From mwilkinson at mrl.ubc.ca Tue Jan 4 19:53:58 2005 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Tue Jan 4 19:18:55 2005 Subject: [MOBY-l] MOBY in The Scientist Message-ID: <1104886438.3699.119.camel@mobycentral.icapture.ubc.ca> Hi all, MOBY and myGrid get good press in the December issue of The Scientist :-) M -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From mwilkinson at mrl.ubc.ca Tue Jan 11 20:07:18 2005 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Tue Jan 11 19:30:39 2005 Subject: [MOBY-l] For anyone who is counting... Message-ID: <1105492038.23571.7.camel@mobycentral.icapture.ubc.ca> Here are the current stats for the public MOBY Central registry and ontologies: # of authorities providing services: 74 # of services: 216 # of registered datatypes: 110 # of registered namespaces: 149 Lets hear it for community-driven development!! :-) I'm running the access log now and I'll post to the list when it is done. M -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From markw at illuminae.com Tue Jan 11 18:09:29 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Tue Jan 11 20:06:58 2005 Subject: [MOBY-l] more stats Message-ID: <41E45CA9.90803@illuminae.com> Google links says... 327 sites currently linking to www.biomoby.org! (that number seems to change dramatically each time I check it, so I don't know how reliable it is...) M From mwilkinson at mrl.ubc.ca Wed Jan 12 12:30:50 2005 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Wed Jan 12 11:53:45 2005 Subject: [MOBY-l] New "Cool Tools" links Message-ID: <1105551050.24758.18.camel@mobycentral.icapture.ubc.ca> Hi all, I've added Eddie Kawas' and Ambrose Ng's tools to the "Cool Tools" page for MOBY-S. These are GUI's that assist in the creation of new MOBY-related resources including Objects, Service types, Namespaces and Service Instance registration. Have fun! Please report any bugs to this list. Cheers! Mark -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From willi at apple.com Wed Jan 12 15:33:32 2005 From: willi at apple.com (Willi Powell) Date: Tue Jan 18 21:40:07 2005 Subject: [MOBY-l] biomoby on Mac OS X Message-ID: <39934000-64D9-11D9-957E-000A95B3E218@apple.com> Hello; I am curious is there anybody on this list that has had experience with BioMoby on Mac Os X Server. We have a prospective customer who has expressed interest in running BioMoby on our Xserves, we think it should run great, but would like to hear if there are any other installs out there. If you have any positive or negative comments, please I would to hear them. Thank you in advance, Willi Powell ---------------------------------------------------------------- Strategic Development Manager Apple willi@apple.com 7495 Birchmount Rd (905) 513 5697 Toronto ON http://www.apple.com/pro/ Canada L3R-5G2 ---------------------------------------------------------------- From bmg at sfu.ca Wed Jan 19 11:00:22 2005 From: bmg at sfu.ca (Benjamin Good) Date: Wed Jan 19 11:06:34 2005 Subject: [MOBY-l] biomoby on Mac OS X In-Reply-To: <39934000-64D9-11D9-957E-000A95B3E218@apple.com> References: <39934000-64D9-11D9-957E-000A95B3E218@apple.com> Message-ID: <1106150422.6060.11.camel@pacifico.mrl.ubc.ca> I have run clients and hosted services from my mac. I haven't tried to install the Perl API, but the Java code didn't produce any problems at all. -Ben On Wed, 2005-01-12 at 12:33, Willi Powell wrote: > Hello; > > I am curious is there anybody on this list that has had experience with > BioMoby on Mac Os X Server. We have a prospective customer who has > expressed interest in running BioMoby on our Xserves, we think it > should run great, but would like to hear if there are any other > installs out there. If you have any positive or negative comments, > please I would to hear them. > > Thank you in advance, > Willi Powell > ---------------------------------------------------------------- > Strategic Development Manager Apple > willi@apple.com 7495 Birchmount Rd > (905) 513 5697 Toronto ON > http://www.apple.com/pro/ Canada L3R-5G2 > ---------------------------------------------------------------- > > _______________________________________________ > moby-l mailing list > moby-l@biomoby.org > http://biomoby.org/mailman/listinfo/moby-l > From markw at illuminae.com Wed Jan 19 23:51:38 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Wed Jan 19 23:47:48 2005 Subject: [MOBY-l] GO services work again Message-ID: <41EF38DA.5010201@illuminae.com> I know a few people have been asking for them to come back on-line... sorry about that! Once flybase closed access to their GO database a few months ago I had trouble finding another public one. I found one today :-) Cheers all! M From simont at mcw.edu Thu Jan 20 17:30:51 2005 From: simont at mcw.edu (Twigger Simon) Date: Thu Jan 20 17:27:00 2005 Subject: [MOBY-l] Taverna & MOBY services Message-ID: Hi there, Im trying to get a quick MOBY service up and running using Taverna and its not working quite as I would like. I deregistered my old keywordToGene service, moved it to a new machine, updated the MOBY code to 0.8 and reregistered the service. Ive checked it out using the gbrowse client and it seems to behave appropriately. Querying with a global_keyword seed text of A2m brings back the correct information. However, if I set something up in Taverna to send the same text to the service it always fails, the stack trace in the terminal seems to indicate a perl problem with an error thrown by XML::Parser I noticed from Mark's last presentation that the taverna workflow shown there seems to have two input objects (blue triangles) - presumably a namespace and an ID that are going into a create_moby_data 'box'. Im wondering if there is more to using MOBY via Taverna than a simple text input object and that is my problem, or if its a more fundamental service problem. I would love to get things working with Taverna so any thoughts would be most appreciated! 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 simont at mcw.edu Thu Jan 20 17:42:23 2005 From: simont at mcw.edu (Twigger Simon) Date: Thu Jan 20 17:38:26 2005 Subject: [MOBY-l] Taverna & MOBY services In-Reply-To: References: Message-ID: <8D4A28CE-6B34-11D9-B93F-000A959D1D82@mcw.edu> Michael, I hadnt seen those, I also didnt read further into the taverna docs and there does seem to be a bunch of MOBY info and examples so I think I need to RTFM some more and that will certainly help! Thanks for pointing out the examples. Simon. On Jan 20, 2005, at 4:36 PM, Michael Jensen wrote: > Did you try the Dragon DB Annotated Images example workflow that comes > with the Taverna examples? That one works well and can be used to help > you figure out others. > > -Michael > > > On Thu, 20 Jan 2005 16:30:51 -0600, Twigger Simon > wrote: >> Hi there, >> >> Im trying to get a quick MOBY service up and running using Taverna and >> its not working quite as I would like. >> >> I deregistered my old keywordToGene service, moved it to a new >> machine, >> updated the MOBY code to 0.8 and reregistered the service. Ive checked >> it out using the gbrowse client and it seems to behave appropriately. >> Querying with a global_keyword seed text of A2m brings back the >> correct >> information. However, if I set something up in Taverna to send the >> same >> text to the service it always fails, the stack trace in the terminal >> seems to indicate a perl problem with an error thrown by XML::Parser >> >> I noticed from Mark's last presentation that the taverna workflow >> shown >> there seems to have two input objects (blue triangles) - presumably a >> namespace and an ID that are going into a create_moby_data 'box'. Im >> wondering if there is more to using MOBY via Taverna than a simple >> text >> input object and that is my problem, or if its a more fundamental >> service problem. >> >> I would love to get things working with Taverna so any thoughts would >> be most appreciated! >> >> 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 >> >> _______________________________________________ >> 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 mdjensen at gmail.com Thu Jan 20 17:36:31 2005 From: mdjensen at gmail.com (Michael Jensen) Date: Thu Jan 20 17:42:08 2005 Subject: [MOBY-l] Taverna & MOBY services In-Reply-To: References: Message-ID: Did you try the Dragon DB Annotated Images example workflow that comes with the Taverna examples? That one works well and can be used to help you figure out others. -Michael On Thu, 20 Jan 2005 16:30:51 -0600, Twigger Simon wrote: > Hi there, > > Im trying to get a quick MOBY service up and running using Taverna and > its not working quite as I would like. > > I deregistered my old keywordToGene service, moved it to a new machine, > updated the MOBY code to 0.8 and reregistered the service. Ive checked > it out using the gbrowse client and it seems to behave appropriately. > Querying with a global_keyword seed text of A2m brings back the correct > information. However, if I set something up in Taverna to send the same > text to the service it always fails, the stack trace in the terminal > seems to indicate a perl problem with an error thrown by XML::Parser > > I noticed from Mark's last presentation that the taverna workflow shown > there seems to have two input objects (blue triangles) - presumably a > namespace and an ID that are going into a create_moby_data 'box'. Im > wondering if there is more to using MOBY via Taverna than a simple text > input object and that is my problem, or if its a more fundamental > service problem. > > I would love to get things working with Taverna so any thoughts would > be most appreciated! > > 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 > > _______________________________________________ > moby-l mailing list > moby-l@biomoby.org > http://biomoby.org/mailman/listinfo/moby-l > > From mwilkinson at mrl.ubc.ca Thu Jan 20 18:23:25 2005 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Thu Jan 20 17:44:18 2005 Subject: [moby] Re: [MOBY-l] Taverna & MOBY services In-Reply-To: <8D4A28CE-6B34-11D9-B93F-000A959D1D82@mcw.edu> References: <8D4A28CE-6B34-11D9-B93F-000A959D1D82@mcw.edu> Message-ID: <1106263404.12776.151.camel@mobycentral.icapture.ubc.ca> yeah, Taverna rocks! You do need to create an input object, as you suggest. There's a "local Java Widget" called "create moby data" in the available widgets/services panel that will do that for you. you similarly need to unpack it at the end using the "parse moby data" widget. Just this morning I was chatting with Martin about creating a more intelligent set of MOBY widgets in Taverna that could fully unpack a MOBY object into its sub-objects, and/or into plain text to pass into other services. We're going to start working on this shortly! M On Thu, 2005-01-20 at 14:42, Twigger Simon wrote: > Michael, > > I hadnt seen those, I also didnt read further into the taverna docs and > there does seem to be a bunch of MOBY info and examples so I think I > need to RTFM some more and that will certainly help! > > Thanks for pointing out the examples. > > Simon. > > > On Jan 20, 2005, at 4:36 PM, Michael Jensen wrote: > > > Did you try the Dragon DB Annotated Images example workflow that comes > > with the Taverna examples? That one works well and can be used to help > > you figure out others. > > > > -Michael > > > > > > On Thu, 20 Jan 2005 16:30:51 -0600, Twigger Simon > > wrote: > >> Hi there, > >> > >> Im trying to get a quick MOBY service up and running using Taverna and > >> its not working quite as I would like. > >> > >> I deregistered my old keywordToGene service, moved it to a new > >> machine, > >> updated the MOBY code to 0.8 and reregistered the service. Ive checked > >> it out using the gbrowse client and it seems to behave appropriately. > >> Querying with a global_keyword seed text of A2m brings back the > >> correct > >> information. However, if I set something up in Taverna to send the > >> same > >> text to the service it always fails, the stack trace in the terminal > >> seems to indicate a perl problem with an error thrown by XML::Parser > >> > >> I noticed from Mark's last presentation that the taverna workflow > >> shown > >> there seems to have two input objects (blue triangles) - presumably a > >> namespace and an ID that are going into a create_moby_data 'box'. Im > >> wondering if there is more to using MOBY via Taverna than a simple > >> text > >> input object and that is my problem, or if its a more fundamental > >> service problem. > >> > >> I would love to get things working with Taverna so any thoughts would > >> be most appreciated! > >> > >> 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 > >> > >> _______________________________________________ > >> 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 > > _______________________________________________ > moby-l mailing list > moby-l@biomoby.org > http://biomoby.org/mailman/listinfo/moby-l -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From senger at ebi.ac.uk Thu Jan 20 17:49:07 2005 From: senger at ebi.ac.uk (Martin Senger) Date: Thu Jan 20 17:45:12 2005 Subject: [MOBY-l] Taverna & MOBY services In-Reply-To: Message-ID: > Im trying to get a quick MOBY service up and running using Taverna and > its not working quite as I would like. > The best would be to give me the name of your service (and perhaps the registry where it can be found - unloess it is in the main Mark's registry) - and the input (in raw XML) that you would like to send to that service. Then I will see what's happening, and perhaps I can find wher is the problem. > text to the service it always fails, the stack trace in the terminal > seems to indicate a perl problem with an error thrown by XML::Parser > That's why I would like to see the full (raw) XML you are sending to that service. > I noticed from Mark's last presentation that the taverna workflow shown > there seems to have two input objects (blue triangles) - presumably a > namespace and an ID that are going into a create_moby_data 'box'. Im > wondering if there is more to using MOBY via Taverna than a simple text > input object and that is my problem, or if its a more fundamental > service problem. > Well, you can always send a raw XML to a moby service in taverna - withou using any of these blue triangles. The create-moby-data widget is there only for simplest cases. The more complex input you have the more probably you need to create XML manually and send it as one input to taverna. Cheers, Martin -- Martin Senger EMBL Outstation - Hinxton Senger@EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From simont at mcw.edu Thu Jan 20 18:01:40 2005 From: simont at mcw.edu (Twigger Simon) Date: Thu Jan 20 17:57:43 2005 Subject: [MOBY-l] Taverna & MOBY services In-Reply-To: References: Message-ID: <3EE053B6-6B37-11D9-B93F-000A959D1D82@mcw.edu> I've managed to get the workflow doing something without breaking, Im a little hamstrung at the moment because Im using a Mac and for some reason I cant expand the processors in the advanced model explorer once I've assigned inputs and outputs - clicking with the mouse doesn't work so its hard to reroute things. (Tom Oinn had mentioned this was a 'feature' a while ago - I'll try on XP tonight) I need to add some more output objects to see if Im getting something sensible back out. I only linked the moby value to the one output object and its blank but I think thats because I have no value in my moby service output, I should try the namespace, etc. I suspect, just to test that things are happening. I'll explore the examples some more and go from there. Thanks for everyone's advice, I think Im on my way. Simon. Here's the XML that comes back from the service when I do a test query with On Jan 20, 2005, at 4:49 PM, Martin Senger wrote: >> Im trying to get a quick MOBY service up and running using Taverna and >> its not working quite as I would like. >> > The best would be to give me the name of your service (and perhaps > the > registry where it can be found - unloess it is in the main Mark's > registry) - and the input (in raw XML) that you would like to send to > that > service. Then I will see what's happening, and perhaps I can find wher > is > the problem. > >> text to the service it always fails, the stack trace in the terminal >> seems to indicate a perl problem with an error thrown by XML::Parser >> > That's why I would like to see the full (raw) XML you are sending to > that service. > >> I noticed from Mark's last presentation that the taverna workflow >> shown >> there seems to have two input objects (blue triangles) - presumably a >> namespace and an ID that are going into a create_moby_data 'box'. Im >> wondering if there is more to using MOBY via Taverna than a simple >> text >> input object and that is my problem, or if its a more fundamental >> service problem. >> > Well, you can always send a raw XML to a moby service in taverna - > withou using any of these blue triangles. The create-moby-data widget > is > there only for simplest cases. The more complex input you have the more > probably you need to create XML manually and send it as one input to > taverna. > > Cheers, > Martin > > -- > Martin Senger > > EMBL Outstation - Hinxton Senger@EBI.ac.uk > European Bioinformatics Institute Phone: (+44) 1223 494636 > Wellcome Trust Genome Campus (Switchboard: 494444) > Hinxton Fax : (+44) 1223 494468 > Cambridge CB10 1SD > United Kingdom > http://industry.ebi.ac.uk/~senger > > _______________________________________________ > 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 senger at ebi.ac.uk Mon Jan 24 03:44:06 2005 From: senger at ebi.ac.uk (Martin Senger) Date: Mon Jan 24 03:40:06 2005 Subject: [MOBY-l] [mygrid-general] Taverna version 1.0 release (fwd) Message-ID: FYI... -- Martin Senger EMBL Outstation - Hinxton Senger@EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger ---------- Forwarded message ---------- Date: Fri, 21 Jan 2005 22:22:58 +0000 From: Tom Oinn To: "Taverna-Users (E-mail)" , taverna-hackers@lists.sourceforge.net, mygrid-general@mygrid.info Subject: [mygrid-general] Taverna version 1.0 release Hi all, We're pleased to announce that Taverna, myGrid's workflow design and enactment environment has finally reached version 1.0 and has been released into the wild! Our website at http://taverna.sf.net will be updated to reflect this on Monday, in the meantime the release and it's accompanying user manual may be downloaded from here : http://sourceforge.net/project/showfiles.php?group_id=74874&package_id=75230&release_id=298786 I'd like to thank everyone involved in the development of this release, particularly Justin, Martin and Kevin within the myGrid project, Jon Blower at Reading eScience center for his help with Styx, the BioMart and External Services groups at the EBI for assistance with development and deployment respectively, the BioMoby developers for their ongoing support and of course the EPSRC for paying for us in the first place! Nothing is ever finished of course and we have plenty of fun stuff planned for the near future - look out for integration with the semantic registry activities, an interactive graphical workflow editor and much more. Cheers guys :) Tom Oinn - Taverna lead -- No virus found in this outgoing message. Checked by AVG Anti-Virus. Version: 7.0.300 / Virus Database: 265.7.0 - Release Date: 17/01/2005 _______________________________________________ myGrid-general mailing list myGrid-general@mygrid.info http://mygrid.info/mailman/listinfo/mygrid-general From mwilkinson at mrl.ubc.ca Tue Jan 4 19:53:58 2005 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Tue, 04 Jan 2005 16:53:58 -0800 Subject: [MOBY-l] MOBY in The Scientist Message-ID: <1104886438.3699.119.camel@mobycentral.icapture.ubc.ca> Hi all, MOBY and myGrid get good press in the December issue of The Scientist :-) M -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From mwilkinson at mrl.ubc.ca Tue Jan 11 20:07:18 2005 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Tue, 11 Jan 2005 17:07:18 -0800 Subject: [MOBY-l] For anyone who is counting... Message-ID: <1105492038.23571.7.camel@mobycentral.icapture.ubc.ca> Here are the current stats for the public MOBY Central registry and ontologies: # of authorities providing services: 74 # of services: 216 # of registered datatypes: 110 # of registered namespaces: 149 Lets hear it for community-driven development!! :-) I'm running the access log now and I'll post to the list when it is done. M -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From markw at illuminae.com Tue Jan 11 18:09:29 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 11 Jan 2005 17:09:29 -0600 Subject: [MOBY-l] more stats Message-ID: <41E45CA9.90803@illuminae.com> Google links says... 327 sites currently linking to www.biomoby.org! (that number seems to change dramatically each time I check it, so I don't know how reliable it is...) M From mwilkinson at mrl.ubc.ca Wed Jan 12 12:30:50 2005 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Wed, 12 Jan 2005 09:30:50 -0800 Subject: [MOBY-l] New "Cool Tools" links Message-ID: <1105551050.24758.18.camel@mobycentral.icapture.ubc.ca> Hi all, I've added Eddie Kawas' and Ambrose Ng's tools to the "Cool Tools" page for MOBY-S. These are GUI's that assist in the creation of new MOBY-related resources including Objects, Service types, Namespaces and Service Instance registration. Have fun! Please report any bugs to this list. Cheers! Mark -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From willi at apple.com Wed Jan 12 15:33:32 2005 From: willi at apple.com (Willi Powell) Date: Wed, 12 Jan 2005 15:33:32 -0500 Subject: [MOBY-l] biomoby on Mac OS X Message-ID: <39934000-64D9-11D9-957E-000A95B3E218@apple.com> Hello; I am curious is there anybody on this list that has had experience with BioMoby on Mac Os X Server. We have a prospective customer who has expressed interest in running BioMoby on our Xserves, we think it should run great, but would like to hear if there are any other installs out there. If you have any positive or negative comments, please I would to hear them. Thank you in advance, Willi Powell ---------------------------------------------------------------- Strategic Development Manager Apple willi at apple.com 7495 Birchmount Rd (905) 513 5697 Toronto ON http://www.apple.com/pro/ Canada L3R-5G2 ---------------------------------------------------------------- From bmg at sfu.ca Wed Jan 19 11:00:22 2005 From: bmg at sfu.ca (Benjamin Good) Date: 19 Jan 2005 08:00:22 -0800 Subject: [MOBY-l] biomoby on Mac OS X In-Reply-To: <39934000-64D9-11D9-957E-000A95B3E218@apple.com> References: <39934000-64D9-11D9-957E-000A95B3E218@apple.com> Message-ID: <1106150422.6060.11.camel@pacifico.mrl.ubc.ca> I have run clients and hosted services from my mac. I haven't tried to install the Perl API, but the Java code didn't produce any problems at all. -Ben On Wed, 2005-01-12 at 12:33, Willi Powell wrote: > Hello; > > I am curious is there anybody on this list that has had experience with > BioMoby on Mac Os X Server. We have a prospective customer who has > expressed interest in running BioMoby on our Xserves, we think it > should run great, but would like to hear if there are any other > installs out there. If you have any positive or negative comments, > please I would to hear them. > > Thank you in advance, > Willi Powell > ---------------------------------------------------------------- > Strategic Development Manager Apple > willi at apple.com 7495 Birchmount Rd > (905) 513 5697 Toronto ON > http://www.apple.com/pro/ Canada L3R-5G2 > ---------------------------------------------------------------- > > _______________________________________________ > moby-l mailing list > moby-l at biomoby.org > http://biomoby.org/mailman/listinfo/moby-l > From markw at illuminae.com Wed Jan 19 23:51:38 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 19 Jan 2005 20:51:38 -0800 Subject: [MOBY-l] GO services work again Message-ID: <41EF38DA.5010201@illuminae.com> I know a few people have been asking for them to come back on-line... sorry about that! Once flybase closed access to their GO database a few months ago I had trouble finding another public one. I found one today :-) Cheers all! M From simont at mcw.edu Thu Jan 20 17:30:51 2005 From: simont at mcw.edu (Twigger Simon) Date: Thu, 20 Jan 2005 16:30:51 -0600 Subject: [MOBY-l] Taverna & MOBY services Message-ID: Hi there, Im trying to get a quick MOBY service up and running using Taverna and its not working quite as I would like. I deregistered my old keywordToGene service, moved it to a new machine, updated the MOBY code to 0.8 and reregistered the service. Ive checked it out using the gbrowse client and it seems to behave appropriately. Querying with a global_keyword seed text of A2m brings back the correct information. However, if I set something up in Taverna to send the same text to the service it always fails, the stack trace in the terminal seems to indicate a perl problem with an error thrown by XML::Parser I noticed from Mark's last presentation that the taverna workflow shown there seems to have two input objects (blue triangles) - presumably a namespace and an ID that are going into a create_moby_data 'box'. Im wondering if there is more to using MOBY via Taverna than a simple text input object and that is my problem, or if its a more fundamental service problem. I would love to get things working with Taverna so any thoughts would be most appreciated! 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 simont at mcw.edu Thu Jan 20 17:42:23 2005 From: simont at mcw.edu (Twigger Simon) Date: Thu, 20 Jan 2005 16:42:23 -0600 Subject: [MOBY-l] Taverna & MOBY services In-Reply-To: References: Message-ID: <8D4A28CE-6B34-11D9-B93F-000A959D1D82@mcw.edu> Michael, I hadnt seen those, I also didnt read further into the taverna docs and there does seem to be a bunch of MOBY info and examples so I think I need to RTFM some more and that will certainly help! Thanks for pointing out the examples. Simon. On Jan 20, 2005, at 4:36 PM, Michael Jensen wrote: > Did you try the Dragon DB Annotated Images example workflow that comes > with the Taverna examples? That one works well and can be used to help > you figure out others. > > -Michael > > > On Thu, 20 Jan 2005 16:30:51 -0600, Twigger Simon > wrote: >> Hi there, >> >> Im trying to get a quick MOBY service up and running using Taverna and >> its not working quite as I would like. >> >> I deregistered my old keywordToGene service, moved it to a new >> machine, >> updated the MOBY code to 0.8 and reregistered the service. Ive checked >> it out using the gbrowse client and it seems to behave appropriately. >> Querying with a global_keyword seed text of A2m brings back the >> correct >> information. However, if I set something up in Taverna to send the >> same >> text to the service it always fails, the stack trace in the terminal >> seems to indicate a perl problem with an error thrown by XML::Parser >> >> I noticed from Mark's last presentation that the taverna workflow >> shown >> there seems to have two input objects (blue triangles) - presumably a >> namespace and an ID that are going into a create_moby_data 'box'. Im >> wondering if there is more to using MOBY via Taverna than a simple >> text >> input object and that is my problem, or if its a more fundamental >> service problem. >> >> I would love to get things working with Taverna so any thoughts would >> be most appreciated! >> >> 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 >> >> _______________________________________________ >> 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 mdjensen at gmail.com Thu Jan 20 17:36:31 2005 From: mdjensen at gmail.com (Michael Jensen) Date: Thu, 20 Jan 2005 16:36:31 -0600 Subject: [MOBY-l] Taverna & MOBY services In-Reply-To: References: Message-ID: Did you try the Dragon DB Annotated Images example workflow that comes with the Taverna examples? That one works well and can be used to help you figure out others. -Michael On Thu, 20 Jan 2005 16:30:51 -0600, Twigger Simon wrote: > Hi there, > > Im trying to get a quick MOBY service up and running using Taverna and > its not working quite as I would like. > > I deregistered my old keywordToGene service, moved it to a new machine, > updated the MOBY code to 0.8 and reregistered the service. Ive checked > it out using the gbrowse client and it seems to behave appropriately. > Querying with a global_keyword seed text of A2m brings back the correct > information. However, if I set something up in Taverna to send the same > text to the service it always fails, the stack trace in the terminal > seems to indicate a perl problem with an error thrown by XML::Parser > > I noticed from Mark's last presentation that the taverna workflow shown > there seems to have two input objects (blue triangles) - presumably a > namespace and an ID that are going into a create_moby_data 'box'. Im > wondering if there is more to using MOBY via Taverna than a simple text > input object and that is my problem, or if its a more fundamental > service problem. > > I would love to get things working with Taverna so any thoughts would > be most appreciated! > > 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 > > _______________________________________________ > moby-l mailing list > moby-l at biomoby.org > http://biomoby.org/mailman/listinfo/moby-l > > From mwilkinson at mrl.ubc.ca Thu Jan 20 18:23:25 2005 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Thu, 20 Jan 2005 15:23:25 -0800 Subject: [moby] Re: [MOBY-l] Taverna & MOBY services In-Reply-To: <8D4A28CE-6B34-11D9-B93F-000A959D1D82@mcw.edu> References: <8D4A28CE-6B34-11D9-B93F-000A959D1D82@mcw.edu> Message-ID: <1106263404.12776.151.camel@mobycentral.icapture.ubc.ca> yeah, Taverna rocks! You do need to create an input object, as you suggest. There's a "local Java Widget" called "create moby data" in the available widgets/services panel that will do that for you. you similarly need to unpack it at the end using the "parse moby data" widget. Just this morning I was chatting with Martin about creating a more intelligent set of MOBY widgets in Taverna that could fully unpack a MOBY object into its sub-objects, and/or into plain text to pass into other services. We're going to start working on this shortly! M On Thu, 2005-01-20 at 14:42, Twigger Simon wrote: > Michael, > > I hadnt seen those, I also didnt read further into the taverna docs and > there does seem to be a bunch of MOBY info and examples so I think I > need to RTFM some more and that will certainly help! > > Thanks for pointing out the examples. > > Simon. > > > On Jan 20, 2005, at 4:36 PM, Michael Jensen wrote: > > > Did you try the Dragon DB Annotated Images example workflow that comes > > with the Taverna examples? That one works well and can be used to help > > you figure out others. > > > > -Michael > > > > > > On Thu, 20 Jan 2005 16:30:51 -0600, Twigger Simon > > wrote: > >> Hi there, > >> > >> Im trying to get a quick MOBY service up and running using Taverna and > >> its not working quite as I would like. > >> > >> I deregistered my old keywordToGene service, moved it to a new > >> machine, > >> updated the MOBY code to 0.8 and reregistered the service. Ive checked > >> it out using the gbrowse client and it seems to behave appropriately. > >> Querying with a global_keyword seed text of A2m brings back the > >> correct > >> information. However, if I set something up in Taverna to send the > >> same > >> text to the service it always fails, the stack trace in the terminal > >> seems to indicate a perl problem with an error thrown by XML::Parser > >> > >> I noticed from Mark's last presentation that the taverna workflow > >> shown > >> there seems to have two input objects (blue triangles) - presumably a > >> namespace and an ID that are going into a create_moby_data 'box'. Im > >> wondering if there is more to using MOBY via Taverna than a simple > >> text > >> input object and that is my problem, or if its a more fundamental > >> service problem. > >> > >> I would love to get things working with Taverna so any thoughts would > >> be most appreciated! > >> > >> 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 > >> > >> _______________________________________________ > >> 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 > > _______________________________________________ > moby-l mailing list > moby-l at biomoby.org > http://biomoby.org/mailman/listinfo/moby-l -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From senger at ebi.ac.uk Thu Jan 20 17:49:07 2005 From: senger at ebi.ac.uk (Martin Senger) Date: Thu, 20 Jan 2005 22:49:07 +0000 (GMT) Subject: [MOBY-l] Taverna & MOBY services In-Reply-To: Message-ID: > Im trying to get a quick MOBY service up and running using Taverna and > its not working quite as I would like. > The best would be to give me the name of your service (and perhaps the registry where it can be found - unloess it is in the main Mark's registry) - and the input (in raw XML) that you would like to send to that service. Then I will see what's happening, and perhaps I can find wher is the problem. > text to the service it always fails, the stack trace in the terminal > seems to indicate a perl problem with an error thrown by XML::Parser > That's why I would like to see the full (raw) XML you are sending to that service. > I noticed from Mark's last presentation that the taverna workflow shown > there seems to have two input objects (blue triangles) - presumably a > namespace and an ID that are going into a create_moby_data 'box'. Im > wondering if there is more to using MOBY via Taverna than a simple text > input object and that is my problem, or if its a more fundamental > service problem. > Well, you can always send a raw XML to a moby service in taverna - withou using any of these blue triangles. The create-moby-data widget is there only for simplest cases. The more complex input you have the more probably you need to create XML manually and send it as one input to taverna. Cheers, Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From simont at mcw.edu Thu Jan 20 18:01:40 2005 From: simont at mcw.edu (Twigger Simon) Date: Thu, 20 Jan 2005 17:01:40 -0600 Subject: [MOBY-l] Taverna & MOBY services In-Reply-To: References: Message-ID: <3EE053B6-6B37-11D9-B93F-000A959D1D82@mcw.edu> I've managed to get the workflow doing something without breaking, Im a little hamstrung at the moment because Im using a Mac and for some reason I cant expand the processors in the advanced model explorer once I've assigned inputs and outputs - clicking with the mouse doesn't work so its hard to reroute things. (Tom Oinn had mentioned this was a 'feature' a while ago - I'll try on XP tonight) I need to add some more output objects to see if Im getting something sensible back out. I only linked the moby value to the one output object and its blank but I think thats because I have no value in my moby service output, I should try the namespace, etc. I suspect, just to test that things are happening. I'll explore the examples some more and go from there. Thanks for everyone's advice, I think Im on my way. Simon. Here's the XML that comes back from the service when I do a test query with On Jan 20, 2005, at 4:49 PM, Martin Senger wrote: >> Im trying to get a quick MOBY service up and running using Taverna and >> its not working quite as I would like. >> > The best would be to give me the name of your service (and perhaps > the > registry where it can be found - unloess it is in the main Mark's > registry) - and the input (in raw XML) that you would like to send to > that > service. Then I will see what's happening, and perhaps I can find wher > is > the problem. > >> text to the service it always fails, the stack trace in the terminal >> seems to indicate a perl problem with an error thrown by XML::Parser >> > That's why I would like to see the full (raw) XML you are sending to > that service. > >> I noticed from Mark's last presentation that the taverna workflow >> shown >> there seems to have two input objects (blue triangles) - presumably a >> namespace and an ID that are going into a create_moby_data 'box'. Im >> wondering if there is more to using MOBY via Taverna than a simple >> text >> input object and that is my problem, or if its a more fundamental >> service problem. >> > Well, you can always send a raw XML to a moby service in taverna - > withou using any of these blue triangles. The create-moby-data widget > is > there only for simplest cases. The more complex input you have the more > probably you need to create XML manually and send it as one input to > taverna. > > Cheers, > Martin > > -- > Martin Senger > > EMBL Outstation - Hinxton Senger at EBI.ac.uk > European Bioinformatics Institute Phone: (+44) 1223 494636 > Wellcome Trust Genome Campus (Switchboard: 494444) > Hinxton Fax : (+44) 1223 494468 > Cambridge CB10 1SD > United Kingdom > http://industry.ebi.ac.uk/~senger > > _______________________________________________ > 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 senger at ebi.ac.uk Mon Jan 24 03:44:06 2005 From: senger at ebi.ac.uk (Martin Senger) Date: Mon, 24 Jan 2005 08:44:06 +0000 (GMT) Subject: [MOBY-l] [mygrid-general] Taverna version 1.0 release (fwd) Message-ID: FYI... -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger ---------- Forwarded message ---------- Date: Fri, 21 Jan 2005 22:22:58 +0000 From: Tom Oinn To: "Taverna-Users (E-mail)" , taverna-hackers at lists.sourceforge.net, mygrid-general at mygrid.info Subject: [mygrid-general] Taverna version 1.0 release Hi all, We're pleased to announce that Taverna, myGrid's workflow design and enactment environment has finally reached version 1.0 and has been released into the wild! Our website at http://taverna.sf.net will be updated to reflect this on Monday, in the meantime the release and it's accompanying user manual may be downloaded from here : http://sourceforge.net/project/showfiles.php?group_id=74874&package_id=75230&release_id=298786 I'd like to thank everyone involved in the development of this release, particularly Justin, Martin and Kevin within the myGrid project, Jon Blower at Reading eScience center for his help with Styx, the BioMart and External Services groups at the EBI for assistance with development and deployment respectively, the BioMoby developers for their ongoing support and of course the EPSRC for paying for us in the first place! Nothing is ever finished of course and we have plenty of fun stuff planned for the near future - look out for integration with the semantic registry activities, an interactive graphical workflow editor and much more. Cheers guys :) Tom Oinn - Taverna lead -- No virus found in this outgoing message. Checked by AVG Anti-Virus. Version: 7.0.300 / Virus Database: 265.7.0 - Release Date: 17/01/2005 _______________________________________________ myGrid-general mailing list myGrid-general at mygrid.info http://mygrid.info/mailman/listinfo/mygrid-general