Camelia, the Perl 6 bug

IRC log for #bioclipse, 2010-09-15

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All times shown according to UTC.

Time Nick Message
05:44 egonw joined #bioclipse
06:07 egonw moin
06:07 zarah hello egonw, you fantastic person you
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08:37 jonalv oh hai
08:37 zarah oh hai jonalv
08:39 sneumann_ @seen samuell
08:39 zarah samuell was last seen 14 h 34 m 22 s ago in #bioclipse saying 'http://stackoverflow.com/questions/3711​520/how-to-convert-a-string-to-an-input​stream-in-bioclipse-javascript-editor'
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08:51 sneumann zarah: tell samuell he could check whether http://www.wikipathways.org is already semantified, it'd be a cool use case, together with e.g. http://metabolomics.jp/wiki/Index:MassBank The latter is by Masanori Arita, if you had requirements I can talk to him
08:51 zarah Consider it noted.
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10:59 sneumann hi samuell
10:59 samuell hi sneumann
10:59 zarah samuell: You have new messages. Write '/msg zarah @messages' to read them.
10:59 sneumann Indeed :-)
11:00 sneumann egonw might want to listen in ...
11:01 samuell sneumann: Yeah, thanks for the message, maybe I should paste it here again
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11:02 edrin hi
11:02 zarah saluton edrin
11:02 samuell 4 h 25 m 26 s ago, egonw said please reply to http://cliqset.com/mndoci/entry/nBLa4sBBhC7wlQee
11:02 samuell 2 h 8 m 14 s ago, sneumann said he could check whether http://www.wikipathways.org is already semantified, it'd be a cool use case, together with e.g. http://metabolomics.jp/wiki/Index:MassBank The latter is by Masanori Arita, if you had requirements I can talk to him
11:02 samuell Oops, skip the first line
11:03 samuell sneumann: Thanks, will check that up! I think egonw is the one to make final decisions though :)
11:09 egonw samuell: we'll go for this malaria/drug-toxicity data first... as we have plenty of ready to use data there...
11:09 egonw samuell, sneumann: but would very much like to keep thinking about metabolomics too... but that would be a separate paper
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11:13 samuell yeah, there should be much interesting stuff that can be done with the bioclipse / smw combo
11:15 sneumann samuell : can you give me an example what semantic malaria wiki data can be used in which way ?
11:15 sneumann Do you already have a blog snippet on that ?
11:17 samuell sneumann: I don't think we have much yet ... but hopefully within this month or so
11:17 samuell If not egonw has some kind of snippet?
11:17 egonw sneumann: http://drugmet.rilspace.org/wiki/Cortisone
11:18 egonw sneumann: a lot of data is added as RDF triples
11:18 egonw which will show up in the 'Facts' box...
11:18 egonw the idea is that after that, the curators jump in and start adding further annotation, like the InChI in the 'plain text' of the wiki
11:18 egonw as in the cortisone example
11:19 egonw samuell: we need to extend this example with a simple 'Box'
11:19 * samuell realizes he has some bioclipse js code for querying the wiki
11:19 samuell egonw: Template you mean?
11:19 samuell Some formatting would be nice indeed
11:20 egonw sneumann: such a box could, for example, annotate the paper where the metabolite was first characterized
11:20 egonw samuell: yeah, like http://en.wikipedia.org/wiki/Template:Chembox
11:21 samuell egonw: Indeed
11:22 egonw sneumann: so, where do the semantics come in on the wikipathways.org site?
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11:26 egonw hi maclean
11:26 maclean hi
11:26 zarah oh hai maclean
11:26 sneumann no clue, I just came across this. I was thinking/hoping, that one could mimick
11:26 sneumann the linking between the pathways and massbank, similar how we did that previously (manually)
11:27 egonw ack
11:27 maclean technically java : http://gist.github.com/580595
11:27 maclean :)
11:27 sneumann with Taverna using KEGG and MassBank SOAP Services.
11:27 sneumann So, if Bioclipse + smw + wikipathwas + wikimassbank could do the trick,
11:27 sneumann that'd be a cool use case
11:27 sneumann Think annotation a whole-genome Metabolite Profile
11:29 samuell sneumann, egonw: Quick little Bioclipse script I made yesterday, which downloads RDF from SMW (Semantic MediaWiki) to a local file, and then queries this data with SPARQL:
11:29 samuell http://gist.github.com/580590
11:30 samuell (Not too fancy yet, but just to show what you can do now)
11:31 * sneumann does not have a current BC installation :-(
11:31 samuell sneumann: Yeah, well, the script requires some bleeding edge versions of some plugins, so not too smooth to install yet
11:32 samuell ... so, just to give an idea.
11:33 egonw sneumann: what's the MyExperiment.org ID for the taverna workflow?
11:33 egonw sneumann: could be cool to write that as BSL script
11:33 egonw BC can call SOAP services, though I would need to ask Ola about the details...
11:36 sneumann mgerlich has quote a range of Workflows
11:37 sneumann http://www.myexperiment.org/users/937/workflows
11:37 sneumann actually we used the BioMoby service for MassBank
11:37 sneumann But really, these suggestions are just "You've got the tool, we've got a problem"
11:38 egonw yeah, bioclipse does feel like that
11:38 egonw sorry about that, I guess
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12:29 sneumann samuell , would this one be a pool for many concepts ?
12:29 sneumann http://www.conceptwiki.org/
12:29 sneumann Although I was unable to find any RDF in there ...
12:31 maclean huh. apparently I am a concept.
12:31 maclean http://www.conceptwiki.org/​index.php/Concept:113547312
12:32 maclean !! Concepts of interest : "Obesity"
12:32 maclean how very dare you, etc.
12:32 egonw conceptwiki was recently funding with *big* money
12:32 egonw we'll see plenty of conceptwiki in the next years
12:32 egonw samuell: I should email Barend Mons about your work...
12:35 egonw samuell: do you fancy Rotterdam?
12:35 samuell egonw: ?
12:36 egonw I think they might be looking for PhD students...
12:36 samuell sneumann: Sorry, didn't understand the question? :)
12:36 samuell egonw: Ah, :) ...well ...
12:39 maclean bloody thing won't let me claim my own page. grrr.
12:39 maclean oh well, back to something useful.
12:39 samuell sneumann: Yeah, not sure if they are using Semantic MediaWiki, or rather some own MediaWiki extensions
12:42 sneumann samuell I was just throwing around pointers, hoping to increase the number of sources you could integrate
12:42 sneumann and hoping that some which are of interest to me might be included in the long term :-)
12:42 samuell This page tells they are not using SMW (and also use quite an outdated MediaWiki, huh ... ) http://www.conceptwiki.org​/index.php/Special:Version
12:42 samuell sneumann: Yeah, IC :)
12:43 egonw samuell: I'm making contact with Barend ... I'
12:43 egonw samuell: I'm making contact with Barend ... I'll get back on ConceptWiki
12:43 egonw btw, Antony Williams (ChemSpider) is also involved in ConceptWiki
12:44 samuell sneumann: There's a list of geneWikis here: http://en.wikipedia.org/wiki/​Portal:Gene_Wiki/Other_Wikis
12:44 samuell know any of them?
12:44 samuell those
12:48 samuell (but never mind ...  of course you already mentioned the ones interested to you ... but that might be a useful list in general )
12:49 samuell egonw: Ok!
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13:38 CIA-58 bioclipse.brunn: jonalv master * r6c371cf / (6 files): fixed bug with parameters in jasper subreports - http://bit.ly/bdvqn5
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13:57 samuell egonw: JFYI: Jena doesn't seem to support SPARQL/Update for remote services ... so have mailed on jena-dev and awaiting answer.
13:58 samuell (In the worst case we'll have to roll an own query method ... might be also that ARC's SPARQL+ is not fully compatible with ARQ's SPARQL/Update. But will see what they say first.)
13:58 CIA-58 bioclipse.brunn: jonalv master * re024ab5 / (2 files in 2 dirs): Merge remote branch 'claes/master' - http://bit.ly/9zVDzR
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14:08 CIA-58 bioclipse.brunn: jonalv master * r2576e8f / (32 files in 8 dirs): Merge remote branch 'claes/masterPlateCopy' - http://bit.ly/drwOrP
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14:43 samuell jonalv: Do you have links to the mediawiki syntax editor, and the basic xml editor for Eclipse, that we thought to use in the documentation publishing project?
14:44 samuell (I guess the XML-editor is not the same as "XML-lite" which is available on right-click in Bioclipse?)
14:45 * samuell grabs a coffe, brb
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14:52 egonw samuell: indeed it is not
14:52 egonw samuell: best to use the xml editor from Web Tools Package
14:53 egonw with XML Schema (and thus validation and autocomplete) support...
14:58 jonalv samuell: ask Gpox
14:59 samuell egonw, jonalv: Ok
15:00 samuell Ok, the XML editor I should find, knowing it is in Web Tools Package
15:00 samuell and maybe there are not too many mediawiki editors for Eclipse either ^^
15:01 Gpox samuell: http://www.eclipse.org/mylyn/ (WikiText)
15:02 samuell Gpox: Thanks!
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15:09 samuell jonalv, Gpox; We were talking about the rich text editor, right (it was a GSoC2010 project, cool)
15:09 samuell http://wiki.eclipse.org/Mylyn/Rich_​Editor_For_Wiki_Markup#Deliverables
15:09 samuell http://wiki.eclipse.org/Mylyn​/Rich_Editor_For_Wiki_Markup
15:10 jonalv samuell: I don't know bt I guess so
15:14 samuell jonalv: ok
15:14 samuell Well, seems to be an extension to the basic mylyn/wikitext thing, but could be nice of course ...
15:15 samuell Seems like ppl have done similar things before, btw: http://fsteeg.wordpress.com/2010/03​/14/generating-documentation-from-a​-wiki-with-ant-and-mylyn-wikitext/
15:15 zarah samuell's link is also http://tinyurl.com/3yxc3ud
15:16 samuell (though we're going the other way around, "eclipse -> wiki" rather than "wiki -> eclipse" )
15:19 samuell Well, seems like the wiki -> eclipse pathway is a lot more supported ... https://bugs.eclipse.org/b​ugs/show_bug.cgi?id=242979
15:20 samuell They seem to be using this in the eclipse project themselves, and specifically use MediaWiki as well ... hmm ...
15:31 egonw samuel -> http://triplemap.com/
15:33 samuell egonw: Requires trial code :/
15:33 samuell Something to watch though, I guess
15:34 egonw yeah, indeed
15:36 samuell Any naming convention for Eclipse plugins for Bioclipse development? (I'm creating one now)
15:37 samuell ... since it's not a bioclipse plugin, should it be named net.bioclipse .... anyway?
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15:37 egonw yahoo... just been called a hero :)
15:37 egonw I love such conference calls :)
15:38 samuell :)
15:38 egonw this triplemap demo will use 'our' chembl rdf :)
15:38 samuell Cool!
15:39 jonalv egonw++ //for being a hero
15:39 jonalv samuell: did you see my anser on stackoverlow?
15:39 samuell jonalv: Not yet, checking ...
15:40 samuell jonalv++
15:40 samuell Nice!
15:41 samuell Btw, I found it a bit confusing that ui.newFile() takes a string, while there is no ui.[***] method to update a file, from a string ... (?)
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15:43 * jonalv did not write the ui manager
15:43 jonalv I think that was masak...
15:43 jonalv samuell: feel free to file bug reports though off course :)
15:43 masak me and olass, yes.
15:44 samuell yeah, true :)
15:45 samuell pele to be up'n running soon?
15:46 samuell or, bugzilla, I mean
15:49 jonalv oh right...
15:50 egonw I hope tomorrow
15:54 samuell ok
15:55 egonw will be at BMC early... I think 8:30 or so...
15:56 samuell btw, what is your views on what is the best place to create the original documentation, the wiki, or some source files in eclipse?
15:56 egonw my views?
15:56 samuell Yeah, all of yours
15:56 egonw on what you are doing? don't know enough about that yet... brief me tomorrow
15:56 samuell egonw, jonalv, masak, Gpox, olass etc
15:57 samuell Ok
15:57 samuell Well, we are looking to avoid duplication of documentation on the wiki, and in the source files
15:58 egonw yeah, indeed
15:58 samuell So question is whether to create docs in wiki and import, or the other way around
15:58 samuell The first one seems much more supported, and used by eclipse project already
15:59 samuell but there might be more pros/cons
15:59 jonalv samuell: please move this discussion to e-mail. I can't give you my undivided attention for the moment...
15:59 samuell jonalv: Ok, sure
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16:30 edrin ciao
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