |
|
olass |
https://sourceforge.net/mail/?group_id=150681 |
| 14:48 |
|
masak |
http://pele.farmbio.uu.se/manager-docs/ |
| 14:48 |
|
zarah |
masak's link is also http://tinyurl.com/aqykgf |
| 14:48 |
|
* masak |
sends to list |
| 15:02 |
|
olass |
masak: bug 296 |
| 15:02 |
|
masak |
@bug 296 |
| 15:02 |
|
zarah |
http://tinyurl.com/c4lue7 |
| 15:02 |
|
masak |
:) |
| 15:02 |
|
masak |
olass: consider it done. |
| 15:03 |
|
olass |
aah |
| 15:03 |
|
olass |
masak++ //effektivare än en tysk |
| 15:03 |
|
olass |
woops, swedish :-) |
| 15:03 |
|
masak |
olass: http://steve-yegge.blogspot.co[…]things-smart.html |
| 15:03 |
|
zarah |
masak's link is also http://tinyurl.com/5pgqco |
| 15:04 |
|
masak |
(not implying that I'm one of them, only that it's a nice ideal) |
| 15:05 |
|
olass |
Gpox: do we have any general manager method for file manipulation (create project, create folder, copy file)? |
| 15:05 |
|
olass |
if not, I'll file a bug |
| 15:05 |
|
Gpox |
no |
| 15:05 |
|
olass |
ok |
| 15:06 |
|
masak |
olass: also, it's not me, it's Perl. :) |
| 15:06 |
|
olass |
masak: would it be possible if zarah listened to pelezilla and reported when someone submitted a bug? |
| 15:06 |
|
olass |
like the commit hook in SVN on SF... |
| 15:06 |
|
masak |
olass: I'm sure. it's probably just a question of RSS. |
| 15:07 |
|
olass |
masak: Iäll file a bug |
| 15:07 |
|
* olass |
likes filing bugs |
| 15:07 |
|
masak |
olass: :) |
| 15:09 |
|
masak |
olass: http://pele.farmbio.uu.se/manager-docs/ |
| 15:09 |
|
zarah |
masak's link is also http://tinyurl.com/aqykgf |
| 15:10 |
|
masak |
I'll have to think some about the layout, but I guess that's good for now. |
| 15:10 |
|
olass |
nice! |
| 15:10 |
|
masak |
hm, I'll have them sorted alphabetically, while am at it. |
| 15:10 |
|
olass |
ok |
| 15:11 |
|
masak |
olass: an index was a 4-line addition. :) |
| 15:11 |
|
olass |
:) |
| 15:12 |
|
olass |
masak: @bug 298 |
| 15:12 |
|
olass |
no rush :-) |
| 15:12 |
|
masak |
zarah: @bug 298 |
| 15:12 |
|
zarah |
masak: that was not so easy for a little bot to understand |
| 15:12 |
|
masak |
zarah: bug 298 |
| 15:13 |
|
zarah |
http://tinyurl.com/dc926e |
| 15:14 |
|
masak |
olass: I like the idea. been trying to add RSS support to zarah before, and failing. I don't know enough about POE to pull it off yet. |
| 15:14 |
|
olass |
no worries |
| 15:15 |
|
CIA-55 |
bioclipse: carl_masak * r8504 /bioclipse2/trunk/manager-apidocs/render-as-html: [managerdocs] now prints an index at the top of the file |
| 15:16 |
|
CIA-55 |
bioclipse: carl_masak * r8505 /bioclipse2/trunk/manager-apidocs/render-as-html: [managerdocs] now sorts managers alphabetically |
| 15:45 |
|
* olass |
will run off to meet eclipse usergroup sweden in Stockholm and hear about Eclipse P2 |
| 15:45 |
|
olass |
cu tomorrow |
| 16:55 |
|
|
shk3 joined #bioclipse |
| 17:52 |
|
CIA-55 |
bioclipse: shk3 * r8506 /bioclipse2/trunk/plugins/net.bioclipse.cml/plugin.xml: solves bug #273 |
| 17:52 |
|
zarah |
bug #273 | http://tinyurl.com/cfvur5 |
| 17:54 |
|
|
de__maas left #bioclipse |
| 18:51 |
|
|
edrin left #bioclipse |
| 19:58 |
|
|
edrin joined #bioclipse |
| 21:33 |
|
CIA-55 |
bioclipse: edrin_t * r8507 /bioclipse2/trunk/plugins/net.bioclipse.webservices/src-axis1/ (4 files in 4 dirs): removed empty directories |
| 21:37 |
|
|
edrin joined #bioclipse |
| 21:40 |
|
CIA-55 |
bioclipse: edrin_t * r8508 /bioclipse2/trunk/plugins/net.bioclipse.webservices/src-axis1/net/bioclipse/webservices/: removed empty dir |
| 21:41 |
|
CIA-55 |
bioclipse: edrin_t * r8509 /bioclipse2/trunk/plugins/net.bioclipse.webservices/src-axis1/com/themindelectric/www/: removed empty dir |
| 21:43 |
|
CIA-55 |
bioclipse: edrin_t * r8510 /bioclipse2/trunk/plugins/net.bioclipse.webservices/src-axis1/ (com/themindelectric/ net/bioclipse/): removed empty dir |
| 22:46 |
|
CIA-55 |
bioclipse: edrin_t * r8511 /bioclipse2/trunk/plugins/net.bioclipse.webservices/src-axis1/ (com/ net/): removed empty dir |
| 23:41 |
|
|
ilogger2 joined #bioclipse |
| 23:44 |
|
|
ilogger2 joined #bioclipse |
| 23:50 |
|
CIA-55 |
bioclipse: edrin_t * r8512 /bioclipse2/trunk/plugins/net.bioclipse.webservices/src/net/bioclipse/webservices/ (5 files in 3 dirs): optimized code. manager still not working, client stub probably invalid atm |
