Camelia, the Perl 6 bug

IRC log for #bioclipse, 2010-07-09

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All times shown according to UTC.

Time Nick Message
06:02 annzi joined #bioclipse
06:18 olass joined #bioclipse
06:18 olass moin
06:18 zarah oh hai olass
06:55 slyrus olass: I'm still out the layout stage. haven't gotten to the drawing yet.
06:56 olass slyrus: what are you working on, if I may ask?
06:57 slyrus a 2d molecule drawing library :)
06:57 slyrus I've been playing around with a couple different approaches
06:58 olass in Java?
06:58 slyrus well, no, not really :)
06:58 olass oh
06:58 slyrus sort of though...
06:58 olass ?
06:59 slyrus I'm a lisp programmer at heart. I had been working on my own cheminformatics-y library in common lisp when I learned about cdk
06:59 olass ah
06:59 slyrus so, I figured, ah! I'll just switch over to clojure and leverage it's awesome java interop capabilities to use all of the cdk goodness
06:59 slyrus then I discovered that cdk's 2d drawing routines are actually pretty weak
07:00 slyrus and that the SMILES parsing code had the same limitations that I had bumped into in my own code
07:00 slyrus (esp. configuration around double bonds)
07:01 olass so are you pursuing to fill those gaps?
07:01 slyrus so... now I've got a nice, but unfinished, library in common lisp, some clojure code that calls cdk, and a nascent approach at rewriting all of my common lisp chemistry stuff in clojure.
07:01 slyrus why reinvent one wheel when you could have 3?
07:01 olass hehe
07:02 slyrus I'm not sure if I'm going to fill those gaps or not. I'd like for them to be filled, but I still haven't decided on the best approach.
07:02 * olass and Bioclipse would be happy if you filled some gaps
07:02 slyrus i noticed from a sf.net bug report (that's another pet peeve -- I pretty much loathe any sourceforge interface) that the cdk 2d layout code is due for a rewrite
07:03 slyrus it's not clear to me that implementing improved functionality (over cdk) in clojure would benefit bioclipse, but that would probably be my first choice, rather than writing in java directly
07:04 olass I guess if you solved some problems, and porting to java/CDK would be simplified?
07:04 olass s/and/then
07:05 slyrus yes, or perhaps there would be a way for cdk/bioclipse to use what I might write in clojure. the interop stuff works both ways, which is nice.
07:06 slyrus otoh, if what I was doing were to be strictly in common lisp, that would be a non-starter, I imagine...
07:08 slyrus the missing pieces that I would like to see are: 1) better smiles parsing and 2-d drawing (chirality, configuration around double bonds) and 2) a molecule -> IUPAC name routine (I think the inverse sort of exists)
07:08 slyrus nice pdf output of multi-step reactions would be a big plus too
07:09 slyrus and you, what are you working on? :)
07:10 Gpox joined #bioclipse
07:15 olass slyrus: I am now more into applying Bioclipse for different drug discovery scenarios
07:15 olass integrate models for safety predictions etc
07:15 olass which requires Bioclipse to be continuously developed
07:16 slyrus Yeah, the 2 points I mentioned above are things that I think would make bioclipse work better for the drug discovery efforts i'm involved with
07:16 olass which are..?
07:17 olass your DD efforts I mean
07:17 slyrus small molecules that target the estrogen receptor
07:17 slyrus s
07:17 olass I see
07:28 CIA-71 bioclipse.ds: Ola Spjuth 2.4.x * ree673ae / features/net.bioclipse.ds_feature/feature.xml : Removed ADME endpoint from feature. - http://bit.ly/bickvJ
07:28 CIA-71 bioclipse.ds: Ola Spjuth master * ree673ae / features/net.bioclipse.ds_feature/feature.xml : Removed ADME endpoint from feature. (+29 more commits...) - http://bit.ly/bickvJ
07:32 CIA-71 bioclipse.balloon: Ola Spjuth 2.4.x * r9996995 / (3 files in 3 dirs): Removed hardcoded version dependency. - http://bit.ly/bELCl2
07:32 CIA-71 bioclipse.balloon: Ola Spjuth master * r9996995 / (3 files in 3 dirs): Removed hardcoded version dependency. (+7 more commits...) - http://bit.ly/bELCl2
07:39 abereles joined #bioclipse
07:42 edrin joined #bioclipse
07:42 edrin hi
07:42 zarah hi edrin
07:50 abereles left #bioclipse
08:19 jonalv joined #bioclipse
08:55 olass number_of_cups_coffe_today++
08:58 jonalv hm zarah how do you suggest we go about resettting that value at end of day?
09:08 s_wolf joined #bioclipse
09:38 masak joined #bioclipse
13:39 CIA-71 bioclipse.core: jonalv 2.4.x * rf88f75b / (2 files in 2 dirs):
13:39 CIA-71 bioclipse.core: Revert "changed rom deloped mode to release mode"
13:39 CIA-71 bioclipse.core: This reverts commit 54392a4a1f7cac6013a0f6fe9d4e172a7a9b1801.
13:39 CIA-71 bioclipse.core: So no we are back in development mode (+9 more commits...) - http://bit.ly/ccDTb0
13:39 CIA-71 bioclipse.core: jonalv master * rf58ccde / (107 files in 64 dirs): Merge branch '2.4.x' (+65 more commits...) - http://bit.ly/92aqOH
13:48 olass TADA! http://bioclipse.blogspot.com/20​10/07/bioclipse-24-released.html
13:48 zarah olass's link is also http://tinyurl.com/36dxlrm
13:50 edrin olass: site-of-metabolism prediction <- what does this mean?
13:52 olass edrin: see: http://www.biomedcentral.com/1471-2105/11/362
13:52 zarah olass's link is also http://tinyurl.com/2ww2byc
13:53 olass edrin: pinpoint at what atom metabolism occurs first in a molecule
14:09 CIA-71 bioclipse.balloon: Ola Spjuth master * rd16e472 / (3 files in 3 dirs): Removed hardcoded version dependency. - http://bit.ly/aGlnZj
14:09 CIA-71 bioclipse.balloon: Ola Spjuth 2.4.x * rd16e472 / (3 files in 3 dirs): Removed hardcoded version dependency. - http://bit.ly/aGlnZj
14:09 CIA-71 bioclipse.balloon: jonalv master * r3478967 / plugins/net.bioclipse.balloo​n.business/about.properties : removed build id from about.properties - http://bit.ly/9o9TP2
14:09 CIA-71 bioclipse.balloon: jonalv 2.4.x * r3478967 / plugins/net.bioclipse.balloo​n.business/about.properties : removed build id from about.properties - http://bit.ly/9o9TP2
14:09 CIA-71 bioclipse.balloon: Ola Spjuth master * rc18acea / (2 files in 2 dirs): Merge remote branch 'jonalv/2.4.0' into 2.4.x - http://bit.ly/alhsbQ
14:09 CIA-71 bioclipse.balloon: Ola Spjuth 2.4.x * rc18acea / (2 files in 2 dirs): Merge remote branch 'jonalv/2.4.0' into 2.4.x -
14:44 CIA-71 bioclipse.ds: Ola Spjuth 2.4.x * rb5a2474 / features/net.bioclipse.ds_feature/feature.xml : Removed ADME endpoint from feature. - http://bit.ly/9fjkOa
14:44 CIA-71 bioclipse.ds: jonalv 2.4.x * r5a1e286 / (2 files in 2 dirs): removed build id from about.properties - http://bit.ly/cbgu1h
14:44 CIA-71 bioclipse.ds: Ola Spjuth 2.4.x * rd68a8d3 / (16 files in 16 dirs): merge with jonalv/2.4.0 - http://bit.ly/aAuWMj
14:44 CIA-71 bioclipse.ds: Ola Spjuth master * rb5a2474 / features/net.bioclipse.ds_feature/feature.xml : Removed ADME endpoint from feature. - http://bit.ly/9fjkOa
14:44 CIA-71 bioclipse.ds: jonalv master * r5a1e286 / (2 files in 2 dirs): removed build id from about.properties - http://bit.ly/cbgu1h
14:44 CIA-71 bioclipse.ds: Ola Spjuth master * rd68a8d3 / (16 files in 16 dirs): merge with jonalv/2.4.0 - http://bit.ly/aAuWMj
14:55 CIA-71 bioclipse.qsar: Ola Spjuth 2.4.x * ra8926af / (5 files in 2 dirs): Updated cheatsheets in QSAR. - http://bit.ly/ds9k5x
14:55 CIA-71 bioclipse.qsar: jonalv 2.4.x * r711b0d7 / (2 files in 2 dirs): removed build id from about.properties - http://bit.ly/akoKC2
14:55 CIA-71 bioclipse.qsar: Ola Spjuth 2.4.x * rf1e7c23 / (13 files in 13 dirs): Merge remote branch 'jonalv/2.4.0' into 2.4.x - http://bit.ly/9lPWk3
14:55 CIA-71 bioclipse.qsar: Ola Spjuth master * rf1e7c23 / (13 files in 13 dirs): Merge remote branch 'jonalv/2.4.0' into 2.4.x (+26 more commits...) - http://bit.ly/9lPWk3
14:57 CIA-71 bioclipse.statistics: jonalv 2.4.x * r6e85ede / (5 files in 5 dirs): set version 2.4.0.20100709 - http://bit.ly/b6KIU6
14:57 CIA-71 bioclipse.statistics: jonalv 2.4.x * r53f4e62 / plugins/net.bioclipse.statistics/about.properties : removed build id from about.properties - http://bit.ly/aPnk0a
14:57 CIA-71 bioclipse.statistics: jonalv master * rfea3dcd / features/net.bioclipse.stat​istics_feature/feature.xml : Set version to 2.4.0.RC2 - http://bit.ly/d4TYAL
14:57 CIA-71 bioclipse.statistics: jonalv master * rc023bba / (5 files in 5 dirs): set version 2.4.0.RC3 - http://bit.ly/9nQhz7
14:57 CIA-71 bioclipse.statistics: jonalv master * r6e85ede / (5 files in 5 dirs): set version 2.4.0.20100709 - http://bit.ly/b6KIU6
14:57 CIA-71 bioclipse.statistics: jonalv master * r53f4e62 / plugins/net.bioclipse.statistics/about.properties : removed build id from about.properties - http://bit.ly/aPnk0a
15:23 samuell joined #bioclipse

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