Camelia, the Perl 6 bug

IRC log for #bioclipse, 2010-03-15

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All times shown according to UTC.

Time Nick Message
06:11 sneumann joined #bioclipse
06:29 egonw joined #bioclipse
07:02 annzi joined #bioclipse
07:49 egonw annzi: when are you away for canada exactly?
07:51 annzi egonw: I will leave 31 Mars and be back 29 April(and start working again 3 May)
07:51 egonw ack, me is adding note to agenda
07:51 annzi egonw: when will you be on summer vacation?
07:52 egonw 30 juni - 21 july
08:01 olass joined #bioclipse
08:03 Gpox joined #bioclipse
08:10 s_wolf joined #bioclipse
08:12 egonw annzi: had I asked you to write up some text about your SPARQL queries for Maris and Martin?
08:12 egonw annzi: or have I forgotten that?
08:12 annzi egonw: no you have not
08:13 egonw do you have time right now to write up a paragraph on that?
08:14 annzi what is the aim?
08:15 egonw to briefly describe the two SPARQL queries
08:16 annzi ok
08:16 annzi I'm on it
08:20 egonw the paper is quite long...
08:20 mgerlich joined #bioclipse
08:20 egonw really takes a lot of time...
08:20 egonw not all is in, and at 25 pages already ...
08:20 * egonw is happy BioMed Central does not charge per page :)
08:21 olass egonw: will you send a proof today?
08:21 egonw yes, before lunch I am hoping...
08:21 egonw now working on your section, then martin's and annzi's...
08:21 olass nice
08:21 egonw Maris' part I have not received yet
08:22 egonw the formatted version without images is 8 pages :)
08:23 egonw changing the title of the paper
08:27 * egonw is still disappointed that we cannot calculate macromolecular descriptors in Bioclipse yet...
08:27 egonw what is that about??
08:33 Gpox joined #bioclipse
08:47 sneumann joined #bioclipse
09:01 sneumann joined #bioclipse
09:12 annzi egonw: do you know what question maris chosen to work with?
09:14 egonw don't worry about that part
09:14 egonw it's up to me to glue things together
09:14 masak joined #bioclipse
09:16 * egonw is hacking on the from new QSAR from chEMBL wizard
09:17 annzi eognw: oh you won't have the queries in the same place? so I should write two independent texts...
09:22 egonw yes
09:23 egonw this (your) section will show how SPARQL is used to aggregate data for futher processing
09:23 egonw then comes Ola's section on molecular descriptor calculation
09:23 egonw and the bits from Maris and Martin
09:28 egonw OK, done hacking on the from chEMBL wizard...
09:28 egonw let's see if it still works :)
09:29 egonw if it does, it will query the RDF sparql end point and show target info in the wizard and update the list of activities
09:30 egonw cool!
09:30 egonw it's even pretty fast :)
09:30 egonw a thread would be better
09:30 egonw but I won't care about that right now
09:31 egonw this is so damn cool
09:35 egonw olass: ping
09:35 egonw olass: how do I do a proper new line in the wizard
09:36 olass pong
09:37 olass new line?
09:37 egonw yeah, targetID + act on first line
09:37 olass line?
09:37 egonw other Label's on lines below it
09:37 olass are you talking about laying out GUI elements?
09:38 olass http://www.eclipse.org/articles/article.php?f​ile=Article-Understanding-Layouts/index.html
09:38 zarah olass's link is also http://tinyurl.com/nkbykf
09:38 olass if so, this link is super
09:38 olass if not, please explain more...
09:38 egonw yeah, that should do
09:39 egonw I suck at making GUIs
09:39 egonw and I don't really want to learn either
10:02 jonalv joined #bioclipse
10:15 sneumann BioClipse should have an every-now-and-then GUI overhaul by somebody
10:16 sneumann who needn't know bioinformatics, but is proficient with eclipse GUIs
10:16 sneumann maybe on a contract basis ?
10:16 jonalv sneumann: did you have something particular in mind?
10:16 sneumann no
10:16 sneumann just because I can follow egonw s last comment ;-)
10:16 sneumann just because I can follow egonw s last comment :-(
10:17 jonalv what was egonws last comment?
10:17 sneumann " I don't really want to learn either"
10:17 jonalv gui programming?
10:17 sneumann hm
10:20 egonw jonalv: hahahaha
10:20 jonalv egonw: huh?
10:20 egonw oh, I'd love to have someone work on those details, so that I can focus on the algorithms
10:21 * masak too
10:28 * egonw is subscribed to the tweets of an astronaut circling around the earth in the ISS
10:28 * egonw is getting tweets from outer space :)
10:28 egonw I find this concept rather amusing and quite cool
10:30 jonalv yea I did that when our swedish astronaut was out there :)
10:30 jonalv it can be quite intresting
10:30 egonw swedish astronaut?
10:30 egonw they exist?
10:31 egonw nice
10:31 jonalv http://en.wikipedia.org/wiki/Christer_Fuglesang
10:31 zarah jonalv's link is also http://tinyurl.com/y5qmek
10:31 egonw perhaps we should write a grant application to test the speed up of Bioclipse development in zero gravity ...
10:33 olass joined #bioclipse
10:34 egonw almost done with the new FromChEMBL QSAR wizard
10:39 olass egonw: send me a pull request or patches when done
10:39 egonw sure
11:09 CIA-60 bioclipse.rdf: Egon Willighagen master * r46e9f65 / (3 files in 2 dirs): Added method to get the properties of a target: organism, title, and type - http://bit.ly/aNe4Z0
11:11 egonw olass: patch sent
11:20 CIA-60 bioclipse.qsar: Egon Willighagen master * r4c9c755 / (2 files in 2 dirs): Interactively provide the user information about the chosen target, and updating the list of available activities - http://bit.ly/ax2WY7
11:32 samuell joined #bioclipse
11:44 egonw http://chem-bla-ics.blogspot.com/2010/03​/rdf-powered-qsar-wizard-sparql-end.html
11:44 zarah egonw's link is also http://tinyurl.com/yc9m49q
11:55 annzi joined #bioclipse
12:17 jpansanel joined #bioclipse
12:17 jpansanel moin
12:17 zarah oh hai jpansanel
12:17 jpansanel bioclipse.net does not work anymore ??
12:59 egonw jpansanel: I cannot confirm... it works for me
13:10 jpansanel may be a dns pb on my side
13:10 egonw nslookup ?
13:10 egonw or dig ?
14:19 jpansanel 195.47.247.86 for bioclipse.net
14:19 jonalv joined #bioclipse
14:21 egonw jpansanel: ah, so it does find the host
14:33 * egonw is afk, bbl
15:25 samuell joined #bioclipse
15:43 sneumann Hi,
15:43 sneumann has anyone done something like a KEGG importer for BC ?
15:44 * sneumann is looking for a small-ish student project
15:44 sneumann i.e. convert KEGG Reactions into CML reactions,
15:44 sneumann list all the compounds etc.
15:45 jonalv sneumann: I don't think Jchempaint supports reqctons, (but I could be wrong)
15:46 sneumann the old one did
15:46 sneumann http://sourceforge.net/apps/mediawiki/metwa​re/index.php?title=MzAnnot_UseCases#Spectra​l_Trees_with_assigned_Fragmentation_Pattern
15:46 zarah sneumann's link is also http://tinyurl.com/ycouakr
15:46 sneumann image at lower right
15:46 jonalv maybe it does then
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19:16 CIA-60 bioclipse.qsar: Ola Spjuth master * r2f97b58 / (3 files in 2 dirs): Added a 'removeStructuresWithErrorAction'. - http://bit.ly/cqft03
22:43 samuell joined #bioclipse

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