Camelia, the Perl 6 bug

IRC log for #cdk, 2010-09-17

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All times shown according to UTC.

Time Nick Message
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07:46 jerome___ moin
07:46 zarah ni hao jerome___
07:46 jerome___ is now known as alchimiste
07:53 egonw hi alchimiste
07:55 alchimiste hi egonw
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08:40 Topic for #cdk is now The Chemistry Development Kit (http://cdk.sf.net) | JUnit CDK 1.2.7: 15690, 76 fails + 15 errors (0.58%) | Logs at http://moritz.faui2k3.org/​irclog/out.pl?channel=cdk | CDK News Feed: http://friendfeed.com/rooms​/chemistry-development-kit
09:14 egonw alchimiste: congrats with the 0.8.1 release
09:14 egonw happy to hear it is now working on mysql 5.x
09:37 alchimiste :)
09:38 alchimiste it works with MySQL 5.1 since 0.8.0
09:38 alchimiste but I have hit an important bug
09:42 egonw there are no ubuntu packages, are there?
09:43 alchimiste no
09:46 egonw well, I would be happy if I got mysql on our lucid system working anyway
09:46 egonw with or withour mychem
09:52 alchimiste I will try also Mychem with MariaDB
09:59 azeem what about Postgres?
10:03 alchimiste see pgchem
10:03 alchimiste Mychem and pgchem are sharing a lot of code.
10:06 azeem ah right :)
10:07 azeem why can't you support with the same codebase?
10:07 azeem +both
10:07 azeem do you need SQL extensions?
10:07 azeem or is *chem a database extension?
10:12 egonw right
10:15 sneumann [off topic] http://lists.pgfoundry.org/pipermail/​pgchem-devel/2010-August/thread.html
10:15 zarah sneumann's link is also http://tinyurl.com/3axnhva
10:15 sneumann we've been hitting a SMARTS bug (?) with OpenBabel
10:16 sneumann in our Pgchem installation, but independent from pgchem
10:16 sneumann http://sourceforge.net/tracker/?func=detail&amp​;aid=3065756&group_id=40728&atid=428740
10:16 zarah sneumann's link is also http://tinyurl.com/35gqowk
10:19 egonw sneumann++
10:44 sneumann egonw ? You mean for proper bug reporting ?
10:44 egonw and for mentioning it here
10:44 sneumann We'll import at least KEGG, and will try tim import PubChem as well,
10:44 sneumann let's see how it scales :-)
10:45 sneumann alchimiste: have you ever tried to import sth. as large as PubChem into MyChem ?
10:47 alchimiste I did not try to upload a larger base than 100k compounds
10:47 sneumann how did that go w.r.t to performance ?
10:48 alchimiste I can not remember.
10:48 sneumann so not too bad ;-)
10:48 alchimiste However, with large database, you need to split it in small files
10:49 alchimiste Mychem does not support Multithreading (as Open Babel)
10:49 alchimiste I can check on a server
10:50 alchimiste how big is the KEGG db ?
10:51 sneumann just 15000
10:51 sneumann http://www.genome.jp/kegg/compound/
10:51 sneumann It's *the* pathway database, quite important to biologists
10:52 sneumann and for us as small/medium sized test bed ;-)
10:55 alchimiste perfect for Mychem
11:20 s9asad HI
11:20 zarah privet s9asad
11:21 s9asad any enzymologist here :-)
11:22 egonw what does an enzymologist do?
11:23 s9asad I just need anyone with basic knowledge about enzymes
11:23 s9asad I am not an expert
11:24 egonw ok, then I am a enzymologist...
11:24 s9asad someone who understand these IUBMB EC classifications
11:24 s9asad great
11:24 egonw I have only very basic knowledge about enzymes
11:24 egonw ah, I even understand EC classifications...
11:24 egonw at least the syntax of the number :)
11:24 s9asad :-)
11:25 s9asad I am trying to develop a tool to compare enzymes
11:25 * sneumann listens
11:25 s9asad based on these small molecule structure similarity and bond changes
11:25 s9asad for example
11:26 egonw that sounds like work for the Thornton group all right
11:26 egonw s9asad: you should talk to Irene (now in London I think?)
11:26 egonw she has done a lot in that area
11:26 s9asad yeah i guess I need to talk to her at somepoint
11:26 egonw but perhaps left before you arrived
11:26 s9asad yes
11:26 s9asad http://www.ebi.ac.uk/thornton-srv/softw​are/ecBLAST/KEGG/html/ec/1.1.1.10.html
11:26 zarah s9asad's link is also http://tinyurl.com/24zseza
11:27 s9asad my question is ...some one working on enzymes .... will this be helpful...
11:32 s9asad ?
11:32 s9asad any feedback
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11:57 maclean egonw : I've been using the 'hierarchical' renderer ...er...architecture a bit, and it's quite nice.
11:59 maclean also, layouts could prove to be quite useful, if done right.
12:02 egonw ack
12:02 * egonw will try to rebase cdk-jchempaint on 1.3.6 this weekend
12:03 maclean ok, cool.
13:08 egonw "OpenChrom: a cross-platform open source software for the mass spectrometric analysis of chromatographic data" ??
13:08 egonw they write:
13:09 egonw "The Chemistry Development Kit (CDK) [30] implements convenient features to edit chemical data and structures, but it has no appropriate user interface."
13:09 egonw huh??
13:09 egonw taverna, knime, bioclipse, rcdk, various websites, ...
13:09 egonw they are not appriopriate user interfaces?
13:10 azeem maybe the author wants something like the minority report UI
13:10 egonw "Bioclipse is a sophisticated project that is open source and is focused with its algorithms on metabolism analysis and gene sequencing."
13:10 egonw hahaha
13:10 egonw and why don't the cite the bioclipse paper?
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