| 2009-06-23 |
| → sneumann_ joined | 04:19 |
| ← sneumann left | 04:19 |
| → egonw joined | 05:29 |
| → sneumann__ joined | 05:39 |
| ← sneumann__ left | 06:11 |
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sneumann_
| morning | 07:08 |
|
egonw
| morning | 07:08 |
|
sneumann_
| moin | 07:08 |
|
zarah
| saluton sneumann_ | 07:08 |
|
egonw
| BC2 RC3 due today | 07:08 |
|
sneumann_
| :-) | 07:08 |
|
egonw
| almost done with my bug reports | 07:08 |
|
sneumann_
| Need more ? | 07:09 |
|
egonw
| will have Michel Dumontier as guest in our group Thursday | 07:09 |
|
| sure, bring them on | 07:09 |
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sneumann_
| only joking :-) | 07:09 |
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egonw
| Michel is a OWL guru | 07:09 |
|
| involved in bio2rdf on SourceForge | 07:09 |
|
| so, will brush up OWL in BC2 | 07:09 |
|
| and part of that | 07:09 |
|
| will work in a MetWare plugin for BC2 | 07:10 |
|
| finally | 07:10 |
|
sneumann_
| Ah. My questions would be about "inheritance" between our Concepts | 07:10 |
|
egonw
| right | 07:10 |
|
sneumann_
| if we want that, and if so, how to do that | 07:10 |
|
egonw
| not sure how much he worked with SKOS though | 07:10 |
|
| this ArMet design sucks | 07:10 |
|
| clearly made by non IT people | 07:10 |
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sneumann_
| Don't let Nigel hear that | 07:11 |
|
egonw
| at PRI we wanted the compatibility too... | 07:11 |
|
| I'm sure the covers the MRS | 07:11 |
|
| but | 07:11 |
|
| the model is not nice | 07:11 |
|
| OWL without SKOS could do much better | 07:11 |
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| MetWare 2 | 07:11 |
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sneumann_
| Nigel always touted ArMet as a "strawman" to get things started and to talk about | 07:12 |
|
egonw
| first I need to get myself to finish that bloody paper :( | 07:12 |
|
sneumann_
| which measn divergence is not a crime | 07:12 |
|
egonw
| true | 07:12 |
|
sneumann_
| and you can always say "modelled after ArMet Design" | 07:12 |
|
egonw
| try explain that to your peers behind the MS machines | 07:12 |
|
sneumann_
| Hollywood is doing all sorts of nasty things to books | 07:12 |
|
| Have the MS people ever submitted something ArMetty anywhere ? | 07:13 |
|
| We have two metware issues here | 07:13 |
|
| egonw has had way to many political meetings | 07:13 |
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egonw
| file them as bug reports please | 07:13 |
|
| everything you want me to look at... | 07:13 |
|
| with BC2.0.0 about out of the way | 07:14 |
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| I have more time for my own research interests... | 07:14 |
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sneumann_
| Ack | 07:14 |
|
egonw
| aka MS-based metabolomics | 07:14 |
|
| and metabolite identity in particular | 07:14 |
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sneumann_
| have you seen our MetFlow prototype ? | 07:14 |
|
egonw
| no, but I love a demo | 07:15 |
|
sneumann_
| http://msbi.ipb-halle.de/MetFlow/ | 07:15 |
|
zarah
| sneumann_'s link is also http://tinyurl.com/l56utv | 07:15 |
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sneumann_
| the "run workflow" is a bit hard to find, it is a button with screen width ... | 07:15 |
|
| it runs quite a while, because it has 3 external web ressources to call | 07:16 |
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| MassBank, PubChem, KEGG | 07:16 |
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egonw
| I've hit 'Start workflow' | 07:17 |
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sneumann_
| wait 2 mins | 07:17 |
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egonw
| but don't get confirmation it is running | 07:17 |
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sneumann_
| The button is greyed out ? | 07:17 |
|
egonw
| yes, it is | 07:17 |
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sneumann_
| If not, which browser ? | 07:17 |
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egonw
| I confused that for the HTML page bit being selected... | 07:17 |
| → s_wolf joined | 07:18 |
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sneumann_
| We don't (yet) have the Taverna callbacks with progress bar | 07:18 |
|
egonw
| can you have the button(?) title updated too, to, say, Running Workflow... | 07:18 |
|
| ? | 07:18 |
|
sneumann_
| Just told Michael | 07:18 |
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egonw
| OK, got results... | 07:18 |
|
| nice! | 07:19 |
|
sneumann_
| Especially the KEGG Pathways | 07:19 |
|
| with highlights | 07:19 |
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egonw
| can I bookmark this publically on delicious? | 07:19 |
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sneumann_
| Um, yes. | 07:19 |
|
| Currently Michael is working on | 07:19 |
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| the equivalent Workflow with | 07:20 |
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egonw
| really nice! | 07:20 |
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sneumann_
| http://msbi.ipb-halle.de/MetFrag/ | 07:20 |
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zarah
| sneumann_'s link is also http://tinyurl.com/mlamsj | 07:20 |
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egonw
| I never got around to but this fluent in JSF... | 07:20 |
|
| I never got around to *beÄ this fluent in JSF... | 07:20 |
|
| I never got around to *be* this fluent in JSF... | 07:20 |
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sneumann_
| Michael and Sebastion hacked together the prototypes in 2-3 weeks | 07:20 |
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egonw
| s_wolf++ | 07:21 |
|
| mgerlich++ | 07:21 |
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sneumann_
| Currently Michael is working on the equivalent Workflow with MetFrag | 07:21 |
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egonw
| link not found | 07:21 |
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sneumann_
| and then the combination of MetFrag + MassBank | 07:21 |
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egonw
| but I get the point :) | 07:21 |
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sneumann_
| Ahm, MetFrag is not yet public. | 07:21 |
|
| Give me an IP (or Range) and I can open it | 07:21 |
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egonw
| good question | 07:22 |
|
| egonw is looking up his new IP | 07:22 |
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egonw
| btw, this 3G broadband is great | 07:22 |
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sneumann_
| but your IP will be changing on each connect ? | 07:22 |
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egonw
| quite OK speed, ~2.3km from tower, receiver indoors, non-directed | 07:23 |
|
| dunno | 07:23 |
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sneumann_
| it will. | 07:23 |
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egonw
| and receiver is WLAN inside | 07:23 |
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sneumann_
| Do you have dyndns.org ? | 07:23 |
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egonw
| it has a battery! | 07:23 |
|
| I can take the WLAN along on holiday :) | 07:23 |
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sneumann_
| Your wife will love you for that ! | 07:23 |
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egonw
| no need for routers at the camping anymore | 07:23 |
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sneumann_
| Your neighbours will queue for that | 07:24 |
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| Do you have dyndns.org ? | 07:24 |
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egonw
| they can pay the camping :) | 07:24 |
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sneumann_
| Nice businness ahm, holiday plan ! | 07:24 |
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egonw
| Your IP Address Is: 91.149.41.229 | 07:24 |
|
| I let you know if it turns out to be dynamic :) | 07:25 |
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| I'm pretty sure it will change when I log in with this modem from Norway :) | 07:25 |
|
| from the camping | 07:25 |
|
| not sure about relog in... | 07:25 |
|
| or changing transmission tower | 07:25 |
|
| mmm... | 07:25 |
|
| bye bye ADSL | 07:26 |
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sneumann_
| http://msbi.ipb-halle.de/MetFrag/ should be open for you now | 07:26 |
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zarah
| sneumann_'s link is also http://tinyurl.com/mlamsj | 07:26 |
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sneumann_
| If you have a egonslaptop.dyndns.org that will be stable | 07:27 |
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egonw
| yes, I might think about that | 07:27 |
|
| I think I saw my router software support something like that | 07:28 |
|
| MetFrag is interesting... | 07:29 |
|
| ESI-backed? | 07:29 |
|
| ah, no | 07:29 |
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sneumann_
| CDK backed | 07:29 |
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egonw
| this is what came out of our pub talk! | 07:29 |
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sneumann_
| right! | 07:29 |
|
| There was a paper by Hill et al | 07:30 |
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| in 2008 who used MassFrontier | 07:30 |
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| to select all PubChem entries with matching | 07:30 |
|
| parent mass and subject them to MassFrontier for scoring | 07:30 |
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egonw
| nice 'Show Frags' pop up | 07:30 |
|
| needs a scrollbar though | 07:30 |
|
sneumann_
| unfortunately we don't have the Hill PubChem snapshot | 07:30 |
|
| so in 2009 we have ~5 times more potential parent masses to score | 07:31 |
|
egonw
| what's the DOI? | 07:31 |
|
sneumann_
| but if you use relative improvements, we're as good as MassFrontier | 07:31 |
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egonw
| I think I missed this paper | 07:31 |
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sneumann_
| s_wolf is at it | 07:32 |
|
| MetFrag is available as BioMoby service, | 07:32 |
|
egonw
| who should I ++ ? | 07:32 |
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sneumann_
| soon we'll have to find out about queueing systems | 07:32 |
|
| Sebastian :-) | 07:33 |
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egonw
| s_wolf++ | 07:33 |
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s_wolf
| hi egonw | 07:33 |
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egonw
| @karma s_wolf | 07:33 |
|
| hi :) | 07:33 |
|
zarah
| s_wolf has a karma of 2 | 07:33 |
|
s_wolf
| doi is: 10.1021/ac800548g | 07:33 |
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egonw
| s_wolf: thanx! | 07:34 |
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sneumann_
| Both MassBank and MetFrag are going to support mzAnnotate, or better | 07:34 |
|
| serve as Test-Bed ;-) | 07:34 |
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egonw
| cool | 07:35 |
|
s_wolf
| but I just compared to the results in the supporting info because there they didn't add any prior knowledge | 07:35 |
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egonw
| http://friendfeed.com/egonw/faf46379/metflow-taverna-workflows-in-web-browser-for | 07:37 |
|
zarah
| egonw's link is also http://tinyurl.com/lpd85z | 07:38 |
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egonw
| maybe I should subscribe to the Analytical Chemistry RSS ToC | 07:39 |
|
| but noise/value is so high :( | 07:39 |
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sneumann_
| Any clue how to get an RSS of AnalChem with additional search, such as "Mass Spectrometry" ? | 07:48 |
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egonw
| no | 07:48 |
|
| yahoo pipes could help here | 07:48 |
|
| but that requires to create an account | 07:48 |
|
| some Perl script would help too | 07:49 |
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sneumann_
| and different topic: | 07:49 |
|
| a while ago I had asked about webmeeting solutions, e.g. for a webinar | 07:49 |
|
| http://www.webconferencing-test.com/en/webconference_overview.html | 07:49 |
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zarah
| sneumann_'s link is also http://tinyurl.com/adhojy | 07:49 |
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sneumann_
| this is an overview of meeting offers, some of them are free. | 07:49 |
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egonw
| last time, we used Skype and desktop sharing | 07:49 |
|
| that worked pretty well | 07:49 |
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| 'we' -> Chris' and our teams | 07:50 |
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sneumann_
| which desktop sharing ? VNC ? | 07:51 |
|
egonw
| btw, getting quite addicted to the GMail keyboard shortcuts | 07:51 |
|
| damn, that makes reading email fast | 07:51 |
|
| mom, checking | 07:52 |
|
| good question | 07:53 |
|
| what was the name again... | 07:53 |
|
| delicious failing for me again :( | 07:57 |
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| I let you know when I remember | 08:00 |
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sneumann_
| RSS feeds filtered: | 08:05 |
|
| http://www.terkko.helsinki.fi/feednavigator/ | 08:05 |
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zarah
| sneumann_'s link is also http://tinyurl.com/c46s4w | 08:05 |
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egonw
| ah, nice! | 08:09 |
|
| metabolomics: http://www.terkko.helsinki.fi/feednavigator/export.php?my=dae352129 | 08:09 |
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zarah
| egonw's link is also http://tinyurl.com/kucr2v | 08:09 |
|
sneumann_
| MedWorm has some userrss as well: | 08:15 |
|
| http://www.medworm.com/rss/userss.php?qu=Metabolomics&ftc=79&title=MedWorm+Query%3A+Metabolomics | 08:15 |
|
zarah
| sneumann_'s link is also http://tinyurl.com/kt2gqt | 08:15 |
|
sneumann_
| were you able to create an RSS in feednavigator for | 08:16 |
|
| Selected Journals *plus* keyword searches ? | 08:16 |
|
egonw
| did not try that | 08:19 |
|
| 'metabolomics' for all journals seemed sufficient... | 08:19 |
|
| so lost interest in that combo | 08:19 |
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sneumann_
| It doesnt work as soon as you select "MyFeed only" | 08:19 |
|
| and I don't like (citations) which collects about everything ... | 08:20 |
|
| results in duplicates | 08:20 |
|
| Sascha arrived | 08:20 |
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egonw
| 'metabolomics' seems pretty sparse | 08:20 |
|
CIA-47
| metware: sneumann * r946 /ISAimport/trunk/src/main/org/metware/isaimport/IsaToClass.java: Automagically detect file.separator | 08:26 |
|
sneumann_
| We're just discussing metware | 08:29 |
|
| genotype has been renamed to organism at some stage in the past | 08:29 |
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egonw
| ha it? | 08:30 |
|
| that would not be entirely correct | 08:30 |
|
| there may be multiple genotypes for one organism | 08:30 |
|
| unles... | 08:30 |
|
| organism is considered an instance of a species... | 08:30 |
|
| mom... | 08:30 |
|
sneumann_
| Second: growth_environment has no connection to another table within the DB | 08:31 |
|
| Same for treatment. | 08:31 |
|
| We now have entries in these tables, not linked anywhere | 08:32 |
|
egonw
| about Organism... | 08:35 |
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sneumann_
| sf.net wikis are dead slow atm | 08:35 |
|
egonw
| it seems indeed to refer to a instance | 08:35 |
|
| yes, observed that for the CDK too :( | 08:36 |
|
sneumann_
| if we have an instance of an organism pushed into the MS machine | 08:37 |
|
| we should still have a collection of genotypes which are living as seeds | 08:37 |
|
| in the drawer, waiting for the growth location ;-) | 08:38 |
|
egonw
| or growth environment ? | 08:38 |
|
sneumann_
| ye | 08:39 |
|
| s | 08:39 |
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egonw
| those links must be added... | 08:43 |
|
| IIRC, growth environment is part of a protocol in the ArMet design | 08:43 |
|
| bugger... | 08:43 |
|
| I need diagrams | 08:44 |
|
sneumann_
| me too | 08:45 |
|
| I have the postgres snapshot | 08:45 |
|
| http://msbi.ipb-halle.de/~sneumann/metware/postgresschema.pdf | 08:45 |
|
egonw
| yes, that's in front of me too... | 08:45 |
|
zarah
| sneumann_'s link is also http://tinyurl.com/m6ugoo | 08:45 |
|
egonw
| well: http://sourceforge.net/apps/mediawiki/metware/nfs/project/m/me/metware/b/b1/Dbdesigner12.png | 08:46 |
|
| that one actually | 08:46 |
|
zarah
| egonw's link is also http://tinyurl.com/l22af8 | 08:46 |
|
egonw
| I hate the 'protocol' blob | 08:49 |
|
| does not differentiate between the operations the protocol describes | 08:49 |
|
| I also note that the PgSQL does not have a direct link between sample and analysisMaterial | 08:50 |
|
| which the DBdesigner has | 08:50 |
|
| but the growthEnvironment is equally nasty | 08:51 |
|
| the metware:Organism (skos:broader armet:Genotype) is confusing | 08:51 |
|
| (next time slap me in the face, when we go along with people insisting on ArMet compatibility) | 08:52 |
|
| the metware:Organism (skos:broader armet:Genotype) is confusing ... | 08:52 |
|
| it is in the middle of a concept of a species-like thing | 08:52 |
|
| and an instance | 08:52 |
|
| growthEnvironment is definately on the level of instance | 08:52 |
|
| in the earlier DBDesigner, the growthEnvironment would have been linked to AnalysisMaterial | 08:54 |
|
| because: | 08:55 |
|
| the analysis material was extracted from an organismInstance (or GenotypeInstance) which was grown in GrowthEnvironment | 08:55 |
|
sneumann_
| sounds like some reorganisation in the SKOS ... | 09:14 |
|
| I'd like to see more "event" which link-in a "protocol" being applied | 09:15 |
|
| at a certain time | 09:15 |
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egonw
| fully agreed | 09:15 |
|
CIA-47
| metware: sneumann * r947 /ISAimport/trunk/src/main/org/metware/isaimport/IsaToClass.java: Clarify some more mappings | 09:40 |
|
sneumann_
| just came across one of these MOLGENIS object models: | 10:13 |
|
| http://gbicserver1.biol.rug.nl:8080/xgap4exampledatasets/doc/objectmodel.html | 10:13 |
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zarah
| sneumann_'s link is also http://tinyurl.com/mym3vb | 10:13 |
| → jerzyo joined | 10:15 |
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egonw
| hi jerzyo | 10:16 |
|
jerzyo
| hi | 10:17 |
|
zarah
| ni hao jerzyo | 10:18 |
|
jerzyo
| The meeting you e-mailed on the list was yesterday 16:30 (Halle, CEST) OR today? | 10:19 |
|
sneumann_
| please, not another typo in my mail... checking | 10:19 |
|
| Tuesday, 16:30 | 10:20 |
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| I just sent around the "relocation" to #taverna. Somehow #metware was all over my mind :-( | 10:20 |
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egonw
| sneumann_++ | 10:23 |
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jerzyo
| I am new to IRC | 10:23 |
|
| Is this on taverna or on metware | 10:24 |
|
| ? | 10:24 |
|
sneumann_
| no problem. Your IRC client should have "Join channel" somewhere, and just go to "#taverna" | 10:24 |
|
egonw
| this is the #metware channel | 10:24 |
|
sneumann_
| here is #metware | 10:24 |
|
jerzyo
| And BTW what #metware is about? | 10:24 |
|
egonw
| see metware.org | 10:24 |
|
| metabolomics | 10:25 |
|
sneumann_
| metware.org is a collection of projects | 10:25 |
|
| aimed at metabolomics databases, services and workflows. | 10:25 |
|
jerzyo
| It seems you have some RAW data | 10:26 |
|
| Is there any access to it? | 10:26 |
|
sneumann_
| What kind of are you talking about ? | 10:26 |
|
| Xcalibur .RAW files ? | 10:27 |
|
mgerlich
| eqonw: the start worklflow button now changes to "workflow running" and then switches to "workflow finished" | 10:30 |
|
egonw
| great! | 10:32 |
|
jerzyo
| Well, I am searching for text files wiith biological data in many formats | 10:33 |
|
egonw
| with what goal? | 10:33 |
|
jerzyo
| Get some training data for students | 10:35 |
|
egonw
| why text files? | 10:36 |
|
CIA-47
| metware: sneumann * r948 /BigMet/trunk/src/main/resources/metware.skos: Added machine setup as field to run | 10:36 |
|
jerzyo
| because they are easier to handlethan binary files | 10:49 |
|
| there are plenty of different formats | 10:50 |
|
egonw
| yes | 10:50 |
|
| what programming language will the students use? | 10:50 |
|
jerzyo
| and they are much more difficult to handle than XML | 10:50 |
|
| Python | 10:50 |
| → sneumann__ joined | 12:18 |
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egonw
| sneumann__: ping | 12:28 |
|
| first iterating in BC2 would be single database... | 12:28 |
|
| does that make sense? | 12:28 |
|
| that is, directly on MySQL... | 12:28 |
|
| grabbing content from other DBs via RDF is scheduled for later... | 12:28 |
| ← sneumann__ left | 12:55 |
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sneumann_
| egonw: pong | 14:16 |
|
egonw
| :) | 14:16 |
|
| yeah, it's a long distance :) | 14:17 |
|
CIA-47
| metware: sneumann * r949 /ISAimport/trunk/src/main/org/metware/isaimport/IsaToJava.java: Removed one of the early prototypes | 14:28 |
|
jerzyo
| Got to go | 15:26 |
|
| bye | 15:26 |
| ← jerzyo left | 15:26 |
|
| egonw is commiting the intial Bioclipse plugin code | 15:57 |
|
egonw
| took me some time to get the preference page working correctly :( | 15:57 |
|
| now setting up a bioclipse manager for Metware | 16:07 |
|
| INFO - Bioclipse manager: metware added to Javascript environment | 16:16 |
|
| :) | 16:17 |
| → sneumann__ joined | 17:18 |
|
CIA-47
| metware: SaschaRichter * r950 /ISAimport/trunk/src/main/org/metware/isaimport/IsaToClass.java: | 17:54 |
|
| metware: "line.separator-problem" solved. | 17:54 |
|
| metware: (Had nothing to do with line.separator but with counting lines.) | 17:54 |
|
sneumann__
| egonw: still around ? | 18:16 |
|
| I'd like to see how to push the SKOS -> SQL DDL generation step. | 18:16 |
|
| Either with or without the BioMart support. | 18:17 |
|
| Preferrably with. | 18:17 |
|
egonw
| back | 18:30 |
|
| not sure for how long... | 18:30 |
|
| starting to feel ill | 18:30 |
|
sneumann__
| Question is | 18:32 |
|
| whether we try to generate the SQL purely from Concepts | 18:33 |
|
| or add some SKOS annotation that helps SQL | 18:33 |
|
egonw
| as we did so far... (?) | 18:33 |
|
| we currently use some annotation | 18:33 |
|
sneumann__
| hm, the <metware> tags were the _only_ hint for the SQL | 18:33 |
|
egonw
| I remember we talked about trying to remove that annotation | 18:33 |
|
sneumann__
| exactly | 18:33 |
|
egonw
| yes, but an important hint | 18:34 |
|
| it is currently used to decide what belongs to which table | 18:34 |
|
| and what the field names are | 18:34 |
|
| which was needed for the biomart compatibility | 18:34 |
|
sneumann__
| one idea we had was that every concept below the collection becomes a table | 18:34 |
|
| and every concept below the table becomes a field | 18:34 |
|
egonw
| right | 18:35 |
|
sneumann__
| which breaks if we leave that somple scheme | 18:35 |
|
| what's missing is a hint | 18:35 |
|
| whether we have 1:1 1:n or n:m relations between concepts | 18:35 |
|
| every 1:1 can become a field | 18:35 |
|
| every 1:n becomes a link | 18:35 |
|
| and every n:m needs a "koppeltabelle" | 18:35 |
|
egonw
| rdf:type sql:Table etc? | 18:36 |
|
sneumann__
| that is very explicit. | 18:36 |
|
| it talks about SQL tables | 18:36 |
|
egonw
| yes | 18:36 |
|
sneumann__
| and won't help if we want to use the information | 18:37 |
|
| also e.g. for the JSF pages or Java Beans | 18:37 |
|
egonw
| true | 18:37 |
|
| mom | 18:37 |
|
| check the metware.skos | 18:37 |
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sneumann__
| Cardinality between concepts | 18:37 |
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egonw
| i added some OWL axioms | 18:37 |
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sneumann__
| similar to broader | 18:37 |
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egonw
| right | 18:38 |
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| we could have a field have a skos:broader to another table... | 18:38 |
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| but the trick would be too see ... | 18:38 |
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| which of the two or more (because Armet is a broader too), is the table pointed too | 18:39 |
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| instead of the table to which the field belongs to itself | 18:39 |
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| we could subclass skos:broader | 18:39 |
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| into metware:propertyOf | 18:40 |
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| and metware:pointsTo | 18:40 |
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| or refersTo | 18:40 |
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| refersToA perhaps | 18:40 |
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sneumann__
| makes sense | 18:40 |
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| this will allow more idioms checking | 18:41 |
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| and is more in line with SKOS thinking | 18:41 |
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egonw
| yes | 18:41 |
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sneumann
| get better, see you | 19:57 |
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| steffen | 19:57 |
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| ← egonw left | 21:51 |
