Camelia, the Perl 6 bug

IRC log for #bioclipse, 2010-02-09

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All times shown according to UTC.

Time Nick Message
05:28 egonw joined #bioclipse
05:49 sneumann_ joined #bioclipse
06:52 annzi joined #bioclipse
07:30 Gpox joined #bioclipse
07:33 Gpoks joined #bioclipse
07:34 egonw hi Gpox and Gpoks
07:36 Gpox only one of us here now
07:46 sneumann_ joined #bioclipse
09:06 egonw joined #bioclipse
09:15 egonw moin
09:15 zarah privet egonw
09:16 egonw managed to reduce my inbox to <100 unread
09:25 annzi egonw: is there a way in cdk to convert to SMILES?
09:26 egonw sure
09:26 egonw I guess a IMolecule to SMILES?
09:26 annzi do you know the name of the method?
09:26 egonw IMolecule.getSMILES() I think
09:38 annzi egonw: found toSMILES
09:38 egonw ah, good
09:38 egonw http://chem-bla-ics.blogspot.com/2010​/02/chembl-rdf-1sparql-end-point.html
09:38 zarah egonw's link is also http://tinyurl.com/yk5e5cw
09:40 annzi about moss,
09:41 annzi egonw: I see two ways, one keep the file system or two add molecules manually
09:41 egonw explain in more detail, please
09:42 annzi well at the moment I'm trying to deal with SMILES collected via sparql
09:43 annzi moss takes files that are built a certain way and for me to be able to run moss I need to save the compunds into this kind o file
09:43 annzi I believe that when working in large subsets files is the way to go
09:44 annzi but on the other hand it could also be nice if the compounds was read in to moss directly
09:44 annzi without having to save to file
09:45 annzi but do not know if this is possible¨
09:47 sneumann_ MetFrag als wants to read/run on hundreds of candidate molecules,
09:47 sneumann_ I am currently only testing with a few dozens. The MolTable is supposed to be able
09:47 sneumann_ to keep huge (read: PubChem) numbers of molecules.
09:48 egonw sneumann_: I managed to get stefan's repositories to check out about an hour ago... not restarted eclipse WS yet
09:48 sneumann_ egonw: cool
09:48 sneumann_ annzi: I'd love to run MoSS if there is a preview available
09:50 sneumann_ MetFrag will give you a zoo of molecular fragments determined via Mass Spectrometry
09:50 egonw annzi: I think indeed we should not aim at trying to run MoSS in a better way
09:50 egonw annzi: so, saving the SMILES directly to file should be ideal... what about composing a large string, and save that as file content?
09:50 annzi well the moss plugin I worked with 2 years ago need some serious polishing (runs really slow)but it is available
09:51 egonw and it cannot be operated at a manager level yet, but that's one of the research goals of annzi's project
09:51 sneumann_ I guess I'll wait until that kinda works
09:51 sneumann_ volunteer as beta tester ;-)
09:51 annzi sneumann_ : great :)
09:53 egonw annzi: more SPARQL end points: http://www.freebase.com/view​/user/bio2rdf/public/sparql
09:53 zarah egonw's link is also http://tinyurl.com/y8ketrm
09:54 annzi egonw: I need to catch up on file saving, know any great tutorial?
09:54 annzi Yes, I've been looking at ta
09:54 annzi that page
10:13 egonw annzi: please do blog about cool SPARQL queries :)
10:14 annzi on my todo list :D
10:23 masak joined #bioclipse
10:32 egonw masak: bioinfo request: z-score calculation
10:32 egonw masak: shall I file on pelezilla?
10:32 masak please do.
10:33 masak I'm sorta handing over the bioinfo feature to jonalv++... a bit disinclined to start on new stuff.
10:34 egonw ack, next time we meet physically, you have to tell me about your new exiting endaevour (without disclosing trade secrets, of course :)
10:34 egonw I wish zarah could file bug reports ...
10:34 masak :)
10:34 masak egonw: seems there are fewer trade secrets this time around. :)
10:35 masak egonw: also, I'm using Perl 6 for prototyping, so I'm a happy puppy :)
10:35 egonw "Perl 6 for prototyping" ... what's that?
10:35 egonw mock ups?
10:38 masak "I'm using [Perl 6] for prototyping"
10:39 masak "I'm using [Perl 6] for prototyping [the application I'm supposed to write]"
10:39 egonw ack, right
10:57 sneumann__ joined #bioclipse
13:28 egonw annzi: http://friendfeed.com/egonw/dccb8​201/chembl-rdf-1-sparql-end-point
13:28 zarah egonw's link is also http://tinyurl.com/ycakdej
14:34 annzi egonw: is there by any chance a way to rename activitiy to activity( <http://rdf.farmbio.uu.se/chembl/snorq​l/?describe=http%3A%2F%2Frdf.farmbio.​uu.se%2Fchembl%2Factivitiy%2Fa32195)
14:34 zarah annzi's link is also http://tinyurl.com/yjf33uz
14:35 annzi I kepp on writing activity
14:36 egonw mom
14:37 egonw crap :(
14:37 egonw sorry about that
14:40 annzi I can live with it ;)
14:43 egonw please file it as bug report here: http://github.com/egonw/chembl.rdf
14:43 zarah egonw's link is also http://tinyurl.com/ygu5bqw
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23:28 sneumann joined #bioclipse

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