| Time |
S |
Nick |
Message |
| 04:13 |
|
|
egonw joined #bioclipse |
| 05:15 |
|
|
sneumann joined #bioclipse |
| 06:20 |
|
|
egonw joined #bioclipse |
| 06:43 |
|
|
Gpox joined #bioclipse |
| 06:54 |
|
|
annzi joined #bioclipse |
| 06:54 |
|
egonw |
annzi: http://www.techscreencast.com/[…]active-adding/791 |
| 06:54 |
|
zarah |
egonw's link is also http://tinyurl.com/2wx4gbf |
| 07:09 |
|
|
jpansanel joined #bioclipse |
| 07:21 |
|
egonw |
hi jpansanel |
| 07:21 |
|
egonw |
jpansanel: what's your progress with porting MyChem to the newer MySQL? |
| 07:22 |
|
egonw |
Gpox: this is the same bnd, correct? http://njbartlett.name/blog/20[…]ools-for-eclipse/ |
| 07:22 |
|
zarah |
egonw's link is also http://tinyurl.com/38yn4oh |
| 07:23 |
|
|
sneumann joined #bioclipse |
| 07:24 |
|
Gpox |
yes, and a nice tool for using it. |
| 07:28 |
|
egonw |
yeah, gonna have to look at it |
| 07:56 |
|
|
faceface joined #bioclipse |
| 07:56 |
|
faceface |
hi |
| 07:56 |
|
zarah |
hello faceface, you fantastic person you |
| 07:56 |
|
egonw |
hi faceface |
| 07:56 |
|
faceface |
why ty |
| 07:56 |
|
egonw |
zarah is a bot |
| 07:56 |
|
faceface |
hello |
| 07:56 |
|
zarah |
saluton faceface |
| 07:56 |
|
faceface |
;-) |
| 07:56 |
|
egonw |
never mind here :) |
| 07:56 |
|
faceface |
Bioclipse is a free and open source workbench for the life sciences. |
| 07:56 |
|
faceface |
interesting! |
| 07:57 |
|
egonw |
thanx :) |
| 07:57 |
|
faceface |
Samuel Lampa about? |
| 07:57 |
|
faceface |
I'm reading his GSoC project |
| 07:58 |
|
faceface |
sorry to say I only just heard about bioclipse |
| 07:58 |
|
egonw |
no, have not seen him yet |
| 07:58 |
|
egonw |
but got an appointment with him later this morning |
| 07:58 |
|
egonw |
faceface: no worries :) |
| 07:58 |
|
egonw |
welcome! |
| 07:58 |
|
faceface |
cool |
| 07:58 |
|
egonw |
you're his mentor? |
| 07:58 |
|
faceface |
Cheminformatics and Metabolism Team at the European Bioinformatics Institute |
| 07:58 |
|
faceface |
nice |
| 07:58 |
|
faceface |
no |
| 07:58 |
|
faceface |
just a person :-) |
| 07:58 |
|
egonw |
EBI is one part of the development team |
| 07:58 |
|
faceface |
awesome |
| 07:59 |
|
egonw |
Uppsala University is the other part |
| 07:59 |
|
egonw |
where Bioclipse originates |
| 07:59 |
|
egonw |
and the largest developer concentration |
| 07:59 |
|
faceface |
one thing that attracts me here is the connection between semantic mediawiki and eclipse... SMW despirately needs an IDE |
| 08:00 |
|
* faceface |
grabs the paper |
| 08:00 |
|
faceface |
its all java I guess? |
| 08:00 |
|
egonw |
yeah, the core parts yes |
| 08:00 |
|
egonw |
some plugins use C/C++ code in the background |
| 08:00 |
|
egonw |
but not the Bioclipse core |
| 08:00 |
|
egonw |
faceface: there are now two Bioclipse papers |
| 08:00 |
|
egonw |
both OA |
| 08:01 |
|
faceface |
my colleagues are developing an interesting java library - do you think that kind of java analysis toolkit can be easily added to bioclipse? (sorry for nieve questions) |
| 08:01 |
|
egonw |
yes |
| 08:01 |
|
faceface |
2009? |
| 08:01 |
|
egonw |
yes |
| 08:01 |
|
faceface |
oic |
| 08:01 |
|
faceface |
2007 / 2009 |
| 08:01 |
|
faceface |
cheminformatics is so cool |
| 08:02 |
|
egonw |
:) |
| 08:02 |
|
egonw |
yeah, I think so too :) |
| 08:02 |
|
egonw |
what's the library about? |
| 08:02 |
|
|
jonalv joined #bioclipse |
| 08:02 |
|
faceface |
protein structure analysis and prediction |
| 08:02 |
|
egonw |
sounds interesting... |
| 08:03 |
|
egonw |
not too much of that in Bioclipse yet |
| 08:03 |
|
faceface |
yeah, the core devs are great |
| 08:03 |
|
egonw |
so, would be a welcome addition, I'd say |
| 08:04 |
|
faceface |
http://www.bioinformatics.org/[…]ps/?group_id=1014 |
| 08:04 |
|
zarah |
faceface's link is also http://tinyurl.com/3ynxxh4 |
| 08:04 |
|
faceface |
ty zarah |
| 08:05 |
|
egonw |
are you present on the social web? |
| 08:05 |
|
faceface |
erm... |
| 08:05 |
|
faceface |
I have a twitter account, but its mostly me spamming music I like ;-) |
| 08:05 |
|
faceface |
danbolser |
| 08:05 |
|
egonw |
:) |
| 08:05 |
|
egonw |
PDBHighlight |
| 08:05 |
|
egonw |
that's cool! |
| 08:05 |
|
faceface |
:-P |
| 08:06 |
|
egonw |
I have been thinking about that for a very long time |
| 08:06 |
|
faceface |
check the year |
| 08:06 |
|
faceface |
hehehe |
| 08:06 |
|
egonw |
well, with Jmol script then |
| 08:06 |
|
faceface |
right |
| 08:06 |
|
egonw |
with make a very nice Bioclipse plugin too! |
| 08:06 |
|
egonw |
2003 :) |
| 08:06 |
|
faceface |
back then I was also talking to ... bernstein and .... the spanish jmol developer(?) about standardizing the scripting language for molecular interaction |
| 08:06 |
|
egonw |
angel |
| 08:06 |
|
faceface |
right |
| 08:07 |
|
egonw |
bernstein? |
| 08:07 |
|
faceface |
rasmol dude |
| 08:07 |
|
egonw |
ah, ic... |
| 08:07 |
|
faceface |
we talked about writing a grant to develop the idea of a query language based on sql |
| 08:07 |
|
egonw |
yeah, have been talking to the late Warren about it too |
| 08:07 |
|
faceface |
but I didn' thave time |
| 08:07 |
|
faceface |
... |
| 08:07 |
|
egonw |
same here |
| 08:07 |
|
faceface |
he's still on irc? |
| 08:08 |
|
egonw |
warren? no, don't think so |
| 08:08 |
|
egonw |
or angel? |
| 08:08 |
|
faceface |
egonw: my latest idea is now to develop jmol - structure DAS integration and organize it via a wiki |
| 08:09 |
|
faceface |
oh... 'have been talking', better 'I was previously talking' ... |
| 08:09 |
|
egonw |
right |
| 08:09 |
|
egonw |
sorry |
| 08:09 |
|
egonw |
had been |
| 08:09 |
|
faceface |
:( |
| 08:10 |
|
faceface |
I'm amazed at my dedication to random ideas back then: http://www.bioinformatics.org/pdbHighlight/ |
| 08:10 |
|
zarah |
faceface's link is also http://tinyurl.com/2vyy2hq |
| 08:10 |
|
faceface |
zarah: are you judging me, or just trying to be helpfull? |
| 08:10 |
|
zarah |
faceface: please rephrase or stop trying to be witty :) |
| 08:10 |
|
faceface |
;-P |
| 08:10 |
|
egonw |
annzi: read this: http://blog.madism.org/index.p[…]nteractive-?cos=1 |
| 08:10 |
|
zarah |
egonw's link is also http://tinyurl.com/37mpqm7 |
| 08:11 |
|
egonw |
faceface: http://wiki.jmol.org/index.php[…]bsites_Using_Jmol |
| 08:11 |
|
zarah |
egonw's link is also http://tinyurl.com/2uz6jw5 |
| 08:12 |
|
egonw |
faceface: but this one in particular: |
| 08:12 |
|
egonw |
http://www.proteopedia.org/wik[…]dex.php/Main_Page |
| 08:12 |
|
zarah |
egonw's link is also http://tinyurl.com/5mafn3 |
| 08:12 |
|
faceface |
egonw: I'm vaguely aware of PP ;-) |
| 08:12 |
|
egonw |
all the green links are Jmol script, to emphasize that particular word in the Jmol window |
| 08:12 |
|
faceface |
I'm one of the authors of PDBWiki ... sigh |
| 08:13 |
|
faceface |
We were the first to develop a MW PDB agunct (sp?), but PP has stolen our thunder with that awesome Jmol app |
| 08:13 |
|
faceface |
also they have funding ;-) |
| 08:13 |
|
faceface |
we just work for food |
| 08:14 |
|
egonw |
yeah, these are things in the air... and then it is the one with the most resources immediately available that gets the glory... |
| 08:14 |
|
faceface |
it's a very nice project |
| 08:15 |
|
faceface |
journal commenting systems are really bad |
| 08:16 |
|
egonw |
indeed |
| 08:16 |
|
faceface |
I posted a comment on teh PDBWiki article weeks ago |
| 08:16 |
|
egonw |
DOI? |
| 08:16 |
|
faceface |
setting out why we think we can exist in addition to PP |
| 08:16 |
|
|
mgerlich joined #bioclipse |
| 08:16 |
|
faceface |
doi: 10.1093/database/baq009 |
| 08:17 |
|
faceface |
sadly I don't think they give comments DOI |
| 08:17 |
|
faceface |
well.. nice chatting, $job is calling |
| 08:17 |
|
egonw |
ok, same here |
| 08:17 |
|
egonw |
do come back |
| 08:17 |
|
faceface |
have a nice day |
| 08:17 |
|
egonw |
to chat about plugin options! |
| 08:17 |
|
* faceface |
won't leave! |
| 08:33 |
|
jonalv |
egonw: do you have a moment me and Gpox are having some problems... |
| 08:33 |
|
jonalv |
egonw: do you think you could come over? |
| 08:33 |
|
egonw |
hang on |
| 08:34 |
|
egonw |
annzi: http://www.arthurkoziel.com/20[…]it-configuration/ |
| 08:34 |
|
zarah |
egonw's link is also http://tinyurl.com/2drowwe |
| 08:48 |
|
|
mgerlich joined #bioclipse |
| 09:00 |
|
|
masak joined #bioclipse |
| 09:03 |
|
|
s_wolf joined #bioclipse |
| 10:29 |
|
|
samuell joined #bioclipse |
| 10:43 |
|
egonw |
http://code.google.com/p/freebase-gridworks/ |
| 10:43 |
|
zarah |
egonw's link is also http://tinyurl.com/29t9gfx |
| 10:43 |
|
egonw |
looks pretty cool |
| 11:08 |
|
|
s_wolf joined #bioclipse |
| 11:40 |
|
|
olass joined #bioclipse |
| 12:17 |
|
egonw |
jonalv: http://jni-inchi.sourceforge.net/ |
| 12:17 |
|
zarah |
egonw's link is also http://tinyurl.com/2ur8aob |
| 12:19 |
|
olas |
egonw: are you pushing Gpox's cheminfo patches now? |
| 12:20 |
|
olas |
then I can try to export.. |
| 12:20 |
|
egonw |
hang on |
| 12:24 |
|
* olas |
is hanging on |
| 12:29 |
|
egonw |
good |
| 12:29 |
|
egonw |
keep hanging |
| 12:29 |
|
egonw |
eclipse is rebuilding |
| 12:30 |
|
egonw |
Gpox: what platform file should I be using? |
| 12:30 |
|
egonw |
the new- one? |
| 12:30 |
|
Gpox |
yes |
| 12:30 |
|
egonw |
can you make a patch then to have it replace the old target platform file? |
| 12:32 |
|
egonw |
Gpox: can you join? it does not work here... |
| 12:37 |
|
egonw |
olas: ping |
| 12:37 |
|
egonw |
olas: cannot build here... |
| 12:37 |
|
egonw |
I can commit Gpox' patches, but no clue if they compile properly |
| 12:37 |
|
egonw |
Gpox is looking into the set target platform problem jonalv is seeing too |
| 12:49 |
|
egonw |
fika |
| 12:49 |
|
egonw |
who joins? |
| 13:02 |
|
egonw |
Gpox: might it just be a timing issue? |
| 13:02 |
|
egonw |
Gpox: it now seems to work |
| 13:02 |
|
egonw |
the difference seems to be that the http:// folders are now populated |
| 13:23 |
|
CIA-61 |
bioclipse.core: jonalv 2.4.x * r7fdbe2d / plugins/net.bioclipse.ui.business/src/net/bioclipse/ui/business/PasteAsNewTester.java : |
| 13:23 |
|
CIA-61 |
bioclipse.core: fix for bug: 1964 |
| 13:23 |
|
CIA-61 |
bioclipse.core: If GUI stuff is null then we might as well not show it. At least that seems like the reasonable action right now. - http://bit.ly/abs7W0 |
| 13:23 |
|
zarah |
bug #1964 | http://tinyurl.com/2voe4pc |
| 13:49 |
|
CIA-61 |
bioclipse.core: Egon Willighagen 2.4.x * r314be8e / plugins/net.bioclipse.scripting/src/net/bioclipse/scripting/JsEnvironment.java : Removed an unused import which caused a compile fail here - http://bit.ly/d04rRQ |
| 13:51 |
|
egonw |
olas: I get a compile error in cdk.smartsmatching |
| 13:51 |
|
egonw |
olas: do you have a pending commit for that? |
| 14:26 |
|
CIA-61 |
bioclipse.cheminformatics: Egon Willighagen 2.4.x * r830759d / plugins/net.bioclipse.cdk.smartsmatching/META-INF/MANIFEST.MF : Added missing dependency on vecmath - http://bit.ly/dzS6SU |
| 14:37 |
|
CIA-61 |
bioclipse.joelib: Egon Willighagen 2.4.x * r7044cc0 / externals/net.sourceforge.joelib/.classpath : Excluded two files that depended on Log4J itself, and are not used anyway - http://bit.ly/at1yC5 |
| 14:39 |
|
|
s_wolf joined #bioclipse |
| 16:22 |
|
CIA-61 |
bioclipse.balloon: Arvid Berg master * r618e710 / (3 files in 3 dirs): Removed log4j version - http://bit.ly/d1Fno2 |
| 16:23 |
|
CIA-61 |
bioclipse.balloon: Arvid Berg master * r8bc974d / (3 files in 3 dirs): Removed bundle and package versions - http://bit.ly/9D4udI |
| 16:23 |
|
CIA-61 |
bioclipse.balloon: Arvid Berg master * rd856c92 / (3 files): Added update site feature - http://bit.ly/atXuao |
| 16:51 |
|
|
samuell joined #bioclipse |
| 20:22 |
|
|
egonw joined #bioclipse |
| 20:43 |
|
|
olass joined #bioclipse |
| 20:43 |
|
olass |
egonw: ping |
| 20:43 |
|
olass |
org.openscience.cdk.log4j does not compile for me |
| 20:43 |
|
egonw |
pong |
| 20:43 |
|
olass |
seems like a logging issue |
| 20:43 |
|
olass |
am I using wrong branch? |
| 20:43 |
|
egonw |
olass: that's because someone removed org.apache.log4j from the classpath |
| 20:44 |
|
olass |
bioclipse2.4 |
| 20:44 |
|
olass |
yes |
| 20:44 |
|
egonw |
indeed |
| 20:44 |
|
olass |
I thought arvid had fixed that |
| 20:44 |
|
olass |
did he not send you a patch? |
| 20:44 |
|
egonw |
yes, that's why you get the error :) |
| 20:44 |
|
egonw |
ok, here's the story |
| 20:44 |
|
egonw |
org.openscience.cdk.log4j requires log4j |
| 20:44 |
|
egonw |
it's the LoggingTool impl for the CDK using log4j |
| 20:45 |
|
egonw |
hence the dependency |
| 20:45 |
|
egonw |
now, Bioclipse does not use log4j |
| 20:45 |
|
egonw |
but which does not expose everything |
| 20:45 |
|
egonw |
hence the error |
| 20:45 |
|
egonw |
but |
| 20:45 |
|
egonw |
bioclipse2.4 is not using cdk.log4j |
| 20:45 |
|
egonw |
so, the answer is to just remove that plugin |
| 20:45 |
|
egonw |
so, the answer is to just remove that bundle |
| 20:45 |
|
egonw |
so, the answer is to just remove that thing |
| 20:45 |
|
olass |
ok |
| 20:46 |
|
olass |
hmm, is it in the feature too? |
| 20:46 |
|
olass |
yes |
| 20:46 |
|
olass |
so will remove it from there too |
| 20:47 |
|
egonw |
yes, that remains to be fixed |
| 20:47 |
|
egonw |
talked with Gpox about that |
| 20:47 |
|
egonw |
we need more CDK features |
| 20:47 |
|
egonw |
more finetuned |
| 20:52 |
|
olass |
how do I turn off the OSGI logging? |
| 20:53 |
|
olass |
egonw? |
| 20:56 |
|
egonw |
was wondering about that too |
| 20:56 |
|
egonw |
I have no clue |
| 20:58 |
|
olass |
ok, let's ask gpox tomorrow |
| 20:58 |
|
olass |
goodnight |
| 20:58 |
|
egonw |
will have course day tomorrow |
