From mwilkinson at mrl.ubc.ca Tue Dec 7 12:21:02 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Tue Dec 7 11:52:59 2004 Subject: [MOBY-l] [Fwd: [personal] Re: Intermittent loss of MOBY from Europe] Message-ID: <1102440061.16721.22.camel@mobycentral.icapture.ubc.ca> Hi all, Since your reports are generally coming in while I am sleeping and the problem is fixed by the time I wake up, can I ask you to do these tests next time you find that you cannot connect to MOBY Central? It's happened a few times in the past two weeks, and I'd like to know what the source of the problem is. thanks! M > Hi Mark, > > All of our tests show that the Moby service is reachable via Europe. > Next time you suspect connectivity problems, please go to: > > www.traceroute.org > > and try a few tests from the various links in Europe to see where the > problem lies. Then, if you can send us the output from your tests, we > should be able to determine if the problem lies in our network or > externally. Most of the links on this site have options to traceroute to > an IP (others have ping and other services available). -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From markw at illuminae.com Sat Dec 11 12:38:57 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Sat Dec 11 12:36:17 2004 Subject: [MOBY-l] A few new tools and updates Message-ID: <41BB30B1.8040105@illuminae.com> Hi all, Here's an update of the latest goings-on with MOBY-S and MOBY-S tooling: 1) Eddie has finished writing applets that help in the construction of new tools for creating objects,service types, and registering new service instances. Try them at: http://mobycentral.cbr.nrc.ca/applets (note that this is operating on the "live" database) 2) For a variety of reasons we've decided to change the structure of the Service Instance RDF. As such, I have temporarily switched the deregisterService function back 'on' in MOBY Central. You can deregister services as before using the API. 3) Once we have a good RDF generator, we will ask you again to retrieve the RDF of your services and we'll switch Nina's agent on. I'll then switch the deregisterService function 'off' again. Cheers all! Mark P.S. I'm planning to host the next (possibly last, depending on funding...) MOBY developers meeting in Vancouver in early May, 2005. Does anyone know of other conferences going on that we should avoid conflicting with? From rebecca.ernst at gsf.de Mon Dec 13 11:20:27 2004 From: rebecca.ernst at gsf.de (Rebecca Ernst) Date: Mon Dec 13 12:18:52 2004 Subject: [MOBY-l] registration of services not possible yet In-Reply-To: <41BB30B1.8040105@illuminae.com> References: <41BB30B1.8040105@illuminae.com> Message-ID: <41BDC14B.1020804@gsf.de> Hi Mark! I just tried to deregister/register my services - it still tells me that I am not allowed to deregister a service that is registered having a RDF!! Rebecca Mark Wilkinson wrote: > Hi all, > > Here's an update of the latest goings-on with MOBY-S and MOBY-S tooling: > > 1) Eddie has finished writing applets that help in the construction > of new tools for creating objects,service types, and registering new > service instances. Try them at: > http://mobycentral.cbr.nrc.ca/applets (note that this is operating on > the "live" database) > > 2) For a variety of reasons we've decided to change the structure of > the Service Instance RDF. As such, I have temporarily switched the > deregisterService function back 'on' in MOBY Central. You can > deregister services as before using the API. > > 3) Once we have a good RDF generator, we will ask you again to > retrieve the RDF of your services and we'll switch Nina's agent on. > I'll then switch the deregisterService function 'off' again. > > Cheers all! > Mark > > P.S. I'm planning to host the next (possibly last, depending on > funding...) MOBY developers meeting in Vancouver in early May, 2005. > Does anyone know of other conferences going on that we should avoid > conflicting with? > _______________________________________________ > moby-l mailing list > moby-l@biomoby.org > http://biomoby.org/mailman/listinfo/moby-l > -- Rebecca Ernst MIPS, Inst. for Bioinformatics GSF Research Center for Environment and Health Ingolstaedter Landstr. 1 85764 Neuherberg fon: +49 89 3187 3583 email: Rebecca.Ernst@gsf.de From mwilkinson at mrl.ubc.ca Mon Dec 13 12:53:21 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Mon Dec 13 12:24:45 2004 Subject: [moby] [MOBY-l] registration of services not possible yet In-Reply-To: <41BDC14B.1020804@gsf.de> References: <41BB30B1.8040105@illuminae.com> <41BDC14B.1020804@gsf.de> Message-ID: <1102960400.30331.26.camel@mobycentral.icapture.ubc.ca> Doh! I forgot to restart the server. Try now... M On Mon, 2004-12-13 at 08:20, Rebecca Ernst wrote: > Hi Mark! > > I just tried to deregister/register my services - it still tells me that > I am not allowed to deregister a service that is registered having a RDF!! > > Rebecca > > > > > Mark Wilkinson wrote: > > > Hi all, > > > > Here's an update of the latest goings-on with MOBY-S and MOBY-S tooling: > > > > 1) Eddie has finished writing applets that help in the construction > > of new tools for creating objects,service types, and registering new > > service instances. Try them at: > > http://mobycentral.cbr.nrc.ca/applets (note that this is operating on > > the "live" database) > > > > 2) For a variety of reasons we've decided to change the structure of > > the Service Instance RDF. As such, I have temporarily switched the > > deregisterService function back 'on' in MOBY Central. You can > > deregister services as before using the API. > > > > 3) Once we have a good RDF generator, we will ask you again to > > retrieve the RDF of your services and we'll switch Nina's agent on. > > I'll then switch the deregisterService function 'off' again. > > > > Cheers all! > > Mark > > > > P.S. I'm planning to host the next (possibly last, depending on > > funding...) MOBY developers meeting in Vancouver in early May, 2005. > > Does anyone know of other conferences going on that we should avoid > > conflicting with? > > _______________________________________________ > > 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 r.page at bio.gla.ac.uk Mon Dec 13 12:45:26 2004 From: r.page at bio.gla.ac.uk (Roderic D. M. Page) Date: Mon Dec 13 12:42:42 2004 Subject: [MOBY-l] LSID protocol handler for Mozilla/Firefox Message-ID: I'm not sure whether this is of interest to BioMoby members, but I've put together a very simple extension that enables Mozilla and Firefox to handle the "lsidres" protocol used in IBM's Launchpad to resolve LSIDs. The extension redirects the browser to the http://lsid.biopathways.org LSID resolver. Once the extension is installed, links such as lsidres://urn:lsid:ncbi.nlm.nih.gov.lsid.biopathways.org:pubmed:12441807 become clickable. This is a bit primitive compared to Launchpad, but means that people who don't use Internet Explorer 6 on Windows can have clickable LSIDs. The extension has been tested (I use that term loosely) on Windows 2000, Mac OS X, and Red Hat 8, with Firefox 0.9.2 - 1.0. The extension is available from http://darwin.zoology.gla.ac.uk/~rpage/lsid/ . Regards Rod -- -------------------------------------------------------- Professor Roderic D. M. Page Editor Elect, Systematic Biology DEEB, IBLS Graham Kerr Building University of Glasgow Glasgow G12 8QP United Kingdom Phone: +44 141 330 4778 Fax: +44 141 330 2792 email: r.page@bio.gla.ac.uk web: http://taxonomy.zoology.gla.ac.uk/rod/rod.html reprints: http://taxonomy.zoology.gla.ac.uk/rod/pubs.html Subscribe to Systematic Biology through the Society of Systematic Biologists Website: http://systematicbiology.org From rebecca.ernst at gsf.de Tue Dec 14 04:01:37 2004 From: rebecca.ernst at gsf.de (Rebecca Ernst) Date: Tue Dec 14 05:43:52 2004 Subject: [MOBY-l] service deregistration Message-ID: <41BEABF1.4050902@gsf.de> Hi Mark! the server restart didn't solve the problem. I still can only deregister services which are registered without RDF. Rebecca -- Rebecca Ernst MIPS, Inst. for Bioinformatics GSF Research Center for Environment and Health Ingolstaedter Landstr. 1 85764 Neuherberg fon: +49 89 3187 3583 email: Rebecca.Ernst@gsf.de From p.lord at cs.man.ac.uk Tue Dec 14 07:37:41 2004 From: p.lord at cs.man.ac.uk (Phillip Lord) Date: Tue Dec 14 07:38:29 2004 Subject: [MOBY-l] Re: [MOBY-dev] service deregistration In-Reply-To: <41BEABF1.4050902@gsf.de> References: <41BEABF1.4050902@gsf.de> Message-ID: >>>>> "Rebecca" == Rebecca Ernst writes: Rebecca> Hi Mark! Rebecca> the server restart didn't solve the problem. I still can Rebecca> only deregister services which are registered without RDF. Rebecca> Rebecca What do you mean? Turning it off and on again did not solve the problem? How can this be true? Phil From mwilkinson at mrl.ubc.ca Tue Dec 14 11:06:38 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Tue Dec 14 10:36:45 2004 Subject: [moby] [MOBY-l] Re: [MOBY-dev] service deregistration In-Reply-To: References: <41BEABF1.4050902@gsf.de> Message-ID: <1103040398.32326.4.camel@mobycentral.icapture.ubc.ca> On Tue, 2004-12-14 at 04:37, Phillip Lord wrote: > What do you mean? Turning it off and on again did not solve the > problem? How can this be true? Come over here and say that! I'll switch YOU off boy-o! ;-) M -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From mwilkinson at mrl.ubc.ca Tue Dec 14 11:37:44 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Tue Dec 14 11:07:56 2004 Subject: [moby] [MOBY-l] service deregistration In-Reply-To: <41BEABF1.4050902@gsf.de> References: <41BEABF1.4050902@gsf.de> Message-ID: <1103042264.32326.34.camel@mobycentral.icapture.ubc.ca> Doh! DOH! You're right. The MOBY Central code is currently broken. Eddie is going to troubleshoot, and hopefully we'll have it up by the end of the day. In the meantime, MOBY Central is running on an older codebase, so almost everything is functioning properly. I'll restart the server again when the problem is identified. Sorry! M On Tue, 2004-12-14 at 01:01, Rebecca Ernst wrote: > Hi Mark! > > the server restart didn't solve the problem. I still can only deregister > services which are registered without RDF. > > Rebecca -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From gordonp at cbr.nrc.ca Thu Dec 16 15:51:15 2004 From: gordonp at cbr.nrc.ca (Paul Gordon) Date: Thu Dec 16 15:48:28 2004 Subject: [MOBY-l] LSID protocol handler for Mozilla/Firefox In-Reply-To: References: Message-ID: <41C1F543.7030801@cbr.nrc.ca> I've tested this using Firefox 1.0 under Solaris and it works fine, thanks! This leads me to ask a question that I've seen floating around but not sure if it has been implemented with the new RDF scheme: Do we have a standard LSID representation for MOBY Objects? Roderic D. M. Page wrote: > I'm not sure whether this is of interest to BioMoby members, but I've > put together a very simple extension that enables Mozilla and Firefox > to handle the "lsidres" protocol used in IBM's Launchpad to resolve > LSIDs. The extension redirects the browser to the > http://lsid.biopathways.org LSID resolver. Once the extension is > installed, links such as > lsidres://urn:lsid:ncbi.nlm.nih.gov.lsid.biopathways.org:pubmed:12441807 > become clickable. > > This is a bit primitive compared to Launchpad, but means that people > who don't use Internet Explorer 6 on Windows can have clickable LSIDs. > The extension has been tested (I use that term loosely) on Windows > 2000, Mac OS X, and Red Hat 8, with Firefox 0.9.2 - 1.0. > > The extension is available from > http://darwin.zoology.gla.ac.uk/~rpage/lsid/ . > > Regards > > Rod > > From mwilkinson at mrl.ubc.ca Tue Dec 7 12:21:02 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Tue, 07 Dec 2004 09:21:02 -0800 Subject: [MOBY-l] [Fwd: [personal] Re: Intermittent loss of MOBY from Europe] Message-ID: <1102440061.16721.22.camel@mobycentral.icapture.ubc.ca> Hi all, Since your reports are generally coming in while I am sleeping and the problem is fixed by the time I wake up, can I ask you to do these tests next time you find that you cannot connect to MOBY Central? It's happened a few times in the past two weeks, and I'd like to know what the source of the problem is. thanks! M > Hi Mark, > > All of our tests show that the Moby service is reachable via Europe. > Next time you suspect connectivity problems, please go to: > > www.traceroute.org > > and try a few tests from the various links in Europe to see where the > problem lies. Then, if you can send us the output from your tests, we > should be able to determine if the problem lies in our network or > externally. Most of the links on this site have options to traceroute to > an IP (others have ping and other services available). -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From markw at illuminae.com Sat Dec 11 12:38:57 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Sat, 11 Dec 2004 09:38:57 -0800 Subject: [MOBY-l] A few new tools and updates Message-ID: <41BB30B1.8040105@illuminae.com> Hi all, Here's an update of the latest goings-on with MOBY-S and MOBY-S tooling: 1) Eddie has finished writing applets that help in the construction of new tools for creating objects,service types, and registering new service instances. Try them at: http://mobycentral.cbr.nrc.ca/applets (note that this is operating on the "live" database) 2) For a variety of reasons we've decided to change the structure of the Service Instance RDF. As such, I have temporarily switched the deregisterService function back 'on' in MOBY Central. You can deregister services as before using the API. 3) Once we have a good RDF generator, we will ask you again to retrieve the RDF of your services and we'll switch Nina's agent on. I'll then switch the deregisterService function 'off' again. Cheers all! Mark P.S. I'm planning to host the next (possibly last, depending on funding...) MOBY developers meeting in Vancouver in early May, 2005. Does anyone know of other conferences going on that we should avoid conflicting with? From rebecca.ernst at gsf.de Mon Dec 13 11:20:27 2004 From: rebecca.ernst at gsf.de (Rebecca Ernst) Date: Mon, 13 Dec 2004 17:20:27 +0100 Subject: [MOBY-l] registration of services not possible yet In-Reply-To: <41BB30B1.8040105@illuminae.com> References: <41BB30B1.8040105@illuminae.com> Message-ID: <41BDC14B.1020804@gsf.de> Hi Mark! I just tried to deregister/register my services - it still tells me that I am not allowed to deregister a service that is registered having a RDF!! Rebecca Mark Wilkinson wrote: > Hi all, > > Here's an update of the latest goings-on with MOBY-S and MOBY-S tooling: > > 1) Eddie has finished writing applets that help in the construction > of new tools for creating objects,service types, and registering new > service instances. Try them at: > http://mobycentral.cbr.nrc.ca/applets (note that this is operating on > the "live" database) > > 2) For a variety of reasons we've decided to change the structure of > the Service Instance RDF. As such, I have temporarily switched the > deregisterService function back 'on' in MOBY Central. You can > deregister services as before using the API. > > 3) Once we have a good RDF generator, we will ask you again to > retrieve the RDF of your services and we'll switch Nina's agent on. > I'll then switch the deregisterService function 'off' again. > > Cheers all! > Mark > > P.S. I'm planning to host the next (possibly last, depending on > funding...) MOBY developers meeting in Vancouver in early May, 2005. > Does anyone know of other conferences going on that we should avoid > conflicting with? > _______________________________________________ > moby-l mailing list > moby-l at biomoby.org > http://biomoby.org/mailman/listinfo/moby-l > -- Rebecca Ernst MIPS, Inst. for Bioinformatics GSF Research Center for Environment and Health Ingolstaedter Landstr. 1 85764 Neuherberg fon: +49 89 3187 3583 email: Rebecca.Ernst at gsf.de From mwilkinson at mrl.ubc.ca Mon Dec 13 12:53:21 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Mon, 13 Dec 2004 09:53:21 -0800 Subject: [moby] [MOBY-l] registration of services not possible yet In-Reply-To: <41BDC14B.1020804@gsf.de> References: <41BB30B1.8040105@illuminae.com> <41BDC14B.1020804@gsf.de> Message-ID: <1102960400.30331.26.camel@mobycentral.icapture.ubc.ca> Doh! I forgot to restart the server. Try now... M On Mon, 2004-12-13 at 08:20, Rebecca Ernst wrote: > Hi Mark! > > I just tried to deregister/register my services - it still tells me that > I am not allowed to deregister a service that is registered having a RDF!! > > Rebecca > > > > > Mark Wilkinson wrote: > > > Hi all, > > > > Here's an update of the latest goings-on with MOBY-S and MOBY-S tooling: > > > > 1) Eddie has finished writing applets that help in the construction > > of new tools for creating objects,service types, and registering new > > service instances. Try them at: > > http://mobycentral.cbr.nrc.ca/applets (note that this is operating on > > the "live" database) > > > > 2) For a variety of reasons we've decided to change the structure of > > the Service Instance RDF. As such, I have temporarily switched the > > deregisterService function back 'on' in MOBY Central. You can > > deregister services as before using the API. > > > > 3) Once we have a good RDF generator, we will ask you again to > > retrieve the RDF of your services and we'll switch Nina's agent on. > > I'll then switch the deregisterService function 'off' again. > > > > Cheers all! > > Mark > > > > P.S. I'm planning to host the next (possibly last, depending on > > funding...) MOBY developers meeting in Vancouver in early May, 2005. > > Does anyone know of other conferences going on that we should avoid > > conflicting with? > > _______________________________________________ > > 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 r.page at bio.gla.ac.uk Mon Dec 13 12:45:26 2004 From: r.page at bio.gla.ac.uk (Roderic D. M. Page) Date: Mon, 13 Dec 2004 17:45:26 +0000 Subject: [MOBY-l] LSID protocol handler for Mozilla/Firefox Message-ID: I'm not sure whether this is of interest to BioMoby members, but I've put together a very simple extension that enables Mozilla and Firefox to handle the "lsidres" protocol used in IBM's Launchpad to resolve LSIDs. The extension redirects the browser to the http://lsid.biopathways.org LSID resolver. Once the extension is installed, links such as lsidres://urn:lsid:ncbi.nlm.nih.gov.lsid.biopathways.org:pubmed:12441807 become clickable. This is a bit primitive compared to Launchpad, but means that people who don't use Internet Explorer 6 on Windows can have clickable LSIDs. The extension has been tested (I use that term loosely) on Windows 2000, Mac OS X, and Red Hat 8, with Firefox 0.9.2 - 1.0. The extension is available from http://darwin.zoology.gla.ac.uk/~rpage/lsid/ . Regards Rod -- -------------------------------------------------------- Professor Roderic D. M. Page Editor Elect, Systematic Biology DEEB, IBLS Graham Kerr Building University of Glasgow Glasgow G12 8QP United Kingdom Phone: +44 141 330 4778 Fax: +44 141 330 2792 email: r.page at bio.gla.ac.uk web: http://taxonomy.zoology.gla.ac.uk/rod/rod.html reprints: http://taxonomy.zoology.gla.ac.uk/rod/pubs.html Subscribe to Systematic Biology through the Society of Systematic Biologists Website: http://systematicbiology.org From rebecca.ernst at gsf.de Tue Dec 14 04:01:37 2004 From: rebecca.ernst at gsf.de (Rebecca Ernst) Date: Tue, 14 Dec 2004 10:01:37 +0100 Subject: [MOBY-l] service deregistration Message-ID: <41BEABF1.4050902@gsf.de> Hi Mark! the server restart didn't solve the problem. I still can only deregister services which are registered without RDF. Rebecca -- Rebecca Ernst MIPS, Inst. for Bioinformatics GSF Research Center for Environment and Health Ingolstaedter Landstr. 1 85764 Neuherberg fon: +49 89 3187 3583 email: Rebecca.Ernst at gsf.de From p.lord at cs.man.ac.uk Tue Dec 14 07:37:41 2004 From: p.lord at cs.man.ac.uk (Phillip Lord) Date: 14 Dec 2004 12:37:41 +0000 Subject: [MOBY-l] Re: [MOBY-dev] service deregistration In-Reply-To: <41BEABF1.4050902@gsf.de> References: <41BEABF1.4050902@gsf.de> Message-ID: >>>>> "Rebecca" == Rebecca Ernst writes: Rebecca> Hi Mark! Rebecca> the server restart didn't solve the problem. I still can Rebecca> only deregister services which are registered without RDF. Rebecca> Rebecca What do you mean? Turning it off and on again did not solve the problem? How can this be true? Phil From mwilkinson at mrl.ubc.ca Tue Dec 14 11:06:38 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Tue, 14 Dec 2004 08:06:38 -0800 Subject: [moby] [MOBY-l] Re: [MOBY-dev] service deregistration In-Reply-To: References: <41BEABF1.4050902@gsf.de> Message-ID: <1103040398.32326.4.camel@mobycentral.icapture.ubc.ca> On Tue, 2004-12-14 at 04:37, Phillip Lord wrote: > What do you mean? Turning it off and on again did not solve the > problem? How can this be true? Come over here and say that! I'll switch YOU off boy-o! ;-) M -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From mwilkinson at mrl.ubc.ca Tue Dec 14 11:37:44 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Tue, 14 Dec 2004 08:37:44 -0800 Subject: [moby] [MOBY-l] service deregistration In-Reply-To: <41BEABF1.4050902@gsf.de> References: <41BEABF1.4050902@gsf.de> Message-ID: <1103042264.32326.34.camel@mobycentral.icapture.ubc.ca> Doh! DOH! You're right. The MOBY Central code is currently broken. Eddie is going to troubleshoot, and hopefully we'll have it up by the end of the day. In the meantime, MOBY Central is running on an older codebase, so almost everything is functioning properly. I'll restart the server again when the problem is identified. Sorry! M On Tue, 2004-12-14 at 01:01, Rebecca Ernst wrote: > Hi Mark! > > the server restart didn't solve the problem. I still can only deregister > services which are registered without RDF. > > Rebecca -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From gordonp at cbr.nrc.ca Thu Dec 16 15:51:15 2004 From: gordonp at cbr.nrc.ca (Paul Gordon) Date: Thu, 16 Dec 2004 13:51:15 -0700 Subject: [MOBY-l] LSID protocol handler for Mozilla/Firefox In-Reply-To: References: Message-ID: <41C1F543.7030801@cbr.nrc.ca> I've tested this using Firefox 1.0 under Solaris and it works fine, thanks! This leads me to ask a question that I've seen floating around but not sure if it has been implemented with the new RDF scheme: Do we have a standard LSID representation for MOBY Objects? Roderic D. M. Page wrote: > I'm not sure whether this is of interest to BioMoby members, but I've > put together a very simple extension that enables Mozilla and Firefox > to handle the "lsidres" protocol used in IBM's Launchpad to resolve > LSIDs. The extension redirects the browser to the > http://lsid.biopathways.org LSID resolver. Once the extension is > installed, links such as > lsidres://urn:lsid:ncbi.nlm.nih.gov.lsid.biopathways.org:pubmed:12441807 > become clickable. > > This is a bit primitive compared to Launchpad, but means that people > who don't use Internet Explorer 6 on Windows can have clickable LSIDs. > The extension has been tested (I use that term loosely) on Windows > 2000, Mac OS X, and Red Hat 8, with Firefox 0.9.2 - 1.0. > > The extension is available from > http://darwin.zoology.gla.ac.uk/~rpage/lsid/ . > > Regards > > Rod > >