Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-08-25

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All times shown according to UTC.

Time Nick Message
02:26 ank joined #bioperl
03:49 rbuels phpmyadmin kind of reminds me of tajikistan.
03:55 CIA-95 Bio-FeatureIO: Chris Fields master * r98d2333 / lib/Bio/FeatureIO/gtf.pm : small link fix - http://bit.ly/az02fc
03:55 CIA-95 Bio-FeatureIO: Chris Fields master * r7122446 / (lib/Bio/FeatureIO.pm lib/Bio/FeatureIO/gff.pm t/bed.t): bed passes, but needs real tests - http://bit.ly/cGhJ3C
04:02 * deafferret blinks
06:45 dnewkirk still at work, eh
07:06 dnewkirk left #bioperl
07:11 bag_ joined #bioperl
07:27 ank left #bioperl
07:54 kai morning folks
09:18 brandi1 joined #bioperl
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09:51 dbolser gutten tag
10:17 kai only one t, but otherwise not too bad :)
10:47 carandraug joined #bioperl
12:12 dbolser tol!
13:13 ank joined #bioperl
13:16 kai toll however has a double-l
13:16 kai :)
13:44 dbolser ich bin... ashamed
14:02 kai is there a good way of turning smiles into a vector graphic of the structural formular? looking for smiles and perl, all I can find is PerlMol, but that can't do structural formulas, it seems
14:45 dbolser kai: I'd guess chembl has all that stuff
14:50 kai nothing that catches the eye
15:02 dnewkirk joined #bioperl
15:03 dbolser kai: yeah... weird... I thought they had all sorts of webservices for this kind of ting
15:57 kblin I guess I'll have to roll my own then
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16:16 perl_splut what are smiles (other than the facial gesture made by people and some other animals)
17:39 kblin http://en.wikipedia.org/wiki/Simplified_​molecular_input_line_entry_specification
17:39 kblin though I'm sure that's a backronym
17:54 perl_splut ahh
17:54 perl_splut pymol might handle those
17:55 kblin I wonder if I should use InChIs instead
17:56 kblin I keep forgetting SMILES are commercial
17:59 perl_splut http://www.opensmiles.org/
18:08 kblin yeah
18:08 kblin but IUPAC came up with InChI, wikipedia uses it..
18:11 perl_splut http://inchi.sourceforge.net/
18:13 kblin yeah
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18:18 CIA-95 Bio-FeatureIO: Chris Fields master * r16c06a6 / (4 files in 3 dirs): finish initial work on bed format, work on ptt - http://bit.ly/bWKOKb
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22:04 CIA-95 bioperl-live: Chris Fields master * rd5faf5e / Bio/SeqFeature/Generic.pm : add primary_id as a constructor parameter - http://bit.ly/cUSGcU
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22:28 CIA-95 Bio-FeatureIO: Chris Fields master * r1de5552 / (5 files in 3 dirs): make all arguments specific to the bioperl interface - http://bit.ly/cX9tl9
23:26 rbuels i've a mind to write a simple, fast set of gff3 tools and put them on cpan.  a stupid parser, a stupid formatter, and an actual decent validator
23:26 rbuels that are not tied to the bioperl data model
23:26 rbuels because sometimes the data model is overkill.
23:26 rbuels (and sometimes it isn't)
23:29 rbuels and then the next-gen bioperl gff3 functions can use them
23:29 * rbuels puts that on the list of things to do, #296
23:49 perl_splut just a small list, rbuels?

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