Camelia, the Perl 6 bug

IRC log for #bioclipse, 2010-02-04

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All times shown according to UTC.

Time Nick Message
06:29 egonw joined #bioclipse
06:36 s_wolf joined #bioclipse
06:36 mgerlich joined #bioclipse
07:20 annzi joined #bioclipse
07:51 sneumann_ joined #bioclipse
07:52 Gpox joined #bioclipse
08:08 sneumann_ morning
08:16 CIA-71 bioclipse.metabolomics: Steffen Neumann master * r4b0db38 / (3 files in 2 dirs): First successful calls to MetFrag from BC - http://bit.ly/cSEIbq
08:51 egonw joined #bioclipse
09:21 * sneumann_ is makeing his proof-of-concept MetFrag plugin more BC friendly
09:22 sneumann_ The manager doesn't find the DefaultChemObjectBuilder
09:22 sneumann_ Caused by: java.lang.NoClassDefFoundError: org/openscience/cdk/DefaultChemObjectBuilder
09:22 sneumann_ But I have Require-Bundle: org.openscience.cdk.data,
09:34 sneumann Ah, I probably need to put org.openscience.data into the metfrag_feature ?
09:34 sneumann or better n.bc.cdk.business ?
09:39 sneumann no, didn't help. Tried n.bc.cdk feature in both metfrag product and metfrag feature.
09:55 sneumann Kinda lost now
10:18 annzi1 joined #bioclipse
10:31 egonw sneumann: just got back from the IT department
10:31 egonw for setting up a RDF server
10:32 egonw metfrag_feature depends on platform_feature
10:32 egonw which includes all the CDK plugins via the cheminformatics_feature dep of platform_f
10:45 jonalv joined #bioclipse
10:47 sneumann egonw: so in theory my problem should not exist ...
10:47 egonw indeed
10:47 egonw pastebin?
10:48 sneumann http://pastebin.com/m5189c544
10:48 sneumann looks identical to the notfounds I had with stuff from the jars shipped with d.i.metfrag
10:49 sneumann going for lunch, will try everything you throw at me in the meantime ;-)
10:53 egonw sneumann: can you commit stuff before you leave?
11:00 masak joined #bioclipse
11:36 sneumann Storage server temporarily offline. Please try again in a few minutes or contact GitHub.
11:36 egonw ack
11:41 sneumann Is it worth sending patches via mail ?
11:41 egonw git format-patch
11:42 egonw yes, very efficient
11:47 CIA-71 bioclipse.metabolomics: Steffen Neumann master * r3e427f6 / (2 files): Refactoring towards molecule arguments, removing KEGG stuff - http://bit.ly/bwdYXc
11:47 sneumann github is back online
11:47 sneumann also committed d.i.metfrag to my repo
12:03 egonw so, no manual patches to apply anymore ?
12:03 sneumann nope
12:28 egonw sneumann: sorry... I'm shit deep in server configuration today...
12:28 egonw Gpox: tomcat6-admin was not installed, which I now just did...
12:37 Gpox ok
12:43 annzi1 egonw: may I ask you about different id on pele/chembl?
12:43 egonw sure
12:45 annzi1 moleculeId, resourceId for examples are they indices you use localy?
12:46 egonw no, they are unique IDs
12:46 annzi1 the only connection I find between sarfari and pele is the activityId, or is there other connections?
12:46 egonw better, global IDs
12:46 egonw ah, right
12:46 egonw moleculeId actually is in the db
12:46 egonw but deprecated
12:46 annzi1 so what for example does moleculeId stand for?
12:46 egonw Anna asked me to use the ChEBI id instead
12:47 egonw the moleculeId on pele is from ChEMBL but only supposed to be used for internal reasons
12:48 annzi1 ok, as I figured, thanx
12:49 annzi1 and I do think that ChEBI Id would be great
12:49 egonw yes, will come soon
12:49 annzi1 nice :)
13:00 olass joined #bioclipse
13:09 sneumann hi olas,
13:10 sneumann I am looking for a way to script m2d
13:10 olass hi sneumann
13:10 olass that should be possible
13:10 olass have you seen the gist: http://gist.github.com/170410 ?
13:10 olass Does it not work?
13:11 olass see page http://wiki.bioclipse.net/i​ndex.php?title=MetaPrint2D
13:11 zarah olass's link is also http://tinyurl.com/yjtwuus
13:11 sneumann yes, and it works.
13:11 sneumann I was looking how to get a moltable  back
13:11 sneumann much in the way of
13:11 sneumann MetaPrint2D-React (experimental)
13:12 sneumann metabolite generator
13:12 sneumann on the website
13:12 olass what website are you talking about? That on cambridge?
13:12 sneumann yup
13:13 olass that is not in Bioclipse yet
13:13 olass so in the pipe
13:13 olass but might take a while
13:13 sneumann ack, will wait a vew month ...
13:13 sneumann ack, will wait a few month ...
13:13 olass ok :)
13:13 sneumann targeted for 2.4 ?
13:13 olass unfortunately no
13:13 olass but who knows
13:14 olass it is a collaboration so not only up to me
13:14 olass I'll kepp you posted ;)
13:14 olass kepp
13:14 olass keep
13:14 olass *gah*
13:14 * olass is looking forward to see what sneumann is producing
13:15 sneumann preview: pipe metaprint2dreact into metfrag ;-)
14:11 annzi joined #bioclipse
14:33 sneumann @tell egonw that I didn't do anything, but cdk stuff in metfrag works
14:33 zarah Consider it noted.
15:12 sneumann @tell egonw that the classNotFound is back. I didn't do anything. Really.
15:12 zarah Consider it noted.
15:22 CIA-71 bioclipse.metabolomics: Steffen Neumann master * rc342ca9 / (4 files in 3 dirs): Using IMolecule, Added Speclipse Dependency - http://bit.ly/c9nw7n
15:32 sneumann_ joined #bioclipse
16:42 CIA-71 bioclipse.metabolomics: Steffen Neumann master * rf658eaf / (2 files in 2 dirs): Moving MetFrag towards using ISpectrum - http://bit.ly/9pkCWO
16:55 egonw joined #bioclipse
17:04 CIA-71 bioclipse.rdf: Egon Willighagen master * ra2ffc5c / (6 files in 4 dirs): Added function to create a RDF only TDB store - http://bit.ly/9qXFAh
18:03 sneumann_ joined #bioclipse
18:15 annzi joined #bioclipse
19:57 * sneumann is adding more methods to metfrag manager for the anticipated use of molecules, moleculeLists and ISpectrum
20:43 sneumann joined #bioclipse

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