Camelia, the Perl 6 bug

IRC log for #cdk, 2010-07-19

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All times shown according to UTC.

Time Nick Message
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09:26 jkerssem hi everyone
09:39 egonw hi jkerssem!
09:39 egonw welcome!
09:39 egonw jkerssem: note that there are a few bots here... zarah, _ilbot2, CIA-47
09:40 egonw zarah: you're silent today?
09:40 zarah egonw: eh... wha'?
09:40 jkerssem Hi egon
09:40 jkerssem I would be Jules
09:41 jkerssem but sadly, there are more people using that as a nick :)
09:41 egonw yes, got that :)
09:41 egonw I can imagine
09:41 jkerssem hi zarah
09:41 jkerssem hi _ilbot2
09:41 egonw I can recommend registering your account
09:41 jkerssem hi CIA-47
09:41 egonw the latter two do not talk
09:41 egonw only zarah, but not so much today
09:41 jkerssem ah, ok
09:41 jkerssem they're only for services?
09:42 egonw right
09:42 egonw CIA reports commit messages here
09:42 egonw is a log bot
09:42 jkerssem ah, ok
09:42 egonw so that people offline can see what we discuss here too
09:42 jkerssem I'm familiar with the concept of bots and logging
09:42 jkerssem just not with the specific bots
09:43 egonw ack
09:45 jkerssem okay, that's the registration done
09:46 egonw did you also register jkerssem_ as second nick?
09:46 jkerssem no.. is that a good thing?
09:46 egonw which is useful because of network splits that happen now and then
09:46 jkerssem ah
09:48 jkerssem ah, GROUP works nicely :)
09:49 jkerssem thanks for the tips
09:49 jkerssem now for git patches
09:49 jkerssem I've finished the whole "apt-get install git"
09:51 jkerssem now do I want the "git clone ssh.." command (read/write) or the "git clone .." (read only) command?
09:51 jkerssem (from the CDK SF develop section)
10:00 jkerssem (no clue what the ssh password should be, going for the read-only variant)
10:17 jkerssem okay, I got the read-only clone all downloaded
10:25 s9asad joined #cdk
10:34 egonw sorry, was afk for a while
10:35 egonw use:
10:35 egonw git clone git://github.com/cdk/cdk.git
10:36 egonw no pwd needed; it's read-only
10:36 egonw oh...
10:36 egonw only now I read your last line :)
10:36 egonw jkerssem: btw, please meet s9asad (Asad), working at the EBI
10:37 egonw jkerssem: s_wolf mgerlich sneumann are metabolomics wizards
10:37 egonw stain: is Taverna developer
10:37 egonw jpansanel: is of MyChem
10:37 egonw jbrefort: of general open source cheminformatics
10:37 egonw Conrad: just lingers here out of interest
10:38 egonw azeem_: is working as Debian Developer on Jmol.deb
10:38 jkerssem hello everyone :)
10:38 egonw slyrus is CDK user
10:38 egonw bag_: I forgot what you are working on..
10:39 egonw s9asad: is author of the SMSD paper, of which the code is now in the CDK... you might find mutual interests
10:39 jkerssem jkerssem: new phd student working on metabolomic database, uses CDK
10:39 egonw s9asad: jkerssem works in Nijmegen on the future BioMeta
10:39 jkerssem I already came across the SMSD paper, cool stuff indeed
10:40 s9asad Hi Everyone
10:40 egonw hi s9asad
10:40 s9asad Sorry I was over teh phone
10:40 jkerssem BioMeta is actually known  here? wow :)
10:40 jkerssem hello asad
10:40 egonw jkerssem: I am an old friend of Martin :)
10:40 jkerssem ah, in that way :)
10:40 s9asad I will join you guys in 5 mins :-)
10:40 jkerssem s9asad, take your time :)
10:41 egonw jkerssem: if you want links to mass spectroscopy, sneumann is your man
10:41 egonw with sneumann I work on metware.org
10:41 egonw so, more metabolite stuff
10:42 s9asad So great to meet you you all
10:42 jkerssem likewise :)
10:43 jkerssem @metware: cool, my other first assignement is a "write a review of everything metabolomics"..
10:43 jkerssem so all info is welcome
10:43 s9asad I was working on metabolomics in PhD now as postdoc I am more working on Enzyme reaction chemistry :-) and metabolomics is very interesting to me
10:44 jkerssem asad, which EBI group are you with?
10:44 s9asad Thornton grp
10:44 s9asad how about you?
10:44 jkerssem I did a short traineeship with IntAct (Henning Hermjakob) for my masters degree
10:44 s9asad Great
10:45 jkerssem now I work at the bioinformatics department of Radboud University, Nijmegen (NL)
10:45 jkerssem The EBI taught me a lot :)
10:45 jkerssem so thanks ;-)
10:45 s9asad I am still learning :-)
10:45 s9asad So what are you working on?
10:46 s9asad BioMeta?
10:46 jkerssem yup
10:46 s9asad Reaction stuff
10:46 jkerssem reaction stuff with an endeavor to go into systems biology
10:47 s9asad Well indeed as per the trend
10:47 jkerssem yup, gotta hop on the systems bandwagon :)
10:47 s9asad I was working on metabolic netwroks before I choose to me more into EC
10:47 egonw BioMeta is a cleaned KEGG
10:48 jkerssem but right now, I'm more on the "figure out what/how my predecessor dit it and update it to current standards"
10:48 egonw jkerssem: are you in contact with Martin?
10:48 jkerssem egonw, incidentally
10:48 jkerssem he's now at Leeds
10:48 egonw lhasa, right?
10:48 jkerssem yup
10:48 egonw havent' spoken with him since he left cmbi myself
10:48 jkerssem but he keeps in touch
10:49 jkerssem well, I'll let you know the next time he's around, maybe it'll coincide with a visit of yourself :)
10:50 s9asad Martin did a good work with biometa
10:50 jkerssem exactly
10:50 jkerssem it still stuns me sometimes when I see the kegg notation
10:50 jkerssem and how heavily it was fixed
10:50 jkerssem I'm a molecular life scientist myself
10:51 jkerssem so I can actually understand a chemical drawing
10:51 s9asad Oh great! so did you update it recently?
10:51 jkerssem 'recently' is what I'm doing right now :)
10:51 jkerssem it's taking me some getting-used to
10:51 jkerssem I only started in april
10:52 jkerssem I'm aiming to automate Martin's insights
10:52 s9asad We might be interested in your curated DB :-)
10:52 jkerssem because at 400+ changes, manual work (especially in the future) is becoming unmaintainable
10:52 jkerssem 'We' = EBI?
10:52 s9asad Like wise as Egon pointed out you might get back something interesting "Symbiotic"
10:53 s9asad We="Thornton Grp"
10:53 jkerssem symbiosis is the way forward, so who knows :)
10:54 s9asad The CDK might be a good starting point
10:54 jkerssem in the very least i'll let you know once I've updated things
10:54 jkerssem I'm already using the CDK
10:54 jkerssem I shudder to think how long it would have taken me to write all the structure stuff myself :)
10:54 s9asad I can help you in the MCS part or in reaction chem
10:54 jkerssem so good job CDK-ists :)
10:55 egonw s9asad: you still need to write a simple tutorial, with lots of code snippets
10:55 s9asad Egon: yes :-)
10:55 egonw so that people can basically copy/paste your code to get SMSD going
10:55 egonw no one has any clue where to start, it seems
10:55 jkerssem UniversalIsomorphismTester, no?
10:56 egonw not for smsd, I think
10:56 egonw s9asad: ?
10:56 s9asad if you need command line option you can download it from http://github.com/asad/SMSD-CMD/downloads
10:56 zarah s9asad's link is also http://tinyurl.com/2v4d79x
10:57 egonw s9asad: people need to know how to use it programmatically
10:57 egonw at a CDK API level
10:57 s9asad Well as a developer I might overlook some obvious to do list to run it but I am here to help anyone
10:57 egonw that model is not working well
10:57 egonw people need some idea on how to get started
10:58 jkerssem hmm, there's this nice SMSD class fairly well documented in the 1.3.5 javadoc...
10:58 jkerssem with code samples even
10:58 egonw a simple a4 describing which class to use
10:58 egonw yeah, once you noticed that is the class to use
10:58 s9asad @member:jkerssem: I thought that was good enough
10:58 s9asad but I can write more
10:58 egonw think of it as vignettes for R
10:58 egonw the R documentation for the methods was not helping
10:58 jkerssem the javadoc is excellent
10:59 egonw so they came up with the vignette idea
10:59 jkerssem but if I understand egon correctly
10:59 egonw s9asad: I'm not talking about JavaDoc
10:59 jkerssem no-one finds the SMSD javadoc because there is no tutorial saying "substructure search? use SMSD!"
10:59 egonw I am talking about a short tutorial on the concepts, and how to apply those concepts with Java source code
11:00 s9asad @Egon: fair enough but where should I put that?
11:00 egonw s9asad: one idea could be to compare the performance of the UIT and the VFLib impl using the SMSD functionality...
11:00 egonw s9asad: in your blog?
11:00 s9asad doesn't CDK contain a module discription?
11:00 egonw jkerssem: do you blog?
11:00 egonw module description? not that I am aware of
11:00 egonw good idea though :)
11:00 jkerssem no, I don't blog, I don't even have a website (gasp!)
11:01 egonw my blog is more or less my website :)
11:01 jkerssem I've thought about it a few times though :)
11:01 s9asad I think we should have a module description page and I am also happy to blog about it.
11:01 jkerssem and a very helpfull website it is
11:01 egonw s9asad: yeah, more module info would be nice
11:02 egonw s9asad: there is some preliminary code to create webpages for modules
11:02 s9asad @jkerssem: Yes Egon's blog is very useful
11:02 egonw with links to test results,etc
11:03 s9asad @egon: I remember a script do compare UIT MCS with some other s/w. I guees I can use that
11:03 egonw description info, maintainer, etc, could easily be added there
11:03 s9asad pointer pls
11:03 egonw git cdk/createModulePages.groovy or so
11:04 s9asad okay will try this
11:04 s9asad @member:jkerssem: Let me know if you need any help :-)
11:05 jkerssem I will :)
11:05 s9asad This is an old blog
11:05 s9asad http://chembioinfo.wordpress.com/20​10/04/26/smsd-integrated-with-cdk/
11:06 zarah s9asad's link is also http://tinyurl.com/3xggumb
11:06 jkerssem my guess is that once I get the source data up-to-date for Kegg54 (currently = Kegg v36 :-O)
11:06 jkerssem I'll start 'true' work
11:06 s9asad sure
11:08 jkerssem thanks for the offer in the very least :)
11:10 egonw I got 6: http://github.com/egonw/cdk/blob/cd2c9c772489​130c2cca16f0e48fecbca30d3821/src/test/org/ope​nscience/cdk/geometry/cip/CIPSMILESTest.java
11:10 zarah egonw's link is also http://tinyurl.com/37l698c
11:10 egonw wrong window :)
11:16 bag_ egonw, i'm a bioinformatition, working on protein-protein interactions and drugs-design :)
11:16 egonw bag_: ack :)
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22:38 CIA-47 cdk: Rajarshi Guha master * re6fecf2 / src/main/org/openscience/cdk/fing​erprint/PubchemFingerprinter.java : Updated fingerprinter javadoc - http://bit.ly/9wORAo

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