| Time |
S |
Nick |
Message |
| 06:59 |
|
|
viklund joined #bioclipse |
| 07:27 |
|
|
viklund joined #bioclipse |
| 08:12 |
|
|
jonalv joined #bioclipse |
| 08:32 |
|
|
olas joined #bioclipse |
| 08:33 |
|
olas |
hi |
| 08:33 |
|
|
EskilA joined #bioclipse |
| 08:33 |
|
CIA-31 |
bioclipse: ospjuth * r3977 /trunk/playground/plugins/net.bioclipse.biomoby/src/net/bioclipse/actions/ (TestBiomoby3.java TestBiomoby4.java): The BioMoby tests now run (fixed secondary data) |
| 08:34 |
|
olas |
viklund: how are things progressing with the service? |
| 08:34 |
|
olas |
I am expecting a mail with input/output once you have decided on that |
| 08:54 |
|
|
egonw joined #bioclipse |
| 08:55 |
|
viklund |
olas: jodå, det går frammåt, sakta men säkert. |
| 08:55 |
|
viklund |
Jag tänker slänga upp en mockup idag |
| 08:57 |
|
viklund |
oops, wrong language... |
| 08:57 |
|
viklund |
whatever... |
| 09:01 |
|
egonw |
new PFAAT release: http://www.biomedcentral.com/1471-2105/8/381 |
| 09:13 |
|
olas |
Can we include that in Bioclipse? |
| 09:13 |
|
olas |
egonw: that and JalView are strong candidates |
| 09:13 |
|
olas |
viklund: could you at EBC not compare the two tools? |
| 09:14 |
|
olas |
PFAAT2 and JalView |
| 09:14 |
|
viklund |
I guess we can, yes, |
| 09:14 |
|
viklund |
I'm not probably the right person to do it though. |
| 09:15 |
|
egonw |
olas: did you not have contact in the past with someone behind PFAAT? |
| 09:15 |
|
olas |
no, but JalView |
| 09:31 |
|
egonw |
olas: your biomoby commit is just about using one, right? not setting one up, right? |
| 09:31 |
|
olas |
yes |
| 09:32 |
|
olas |
Bioclispe is a client |
| 09:32 |
|
olas |
(right now at least) |
| 09:32 |
|
egonw |
ok, just making sure :) |
| 09:32 |
|
egonw |
what was this with biomart? |
| 09:32 |
|
olas |
well, just wanted to know what it is and what we can use it for |
| 09:32 |
|
egonw |
you had that page online... |
| 09:33 |
|
egonw |
it seems that our group is going to use it |
| 09:33 |
|
olas |
not experienced with it but heard a lot about it :-) |
| 09:33 |
|
olas |
we should maybe have a biomart plugin |
| 09:34 |
|
egonw |
yes, very possibly indeed... |
| 09:34 |
|
egonw |
would fit well with the current db things in progress |
| 09:35 |
|
jonalv |
oh, what is it? |
| 09:35 |
|
egonw |
a database architecture for life science data... |
| 09:35 |
|
olas |
jonalv: please read on www.biomart.org |
| 09:35 |
|
olas |
http://www.biomart.org/install.html |
| 09:36 |
|
egonw |
it has a SOAP interface to access data... |
| 09:36 |
|
egonw |
would be great to have a node in the Bioclipse2 navigator to open biomart databases |
| 09:36 |
|
olas |
yes |
| 09:36 |
|
olas |
Extremely good |
| 09:37 |
|
olas |
http://www.genome.org/cgi/content/full/14/1/160 is a publication |
| 09:37 |
|
jonalv |
It seems interesting although I am not quite sure I understand exactly what it is |
| 09:38 |
|
egonw |
btw, did you see: http://www.bioclips.com/ |
| 09:38 |
|
olas |
no |
| 09:38 |
|
jonalv |
Eclipse crached again... :( |
| 09:38 |
|
olas |
:-) |
| 09:38 |
|
olas |
haha |
| 09:38 |
|
olas |
BioClips |
| 09:39 |
|
egonw |
they are around longer than bioclipse.net :( |
| 09:39 |
|
jonalv |
wow |
| 09:39 |
|
egonw |
maybe time for a BioClipse plugin for Bioclipse ? :) |
| 09:39 |
|
egonw |
maybe time for a BioClips plugin for Bioclipse ? :) |
| 09:39 |
|
jonalv |
hehe |
| 09:51 |
|
viklund |
olas: Can you pleas just check this wsdl: |
| 09:52 |
|
viklund |
http://artedi.ebc.uu.se/course/temperatures.wsdl |
| 09:53 |
|
olas |
ok |
| 09:53 |
|
viklund |
I get an infinite loop in my perl-test-script when I try to load it |
| 09:53 |
|
egonw |
lunch time |
| 09:53 |
|
viklund |
so it's not actually using it that needs testing, it dosn't work |
| 09:53 |
|
olas |
it's valid |
| 09:54 |
|
olas |
do you want me to build a java client? |
| 09:54 |
|
viklund |
hmm, strange... I get an infinite loop in my SOAP::Lite... |
| 09:54 |
|
viklund |
nope |
| 09:54 |
|
viklund |
the service dosnt exist ;p |
| 09:54 |
|
olas |
Just because it's valid doesn't mean it works... |
| 09:55 |
|
olas |
targetNamespace="http://localhost/Temperatures" |
| 09:55 |
|
olas |
I see |
| 09:55 |
|
viklund |
yep |
| 09:55 |
|
viklund |
you can try a new one very soon though |
| 09:55 |
|
olas |
ok |
| 09:55 |
|
viklund |
now |
| 09:55 |
|
olas |
now? |
| 09:56 |
|
viklund |
redownload the wsdl, and test it, targetNamespace is accesible now |
| 09:56 |
|
olas |
ok |
| 09:58 |
|
olas |
no |
| 09:58 |
|
olas |
Denied access to method (as_celsius) in class (Temperatures) at /usr/lib/perl5/vendor_perl/5.8.8/SOAP/Lite.pm line 2509. |
| 09:59 |
|
viklund |
hmm |
| 09:59 |
|
viklund |
I thought some things would be easier with objects, but maybe not... |
| 10:02 |
|
olas |
It is |
| 10:02 |
|
olas |
we really should have a model object |
| 10:02 |
|
olas |
holding all information |
| 10:02 |
|
olas |
for more complex cases, that is a must |
| 10:02 |
|
viklund |
yes... |
| 10:02 |
|
viklund |
maybe test another thing then.. |
| 10:02 |
|
olas |
I would strongly suggest you looking into BioMoby |
| 10:03 |
|
olas |
They are standardizing these things and have generators to generate perl |
| 10:03 |
|
viklund |
I'll try to access the stuff without wsdl and see if that works |
| 10:03 |
|
viklund |
I will |
| 10:03 |
|
olas |
good |
| 10:03 |
|
olas |
We (in Bioclipse) think BioMoby is the future for services |
| 10:15 |
|
viklund |
;) |
| 10:27 |
|
|
olas left #bioclipse |
| 11:10 |
|
viklund |
the service should work not though... |
| 11:10 |
|
viklund |
does someone else now how to test it? |
| 11:10 |
|
viklund |
not a yn00 service but the previous service... |
| 14:27 |
|
|
viklund joined #bioclipse |
| 20:57 |
|
|
egonw joined #bioclipse |
| 22:19 |
|
|
bjarni joined #bioclipse |
| 22:19 |
|
|
ilogger2 joined #bioclipse |
| 22:19 |
|
|
ChanServ joined #bioclipse |
| 22:20 |
|
|
CIA-31 joined #bioclipse |
