From bgulden at purdue.edu Wed Jun 1 13:16:42 2005 From: bgulden at purdue.edu (bgulden@purdue.edu) Date: Wed Jun 1 13:13:15 2005 Subject: [MOBY-l] Parameters for services Message-ID: <1117646202.429ded7a59449@webmail.purdue.edu> Is there any way to determine dynamically the parameters that a given service can take? For example, if I have a service that can run blastp or blastn, could I have a parameter that would determine which one to run or would they be better described as two entirely different services? Also, a blast service could have other options that could be set. Would those options be placed in the "input" section of the service description? Thanks for any help, Brian Gulden From bmg at sfu.ca Wed Jun 1 19:08:41 2005 From: bmg at sfu.ca (Benjamin Good) Date: Wed Jun 1 19:02:22 2005 Subject: [MOBY-l] Parameters for services In-Reply-To: <1117646202.429ded7a59449@webmail.purdue.edu> References: <1117646202.429ded7a59449@webmail.purdue.edu> Message-ID: <429E3FF9.3000802@sfu.ca> In short, yes Search for "Secondary Parameters" here http://www.biomoby.org/twiki/bin//view/Moby/MobySAPI You may find the service registration applet informative as well - http://mobycentral.cbr.nrc.ca/applets/ sorry I can't offer a more detailed explanation right now -ben bgulden@purdue.edu wrote: >Is there any way to determine dynamically the parameters that a given service >can take? For example, if I have a service that can run blastp or blastn, could >I have a parameter that would determine which one to run or would they be better >described as two entirely different services? Also, a blast service could have >other options that could be set. Would those options be placed in the "input" >section of the service description? >Thanks for any help, >Brian Gulden > > >_______________________________________________ >moby-l mailing list >moby-l@biomoby.org >http://biomoby.org/mailman/listinfo/moby-l > > > > From edward.kawas at gmail.com Thu Jun 2 16:25:50 2005 From: edward.kawas at gmail.com (Eddie Kawas) Date: Thu Jun 2 16:21:49 2005 Subject: [MOBY-l] Prototype Biomoby Taverna Plugin Message-ID: <429f6b52.3015ac83.0158.38da@mx.gmail.com> Hi, http://bioinfo.icapture.ubc.ca/ekawas/biomobyPlugin.zip The above link is to a zip file consisting of 6 jar files. If you place these jar files in the lib directory, where you installed Taverna, typically /taverna-workbench-1.1/lib/ and you delete /taverna-workbench-1.1/lib/jmoby.jar, you *may* have new and improved Moby support for Taverna. The reason that I say may have, is because I have only tried this on my windows machine. Note that right now, the plugin only queries the Mobycentral registry. You can still ask it to use yours, but it will not work 100%. Also note that the local widgets do not work (well, that's a lie, the create collection widget works). http://bioinfo.icapture.ubc.ca/ekawas/workflow.xml http://bioinfo.icapture.ubc.ca/ekawas/workflowInput.xml Above is are urls to a workflow definition file (you can load it into Taverna) as well as its inputs, as an example of how to use the plugin. I have added some context (right) click information to Moby objects and services. You can try this from the window labeled 'Advanced Model Explorer'. Basically, right-click a Moby related object or service instance from the 'Processors' list and choose either 'Moby Object Details' or 'Moby Service Details'. I am interested in all feedback both good and bad. I still have a lot to do, but I figure that the more eyes trying (testing) will help me make it better. This is a working prototype, in the spirit of BioMoby ;-) If I make significant changes, I will let you know. Thanks, Eddie Kawas edward.kawas@gmail.com From tmo at ebi.ac.uk Thu Jun 2 17:34:54 2005 From: tmo at ebi.ac.uk (Tom Oinn) Date: Thu Jun 2 17:26:50 2005 Subject: [MOBY-l] Prototype Biomoby Taverna Plugin In-Reply-To: <429f6b52.3015ac83.0158.38da@mx.gmail.com> References: <429f6b52.3015ac83.0158.38da@mx.gmail.com> Message-ID: <429F7B7E.2070900@ebi.ac.uk> Eddie Kawas wrote: > Hi, > > http://bioinfo.icapture.ubc.ca/ekawas/biomobyPlugin.zip > > The above link is to a zip file consisting of 6 jar files. > If you place these jar files in the lib directory, where you > installed Taverna, typically /taverna-workbench-1.1/lib/ and > you delete > /taverna-workbench-1.1/lib/jmoby.jar, > you *may* have new and improved Moby support for Taverna. > The reason that I say may have, is because I have only tried > this on my windows machine. Eddie - I get 'no such method' errors here, do you have any XML APIs in your system classpath (/jre/lib/ext and friends) and which version of Java are you using? I'm running a clean install (yesterday) of WinXP SP2 with Java5 SDK. Looks promising though - we're going for a Taverna 1.2 release in two weeks time so with a bit of luck this will all be there for ISMB / BOSC :) Tom From edward.kawas at gmail.com Thu Jun 2 17:59:23 2005 From: edward.kawas at gmail.com (Eddie Kawas) Date: Thu Jun 2 17:51:27 2005 Subject: [MOBY-l] Prototype Biomoby Taverna Plugin In-Reply-To: <429F7B7E.2070900@ebi.ac.uk> Message-ID: <429f8140.3e43073a.570e.57f4@mx.gmail.com> I have to say that I am confused. I just went to a machine that I have never been on. It is a windows machine with java 1.4 (I am running 1.5 on my work station). I downloaded the Taverna workbench from http://prdownloads.sourceforge.net/taverna/taverna-workbench -1.1.zip?download And then I downloaded my zip file. I unzipped the file into the /taverna-workbench-1.1/lib/ and removed jmoby.jar. I ran Taverna using runme.bat. I then successfully added Moby processors to the workflow. Tom, what errors are you seeing? As for the /lib/ext question, I haven't added any libraries here and I don't have any endorsed libraries either. Eddie > -----Original Message----- > From: Tom Oinn [mailto:tmo@ebi.ac.uk] > Sent: Thursday, June 02, 2005 2:35 PM > To: Eddie Kawas > Cc: moby-l@biomoby.org; dgpisano@cnb.uam.es > Subject: Re: [MOBY-l] Prototype Biomoby Taverna Plugin > > Eddie Kawas wrote: > > Hi, > > > > http://bioinfo.icapture.ubc.ca/ekawas/biomobyPlugin.zip > > > > The above link is to a zip file consisting of 6 jar > files. > > If you place these jar files in the lib directory, where > you > > installed Taverna, typically /taverna-workbench-1.1/lib/ > and > > you delete > > /taverna-workbench-1.1/lib/jmoby.jar, > > you *may* have new and improved Moby support for Taverna. > > The reason that I say may have, is because I have only > tried > > this on my windows machine. > > Eddie - I get 'no such method' errors here, do you have > any XML APIs in > your system classpath (/jre/lib/ext and friends) and which > version of > Java are you using? I'm running a clean install > (yesterday) of WinXP SP2 > with Java5 SDK. > > Looks promising though - we're going for a Taverna 1.2 > release in two > weeks time so with a bit of luck this will all be there > for ISMB / BOSC :) > > Tom From tmo at ebi.ac.uk Thu Jun 2 18:39:39 2005 From: tmo at ebi.ac.uk (Tom Oinn) Date: Thu Jun 2 18:31:27 2005 Subject: [MOBY-l] Prototype Biomoby Taverna Plugin In-Reply-To: <429f8140.3e43073a.570e.57f4@mx.gmail.com> References: <429f8140.3e43073a.570e.57f4@mx.gmail.com> Message-ID: <429F8AAB.5010407@ebi.ac.uk> Eddie Kawas wrote: > I have to say that I am confused. > > I just went to a machine that I have never been on. It is a > windows machine with java 1.4 (I am running 1.5 on my work > station). I downloaded the Taverna workbench from > http://prdownloads.sourceforge.net/taverna/taverna-workbench > -1.1.zip?download > And then I downloaded my zip file. I unzipped the file into > the /taverna-workbench-1.1/lib/ and removed jmoby.jar. I ran > Taverna using runme.bat. I then successfully added Moby > processors to the workflow. > > Tom, what errors are you seeing? As for the /lib/ext > question, I haven't added any libraries here and I don't > have any endorsed libraries either. Can add processors, just not run the thing. Tom From harttig at mail.dife.de Fri Jun 3 04:17:23 2005 From: harttig at mail.dife.de (Ulrich Harttig) Date: Fri Jun 3 04:09:42 2005 Subject: [MOBY-l] Non-default registryname handling in MOBY::Client::Central.pm Message-ID: <42A01213.70604@mail.dife.de> Dear all I'm using biomoby with my own local MOBY Central Registry (Perl version) I noticed that when I try to use a registry with a name different from 'mobycentral' then Service registration does not work. The problem here seems to be that the registerXXX functions in the MOBY/Client/Central.pm module do not care about the registry name but pass 'default' to the _call function causing it to look forever for a not-exisiting connection with the default 'mobycentral' name (endless loop in $self->Connection( $reg ). I wonder if there is a reason for this behavior or did I miss something here ? For instance the retrieveXXXX functions all accept a parameter defining the registry name. The biomoby version I use was retrieved from cvs on 24. Mai 2005, MOBY/Client/Central.pm has version No 1.94 Thanks for your help Best regards Ulrich Harttig -- Ulrich Harttig. Ph.D German Institute of Human Nutrition Potsdam-Rehbruecke Dept. of Epidemiology Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany phone: +49 (0)33200 88-729, fax: +49 (0)33200 88-721 From harttig at mail.dife.de Fri Jun 3 04:17:23 2005 From: harttig at mail.dife.de (Ulrich Harttig) Date: Fri Jun 3 04:18:02 2005 Subject: [MOBY-l] Non-default registryname handling in MOBY::Client::Central.pm Message-ID: <42A01213.70604@mail.dife.de> Dear all I'm using biomoby with my own local MOBY Central Registry (Perl version) I noticed that when I try to use a registry with a name different from 'mobycentral' then Service registration does not work. The problem here seems to be that the registerXXX functions in the MOBY/Client/Central.pm module do not care about the registry name but pass 'default' to the _call function causing it to look forever for a not-exisiting connection with the default 'mobycentral' name (endless loop in $self->Connection( $reg ). I wonder if there is a reason for this behavior or did I miss something here ? For instance the retrieveXXXX functions all accept a parameter defining the registry name. The biomoby version I use was retrieved from cvs on 24. Mai 2005, MOBY/Client/Central.pm has version No 1.94 Thanks for your help Best regards Ulrich Harttig -- Ulrich Harttig. Ph.D German Institute of Human Nutrition Potsdam-Rehbruecke Dept. of Epidemiology Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany phone: +49 (0)33200 88-729, fax: +49 (0)33200 88-721 From markw at illuminae.com Fri Jun 3 07:16:07 2005 From: markw at illuminae.com (mark wilkinson) Date: Fri Jun 3 07:11:10 2005 Subject: [MOBY-l] Non-default registryname handling inMOBY::Client::Central.pm Message-ID: <517876797-1117797432-cardhu_blackberry.rim.net-31714-@engine09-cell01> The easiest way to get the perl libraries to talk to a non-standard mobycentral is to set two environment variables: MOBY_SERVER and MOBY_URI. MOBY_SERVER=http://your.server/path/to/mobycentral.pl MOBY_URI=http://your.server/MOBY/Central (The latter is exactly as typed above, just change the domain name section, nothing else) There are other ways too, but this is the easiest. See the MOBY::Client::Central documentation for all the gorey details, including querying multiple mobycentrals. Good luck! Mark -----Original Message----- From: Ulrich Harttig Date: Fri, 03 Jun 2005 10:17:23 To:moby-l@biomoby.org Subject: [MOBY-l] Non-default registryname handling in MOBY::Client::Central.pm Dear all I'm using biomoby with my own local MOBY Central Registry (Perl version) I noticed that when I try to use a registry with a name different from 'mobycentral' then Service registration does not work. The problem here seems to be that the registerXXX functions in the MOBY/Client/Central.pm module do not care about the registry name but pass 'default' to the _call function causing it to look forever for a not-exisiting connection with the default 'mobycentral' name (endless loop in $self->Connection( $reg ). I wonder if there is a reason for this behavior or did I miss something here ? For instance the retrieveXXXX functions all accept a parameter defining the registry name. The biomoby version I use was retrieved from cvs on 24. Mai 2005, MOBY/Client/Central.pm has version No 1.94 Thanks for your help Best regards Ulrich Harttig -- Ulrich Harttig. Ph.D German Institute of Human Nutrition Potsdam-Rehbruecke Dept. of Epidemiology Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany phone: +49 (0)33200 88-729, fax: +49 (0)33200 88-721 _______________________________________________ moby-l mailing list moby-l@biomoby.org http://biomoby.org/mailman/listinfo/moby-l -- Mark Wilkinson ...on the road! From markw at illuminae.com Fri Jun 3 08:08:36 2005 From: markw at illuminae.com (mark wilkinson) Date: Fri Jun 3 08:05:03 2005 Subject: [MOBY-l] Non-default registryname handling inMOBY::Client::Central.pm Message-ID: <624376559-1117800581-cardhu_blackberry.rim.net-4149-@engine13-cell01> B.t.w. Once you have set the environment variables, try running the testMOBYClientCentral05.pl script in the moby-live/perl/scripts folder to test your registry. M -----Original Message----- From: Ulrich Harttig Date: Fri, 03 Jun 2005 10:17:23 To:moby-l@biomoby.org Subject: [MOBY-l] Non-default registryname handling in MOBY::Client::Central.pm Dear all I'm using biomoby with my own local MOBY Central Registry (Perl version) I noticed that when I try to use a registry with a name different from 'mobycentral' then Service registration does not work. The problem here seems to be that the registerXXX functions in the MOBY/Client/Central.pm module do not care about the registry name but pass 'default' to the _call function causing it to look forever for a not-exisiting connection with the default 'mobycentral' name (endless loop in $self->Connection( $reg ). I wonder if there is a reason for this behavior or did I miss something here ? For instance the retrieveXXXX functions all accept a parameter defining the registry name. The biomoby version I use was retrieved from cvs on 24. Mai 2005, MOBY/Client/Central.pm has version No 1.94 Thanks for your help Best regards Ulrich Harttig -- Ulrich Harttig. Ph.D German Institute of Human Nutrition Potsdam-Rehbruecke Dept. of Epidemiology Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany phone: +49 (0)33200 88-729, fax: +49 (0)33200 88-721 _______________________________________________ moby-l mailing list moby-l@biomoby.org http://biomoby.org/mailman/listinfo/moby-l -- Mark Wilkinson ...on the road! From markw at illuminae.com Fri Jun 3 16:20:12 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Fri Jun 3 16:12:23 2005 Subject: [MOBY-l] Prototype Biomoby Taverna Plugin In-Reply-To: <429f8140.3e43073a.570e.57f4@mx.gmail.com> References: <429f8140.3e43073a.570e.57f4@mx.gmail.com> Message-ID: <42A0BB7C.1080300@illuminae.com> Works for me...??? Nice!! M Eddie Kawas wrote: >I have to say that I am confused. > >I just went to a machine that I have never been on. It is a >windows machine with java 1.4 (I am running 1.5 on my work >station). I downloaded the Taverna workbench from >http://prdownloads.sourceforge.net/taverna/taverna-workbench >-1.1.zip?download >And then I downloaded my zip file. I unzipped the file into >the /taverna-workbench-1.1/lib/ and removed jmoby.jar. I ran >Taverna using runme.bat. I then successfully added Moby >processors to the workflow. > >Tom, what errors are you seeing? As for the /lib/ext >question, I haven't added any libraries here and I don't >have any endorsed libraries either. > >Eddie > > > > > >>-----Original Message----- >>From: Tom Oinn [mailto:tmo@ebi.ac.uk] >>Sent: Thursday, June 02, 2005 2:35 PM >>To: Eddie Kawas >>Cc: moby-l@biomoby.org; dgpisano@cnb.uam.es >>Subject: Re: [MOBY-l] Prototype Biomoby Taverna Plugin >> >>Eddie Kawas wrote: >> >> >>>Hi, >>> >>>http://bioinfo.icapture.ubc.ca/ekawas/biomobyPlugin.zip >>> >>>The above link is to a zip file consisting of 6 jar >>> >>> >>files. >> >> >>>If you place these jar files in the lib directory, where >>> >>> >>you >> >> >>>installed Taverna, typically /taverna-workbench-1.1/lib/ >>> >>> >>and >> >> >>>you delete >>>/taverna-workbench-1.1/lib/jmoby.jar, >>>you *may* have new and improved Moby support for >>> >>> >Taverna. > > >>>The reason that I say may have, is because I have only >>> >>> >>tried >> >> >>>this on my windows machine. >>> >>> >>Eddie - I get 'no such method' errors here, do you have >>any XML APIs in >>your system classpath (/jre/lib/ext and friends) and which >>version of >>Java are you using? I'm running a clean install >>(yesterday) of WinXP SP2 >>with Java5 SDK. >> >>Looks promising though - we're going for a Taverna 1.2 >>release in two >>weeks time so with a bit of luck this will all be there >>for ISMB / BOSC :) >> >>Tom >> >> > >_______________________________________________ >moby-l mailing list >moby-l@biomoby.org >http://biomoby.org/mailman/listinfo/moby-l > > > > From edward.kawas at gmail.com Fri Jun 3 19:04:14 2005 From: edward.kawas at gmail.com (Eddie Kawas) Date: Fri Jun 3 18:56:24 2005 Subject: [MOBY-l] RE: Prototype Biomoby Taverna Plugin Message-ID: <42a0e1f2.5a0b2bf3.4db9.ffff93a3@mx.gmail.com> Hi Again, I have just uploaded my java 1.4.x compatible BioMoby plugin for Taverna. Please direct all feed back to me as I am greatly interested in seeing how actual users find the tools experience. Thanks, Eddie ------------------------------------------ Hi, http://bioinfo.icapture.ubc.ca/ekawas/biomobyPlugin.zip The above link is to a zip file consisting of 6 jar files. If you place these jar files in the lib directory, where you installed Taverna, typically /taverna-workbench-1.1/lib/ and you delete /taverna-workbench-1.1/lib/jmoby.jar, you *may* have new and improved Moby support for Taverna. The reason that I say may have, is because I have only tried this on my windows machine. Note that right now, the plugin only queries the Mobycentral registry. You can still ask it to use yours, but it will not work 100%. Also note that the local widgets do not work (well, that's a lie, the create collection widget works). http://bioinfo.icapture.ubc.ca/ekawas/workflow.xml http://bioinfo.icapture.ubc.ca/ekawas/workflowInput.xml Above is are urls to a workflow definition file (you can load it into Taverna) as well as its inputs, as an example of how to use the plugin. I have added some context (right) click information to Moby objects and services. You can try this from the window labeled 'Advanced Model Explorer'. Basically, right-click a Moby related object or service instance from the 'Processors' list and choose either 'Moby Object Details' or 'Moby Service Details'. I am interested in all feedback both good and bad. I still have a lot to do, but I figure that the more eyes trying (testing) will help me make it better. This is a working prototype, in the spirit of BioMoby ;-) If I make significant changes, I will let you know. Thanks, Eddie Kawas edward.kawas@gmail.com From markw at illuminae.com Fri Jun 3 19:05:38 2005 From: markw at illuminae.com (mark wilkinson) Date: Fri Jun 3 18:58:42 2005 Subject: [MOBY-l] RE: Prototype Biomoby Taverna Plugin Message-ID: <987861068-1117840004-cardhu_blackberry.rim.net-6556-@engine13-cell01> Uploaded to where? -----Original Message----- From: "Eddie Kawas" Date: Fri, 3 Jun 2005 16:04:14 To:"'Eddie Kawas'" , Cc:dgpisano@cnb.uam.es Subject: [MOBY-l] RE: Prototype Biomoby Taverna Plugin Hi Again, I have just uploaded my java 1.4.x compatible BioMoby plugin for Taverna. Please direct all feed back to me as I am greatly interested in seeing how actual users find the tools experience. Thanks, Eddie ------------------------------------------ Hi, http://bioinfo.icapture.ubc.ca/ekawas/biomobyPlugin.zip The above link is to a zip file consisting of 6 jar files. If you place these jar files in the lib directory, where you installed Taverna, typically /taverna-workbench-1.1/lib/ and you delete /taverna-workbench-1.1/lib/jmoby.jar, you *may* have new and improved Moby support for Taverna. The reason that I say may have, is because I have only tried this on my windows machine. Note that right now, the plugin only queries the Mobycentral registry. You can still ask it to use yours, but it will not work 100%. Also note that the local widgets do not work (well, that's a lie, the create collection widget works). http://bioinfo.icapture.ubc.ca/ekawas/workflow.xml http://bioinfo.icapture.ubc.ca/ekawas/workflowInput.xml Above is are urls to a workflow definition file (you can load it into Taverna) as well as its inputs, as an example of how to use the plugin. I have added some context (right) click information to Moby objects and services. You can try this from the window labeled 'Advanced Model Explorer'. Basically, right-click a Moby related object or service instance from the 'Processors' list and choose either 'Moby Object Details' or 'Moby Service Details'. I am interested in all feedback both good and bad. I still have a lot to do, but I figure that the more eyes trying (testing) will help me make it better. This is a working prototype, in the spirit of BioMoby ;-) If I make significant changes, I will let you know. Thanks, Eddie Kawas edward.kawas@gmail.com _______________________________________________ moby-l mailing list moby-l@biomoby.org http://biomoby.org/mailman/listinfo/moby-l -- Mark Wilkinson ...on the road! From simont at mcw.edu Mon Jun 6 11:51:06 2005 From: simont at mcw.edu (Twigger Simon) Date: Mon Jun 6 11:43:01 2005 Subject: [MOBY-l] MySQL down on Moby Central? Message-ID: <3BAF26C5-F4E0-41A5-8702-9B956B1E3C24@mcw.edu> I was getting some database errors from MOBY Central this morning, it might need to be kicked into life after a hard weekend. Simon. -- Simon N. Twigger, Ph.D. Assistant Professor, Department of Physiology Medical College of Wisconsin 8701 Watertown Plank Road, Milwaukee, WI, USA tel: 414-456-8802 fax: 414-456-6595 AIM/iChat: simontatmcw From simont at mcw.edu Mon Jun 6 14:05:09 2005 From: simont at mcw.edu (Twigger Simon) Date: Mon Jun 6 13:57:03 2005 Subject: [MOBY-l] Prototype Biomoby Taverna Plugin In-Reply-To: <429f6b52.3015ac83.0158.38da@mx.gmail.com> References: <429f6b52.3015ac83.0158.38da@mx.gmail.com> Message-ID: <708BED47-7159-4D02-B5E9-209E5AC84F53@mcw.edu> Installing the new jars seemed to break my Mac version of taverna 1.1, no MOBY list came up in the available processors and I couldnt make it create a new one from MOBY Central. Simon. On Jun 2, 2005, at 3:25 PM, Eddie Kawas wrote: > Hi, > > http://bioinfo.icapture.ubc.ca/ekawas/biomobyPlugin.zip > > The above link is to a zip file consisting of 6 jar files. > If you place these jar files in the lib directory, where you > installed Taverna, typically /taverna-workbench-1.1/lib/ and > you delete > /taverna-workbench-1.1/lib/jmoby.jar, > you *may* have new and improved Moby support for Taverna. > The reason that I say may have, is because I have only tried > this on my windows machine. > > Note that right now, the plugin only queries the Mobycentral > registry. You can still ask it to use yours, but it will not > work 100%. > > Also note that the local widgets do not work (well, that's a > lie, the create collection widget works). > > http://bioinfo.icapture.ubc.ca/ekawas/workflow.xml > http://bioinfo.icapture.ubc.ca/ekawas/workflowInput.xml > > Above is are urls to a workflow definition file (you can > load it into Taverna) as well as its inputs, as an example > of how to use the plugin. > > I have added some context (right) click information to Moby > objects and services. You can try this from the window > labeled 'Advanced Model Explorer'. Basically, right-click a > Moby related object or service instance from the > 'Processors' list and choose either 'Moby Object Details' or > 'Moby Service Details'. > > I am interested in all feedback both good and bad. I still > have a lot to do, but I figure that the more eyes trying > (testing) will help me make it better. This is a working > prototype, in the spirit of BioMoby ;-) > > If I make significant changes, I will let you know. > > Thanks, > > Eddie Kawas > edward.kawas@gmail.com > > > _______________________________________________ > moby-l mailing list > moby-l@biomoby.org > http://biomoby.org/mailman/listinfo/moby-l > -- Simon N. Twigger, Ph.D. Assistant Professor, Department of Physiology Medical College of Wisconsin 8701 Watertown Plank Road, Milwaukee, WI, USA tel: 414-456-8802 fax: 414-456-6595 AIM/iChat: simontatmcw From markw at illuminae.com Fri Jun 10 14:38:07 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Fri Jun 10 14:29:54 2005 Subject: [MOBY-l] going offline for a couple of weeks Message-ID: <1118428687.27504.60.camel@mobycentral.mrl.ubc.ca> Hi all, There are Genome Canada face-to-face reviews coming up next week, followed by ISMB. I also have a meeting in Rome starting Tuesday. As such, I anticipate being "unavailable" as of this afternoon until ~June 25th. I just want to let the other developers know this so that you can quickly jump in and respond to questions that get posted to the list. We've got a pretty good reputation for rapid response :-) :-) Cheers all! See you on the other side! M -- Mark Wilkinson Asst. Professor Dept. of Medical Genetics University of British Columbia PI in Bioinformatics iCAPTURE Centre St. Paul's Hospital Vancouver, BC From paolo at ist.unige.it Thu Jun 16 06:52:32 2005 From: paolo at ist.unige.it (Paolo Romano) Date: Thu Jun 16 05:42:32 2005 Subject: [MOBY-l] NETTAB 2005 oral communications deadline postponed Message-ID: <200506161052.j5GAqWAP014998@ibm43p.biotech.ist.unige.it> Dear colleagues, the deadline for the submission of abstracts for oral communications to the NETTAB 2005 workshop on "Workflows management: new abilities for the biological information overflow" has been postponed to next June 27 ,2005. I'm therefore resending here some essential information on the workshop and the Call for Papers. Best regards. Paolo Romano ---- NETTAB 2005 Workflows management: new abilities for the biological information overflow http://www.nettab.org/2005/ 5-7 October, 2005 Second University of Naples, Naples, Italy CALL FOR PAPERS NETTAB 2005 workshop is organized in sessions and open discussions. Invited speakers will present the state of art of the session's topic, a number of submissions will be accepted for oral presentation, and a poster session is also foreseen. Open discussions will also be based upon submitted issues and topics. A call for position papers, posters and oral presentations is now open. Information will soon be added to the web site. Workshop topics Submitted contributions should address one or more of the following topics: Technologies and technological platforms of interest to the field, with emphasis on: - Web Services (SOAP, WSDL, WSFL, UDDI, ....) - Web Services Choreography and Orchestration - Semantic Web (RDF, LSID, OWL, ...) - comparison of available technologies, limitations, pros and cons - Knowledge representation - Biological data and knowledge modeling tools - Ontologies, Databases and Applications of Semantics in Bioinformatics Workflow management systems in bioinformatics: - implementations of web services - implementations of registries - reuse and versioning of web services and workflows - workflow management systems - web interfaces for accessing and executing workflows - interactive systems to support work flows Applications of workflow management systems in bioinformatics - Methodologies for life sciences analysis: gene expression, genome annotation, mass spec peptide fragment identification, etc... - Encoding of the above in workflows - Case studies - Scenarios and use cases Submission of contributions Authors are invited to submit: Oral Presentations: submit an extended abstract (4-5 A4 pages, size 12pt, MS Word format). Abstracts will be reviewed and acceptance or rejection will be communicated to authors. All submissions for oral presentation which are not selected will automatically be considered for posters presentation. Posters: submit an extended abstract (2-3 A4 pages, size 12pt, MS Word format). Abstracts will be reviewed by relevance and acceptance or rejection will be communicated to authors. Position papers: submit a short abstract (max 1 A4 pages in length, size 12pt, MS Word format) specifying research interests and issues to be debated during the workshop. Authors submitting position papers do not engage themselves to present a poster. Instead, they will be invited to introduce the issues they arose before open discussion sessions. Abstracts can be submitted from May 1st, 2005, through the NETTAB 2005 Paper Review System availble at the workshop web site. Contributions will be reviewed by the scientific committee for relevance, clarity and novelty of results. Accepted oral presentations, posters and position papers will be published in the conference proceedings. Authors of a selection of best papers will be asked to submit an extended version of their paper in view of a joint submission to a peer-reviewed international journal. Deadlines - Oral presentations due: June 27, 2005. - Notification to authors: July 29, 2005. - Posters and position papers due: August 26, 2005. Registration: - Early registration: August 26, 2005 -- Paolo Romano (paolo.romano@istge.it) Bioinformatics and Structural Proteomics National Cancer Research Institute (IST) Largo Rosanna Benzi, 10, I-16132, Genova, Italy Tel: +39-010-5737-288 Fax: +39-010-5737-295 Web: http://www.nettab.org/promano/ From simont at mcw.edu Thu Jun 16 11:46:38 2005 From: simont at mcw.edu (Twigger Simon) Date: Thu Jun 16 11:38:24 2005 Subject: [MOBY-l] Comments from recent Taverna/services demo Message-ID: <82EBEA28-EBB3-405E-81DF-6D612647F587@mcw.edu> Hi there, Just thought I'd share some of the comments I heard from our lab folks following a taverna/webservice demo I just did. I expect these are not new to most people but they do represent barriers to potential users of this technology that we need to actively address so I thought a quick reminder/discussion wouldnt hurt. Provenance: How do we know what data a service is running on, what version of an algorithm, what parameters its using, when the database was last updated, etc? This seemed to be the biggest concern - not knowing what was going on under the hood and having no way to find it out. Workflows and services provide great ways to automate things but theres a distrust of the 'black box' that this creates. From a MOBY perspective, if we could somehow enforce the provision information block so that service providers had to fill in something sensible for the service (algorithm version, database version, date last updated, etc.) this could be a very good selling point. "Use MOBY services where possible because at least then you can get a list of what went on in your workflow, what databases were searched, etc." Some sort of report at the end of a taverna workflow that compiled all this provision data into a human readable document would be great. In reality, this is the same as getting data off a website - how do you know what's going on? Good websites tell you what algorithm and database they use, others dont. I suspect people are more familiar and hence more trusting of websites and havent yet got comfortable with webservices/workflows so the level of (blind?) trust isnt there. Input's and Outputs - How do I know what data I should pass in? Again, MOBY is nice in that it defines the objects and should ameliorate a lot of these problems but joining the dots is harder than it should be, particularly outside of MOBY-land. Make it even easier to use "Is taverna something even I could use?", "I got lost with all these service options" Drag and drop, connect the dots services seems pretty straight forward but it may still be too much for your average (or even above average) lab scientist. How have other people found this technology has been accepted? A web front end to all these services and workflows seems to be one of the best ways we could get this technology in use by the largest number of people. I'd love to hear any comments/thoughts about these issues from others. Cheers, Simon. -- Simon N. Twigger, Ph.D. Assistant Professor, Department of Physiology Medical College of Wisconsin 8701 Watertown Plank Road, Milwaukee, WI, USA tel: 414-456-8802 fax: 414-456-6595 AIM/iChat: simontatmcw From ywong at infobiogen.fr Thu Jun 16 14:05:57 2005 From: ywong at infobiogen.fr (ywong@infobiogen.fr) Date: Thu Jun 16 13:57:32 2005 Subject: [MOBY-l] Object ontology browser Message-ID: <1476.82.66.216.27.1118945157.squirrel@82.66.216.27> Hello, I've Built a ontology object browser in Java. It has the same functionalities than the Python version. For people using unix and windows: http://yan.wong.free.fr/Public/jMOBrowser.zip unzip the file and launch the objectBrowser script For people using MacOS X (you'll need Java machine 1.4+): http://yan.wong.free.fr/Public/jMOBrowser.dmg if you are asked for a password and login: login: Invite password: invite No third party libraries required! just drag'n drop the application to a location on your disk and double click! From d.haase at gsf.de Mon Jun 27 10:58:21 2005 From: d.haase at gsf.de (Dirk Haase) Date: Mon Jun 27 10:49:39 2005 Subject: [MOBY-l] Object ontology browser In-Reply-To: <1476.82.66.216.27.1118945157.squirrel@82.66.216.27> References: <1476.82.66.216.27.1118945157.squirrel@82.66.216.27> Message-ID: <200506271658.21277.d.haase@gsf.de> Hi Yan, On Thursday 16 June 2005 20:05, ywong@infobiogen.fr wrote: > Hello, > > I've Built a ontology object browser in Java. It has the same > functionalities than the Python version. > > For people using unix and windows: > http://yan.wong.free.fr/Public/jMOBrowser.zip > > unzip the file and launch the objectBrowser script I just tried your object ontology browser and it works nice on our Linux boxes. Just one remark: in the dialog which opens after selecting 'Browse a Moby directory', I found the labels for the input fields very confusing. I would prefer "Moby Central URL" instead of just "URL" and - even more important - "Moby Central URI" instead of 'Namespace'. I first tried to insert namespaces like "Global_Keyword" in the latter one and got obscure error messages... Clicking the Root node always leads to a NPE - which does no harm besides spoiling the start shell with ugly java errors... But the rest of it is very nice! Regards, dirk From ywong at infobiogen.fr Tue Jun 28 05:50:03 2005 From: ywong at infobiogen.fr (Yan Wong) Date: Tue Jun 28 05:41:35 2005 Subject: [MOBY-l] Object ontology browser In-Reply-To: <200506271658.21277.d.haase@gsf.de> References: <1476.82.66.216.27.1118945157.squirrel@82.66.216.27> <200506271658.21277.d.haase@gsf.de> Message-ID: <42C11D4B.1040502@infobiogen.fr> Dirk Haase wrote: >Hi Yan, > >On Thursday 16 June 2005 20:05, ywong@infobiogen.fr wrote: > > >>Hello, >> >>I've Built a ontology object browser in Java. It has the same >>functionalities than the Python version. >> >>For people using unix and windows: >> http://yan.wong.free.fr/Public/jMOBrowser.zip >> >>unzip the file and launch the objectBrowser script >> >> > >I just tried your object ontology browser and it works nice on our Linux >boxes. Just one remark: in the dialog which opens after selecting 'Browse a >Moby directory', I found the labels for the input fields very confusing. I >would prefer "Moby Central URL" instead of just "URL" and - even more >important - "Moby Central URI" instead of 'Namespace'. I first tried to >insert namespaces like "Global_Keyword" in the latter one and got obscure >error messages... > >Clicking the Root node always leads to a NPE - which does no harm besides >spoiling the start shell with ugly java errors... > >But the rest of it is very nice! > >Regards, >dirk >_______________________________________________ >moby-l mailing list >moby-l@biomoby.org >http://biomoby.org/mailman/listinfo/moby-l > > > OK I posted the modifications this morning... If I have time, I'll implement some search functionalities... From markw at illuminae.com Tue Jun 28 09:52:36 2005 From: markw at illuminae.com (mark wilkinson) Date: Tue Jun 28 09:48:31 2005 Subject: [MOBY-l] Object ontology browser Message-ID: <1293586438-1119967038-cardhu_blackberry.rim.net-3291-@engine10-cell01> Do you want me to add this to the "cool tools" page? M -----Original Message----- From: Yan Wong Date: Tue, 28 Jun 2005 11:50:03 To:Dirk Haase Cc:moby-l@biomoby.org Subject: Re: [MOBY-l] Object ontology browser Dirk Haase wrote: >Hi Yan, > >On Thursday 16 June 2005 20:05, ywong@infobiogen.fr wrote: > > >>Hello, >> >>I've Built a ontology object browser in Java. It has the same >>functionalities than the Python version. >> >>For people using unix and windows: >> http://yan.wong.free.fr/Public/jMOBrowser.zip >> >>unzip the file and launch the objectBrowser script >> >> > >I just tried your object ontology browser and it works nice on our Linux >boxes. Just one remark: in the dialog which opens after selecting 'Browse a >Moby directory', I found the labels for the input fields very confusing. I >would prefer "Moby Central URL" instead of just "URL" and - even more >important - "Moby Central URI" instead of 'Namespace'. I first tried to >insert namespaces like "Global_Keyword" in the latter one and got obscure >error messages... > >Clicking the Root node always leads to a NPE - which does no harm besides >spoiling the start shell with ugly java errors... > >But the rest of it is very nice! > >Regards, >dirk >_______________________________________________ >moby-l mailing list >moby-l@biomoby.org >http://biomoby.org/mailman/listinfo/moby-l > > > OK I posted the modifications this morning... If I have time, I'll implement some search functionalities... _______________________________________________ moby-l mailing list moby-l@biomoby.org http://biomoby.org/mailman/listinfo/moby-l -- Mark Wilkinson ...on the road! From ywong at infobiogen.fr Tue Jun 28 10:24:05 2005 From: ywong at infobiogen.fr (Yan Wong) Date: Tue Jun 28 10:15:30 2005 Subject: [MOBY-l] Object ontology browser In-Reply-To: <1293586438-1119967038-cardhu_blackberry.rim.net-3291-@engine10-cell01> References: <1293586438-1119967038-cardhu_blackberry.rim.net-3291-@engine10-cell01> Message-ID: <42C15D85.7010707@infobiogen.fr> mark wilkinson wrote: >Do you want me to add this to the "cool tools" page? > >M > > >-----Original Message----- >From: Yan Wong >Date: Tue, 28 Jun 2005 11:50:03 >To:Dirk Haase >Cc:moby-l@biomoby.org >Subject: Re: [MOBY-l] Object ontology browser > >Dirk Haase wrote: > > > >>Hi Yan, >> >>On Thursday 16 June 2005 20:05, ywong@infobiogen.fr wrote: >> >> >> >> >>>Hello, >>> >>>I've Built a ontology object browser in Java. It has the same >>>functionalities than the Python version. >>> >>>For people using unix and windows: >>> http://yan.wong.free.fr/Public/jMOBrowser.zip >>> >>>unzip the file and launch the objectBrowser script >>> >>> >>> >>> >>I just tried your object ontology browser and it works nice on our Linux >>boxes. Just one remark: in the dialog which opens after selecting 'Browse a >>Moby directory', I found the labels for the input fields very confusing. I >>would prefer "Moby Central URL" instead of just "URL" and - even more >>important - "Moby Central URI" instead of 'Namespace'. I first tried to >>insert namespaces like "Global_Keyword" in the latter one and got obscure >>error messages... >> >>Clicking the Root node always leads to a NPE - which does no harm besides >>spoiling the start shell with ugly java errors... >> >>But the rest of it is very nice! >> >>Regards, >>dirk >>_______________________________________________ >>moby-l mailing list >>moby-l@biomoby.org >>http://biomoby.org/mailman/listinfo/moby-l >> >> >> >> >> >OK I posted the modifications this morning... If I have time, I'll >implement some search functionalities... >_______________________________________________ >moby-l mailing list >moby-l@biomoby.org >http://biomoby.org/mailman/listinfo/moby-l > >-- >Mark Wilkinson >...on the road! > > > There is also a Mac OS X (tested on 10.3 and 10.4) version on http://yan.wong.free.fr/Public/jMOBrowser.dmg login: Invite password: invite You can add them to "the cool tools" section if you want ;) From markw at illuminae.com Tue Jun 28 11:56:17 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Tue Jun 28 11:47:28 2005 Subject: [moby] Re: [MOBY-l] Object ontology browser In-Reply-To: <42C15D85.7010707@infobiogen.fr> References: <1293586438-1119967038-cardhu_blackberry.rim.net-3291-@engine10-cell01> <42C15D85.7010707@infobiogen.fr> Message-ID: <1119974177.15887.12.camel@mobycentral.mrl.ubc.ca> On Tue, 2005-06-28 at 16:24 +0200, Yan Wong wrote: > You can add them to "the cool tools" section if you want ;) Done, with pleasure! M -- Mark Wilkinson Asst. Professor Dept. of Medical Genetics University of British Columbia PI in Bioinformatics iCAPTURE Centre St. Paul's Hospital Vancouver, BC From markw at illuminae.com Wed Jun 29 11:25:05 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Wed Jun 29 11:18:00 2005 Subject: [MOBY-l] MOBY Central hacked last night Message-ID: <1120058705.20181.26.camel@mobycentral.mrl.ubc.ca> Hi all, MOBY Central is down for at least a day due to a nasty hack last night. We may have to rebuild from scratch, so it may not be a rapid recovery. Speaks again to the need for a mirroring system! Hey, Heiko... how's the research going? ;-) ;-) You can run, but you can't hide! Sorry for the down-time... M -- Mark Wilkinson Asst. Professor Dept. of Medical Genetics University of British Columbia PI in Bioinformatics iCAPTURE Centre St. Paul's Hospital Vancouver, BC From markw at illuminae.com Thu Jun 30 19:38:45 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Thu Jun 30 19:29:58 2005 Subject: [MOBY-l] MOBY Central Registry up and running at a new location Message-ID: <1120174725.31990.6.camel@mobycentral.mrl.ubc.ca> Hi all, The core of MOBY Central is up and running again at: URL: http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl URI: http://mobycentral.icapture.ubc.ca/MOBY/Central No accessories are functioning, however. Just the registry. Also, none of my services will be working either. No data loss as far as I can tell at the moment, so that is good news! I will begin migrating the accessories over to this new server tomorrow. Hopefully we will have things running again by the end of the weekend, but for the moment at least the registry itself is functional. remember you can use this registry as your default for the Perl libraries by setting the environment variables: MOBY_SERVER= $URL (above) MOBY_URI = $URI (above) This will cause MOBY::Client::Central to connect to this server by default. I will make changes to the test harness in the CVS soon. It doesn't matter, really, because the version in the CVS is non-functional until we can get the Perl LSID resolver stack working }-/ Anyway, sorry for the down-time! What a disaster! (but I did learn a lot about what it takes to install MOBY Central now! So I have lots of good notes for our documentation drive...) M -- Mark Wilkinson Asst. Professor Dept. of Medical Genetics University of British Columbia PI in Bioinformatics iCAPTURE Centre St. Paul's Hospital Vancouver, BC From bgulden at purdue.edu Wed Jun 1 13:16:42 2005 From: bgulden at purdue.edu (bgulden@purdue.edu) Date: Wed, 1 Jun 2005 12:16:42 -0500 Subject: [MOBY-l] Parameters for services Message-ID: <1117646202.429ded7a59449@webmail.purdue.edu> Is there any way to determine dynamically the parameters that a given service can take? For example, if I have a service that can run blastp or blastn, could I have a parameter that would determine which one to run or would they be better described as two entirely different services? Also, a blast service could have other options that could be set. Would those options be placed in the "input" section of the service description? Thanks for any help, Brian Gulden From bmg at sfu.ca Wed Jun 1 19:08:41 2005 From: bmg at sfu.ca (Benjamin Good) Date: Wed, 01 Jun 2005 16:08:41 -0700 Subject: [MOBY-l] Parameters for services In-Reply-To: <1117646202.429ded7a59449@webmail.purdue.edu> References: <1117646202.429ded7a59449@webmail.purdue.edu> Message-ID: <429E3FF9.3000802@sfu.ca> In short, yes Search for "Secondary Parameters" here http://www.biomoby.org/twiki/bin//view/Moby/MobySAPI You may find the service registration applet informative as well - http://mobycentral.cbr.nrc.ca/applets/ sorry I can't offer a more detailed explanation right now -ben bgulden at purdue.edu wrote: >Is there any way to determine dynamically the parameters that a given service >can take? For example, if I have a service that can run blastp or blastn, could >I have a parameter that would determine which one to run or would they be better >described as two entirely different services? Also, a blast service could have >other options that could be set. Would those options be placed in the "input" >section of the service description? >Thanks for any help, >Brian Gulden > > >_______________________________________________ >moby-l mailing list >moby-l at biomoby.org >http://biomoby.org/mailman/listinfo/moby-l > > > > From edward.kawas at gmail.com Thu Jun 2 16:25:50 2005 From: edward.kawas at gmail.com (Eddie Kawas) Date: Thu, 2 Jun 2005 13:25:50 -0700 Subject: [MOBY-l] Prototype Biomoby Taverna Plugin Message-ID: <429f6b52.3015ac83.0158.38da@mx.gmail.com> Hi, http://bioinfo.icapture.ubc.ca/ekawas/biomobyPlugin.zip The above link is to a zip file consisting of 6 jar files. If you place these jar files in the lib directory, where you installed Taverna, typically /taverna-workbench-1.1/lib/ and you delete /taverna-workbench-1.1/lib/jmoby.jar, you *may* have new and improved Moby support for Taverna. The reason that I say may have, is because I have only tried this on my windows machine. Note that right now, the plugin only queries the Mobycentral registry. You can still ask it to use yours, but it will not work 100%. Also note that the local widgets do not work (well, that's a lie, the create collection widget works). http://bioinfo.icapture.ubc.ca/ekawas/workflow.xml http://bioinfo.icapture.ubc.ca/ekawas/workflowInput.xml Above is are urls to a workflow definition file (you can load it into Taverna) as well as its inputs, as an example of how to use the plugin. I have added some context (right) click information to Moby objects and services. You can try this from the window labeled 'Advanced Model Explorer'. Basically, right-click a Moby related object or service instance from the 'Processors' list and choose either 'Moby Object Details' or 'Moby Service Details'. I am interested in all feedback both good and bad. I still have a lot to do, but I figure that the more eyes trying (testing) will help me make it better. This is a working prototype, in the spirit of BioMoby ;-) If I make significant changes, I will let you know. Thanks, Eddie Kawas edward.kawas at gmail.com From tmo at ebi.ac.uk Thu Jun 2 17:34:54 2005 From: tmo at ebi.ac.uk (Tom Oinn) Date: Thu, 02 Jun 2005 22:34:54 +0100 Subject: [MOBY-l] Prototype Biomoby Taverna Plugin In-Reply-To: <429f6b52.3015ac83.0158.38da@mx.gmail.com> References: <429f6b52.3015ac83.0158.38da@mx.gmail.com> Message-ID: <429F7B7E.2070900@ebi.ac.uk> Eddie Kawas wrote: > Hi, > > http://bioinfo.icapture.ubc.ca/ekawas/biomobyPlugin.zip > > The above link is to a zip file consisting of 6 jar files. > If you place these jar files in the lib directory, where you > installed Taverna, typically /taverna-workbench-1.1/lib/ and > you delete > /taverna-workbench-1.1/lib/jmoby.jar, > you *may* have new and improved Moby support for Taverna. > The reason that I say may have, is because I have only tried > this on my windows machine. Eddie - I get 'no such method' errors here, do you have any XML APIs in your system classpath (/jre/lib/ext and friends) and which version of Java are you using? I'm running a clean install (yesterday) of WinXP SP2 with Java5 SDK. Looks promising though - we're going for a Taverna 1.2 release in two weeks time so with a bit of luck this will all be there for ISMB / BOSC :) Tom From edward.kawas at gmail.com Thu Jun 2 17:59:23 2005 From: edward.kawas at gmail.com (Eddie Kawas) Date: Thu, 2 Jun 2005 14:59:23 -0700 Subject: [MOBY-l] Prototype Biomoby Taverna Plugin In-Reply-To: <429F7B7E.2070900@ebi.ac.uk> Message-ID: <429f8140.3e43073a.570e.57f4@mx.gmail.com> I have to say that I am confused. I just went to a machine that I have never been on. It is a windows machine with java 1.4 (I am running 1.5 on my work station). I downloaded the Taverna workbench from http://prdownloads.sourceforge.net/taverna/taverna-workbench -1.1.zip?download And then I downloaded my zip file. I unzipped the file into the /taverna-workbench-1.1/lib/ and removed jmoby.jar. I ran Taverna using runme.bat. I then successfully added Moby processors to the workflow. Tom, what errors are you seeing? As for the /lib/ext question, I haven't added any libraries here and I don't have any endorsed libraries either. Eddie > -----Original Message----- > From: Tom Oinn [mailto:tmo at ebi.ac.uk] > Sent: Thursday, June 02, 2005 2:35 PM > To: Eddie Kawas > Cc: moby-l at biomoby.org; dgpisano at cnb.uam.es > Subject: Re: [MOBY-l] Prototype Biomoby Taverna Plugin > > Eddie Kawas wrote: > > Hi, > > > > http://bioinfo.icapture.ubc.ca/ekawas/biomobyPlugin.zip > > > > The above link is to a zip file consisting of 6 jar > files. > > If you place these jar files in the lib directory, where > you > > installed Taverna, typically /taverna-workbench-1.1/lib/ > and > > you delete > > /taverna-workbench-1.1/lib/jmoby.jar, > > you *may* have new and improved Moby support for Taverna. > > The reason that I say may have, is because I have only > tried > > this on my windows machine. > > Eddie - I get 'no such method' errors here, do you have > any XML APIs in > your system classpath (/jre/lib/ext and friends) and which > version of > Java are you using? I'm running a clean install > (yesterday) of WinXP SP2 > with Java5 SDK. > > Looks promising though - we're going for a Taverna 1.2 > release in two > weeks time so with a bit of luck this will all be there > for ISMB / BOSC :) > > Tom From tmo at ebi.ac.uk Thu Jun 2 18:39:39 2005 From: tmo at ebi.ac.uk (Tom Oinn) Date: Thu, 02 Jun 2005 23:39:39 +0100 Subject: [MOBY-l] Prototype Biomoby Taverna Plugin In-Reply-To: <429f8140.3e43073a.570e.57f4@mx.gmail.com> References: <429f8140.3e43073a.570e.57f4@mx.gmail.com> Message-ID: <429F8AAB.5010407@ebi.ac.uk> Eddie Kawas wrote: > I have to say that I am confused. > > I just went to a machine that I have never been on. It is a > windows machine with java 1.4 (I am running 1.5 on my work > station). I downloaded the Taverna workbench from > http://prdownloads.sourceforge.net/taverna/taverna-workbench > -1.1.zip?download > And then I downloaded my zip file. I unzipped the file into > the /taverna-workbench-1.1/lib/ and removed jmoby.jar. I ran > Taverna using runme.bat. I then successfully added Moby > processors to the workflow. > > Tom, what errors are you seeing? As for the /lib/ext > question, I haven't added any libraries here and I don't > have any endorsed libraries either. Can add processors, just not run the thing. Tom From harttig at mail.dife.de Fri Jun 3 04:17:23 2005 From: harttig at mail.dife.de (Ulrich Harttig) Date: Fri, 03 Jun 2005 10:17:23 +0200 Subject: [MOBY-l] Non-default registryname handling in MOBY::Client::Central.pm Message-ID: <42A01213.70604@mail.dife.de> Dear all I'm using biomoby with my own local MOBY Central Registry (Perl version) I noticed that when I try to use a registry with a name different from 'mobycentral' then Service registration does not work. The problem here seems to be that the registerXXX functions in the MOBY/Client/Central.pm module do not care about the registry name but pass 'default' to the _call function causing it to look forever for a not-exisiting connection with the default 'mobycentral' name (endless loop in $self->Connection( $reg ). I wonder if there is a reason for this behavior or did I miss something here ? For instance the retrieveXXXX functions all accept a parameter defining the registry name. The biomoby version I use was retrieved from cvs on 24. Mai 2005, MOBY/Client/Central.pm has version No 1.94 Thanks for your help Best regards Ulrich Harttig -- Ulrich Harttig. Ph.D German Institute of Human Nutrition Potsdam-Rehbruecke Dept. of Epidemiology Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany phone: +49 (0)33200 88-729, fax: +49 (0)33200 88-721 From harttig at mail.dife.de Fri Jun 3 04:17:23 2005 From: harttig at mail.dife.de (Ulrich Harttig) Date: Fri, 03 Jun 2005 10:17:23 +0200 Subject: [MOBY-l] Non-default registryname handling in MOBY::Client::Central.pm Message-ID: <42A01213.70604@mail.dife.de> Dear all I'm using biomoby with my own local MOBY Central Registry (Perl version) I noticed that when I try to use a registry with a name different from 'mobycentral' then Service registration does not work. The problem here seems to be that the registerXXX functions in the MOBY/Client/Central.pm module do not care about the registry name but pass 'default' to the _call function causing it to look forever for a not-exisiting connection with the default 'mobycentral' name (endless loop in $self->Connection( $reg ). I wonder if there is a reason for this behavior or did I miss something here ? For instance the retrieveXXXX functions all accept a parameter defining the registry name. The biomoby version I use was retrieved from cvs on 24. Mai 2005, MOBY/Client/Central.pm has version No 1.94 Thanks for your help Best regards Ulrich Harttig -- Ulrich Harttig. Ph.D German Institute of Human Nutrition Potsdam-Rehbruecke Dept. of Epidemiology Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany phone: +49 (0)33200 88-729, fax: +49 (0)33200 88-721 From markw at illuminae.com Fri Jun 3 07:16:07 2005 From: markw at illuminae.com (mark wilkinson) Date: Fri, 3 Jun 2005 11:16:07 +0000 GMT Subject: [MOBY-l] Non-default registryname handling inMOBY::Client::Central.pm Message-ID: <517876797-1117797432-cardhu_blackberry.rim.net-31714-@engine09-cell01> The easiest way to get the perl libraries to talk to a non-standard mobycentral is to set two environment variables: MOBY_SERVER and MOBY_URI. MOBY_SERVER=http://your.server/path/to/mobycentral.pl MOBY_URI=http://your.server/MOBY/Central (The latter is exactly as typed above, just change the domain name section, nothing else) There are other ways too, but this is the easiest. See the MOBY::Client::Central documentation for all the gorey details, including querying multiple mobycentrals. Good luck! Mark -----Original Message----- From: Ulrich Harttig Date: Fri, 03 Jun 2005 10:17:23 To:moby-l at biomoby.org Subject: [MOBY-l] Non-default registryname handling in MOBY::Client::Central.pm Dear all I'm using biomoby with my own local MOBY Central Registry (Perl version) I noticed that when I try to use a registry with a name different from 'mobycentral' then Service registration does not work. The problem here seems to be that the registerXXX functions in the MOBY/Client/Central.pm module do not care about the registry name but pass 'default' to the _call function causing it to look forever for a not-exisiting connection with the default 'mobycentral' name (endless loop in $self->Connection( $reg ). I wonder if there is a reason for this behavior or did I miss something here ? For instance the retrieveXXXX functions all accept a parameter defining the registry name. The biomoby version I use was retrieved from cvs on 24. Mai 2005, MOBY/Client/Central.pm has version No 1.94 Thanks for your help Best regards Ulrich Harttig -- Ulrich Harttig. Ph.D German Institute of Human Nutrition Potsdam-Rehbruecke Dept. of Epidemiology Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany phone: +49 (0)33200 88-729, fax: +49 (0)33200 88-721 _______________________________________________ moby-l mailing list moby-l at biomoby.org http://biomoby.org/mailman/listinfo/moby-l -- Mark Wilkinson ...on the road! From markw at illuminae.com Fri Jun 3 08:08:36 2005 From: markw at illuminae.com (mark wilkinson) Date: Fri, 3 Jun 2005 12:08:36 +0000 GMT Subject: [MOBY-l] Non-default registryname handling inMOBY::Client::Central.pm Message-ID: <624376559-1117800581-cardhu_blackberry.rim.net-4149-@engine13-cell01> B.t.w. Once you have set the environment variables, try running the testMOBYClientCentral05.pl script in the moby-live/perl/scripts folder to test your registry. M -----Original Message----- From: Ulrich Harttig Date: Fri, 03 Jun 2005 10:17:23 To:moby-l at biomoby.org Subject: [MOBY-l] Non-default registryname handling in MOBY::Client::Central.pm Dear all I'm using biomoby with my own local MOBY Central Registry (Perl version) I noticed that when I try to use a registry with a name different from 'mobycentral' then Service registration does not work. The problem here seems to be that the registerXXX functions in the MOBY/Client/Central.pm module do not care about the registry name but pass 'default' to the _call function causing it to look forever for a not-exisiting connection with the default 'mobycentral' name (endless loop in $self->Connection( $reg ). I wonder if there is a reason for this behavior or did I miss something here ? For instance the retrieveXXXX functions all accept a parameter defining the registry name. The biomoby version I use was retrieved from cvs on 24. Mai 2005, MOBY/Client/Central.pm has version No 1.94 Thanks for your help Best regards Ulrich Harttig -- Ulrich Harttig. Ph.D German Institute of Human Nutrition Potsdam-Rehbruecke Dept. of Epidemiology Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany phone: +49 (0)33200 88-729, fax: +49 (0)33200 88-721 _______________________________________________ moby-l mailing list moby-l at biomoby.org http://biomoby.org/mailman/listinfo/moby-l -- Mark Wilkinson ...on the road! From markw at illuminae.com Fri Jun 3 16:20:12 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 03 Jun 2005 13:20:12 -0700 Subject: [MOBY-l] Prototype Biomoby Taverna Plugin In-Reply-To: <429f8140.3e43073a.570e.57f4@mx.gmail.com> References: <429f8140.3e43073a.570e.57f4@mx.gmail.com> Message-ID: <42A0BB7C.1080300@illuminae.com> Works for me...??? Nice!! M Eddie Kawas wrote: >I have to say that I am confused. > >I just went to a machine that I have never been on. It is a >windows machine with java 1.4 (I am running 1.5 on my work >station). I downloaded the Taverna workbench from >http://prdownloads.sourceforge.net/taverna/taverna-workbench >-1.1.zip?download >And then I downloaded my zip file. I unzipped the file into >the /taverna-workbench-1.1/lib/ and removed jmoby.jar. I ran >Taverna using runme.bat. I then successfully added Moby >processors to the workflow. > >Tom, what errors are you seeing? As for the /lib/ext >question, I haven't added any libraries here and I don't >have any endorsed libraries either. > >Eddie > > > > > >>-----Original Message----- >>From: Tom Oinn [mailto:tmo at ebi.ac.uk] >>Sent: Thursday, June 02, 2005 2:35 PM >>To: Eddie Kawas >>Cc: moby-l at biomoby.org; dgpisano at cnb.uam.es >>Subject: Re: [MOBY-l] Prototype Biomoby Taverna Plugin >> >>Eddie Kawas wrote: >> >> >>>Hi, >>> >>>http://bioinfo.icapture.ubc.ca/ekawas/biomobyPlugin.zip >>> >>>The above link is to a zip file consisting of 6 jar >>> >>> >>files. >> >> >>>If you place these jar files in the lib directory, where >>> >>> >>you >> >> >>>installed Taverna, typically /taverna-workbench-1.1/lib/ >>> >>> >>and >> >> >>>you delete >>>/taverna-workbench-1.1/lib/jmoby.jar, >>>you *may* have new and improved Moby support for >>> >>> >Taverna. > > >>>The reason that I say may have, is because I have only >>> >>> >>tried >> >> >>>this on my windows machine. >>> >>> >>Eddie - I get 'no such method' errors here, do you have >>any XML APIs in >>your system classpath (/jre/lib/ext and friends) and which >>version of >>Java are you using? I'm running a clean install >>(yesterday) of WinXP SP2 >>with Java5 SDK. >> >>Looks promising though - we're going for a Taverna 1.2 >>release in two >>weeks time so with a bit of luck this will all be there >>for ISMB / BOSC :) >> >>Tom >> >> > >_______________________________________________ >moby-l mailing list >moby-l at biomoby.org >http://biomoby.org/mailman/listinfo/moby-l > > > > From edward.kawas at gmail.com Fri Jun 3 19:04:14 2005 From: edward.kawas at gmail.com (Eddie Kawas) Date: Fri, 3 Jun 2005 16:04:14 -0700 Subject: [MOBY-l] RE: Prototype Biomoby Taverna Plugin Message-ID: <42a0e1f2.5a0b2bf3.4db9.ffff93a3@mx.gmail.com> Hi Again, I have just uploaded my java 1.4.x compatible BioMoby plugin for Taverna. Please direct all feed back to me as I am greatly interested in seeing how actual users find the tools experience. Thanks, Eddie ------------------------------------------ Hi, http://bioinfo.icapture.ubc.ca/ekawas/biomobyPlugin.zip The above link is to a zip file consisting of 6 jar files. If you place these jar files in the lib directory, where you installed Taverna, typically /taverna-workbench-1.1/lib/ and you delete /taverna-workbench-1.1/lib/jmoby.jar, you *may* have new and improved Moby support for Taverna. The reason that I say may have, is because I have only tried this on my windows machine. Note that right now, the plugin only queries the Mobycentral registry. You can still ask it to use yours, but it will not work 100%. Also note that the local widgets do not work (well, that's a lie, the create collection widget works). http://bioinfo.icapture.ubc.ca/ekawas/workflow.xml http://bioinfo.icapture.ubc.ca/ekawas/workflowInput.xml Above is are urls to a workflow definition file (you can load it into Taverna) as well as its inputs, as an example of how to use the plugin. I have added some context (right) click information to Moby objects and services. You can try this from the window labeled 'Advanced Model Explorer'. Basically, right-click a Moby related object or service instance from the 'Processors' list and choose either 'Moby Object Details' or 'Moby Service Details'. I am interested in all feedback both good and bad. I still have a lot to do, but I figure that the more eyes trying (testing) will help me make it better. This is a working prototype, in the spirit of BioMoby ;-) If I make significant changes, I will let you know. Thanks, Eddie Kawas edward.kawas at gmail.com From markw at illuminae.com Fri Jun 3 19:05:38 2005 From: markw at illuminae.com (mark wilkinson) Date: Fri, 3 Jun 2005 23:05:38 +0000 GMT Subject: [MOBY-l] RE: Prototype Biomoby Taverna Plugin Message-ID: <987861068-1117840004-cardhu_blackberry.rim.net-6556-@engine13-cell01> Uploaded to where? -----Original Message----- From: "Eddie Kawas" Date: Fri, 3 Jun 2005 16:04:14 To:"'Eddie Kawas'" , Cc:dgpisano at cnb.uam.es Subject: [MOBY-l] RE: Prototype Biomoby Taverna Plugin Hi Again, I have just uploaded my java 1.4.x compatible BioMoby plugin for Taverna. Please direct all feed back to me as I am greatly interested in seeing how actual users find the tools experience. Thanks, Eddie ------------------------------------------ Hi, http://bioinfo.icapture.ubc.ca/ekawas/biomobyPlugin.zip The above link is to a zip file consisting of 6 jar files. If you place these jar files in the lib directory, where you installed Taverna, typically /taverna-workbench-1.1/lib/ and you delete /taverna-workbench-1.1/lib/jmoby.jar, you *may* have new and improved Moby support for Taverna. The reason that I say may have, is because I have only tried this on my windows machine. Note that right now, the plugin only queries the Mobycentral registry. You can still ask it to use yours, but it will not work 100%. Also note that the local widgets do not work (well, that's a lie, the create collection widget works). http://bioinfo.icapture.ubc.ca/ekawas/workflow.xml http://bioinfo.icapture.ubc.ca/ekawas/workflowInput.xml Above is are urls to a workflow definition file (you can load it into Taverna) as well as its inputs, as an example of how to use the plugin. I have added some context (right) click information to Moby objects and services. You can try this from the window labeled 'Advanced Model Explorer'. Basically, right-click a Moby related object or service instance from the 'Processors' list and choose either 'Moby Object Details' or 'Moby Service Details'. I am interested in all feedback both good and bad. I still have a lot to do, but I figure that the more eyes trying (testing) will help me make it better. This is a working prototype, in the spirit of BioMoby ;-) If I make significant changes, I will let you know. Thanks, Eddie Kawas edward.kawas at gmail.com _______________________________________________ moby-l mailing list moby-l at biomoby.org http://biomoby.org/mailman/listinfo/moby-l -- Mark Wilkinson ...on the road! From simont at mcw.edu Mon Jun 6 11:51:06 2005 From: simont at mcw.edu (Twigger Simon) Date: Mon, 6 Jun 2005 10:51:06 -0500 Subject: [MOBY-l] MySQL down on Moby Central? Message-ID: <3BAF26C5-F4E0-41A5-8702-9B956B1E3C24@mcw.edu> I was getting some database errors from MOBY Central this morning, it might need to be kicked into life after a hard weekend. Simon. -- Simon N. Twigger, Ph.D. Assistant Professor, Department of Physiology Medical College of Wisconsin 8701 Watertown Plank Road, Milwaukee, WI, USA tel: 414-456-8802 fax: 414-456-6595 AIM/iChat: simontatmcw From simont at mcw.edu Mon Jun 6 14:05:09 2005 From: simont at mcw.edu (Twigger Simon) Date: Mon, 6 Jun 2005 13:05:09 -0500 Subject: [MOBY-l] Prototype Biomoby Taverna Plugin In-Reply-To: <429f6b52.3015ac83.0158.38da@mx.gmail.com> References: <429f6b52.3015ac83.0158.38da@mx.gmail.com> Message-ID: <708BED47-7159-4D02-B5E9-209E5AC84F53@mcw.edu> Installing the new jars seemed to break my Mac version of taverna 1.1, no MOBY list came up in the available processors and I couldnt make it create a new one from MOBY Central. Simon. On Jun 2, 2005, at 3:25 PM, Eddie Kawas wrote: > Hi, > > http://bioinfo.icapture.ubc.ca/ekawas/biomobyPlugin.zip > > The above link is to a zip file consisting of 6 jar files. > If you place these jar files in the lib directory, where you > installed Taverna, typically /taverna-workbench-1.1/lib/ and > you delete > /taverna-workbench-1.1/lib/jmoby.jar, > you *may* have new and improved Moby support for Taverna. > The reason that I say may have, is because I have only tried > this on my windows machine. > > Note that right now, the plugin only queries the Mobycentral > registry. You can still ask it to use yours, but it will not > work 100%. > > Also note that the local widgets do not work (well, that's a > lie, the create collection widget works). > > http://bioinfo.icapture.ubc.ca/ekawas/workflow.xml > http://bioinfo.icapture.ubc.ca/ekawas/workflowInput.xml > > Above is are urls to a workflow definition file (you can > load it into Taverna) as well as its inputs, as an example > of how to use the plugin. > > I have added some context (right) click information to Moby > objects and services. You can try this from the window > labeled 'Advanced Model Explorer'. Basically, right-click a > Moby related object or service instance from the > 'Processors' list and choose either 'Moby Object Details' or > 'Moby Service Details'. > > I am interested in all feedback both good and bad. I still > have a lot to do, but I figure that the more eyes trying > (testing) will help me make it better. This is a working > prototype, in the spirit of BioMoby ;-) > > If I make significant changes, I will let you know. > > Thanks, > > Eddie Kawas > edward.kawas at gmail.com > > > _______________________________________________ > moby-l mailing list > moby-l at biomoby.org > http://biomoby.org/mailman/listinfo/moby-l > -- Simon N. Twigger, Ph.D. Assistant Professor, Department of Physiology Medical College of Wisconsin 8701 Watertown Plank Road, Milwaukee, WI, USA tel: 414-456-8802 fax: 414-456-6595 AIM/iChat: simontatmcw From markw at illuminae.com Fri Jun 10 14:38:07 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 10 Jun 2005 11:38:07 -0700 Subject: [MOBY-l] going offline for a couple of weeks Message-ID: <1118428687.27504.60.camel@mobycentral.mrl.ubc.ca> Hi all, There are Genome Canada face-to-face reviews coming up next week, followed by ISMB. I also have a meeting in Rome starting Tuesday. As such, I anticipate being "unavailable" as of this afternoon until ~June 25th. I just want to let the other developers know this so that you can quickly jump in and respond to questions that get posted to the list. We've got a pretty good reputation for rapid response :-) :-) Cheers all! See you on the other side! M -- Mark Wilkinson Asst. Professor Dept. of Medical Genetics University of British Columbia PI in Bioinformatics iCAPTURE Centre St. Paul's Hospital Vancouver, BC From paolo at ist.unige.it Thu Jun 16 06:52:32 2005 From: paolo at ist.unige.it (Paolo Romano) Date: Thu, 16 Jun 2005 12:52:32 +0200 (DFT) Subject: [MOBY-l] NETTAB 2005 oral communications deadline postponed Message-ID: <200506161052.j5GAqWAP014998@ibm43p.biotech.ist.unige.it> Dear colleagues, the deadline for the submission of abstracts for oral communications to the NETTAB 2005 workshop on "Workflows management: new abilities for the biological information overflow" has been postponed to next June 27 ,2005. I'm therefore resending here some essential information on the workshop and the Call for Papers. Best regards. Paolo Romano ---- NETTAB 2005 Workflows management: new abilities for the biological information overflow http://www.nettab.org/2005/ 5-7 October, 2005 Second University of Naples, Naples, Italy CALL FOR PAPERS NETTAB 2005 workshop is organized in sessions and open discussions. Invited speakers will present the state of art of the session's topic, a number of submissions will be accepted for oral presentation, and a poster session is also foreseen. Open discussions will also be based upon submitted issues and topics. A call for position papers, posters and oral presentations is now open. Information will soon be added to the web site. Workshop topics Submitted contributions should address one or more of the following topics: Technologies and technological platforms of interest to the field, with emphasis on: - Web Services (SOAP, WSDL, WSFL, UDDI, ....) - Web Services Choreography and Orchestration - Semantic Web (RDF, LSID, OWL, ...) - comparison of available technologies, limitations, pros and cons - Knowledge representation - Biological data and knowledge modeling tools - Ontologies, Databases and Applications of Semantics in Bioinformatics Workflow management systems in bioinformatics: - implementations of web services - implementations of registries - reuse and versioning of web services and workflows - workflow management systems - web interfaces for accessing and executing workflows - interactive systems to support work flows Applications of workflow management systems in bioinformatics - Methodologies for life sciences analysis: gene expression, genome annotation, mass spec peptide fragment identification, etc... - Encoding of the above in workflows - Case studies - Scenarios and use cases Submission of contributions Authors are invited to submit: Oral Presentations: submit an extended abstract (4-5 A4 pages, size 12pt, MS Word format). Abstracts will be reviewed and acceptance or rejection will be communicated to authors. All submissions for oral presentation which are not selected will automatically be considered for posters presentation. Posters: submit an extended abstract (2-3 A4 pages, size 12pt, MS Word format). Abstracts will be reviewed by relevance and acceptance or rejection will be communicated to authors. Position papers: submit a short abstract (max 1 A4 pages in length, size 12pt, MS Word format) specifying research interests and issues to be debated during the workshop. Authors submitting position papers do not engage themselves to present a poster. Instead, they will be invited to introduce the issues they arose before open discussion sessions. Abstracts can be submitted from May 1st, 2005, through the NETTAB 2005 Paper Review System availble at the workshop web site. Contributions will be reviewed by the scientific committee for relevance, clarity and novelty of results. Accepted oral presentations, posters and position papers will be published in the conference proceedings. Authors of a selection of best papers will be asked to submit an extended version of their paper in view of a joint submission to a peer-reviewed international journal. Deadlines - Oral presentations due: June 27, 2005. - Notification to authors: July 29, 2005. - Posters and position papers due: August 26, 2005. Registration: - Early registration: August 26, 2005 -- Paolo Romano (paolo.romano at istge.it) Bioinformatics and Structural Proteomics National Cancer Research Institute (IST) Largo Rosanna Benzi, 10, I-16132, Genova, Italy Tel: +39-010-5737-288 Fax: +39-010-5737-295 Web: http://www.nettab.org/promano/ From simont at mcw.edu Thu Jun 16 11:46:38 2005 From: simont at mcw.edu (Twigger Simon) Date: Thu, 16 Jun 2005 10:46:38 -0500 Subject: [MOBY-l] Comments from recent Taverna/services demo Message-ID: <82EBEA28-EBB3-405E-81DF-6D612647F587@mcw.edu> Hi there, Just thought I'd share some of the comments I heard from our lab folks following a taverna/webservice demo I just did. I expect these are not new to most people but they do represent barriers to potential users of this technology that we need to actively address so I thought a quick reminder/discussion wouldnt hurt. Provenance: How do we know what data a service is running on, what version of an algorithm, what parameters its using, when the database was last updated, etc? This seemed to be the biggest concern - not knowing what was going on under the hood and having no way to find it out. Workflows and services provide great ways to automate things but theres a distrust of the 'black box' that this creates. From a MOBY perspective, if we could somehow enforce the provision information block so that service providers had to fill in something sensible for the service (algorithm version, database version, date last updated, etc.) this could be a very good selling point. "Use MOBY services where possible because at least then you can get a list of what went on in your workflow, what databases were searched, etc." Some sort of report at the end of a taverna workflow that compiled all this provision data into a human readable document would be great. In reality, this is the same as getting data off a website - how do you know what's going on? Good websites tell you what algorithm and database they use, others dont. I suspect people are more familiar and hence more trusting of websites and havent yet got comfortable with webservices/workflows so the level of (blind?) trust isnt there. Input's and Outputs - How do I know what data I should pass in? Again, MOBY is nice in that it defines the objects and should ameliorate a lot of these problems but joining the dots is harder than it should be, particularly outside of MOBY-land. Make it even easier to use "Is taverna something even I could use?", "I got lost with all these service options" Drag and drop, connect the dots services seems pretty straight forward but it may still be too much for your average (or even above average) lab scientist. How have other people found this technology has been accepted? A web front end to all these services and workflows seems to be one of the best ways we could get this technology in use by the largest number of people. I'd love to hear any comments/thoughts about these issues from others. Cheers, Simon. -- Simon N. Twigger, Ph.D. Assistant Professor, Department of Physiology Medical College of Wisconsin 8701 Watertown Plank Road, Milwaukee, WI, USA tel: 414-456-8802 fax: 414-456-6595 AIM/iChat: simontatmcw From ywong at infobiogen.fr Thu Jun 16 14:05:57 2005 From: ywong at infobiogen.fr (ywong@infobiogen.fr) Date: Thu, 16 Jun 2005 20:05:57 +0200 (CEST) Subject: [MOBY-l] Object ontology browser Message-ID: <1476.82.66.216.27.1118945157.squirrel@82.66.216.27> Hello, I've Built a ontology object browser in Java. It has the same functionalities than the Python version. For people using unix and windows: http://yan.wong.free.fr/Public/jMOBrowser.zip unzip the file and launch the objectBrowser script For people using MacOS X (you'll need Java machine 1.4+): http://yan.wong.free.fr/Public/jMOBrowser.dmg if you are asked for a password and login: login: Invite password: invite No third party libraries required! just drag'n drop the application to a location on your disk and double click! From d.haase at gsf.de Mon Jun 27 10:58:21 2005 From: d.haase at gsf.de (Dirk Haase) Date: Mon, 27 Jun 2005 16:58:21 +0200 Subject: [MOBY-l] Object ontology browser In-Reply-To: <1476.82.66.216.27.1118945157.squirrel@82.66.216.27> References: <1476.82.66.216.27.1118945157.squirrel@82.66.216.27> Message-ID: <200506271658.21277.d.haase@gsf.de> Hi Yan, On Thursday 16 June 2005 20:05, ywong at infobiogen.fr wrote: > Hello, > > I've Built a ontology object browser in Java. It has the same > functionalities than the Python version. > > For people using unix and windows: > http://yan.wong.free.fr/Public/jMOBrowser.zip > > unzip the file and launch the objectBrowser script I just tried your object ontology browser and it works nice on our Linux boxes. Just one remark: in the dialog which opens after selecting 'Browse a Moby directory', I found the labels for the input fields very confusing. I would prefer "Moby Central URL" instead of just "URL" and - even more important - "Moby Central URI" instead of 'Namespace'. I first tried to insert namespaces like "Global_Keyword" in the latter one and got obscure error messages... Clicking the Root node always leads to a NPE - which does no harm besides spoiling the start shell with ugly java errors... But the rest of it is very nice! Regards, dirk From ywong at infobiogen.fr Tue Jun 28 05:50:03 2005 From: ywong at infobiogen.fr (Yan Wong) Date: Tue, 28 Jun 2005 11:50:03 +0200 Subject: [MOBY-l] Object ontology browser In-Reply-To: <200506271658.21277.d.haase@gsf.de> References: <1476.82.66.216.27.1118945157.squirrel@82.66.216.27> <200506271658.21277.d.haase@gsf.de> Message-ID: <42C11D4B.1040502@infobiogen.fr> Dirk Haase wrote: >Hi Yan, > >On Thursday 16 June 2005 20:05, ywong at infobiogen.fr wrote: > > >>Hello, >> >>I've Built a ontology object browser in Java. It has the same >>functionalities than the Python version. >> >>For people using unix and windows: >> http://yan.wong.free.fr/Public/jMOBrowser.zip >> >>unzip the file and launch the objectBrowser script >> >> > >I just tried your object ontology browser and it works nice on our Linux >boxes. Just one remark: in the dialog which opens after selecting 'Browse a >Moby directory', I found the labels for the input fields very confusing. I >would prefer "Moby Central URL" instead of just "URL" and - even more >important - "Moby Central URI" instead of 'Namespace'. I first tried to >insert namespaces like "Global_Keyword" in the latter one and got obscure >error messages... > >Clicking the Root node always leads to a NPE - which does no harm besides >spoiling the start shell with ugly java errors... > >But the rest of it is very nice! > >Regards, >dirk >_______________________________________________ >moby-l mailing list >moby-l at biomoby.org >http://biomoby.org/mailman/listinfo/moby-l > > > OK I posted the modifications this morning... If I have time, I'll implement some search functionalities... From markw at illuminae.com Tue Jun 28 09:52:36 2005 From: markw at illuminae.com (mark wilkinson) Date: Tue, 28 Jun 2005 13:52:36 +0000 GMT Subject: [MOBY-l] Object ontology browser Message-ID: <1293586438-1119967038-cardhu_blackberry.rim.net-3291-@engine10-cell01> Do you want me to add this to the "cool tools" page? M -----Original Message----- From: Yan Wong Date: Tue, 28 Jun 2005 11:50:03 To:Dirk Haase Cc:moby-l at biomoby.org Subject: Re: [MOBY-l] Object ontology browser Dirk Haase wrote: >Hi Yan, > >On Thursday 16 June 2005 20:05, ywong at infobiogen.fr wrote: > > >>Hello, >> >>I've Built a ontology object browser in Java. It has the same >>functionalities than the Python version. >> >>For people using unix and windows: >> http://yan.wong.free.fr/Public/jMOBrowser.zip >> >>unzip the file and launch the objectBrowser script >> >> > >I just tried your object ontology browser and it works nice on our Linux >boxes. Just one remark: in the dialog which opens after selecting 'Browse a >Moby directory', I found the labels for the input fields very confusing. I >would prefer "Moby Central URL" instead of just "URL" and - even more >important - "Moby Central URI" instead of 'Namespace'. I first tried to >insert namespaces like "Global_Keyword" in the latter one and got obscure >error messages... > >Clicking the Root node always leads to a NPE - which does no harm besides >spoiling the start shell with ugly java errors... > >But the rest of it is very nice! > >Regards, >dirk >_______________________________________________ >moby-l mailing list >moby-l at biomoby.org >http://biomoby.org/mailman/listinfo/moby-l > > > OK I posted the modifications this morning... If I have time, I'll implement some search functionalities... _______________________________________________ moby-l mailing list moby-l at biomoby.org http://biomoby.org/mailman/listinfo/moby-l -- Mark Wilkinson ...on the road! From ywong at infobiogen.fr Tue Jun 28 10:24:05 2005 From: ywong at infobiogen.fr (Yan Wong) Date: Tue, 28 Jun 2005 16:24:05 +0200 Subject: [MOBY-l] Object ontology browser In-Reply-To: <1293586438-1119967038-cardhu_blackberry.rim.net-3291-@engine10-cell01> References: <1293586438-1119967038-cardhu_blackberry.rim.net-3291-@engine10-cell01> Message-ID: <42C15D85.7010707@infobiogen.fr> mark wilkinson wrote: >Do you want me to add this to the "cool tools" page? > >M > > >-----Original Message----- >From: Yan Wong >Date: Tue, 28 Jun 2005 11:50:03 >To:Dirk Haase >Cc:moby-l at biomoby.org >Subject: Re: [MOBY-l] Object ontology browser > >Dirk Haase wrote: > > > >>Hi Yan, >> >>On Thursday 16 June 2005 20:05, ywong at infobiogen.fr wrote: >> >> >> >> >>>Hello, >>> >>>I've Built a ontology object browser in Java. It has the same >>>functionalities than the Python version. >>> >>>For people using unix and windows: >>> http://yan.wong.free.fr/Public/jMOBrowser.zip >>> >>>unzip the file and launch the objectBrowser script >>> >>> >>> >>> >>I just tried your object ontology browser and it works nice on our Linux >>boxes. Just one remark: in the dialog which opens after selecting 'Browse a >>Moby directory', I found the labels for the input fields very confusing. I >>would prefer "Moby Central URL" instead of just "URL" and - even more >>important - "Moby Central URI" instead of 'Namespace'. I first tried to >>insert namespaces like "Global_Keyword" in the latter one and got obscure >>error messages... >> >>Clicking the Root node always leads to a NPE - which does no harm besides >>spoiling the start shell with ugly java errors... >> >>But the rest of it is very nice! >> >>Regards, >>dirk >>_______________________________________________ >>moby-l mailing list >>moby-l at biomoby.org >>http://biomoby.org/mailman/listinfo/moby-l >> >> >> >> >> >OK I posted the modifications this morning... If I have time, I'll >implement some search functionalities... >_______________________________________________ >moby-l mailing list >moby-l at biomoby.org >http://biomoby.org/mailman/listinfo/moby-l > >-- >Mark Wilkinson >...on the road! > > > There is also a Mac OS X (tested on 10.3 and 10.4) version on http://yan.wong.free.fr/Public/jMOBrowser.dmg login: Invite password: invite You can add them to "the cool tools" section if you want ;) From markw at illuminae.com Tue Jun 28 11:56:17 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 28 Jun 2005 08:56:17 -0700 Subject: [moby] Re: [MOBY-l] Object ontology browser In-Reply-To: <42C15D85.7010707@infobiogen.fr> References: <1293586438-1119967038-cardhu_blackberry.rim.net-3291-@engine10-cell01> <42C15D85.7010707@infobiogen.fr> Message-ID: <1119974177.15887.12.camel@mobycentral.mrl.ubc.ca> On Tue, 2005-06-28 at 16:24 +0200, Yan Wong wrote: > You can add them to "the cool tools" section if you want ;) Done, with pleasure! M -- Mark Wilkinson Asst. Professor Dept. of Medical Genetics University of British Columbia PI in Bioinformatics iCAPTURE Centre St. Paul's Hospital Vancouver, BC From markw at illuminae.com Wed Jun 29 11:25:05 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 29 Jun 2005 08:25:05 -0700 Subject: [MOBY-l] MOBY Central hacked last night Message-ID: <1120058705.20181.26.camel@mobycentral.mrl.ubc.ca> Hi all, MOBY Central is down for at least a day due to a nasty hack last night. We may have to rebuild from scratch, so it may not be a rapid recovery. Speaks again to the need for a mirroring system! Hey, Heiko... how's the research going? ;-) ;-) You can run, but you can't hide! Sorry for the down-time... M -- Mark Wilkinson Asst. Professor Dept. of Medical Genetics University of British Columbia PI in Bioinformatics iCAPTURE Centre St. Paul's Hospital Vancouver, BC From markw at illuminae.com Thu Jun 30 19:38:45 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 30 Jun 2005 16:38:45 -0700 Subject: [MOBY-l] MOBY Central Registry up and running at a new location Message-ID: <1120174725.31990.6.camel@mobycentral.mrl.ubc.ca> Hi all, The core of MOBY Central is up and running again at: URL: http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl URI: http://mobycentral.icapture.ubc.ca/MOBY/Central No accessories are functioning, however. Just the registry. Also, none of my services will be working either. No data loss as far as I can tell at the moment, so that is good news! I will begin migrating the accessories over to this new server tomorrow. Hopefully we will have things running again by the end of the weekend, but for the moment at least the registry itself is functional. remember you can use this registry as your default for the Perl libraries by setting the environment variables: MOBY_SERVER= $URL (above) MOBY_URI = $URI (above) This will cause MOBY::Client::Central to connect to this server by default. I will make changes to the test harness in the CVS soon. It doesn't matter, really, because the version in the CVS is non-functional until we can get the Perl LSID resolver stack working }-/ Anyway, sorry for the down-time! What a disaster! (but I did learn a lot about what it takes to install MOBY Central now! So I have lots of good notes for our documentation drive...) M -- Mark Wilkinson Asst. Professor Dept. of Medical Genetics University of British Columbia PI in Bioinformatics iCAPTURE Centre St. Paul's Hospital Vancouver, BC