From silvia77 at dist.unige.it Tue Sep 6 06:24:03 2005 From: silvia77 at dist.unige.it (scaglione) Date: Tue Sep 6 06:24:20 2005 Subject: [MOBY-l] Re: sth_collection_ins In-Reply-To: <1124964729.430d9979a03e9@webmail.unige.it> References: <1124964729.430d9979a03e9@webmail.unige.it> Message-ID: <1126002243.431d6e4387d3d@webmail.unige.it> hello, I have finished (hopefully) to install moby central in my machine. I'm working to add some new GOWlab webservices into my moby central (up to now only "MOBY object" and "www.illuminae.com" services are available), to use these webservices into Taverna. Any suggestions? The registerService WSDL ( http://cvs.bioperl.org/cgi- bin/viewcvs/viewcvs.cgi/moby-live/Perl/MOBY/Central.html? cvsroot=biomoby&rev=1.5#registerservicewsdl ) seems to be useful for me, but unfortunately not implemented yet... Isn't it or I'm missing anything? thanks silvia Scrive scaglione : > hello, > I have followed instructions to install a moby central in my machine.I have > tried the testMOBYClientCentral_v05.pl script on my mobycentral and an error > > appeared: > > >perl testMOBYCentral_v05.pl > > Useless use of hash element in void context > at /usr/lib/perl5/site_perl/5.8.5/RDF/Core/Serializer.pm line 52. > Global symbol "$sth_collection_ins" requires explicit package name > at /usr/lib/perl5/site_perl/5.8.5/MOBY/Central.pm line 3426. > Compilation failed in require at testMOBYCentral_v05.pl line 4. > BEGIN failed--compilation aborted at testMOBYCentral_v05.pl line 4. > > what does it mean? > The overall configuration of the moby central seemed to be ok, since the test > > of the same script on the main mobycentral works... > many thanks > silvia > > > > -- > PhD. Silvia Scaglione > DIST University of Genoa > Viale Causa,13 > 16145 Genoa > phone +39 010 353 2789 > phone CBA +39 010 5737 505 > fax +39 010 353 2948 -- PhD. Silvia Scaglione DIST University of Genoa Viale Causa,13 16145 Genoa phone +39 010 353 2789 phone CBA +39 010 5737 505 fax +39 010 353 2948 From markw at illuminae.com Tue Sep 6 12:04:10 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Tue Sep 6 13:22:40 2005 Subject: [moby] [MOBY-l] Re: sth_collection_ins In-Reply-To: <1126002243.431d6e4387d3d@webmail.unige.it> References: <1124964729.430d9979a03e9@webmail.unige.it> <1126002243.431d6e4387d3d@webmail.unige.it> Message-ID: <1126022650.30434.43.camel@bioinfo.icapture.ubc.ca> It is not implemented, and may not be for a very long time (if ever) because it turns out that XML Schema has limitations that prevent us from accurately describing MOBY Objects. As such, we may never be able to *precisely* describe a MOBY service interface from a WSDL document. This is an XSD limitation, not a MOBY limitation :-/ M On Tue, 2005-09-06 at 12:24 +0200, scaglione wrote: > hello, > I have finished (hopefully) to install moby central in my machine. I'm working > to add some new GOWlab webservices into my moby central (up to now only "MOBY > object" and "www.illuminae.com" services are available), to use these > webservices into Taverna. > Any suggestions? > The registerService WSDL ( http://cvs.bioperl.org/cgi- > bin/viewcvs/viewcvs.cgi/moby-live/Perl/MOBY/Central.html? > cvsroot=biomoby&rev=1.5#registerservicewsdl ) seems to be useful for me, but > unfortunately not implemented yet... > Isn't it or I'm missing anything? > thanks > silvia > > Scrive scaglione : > > > hello, > > I have followed instructions to install a moby central in my machine.I have > > tried the testMOBYClientCentral_v05.pl script on my mobycentral and an error > > > > appeared: > > > > >perl testMOBYCentral_v05.pl > > > > Useless use of hash element in void context > > at /usr/lib/perl5/site_perl/5.8.5/RDF/Core/Serializer.pm line 52. > > Global symbol "$sth_collection_ins" requires explicit package name > > at /usr/lib/perl5/site_perl/5.8.5/MOBY/Central.pm line 3426. > > Compilation failed in require at testMOBYCentral_v05.pl line 4. > > BEGIN failed--compilation aborted at testMOBYCentral_v05.pl line 4. > > > > what does it mean? > > The overall configuration of the moby central seemed to be ok, since the test > > > > of the same script on the main mobycentral works... > > many thanks > > silvia > > > > > > > > -- > > PhD. Silvia Scaglione > > DIST University of Genoa > > Viale Causa,13 > > 16145 Genoa > > phone +39 010 353 2789 > > phone CBA +39 010 5737 505 > > fax +39 010 353 2948 > > -- "Ontologists do it with the edges!" Mark Wilkinson Asst. Professor Dept. of Medical Genetics University of British Columbia PI in Bioinformatics iCAPTURE Centre St. Paul's Hospital Rm. 166, 1081 Burrard St. Vancouver, BC, V6Z 1Y6 tel: 604 682 2344 x62129 fax: 604 806 9274 From tmo at ebi.ac.uk Tue Sep 6 13:57:59 2005 From: tmo at ebi.ac.uk (Tom Oinn) Date: Tue Sep 6 15:55:23 2005 Subject: [moby] [MOBY-l] Re: sth_collection_ins In-Reply-To: <1126022650.30434.43.camel@bioinfo.icapture.ubc.ca> References: <1124964729.430d9979a03e9@webmail.unige.it> <1126002243.431d6e4387d3d@webmail.unige.it> <1126022650.30434.43.camel@bioinfo.icapture.ubc.ca> Message-ID: <431DD8A7.2040007@ebi.ac.uk> >>hello, >>I have finished (hopefully) to install moby central in my machine. I'm working >>to add some new GOWlab webservices into my moby central (up to now only "MOBY >>object" and "www.illuminae.com" services are available), to use these >>webservices into Taverna. >>Any suggestions? Um... not to advocate not using Moby or anything but why would you want to convert GOWlab services to Moby ones to use in Taverna? Taverna has full support for GOWlab / SoapLab already and it's generally better than the support for Moby ;) Is there some reason you'd want to do this...? The only thing you don't get of course is registry support but this will appear soon enough (and will be integrated into the moby registry as well). Tom From schoof at mpiz-koeln.mpg.de Mon Sep 12 08:36:19 2005 From: schoof at mpiz-koeln.mpg.de (Heiko Schoof) Date: Mon Sep 12 08:44:52 2005 Subject: [MOBY-l] Moby Dick Message-ID: Hi, I just came across the EU project "Moby Dick" and thought you'd be amused as well... Best, Heiko Closing the gaps in the mobile Internet While mobile services try to provide constant connectivity, there are times, when switching from one network to another, when connections can be dropped. However temporary the network loss may be, it proves annoying for users, and threatens QoS standards. The EU-funded 'Moby Dick' project set out to build and evaluate a mobile network architecture based on the next-generation Internet protocol (IPv6) that addresses this problem. http://www.ccrle.nec.de/Projects/mobydick.htm ______________________ Max Planck Institute for Plant Breeding Research Plant Computational Biology Dr. Heiko Schoof Carl-von-Linne Weg 10 50829 Koeln Germany +49-(0)221 / 5062 - 445 Fax +49 221 5062 413 http://www.mpiz-koeln.mpg.de/english/research/ independent_research_groups/schoof/index.html schoof@mpiz-koeln.mpg.de From cwmoad at gmail.com Mon Sep 12 12:11:43 2005 From: cwmoad at gmail.com (Charlie Moad) Date: Mon Sep 12 12:29:42 2005 Subject: [MOBY-l] bioMoby python timeouts Message-ID: <6382066a0509120911961f50@mail.gmail.com> Hi, I am trying to experiment with the python interface to bioMoby and I am getting timeouts across the board. I am running samples provided in the tutorial as well. Are the services running right now? Thanks, Charlie From ywong at infobiogen.fr Tue Sep 13 17:43:28 2005 From: ywong at infobiogen.fr (ywong@infobiogen.fr) Date: Tue Sep 13 17:51:02 2005 Subject: [MOBY-l] bioMoby python timeouts In-Reply-To: <6382066a0509120911961f50@mail.gmail.com> References: <6382066a0509120911961f50@mail.gmail.com> Message-ID: <49311.82.66.216.27.1126647808.squirrel@82.66.216.27> What kind of problem do you have? Do the problems occur when you try to reach a moby central or a service? If you can't contact the moby central server, the cause maybe that by default, as far as I can remember, the url of the moby server is http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY05/mobycentral.pl Since I had little time these month following the changes on this API, I didn't change the default url. In order to connect to the moby central directory just add to your Client constructor the optional parameter url= you can have a trace of the transaction by changing the debug parameter to True: from bioMoby import Client client=Client(url="http://myown.mobyserver.org/central.pl", debug=True") This will help you diagnose problems with the central server. for the latter, you should execute the service with the debug option set to True, you may have a clue of what's going wrong. Greetings, Yan > Hi, > I am trying to experiment with the python interface to bioMoby and I am > getting timeouts across the board. I am running samples provided in the > tutorial as well. Are the services running right now? > > Thanks, > Charlie > > _______________________________________________ > moby-l mailing list > moby-l@biomoby.org > http://biomoby.org/mailman/listinfo/moby-l > From fgibbons at hms.harvard.edu Thu Sep 15 11:21:53 2005 From: fgibbons at hms.harvard.edu (Frank Gibbons) Date: Thu Sep 15 17:53:20 2005 Subject: [MOBY-l] Using bugzilla to continue RFC on Error-handling in MOBY-S Message-ID: <5.2.1.1.2.20050915105906.012401c8@email.med.harvard.edu> Hi, I've just added a few "bugs" to the bugzilla, to try to preserve the RFC momentum built up over the past few weeks. I propose that, although bugzilla is perhaps not ideal for this, it is what it is, it is what we have, and it will do for now. I'd like to propose that we try to continue development of this RFC through bugzilla (see bug #1863), rather than through the mailing list. Searching through old mail messages (or worse still, through the digest, with all of its repeated messages and long inclusions) is tedious, and I think contributes to the loss in momentum. So far, in Martin's scheme for RFC-processing, we have (numbers are those used in Martin's original suggestion, now available in the codebase as Docs/MOBY-S_API/RFC.html) 1. Had a suggestion made by INB to add this features. It was added to bugzilla, No. 1863 2. Suggested to resolve it by today (Sep-15) 3. Martin backed up the RFC 4. I think we have the resources to make this change - it seems an essential part of a robust API, which version 1.0 should be. 5a. List members have exchanged several comments back and forth, resulting in amended versions of the RFC being posted to the mailing list. 5b. We've also gotten a little side-tracked by the related articleName problem. So it seems to me that it's time to vote on it (step 6 of the Senger seven-step scheme ;-). Martin suggested that Mark would ask a limited number of people to vote on it after the resolution date (today). I guess those people would self-select, or maybe Mark will select them. They will be requested to make a one-year commitment. After that comes step 7, the "fun part": implementation, documentation. We're pretty close to reaching a conclusion on this. The fact is that even if we do nothing, people want this functionality, and they WILL implement it. It is in everybody's interest that we have a specification for what the functionality should be. It may change over time, but I think there has been enough back-and-forth that we have a reasonable first draft, and should vote on it. -Frank P.S. Of course, this message, along with version 1.7.1 of the RFC is attached to the bug on bugzilla PhD, Computational Biologist, Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA 02115, USA. Tel: 617-432-3555 Fax: 617-432-3557 http://llama.med.harvard.edu/~fgibbons From markw at illuminae.com Fri Sep 16 00:20:50 2005 From: markw at illuminae.com (mark wilkinson) Date: Fri Sep 16 00:27:47 2005 Subject: [MOBY-l] Re: [MOBY-dev] taverna update Message-ID: <2044406868-1126844547-cardhu_blackberry.rim.net-21354-@engine13-cell01> This is the kick-ass addition to Taverna that only MOBY can accomplish! I'm really excited about this! Lead the biologist by the hand through workflow creation... It isn't quite a "wizard" but getting there! Thanks Eddie! Your plugin is bare(bear)able! M . -----Original Message----- From: "Eddie Kawas" Date: Thu, 15 Sep 2005 17:04:26 To:, "'Moby Developers'" Subject: [MOBY-dev] taverna update Hi, I have modified the Moby plugin and I was wondering if Moby'ers would like to try it and let me know what you think? I basically added the ability to add Moby objects, and the objects that are contained within the object in the form of has(a), to the workflow. I also added some new things to the popup window that arises when you context (right) click the Moby object/service processor in the 'advance model explorer'. When the window pops up, there is a context menu for certain nodes in the tree that allows you to add services/datatypes to the workflow, after 'discovering' them. I think that it's better just to try it out. The one downside is that you can only use the Vancouver based Mobycentral registry (since I am taking advantage of recent api additions). The link to this 'new' taverna is: http://bioinfo.icapture.ubc.ca/ekawas/taverna-workbench-1.2. zip I would first suggest that you ensure that your old workflows work and then try creating workflows using the 'enhancements'. If you have any problems/suggestions, let me know. Thanks, Eddie _______________________________________________ MOBY-dev mailing list MOBY-dev@biomoby.org http://www.biomoby.org/mailman/listinfo/moby-dev -- Mark Wilkinson ...on the road! From ed.kawas at gmail.com Thu Sep 15 20:04:26 2005 From: ed.kawas at gmail.com (Eddie Kawas) Date: Fri Sep 23 13:35:45 2005 Subject: [MOBY-l] taverna update Message-ID: <432a0c0e.0f0001ad.6fb1.4f25@mx.gmail.com> Hi, I have modified the Moby plugin and I was wondering if Moby'ers would like to try it and let me know what you think? I basically added the ability to add Moby objects, and the objects that are contained within the object in the form of has(a), to the workflow. I also added some new things to the popup window that arises when you context (right) click the Moby object/service processor in the 'advance model explorer'. When the window pops up, there is a context menu for certain nodes in the tree that allows you to add services/datatypes to the workflow, after 'discovering' them. I think that it's better just to try it out. The one downside is that you can only use the Vancouver based Mobycentral registry (since I am taking advantage of recent api additions). The link to this 'new' taverna is: http://bioinfo.icapture.ubc.ca/ekawas/taverna-workbench-1.2. zip I would first suggest that you ensure that your old workflows work and then try creating workflows using the 'enhancements'. If you have any problems/suggestions, let me know. Thanks, Eddie From silvia77 at dist.unige.it Tue Sep 6 06:24:03 2005 From: silvia77 at dist.unige.it (scaglione) Date: Tue, 6 Sep 2005 12:24:03 +0200 Subject: [MOBY-l] Re: sth_collection_ins In-Reply-To: <1124964729.430d9979a03e9@webmail.unige.it> References: <1124964729.430d9979a03e9@webmail.unige.it> Message-ID: <1126002243.431d6e4387d3d@webmail.unige.it> hello, I have finished (hopefully) to install moby central in my machine. I'm working to add some new GOWlab webservices into my moby central (up to now only "MOBY object" and "www.illuminae.com" services are available), to use these webservices into Taverna. Any suggestions? The registerService WSDL ( http://cvs.bioperl.org/cgi- bin/viewcvs/viewcvs.cgi/moby-live/Perl/MOBY/Central.html? cvsroot=biomoby&rev=1.5#registerservicewsdl ) seems to be useful for me, but unfortunately not implemented yet... Isn't it or I'm missing anything? thanks silvia Scrive scaglione : > hello, > I have followed instructions to install a moby central in my machine.I have > tried the testMOBYClientCentral_v05.pl script on my mobycentral and an error > > appeared: > > >perl testMOBYCentral_v05.pl > > Useless use of hash element in void context > at /usr/lib/perl5/site_perl/5.8.5/RDF/Core/Serializer.pm line 52. > Global symbol "$sth_collection_ins" requires explicit package name > at /usr/lib/perl5/site_perl/5.8.5/MOBY/Central.pm line 3426. > Compilation failed in require at testMOBYCentral_v05.pl line 4. > BEGIN failed--compilation aborted at testMOBYCentral_v05.pl line 4. > > what does it mean? > The overall configuration of the moby central seemed to be ok, since the test > > of the same script on the main mobycentral works... > many thanks > silvia > > > > -- > PhD. Silvia Scaglione > DIST University of Genoa > Viale Causa,13 > 16145 Genoa > phone +39 010 353 2789 > phone CBA +39 010 5737 505 > fax +39 010 353 2948 -- PhD. Silvia Scaglione DIST University of Genoa Viale Causa,13 16145 Genoa phone +39 010 353 2789 phone CBA +39 010 5737 505 fax +39 010 353 2948 From markw at illuminae.com Tue Sep 6 12:04:10 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 06 Sep 2005 09:04:10 -0700 Subject: [moby] [MOBY-l] Re: sth_collection_ins In-Reply-To: <1126002243.431d6e4387d3d@webmail.unige.it> References: <1124964729.430d9979a03e9@webmail.unige.it> <1126002243.431d6e4387d3d@webmail.unige.it> Message-ID: <1126022650.30434.43.camel@bioinfo.icapture.ubc.ca> It is not implemented, and may not be for a very long time (if ever) because it turns out that XML Schema has limitations that prevent us from accurately describing MOBY Objects. As such, we may never be able to *precisely* describe a MOBY service interface from a WSDL document. This is an XSD limitation, not a MOBY limitation :-/ M On Tue, 2005-09-06 at 12:24 +0200, scaglione wrote: > hello, > I have finished (hopefully) to install moby central in my machine. I'm working > to add some new GOWlab webservices into my moby central (up to now only "MOBY > object" and "www.illuminae.com" services are available), to use these > webservices into Taverna. > Any suggestions? > The registerService WSDL ( http://cvs.bioperl.org/cgi- > bin/viewcvs/viewcvs.cgi/moby-live/Perl/MOBY/Central.html? > cvsroot=biomoby&rev=1.5#registerservicewsdl ) seems to be useful for me, but > unfortunately not implemented yet... > Isn't it or I'm missing anything? > thanks > silvia > > Scrive scaglione : > > > hello, > > I have followed instructions to install a moby central in my machine.I have > > tried the testMOBYClientCentral_v05.pl script on my mobycentral and an error > > > > appeared: > > > > >perl testMOBYCentral_v05.pl > > > > Useless use of hash element in void context > > at /usr/lib/perl5/site_perl/5.8.5/RDF/Core/Serializer.pm line 52. > > Global symbol "$sth_collection_ins" requires explicit package name > > at /usr/lib/perl5/site_perl/5.8.5/MOBY/Central.pm line 3426. > > Compilation failed in require at testMOBYCentral_v05.pl line 4. > > BEGIN failed--compilation aborted at testMOBYCentral_v05.pl line 4. > > > > what does it mean? > > The overall configuration of the moby central seemed to be ok, since the test > > > > of the same script on the main mobycentral works... > > many thanks > > silvia > > > > > > > > -- > > PhD. Silvia Scaglione > > DIST University of Genoa > > Viale Causa,13 > > 16145 Genoa > > phone +39 010 353 2789 > > phone CBA +39 010 5737 505 > > fax +39 010 353 2948 > > -- "Ontologists do it with the edges!" Mark Wilkinson Asst. Professor Dept. of Medical Genetics University of British Columbia PI in Bioinformatics iCAPTURE Centre St. Paul's Hospital Rm. 166, 1081 Burrard St. Vancouver, BC, V6Z 1Y6 tel: 604 682 2344 x62129 fax: 604 806 9274 From tmo at ebi.ac.uk Tue Sep 6 13:57:59 2005 From: tmo at ebi.ac.uk (Tom Oinn) Date: Tue, 06 Sep 2005 18:57:59 +0100 Subject: [moby] [MOBY-l] Re: sth_collection_ins In-Reply-To: <1126022650.30434.43.camel@bioinfo.icapture.ubc.ca> References: <1124964729.430d9979a03e9@webmail.unige.it> <1126002243.431d6e4387d3d@webmail.unige.it> <1126022650.30434.43.camel@bioinfo.icapture.ubc.ca> Message-ID: <431DD8A7.2040007@ebi.ac.uk> >>hello, >>I have finished (hopefully) to install moby central in my machine. I'm working >>to add some new GOWlab webservices into my moby central (up to now only "MOBY >>object" and "www.illuminae.com" services are available), to use these >>webservices into Taverna. >>Any suggestions? Um... not to advocate not using Moby or anything but why would you want to convert GOWlab services to Moby ones to use in Taverna? Taverna has full support for GOWlab / SoapLab already and it's generally better than the support for Moby ;) Is there some reason you'd want to do this...? The only thing you don't get of course is registry support but this will appear soon enough (and will be integrated into the moby registry as well). Tom From schoof at mpiz-koeln.mpg.de Mon Sep 12 08:36:19 2005 From: schoof at mpiz-koeln.mpg.de (Heiko Schoof) Date: Mon, 12 Sep 2005 14:36:19 +0200 Subject: [MOBY-l] Moby Dick Message-ID: Hi, I just came across the EU project "Moby Dick" and thought you'd be amused as well... Best, Heiko Closing the gaps in the mobile Internet While mobile services try to provide constant connectivity, there are times, when switching from one network to another, when connections can be dropped. However temporary the network loss may be, it proves annoying for users, and threatens QoS standards. The EU-funded 'Moby Dick' project set out to build and evaluate a mobile network architecture based on the next-generation Internet protocol (IPv6) that addresses this problem. http://www.ccrle.nec.de/Projects/mobydick.htm ______________________ Max Planck Institute for Plant Breeding Research Plant Computational Biology Dr. Heiko Schoof Carl-von-Linne Weg 10 50829 Koeln Germany +49-(0)221 / 5062 - 445 Fax +49 221 5062 413 http://www.mpiz-koeln.mpg.de/english/research/ independent_research_groups/schoof/index.html schoof at mpiz-koeln.mpg.de From cwmoad at gmail.com Mon Sep 12 12:11:43 2005 From: cwmoad at gmail.com (Charlie Moad) Date: Mon, 12 Sep 2005 11:11:43 -0500 Subject: [MOBY-l] bioMoby python timeouts Message-ID: <6382066a0509120911961f50@mail.gmail.com> Hi, I am trying to experiment with the python interface to bioMoby and I am getting timeouts across the board. I am running samples provided in the tutorial as well. Are the services running right now? Thanks, Charlie From ywong at infobiogen.fr Tue Sep 13 17:43:28 2005 From: ywong at infobiogen.fr (ywong@infobiogen.fr) Date: Tue, 13 Sep 2005 23:43:28 +0200 (CEST) Subject: [MOBY-l] bioMoby python timeouts In-Reply-To: <6382066a0509120911961f50@mail.gmail.com> References: <6382066a0509120911961f50@mail.gmail.com> Message-ID: <49311.82.66.216.27.1126647808.squirrel@82.66.216.27> What kind of problem do you have? Do the problems occur when you try to reach a moby central or a service? If you can't contact the moby central server, the cause maybe that by default, as far as I can remember, the url of the moby server is http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY05/mobycentral.pl Since I had little time these month following the changes on this API, I didn't change the default url. In order to connect to the moby central directory just add to your Client constructor the optional parameter url= you can have a trace of the transaction by changing the debug parameter to True: from bioMoby import Client client=Client(url="http://myown.mobyserver.org/central.pl", debug=True") This will help you diagnose problems with the central server. for the latter, you should execute the service with the debug option set to True, you may have a clue of what's going wrong. Greetings, Yan > Hi, > I am trying to experiment with the python interface to bioMoby and I am > getting timeouts across the board. I am running samples provided in the > tutorial as well. Are the services running right now? > > Thanks, > Charlie > > _______________________________________________ > moby-l mailing list > moby-l at biomoby.org > http://biomoby.org/mailman/listinfo/moby-l > From fgibbons at hms.harvard.edu Thu Sep 15 11:21:53 2005 From: fgibbons at hms.harvard.edu (Frank Gibbons) Date: Thu, 15 Sep 2005 11:21:53 -0400 Subject: [MOBY-l] Using bugzilla to continue RFC on Error-handling in MOBY-S Message-ID: <5.2.1.1.2.20050915105906.012401c8@email.med.harvard.edu> Hi, I've just added a few "bugs" to the bugzilla, to try to preserve the RFC momentum built up over the past few weeks. I propose that, although bugzilla is perhaps not ideal for this, it is what it is, it is what we have, and it will do for now. I'd like to propose that we try to continue development of this RFC through bugzilla (see bug #1863), rather than through the mailing list. Searching through old mail messages (or worse still, through the digest, with all of its repeated messages and long inclusions) is tedious, and I think contributes to the loss in momentum. So far, in Martin's scheme for RFC-processing, we have (numbers are those used in Martin's original suggestion, now available in the codebase as Docs/MOBY-S_API/RFC.html) 1. Had a suggestion made by INB to add this features. It was added to bugzilla, No. 1863 2. Suggested to resolve it by today (Sep-15) 3. Martin backed up the RFC 4. I think we have the resources to make this change - it seems an essential part of a robust API, which version 1.0 should be. 5a. List members have exchanged several comments back and forth, resulting in amended versions of the RFC being posted to the mailing list. 5b. We've also gotten a little side-tracked by the related articleName problem. So it seems to me that it's time to vote on it (step 6 of the Senger seven-step scheme ;-). Martin suggested that Mark would ask a limited number of people to vote on it after the resolution date (today). I guess those people would self-select, or maybe Mark will select them. They will be requested to make a one-year commitment. After that comes step 7, the "fun part": implementation, documentation. We're pretty close to reaching a conclusion on this. The fact is that even if we do nothing, people want this functionality, and they WILL implement it. It is in everybody's interest that we have a specification for what the functionality should be. It may change over time, but I think there has been enough back-and-forth that we have a reasonable first draft, and should vote on it. -Frank P.S. Of course, this message, along with version 1.7.1 of the RFC is attached to the bug on bugzilla PhD, Computational Biologist, Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA 02115, USA. Tel: 617-432-3555 Fax: 617-432-3557 http://llama.med.harvard.edu/~fgibbons From markw at illuminae.com Fri Sep 16 00:20:50 2005 From: markw at illuminae.com (mark wilkinson) Date: Fri, 16 Sep 2005 04:20:50 +0000 GMT Subject: [MOBY-l] Re: [MOBY-dev] taverna update Message-ID: <2044406868-1126844547-cardhu_blackberry.rim.net-21354-@engine13-cell01> This is the kick-ass addition to Taverna that only MOBY can accomplish! I'm really excited about this! Lead the biologist by the hand through workflow creation... It isn't quite a "wizard" but getting there! Thanks Eddie! Your plugin is bare(bear)able! M . -----Original Message----- From: "Eddie Kawas" Date: Thu, 15 Sep 2005 17:04:26 To:, "'Moby Developers'" Subject: [MOBY-dev] taverna update Hi, I have modified the Moby plugin and I was wondering if Moby'ers would like to try it and let me know what you think? I basically added the ability to add Moby objects, and the objects that are contained within the object in the form of has(a), to the workflow. I also added some new things to the popup window that arises when you context (right) click the Moby object/service processor in the 'advance model explorer'. When the window pops up, there is a context menu for certain nodes in the tree that allows you to add services/datatypes to the workflow, after 'discovering' them. I think that it's better just to try it out. The one downside is that you can only use the Vancouver based Mobycentral registry (since I am taking advantage of recent api additions). The link to this 'new' taverna is: http://bioinfo.icapture.ubc.ca/ekawas/taverna-workbench-1.2. zip I would first suggest that you ensure that your old workflows work and then try creating workflows using the 'enhancements'. If you have any problems/suggestions, let me know. Thanks, Eddie _______________________________________________ MOBY-dev mailing list MOBY-dev at biomoby.org http://www.biomoby.org/mailman/listinfo/moby-dev -- Mark Wilkinson ...on the road! From ed.kawas at gmail.com Thu Sep 15 20:04:26 2005 From: ed.kawas at gmail.com (Eddie Kawas) Date: Thu, 15 Sep 2005 17:04:26 -0700 Subject: [MOBY-l] taverna update Message-ID: <432a0c0e.0f0001ad.6fb1.4f25@mx.gmail.com> Hi, I have modified the Moby plugin and I was wondering if Moby'ers would like to try it and let me know what you think? I basically added the ability to add Moby objects, and the objects that are contained within the object in the form of has(a), to the workflow. I also added some new things to the popup window that arises when you context (right) click the Moby object/service processor in the 'advance model explorer'. When the window pops up, there is a context menu for certain nodes in the tree that allows you to add services/datatypes to the workflow, after 'discovering' them. I think that it's better just to try it out. The one downside is that you can only use the Vancouver based Mobycentral registry (since I am taking advantage of recent api additions). The link to this 'new' taverna is: http://bioinfo.icapture.ubc.ca/ekawas/taverna-workbench-1.2. zip I would first suggest that you ensure that your old workflows work and then try creating workflows using the 'enhancements'. If you have any problems/suggestions, let me know. Thanks, Eddie