From simont at mcw.edu Tue Jul 13 13:29:49 2004 From: simont at mcw.edu (Simon Twigger) Date: Tue Jul 13 13:31:44 2004 Subject: [MOBY-dev] S-MOBY Install on OS X Message-ID: <3E13688F-D4F2-11D8-8910-000A959D1D82@mcw.edu> (I posted this from a different email a/c and the post got held up pending review so I thought I'd repost from my normal account - apologies if you end up getting this twice) I managed to get the S-MOBY reference implementation up and running on my PowerBook this morning. It wasn't completely plain sailing though the install docs are great. Notes from the OS X Install: Tested using Tomcat 5.0.25, Ant 1.6.1, Java 1.4.2 on Mac OSX 10.3.4 When Editing /etc/hosts: /etc/hosts on 10.3.4 claims that it is not used in the hostname lookup process except for single-user mode. Apparently this is incorrect (at least with the current versions) so this file can be modified as detailed for unix/linux. You may also need to modify the lookup order for the lookupd so it checks the flat file /etc/hosts first, before using DNS, etc. Otherwise trying to find www.s-moby.org:8080 ends up searching DNS rather than using localhost. I followed the advice on the web page listed below, modifying to search the Flat File first rather than DNS which is how it is described in the article. I found this was necessary as once I had everything installed and restarted Tomcat5, localhost:8080 wasnt working as expected and was pointing to some site at MIT (!) sudo mkdir /etc/lookupd sudo echo LookupOrder FF Cache NI DNS DS > /etc/lookupd/hosts sudo kill -1 `cat /var/run/lookupd.pid` See www.aplawrence.com/MacOSX/macosxlookupd.html for more information. Running the Ant Build: In the ant build process, you might need to add appropriate entries in ~/.cvspass if it fails when trying to access CVS servers. Presumably this will only happen if you havent had reason to do any previous anon checkouts from these cvs repositories. :pserver:anoncvs@cvs.apache.org:/home/cvspublic A :pserver:anonymous@cvs.sourceforge.net:/cvsroot/jena A Other than these noted issues, the build ran fine and so far seems to work as advertised though I havent really tried to do much yet. Im trying to get some experience with Jena and how it works with OWL, etc. and having a working application that uses this will be very handy. Gary/Damian: I can add these notes to the S-MOBY/ref-impl/INSTALL.html file and commit to the CVS repository if you would like, or I can leave it to you to add in as appropriate. 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 gss at ncgr.org Tue Jul 13 13:51:54 2004 From: gss at ncgr.org (Gary Schiltz) Date: Tue Jul 13 13:57:04 2004 Subject: [MOBY-dev] S-MOBY Install on OS X In-Reply-To: <3E13688F-D4F2-11D8-8910-000A959D1D82@mcw.edu> References: <3E13688F-D4F2-11D8-8910-000A959D1D82@mcw.edu> Message-ID: <40F4213A.7060307@ncgr.org> Simon Twigger wrote: [...] > I managed to get the S-MOBY reference implementation up and running on > my PowerBook this morning. It wasn't completely plain sailing though the > install docs are great. It's great (and a little scary :-) to see someone looking at Semantic MOBY! I'm glad to see that you got it running on OS X - I have assumed that it would work, but haven't had the chance (or hardware) to try it out. [...] > Gary/Damian: I can add these notes to the S-MOBY/ref-impl/INSTALL.html > file and commit to the CVS repository if you would like, or I can leave > it to you to add in as appropriate. > > Simon. I would be quite happy for you to modify INSTALL.html to include the notes that you wrote up (perhaps in a separate "OS-X-NOTES.html" file linked to from INSTALL.html; you make the call). I would be very happy to see someone else get involved with S-MOBY, since NCGR/CSHL funding for the project is winding down. I'm making quite a few changes that haven't been checked in yet, in order to bring the www.semanticmoby.org web site online. The site will include more examples and keyword-based search. Now I have incentive to make sure my changes don't break anyone else's installation when I do check them in :-) // Gary From simont at aa9pw.com Mon Jul 12 11:14:22 2004 From: simont at aa9pw.com (Simon Twigger) Date: Wed Jul 14 13:32:44 2004 Subject: [MOBY-dev] S-MOBY install on OS X Message-ID: <276F663C-D416-11D8-96F3-000A959D1D82@aa9pw.com> I managed to get the S-MOBY reference implementation up and running on my PowerBook this morning. It wasn't completely plain sailing though the install docs are great. Notes from the OS X Install: Tested using Tomcat 5.0.25, Ant 1.6.1, Java 1.4.2 on Mac OSX 10.3.4 When Editing /etc/hosts: /etc/hosts on 10.3.4 claims that it is not used in the hostname lookup process except for single-user mode. Apparently this is incorrect (at least with the current versions) so this file can be modified as detailed for unix/linux. You may also need to modify the lookup order for the lookupd so it checks the flat file /etc/hosts first, before using DNS, etc. Otherwise trying to find www.s-moby.org:8080 ends up searching DNS rather than using localhost. I followed the advice on the web page listed below, modifying to search the Flat File first rather than DNS which is how it is described in the article. I found this was necessary as once I had everything installed and restarted Tomcat5, localhost:8080 wasnt working as expected and was pointing to some site at MIT (!) sudo mkdir /etc/lookupd sudo echo LookupOrder FF Cache NI DNS DS > /etc/lookupd/hosts sudo kill -1 `cat /var/run/lookupd.pid` See www.aplawrence.com/MacOSX/macosxlookupd.html for more information. Running the Ant Build: In the ant build process, you might need to add appropriate entries in ~/.cvspass if it fails when trying to access CVS servers. Presumably this will only happen if you havent had reason to do any previous anon checkouts from these cvs repositories. :pserver:anoncvs@cvs.apache.org:/home/cvspublic A :pserver:anonymous@cvs.sourceforge.net:/cvsroot/jena A Other than these noted issues, the build ran fine and so far seems to work as advertised though I havent really tried to do much yet. Im trying to get some experience with Jena and how it works with OWL, etc. and having a working application that uses this will be very handy. Gary/Damian: I can add these notes to the S-MOBY/ref-impl/INSTALL.html file and commit to the CVS repository if you would like, or I can leave it to you to add in as appropriate. 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 yanwong at ebgm.jussieu.fr Thu Jul 22 04:55:09 2004 From: yanwong at ebgm.jussieu.fr (Yan Wong) Date: Thu Jul 22 04:56:49 2004 Subject: [MOBY-dev] Are there people in the biomoby list who are working on structures? Message-ID: <1090486509.27675.21.camel@prot1.rpbs.jussieu.fr> I would like to have some points of view of people who are working on protein structures. From mwilkinson at mrl.ubc.ca Thu Jul 29 21:08:08 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Thu Jul 29 21:09:43 2004 Subject: [MOBY-dev] API finally RDF-ized to what we decided on at the last MOBY meeting Message-ID: <1091149688.22146.155.camel@myhost.mydomain> Hi all, between Nina and I we have now come fairly close to a working ~distributed model for service registration/deregistration/updates, as we had decided at the CSHL MOBY Meeting. Here's the way it works: There is a new optional parameter in the registerService call - signatureURL. In that parameter, you enter the URL that the MOBY Central agent should look to for an RDF describing your service. If your registration was successful, you will receive a Registration object, as usual, but the registration object now contains an extra element that contains the RDF describing your service signature. You should place that RDF at the location you indicated in your signatureURL. Nina's agent will come around occasionally and check that document for any updates/additions, etc. If the document is removed, your service will be deregistered. Any RDF tags present in that document that are not familiar to MOBY will be ignored - thus you can annotate your service as much as you wish without affecting the registry agent. Services registered with a signatureURL **cannot be deleted by the deregisterService call!!**, only by the agent. You can temporarily register a service by registering it without a signatureURL - the next time the agent goes exploring, it will delete your service (i.e. it deletes services if it finds no RDF at the URL, or if there is no URL to look to) Once MOBY Central knows your URL, you can add new services without using the MOBY Central API at all! Simply add a new signature to the RDF document, and the agent will register your new service next time it explores your site. Of course, if you don't want to write the RDF yourself (and who would?!?) you can simply use the registerService call of MOBY Central as usual, and it will return the RDF to you. In the next few days, I will be setting up a temporary method call to be used by all existing service providers that will allow you to send a signautureURL to MOBY Central and retrieve an RDF document for all of the services you currently have registered, so you will NOT have to re-register them all! :-) This will bring the database up to date with a URL for everyone. NOTE TO THOSE WITH THEIR OWN MOBY CENTRAL INSTALLATIONS There is now an extra field in the service_instances table: signatureURL varchar(255) null is allowed. You will need to alter your database the next time you cvs update. Shortly - probably this weekend - I will be sending messages only to those who have services registered with information on how to retrieve your RDF signatures. At the moment, all tests pass, so I think it should be a ~painless transition. Lete me know if you experience difficulties. Best wishes all! Mark -- Mark Wilkinson (mwilkinson@mrl.ubc.ca) University of British Columbia iCAPTURE Centre From simont at mcw.edu Tue Jul 13 13:29:49 2004 From: simont at mcw.edu (Simon Twigger) Date: Tue, 13 Jul 2004 12:29:49 -0500 Subject: [MOBY-dev] S-MOBY Install on OS X Message-ID: <3E13688F-D4F2-11D8-8910-000A959D1D82@mcw.edu> (I posted this from a different email a/c and the post got held up pending review so I thought I'd repost from my normal account - apologies if you end up getting this twice) I managed to get the S-MOBY reference implementation up and running on my PowerBook this morning. It wasn't completely plain sailing though the install docs are great. Notes from the OS X Install: Tested using Tomcat 5.0.25, Ant 1.6.1, Java 1.4.2 on Mac OSX 10.3.4 When Editing /etc/hosts: /etc/hosts on 10.3.4 claims that it is not used in the hostname lookup process except for single-user mode. Apparently this is incorrect (at least with the current versions) so this file can be modified as detailed for unix/linux. You may also need to modify the lookup order for the lookupd so it checks the flat file /etc/hosts first, before using DNS, etc. Otherwise trying to find www.s-moby.org:8080 ends up searching DNS rather than using localhost. I followed the advice on the web page listed below, modifying to search the Flat File first rather than DNS which is how it is described in the article. I found this was necessary as once I had everything installed and restarted Tomcat5, localhost:8080 wasnt working as expected and was pointing to some site at MIT (!) sudo mkdir /etc/lookupd sudo echo LookupOrder FF Cache NI DNS DS > /etc/lookupd/hosts sudo kill -1 `cat /var/run/lookupd.pid` See www.aplawrence.com/MacOSX/macosxlookupd.html for more information. Running the Ant Build: In the ant build process, you might need to add appropriate entries in ~/.cvspass if it fails when trying to access CVS servers. Presumably this will only happen if you havent had reason to do any previous anon checkouts from these cvs repositories. :pserver:anoncvs at cvs.apache.org:/home/cvspublic A :pserver:anonymous at cvs.sourceforge.net:/cvsroot/jena A Other than these noted issues, the build ran fine and so far seems to work as advertised though I havent really tried to do much yet. Im trying to get some experience with Jena and how it works with OWL, etc. and having a working application that uses this will be very handy. Gary/Damian: I can add these notes to the S-MOBY/ref-impl/INSTALL.html file and commit to the CVS repository if you would like, or I can leave it to you to add in as appropriate. 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 gss at ncgr.org Tue Jul 13 13:51:54 2004 From: gss at ncgr.org (Gary Schiltz) Date: Tue, 13 Jul 2004 11:51:54 -0600 Subject: [MOBY-dev] S-MOBY Install on OS X In-Reply-To: <3E13688F-D4F2-11D8-8910-000A959D1D82@mcw.edu> References: <3E13688F-D4F2-11D8-8910-000A959D1D82@mcw.edu> Message-ID: <40F4213A.7060307@ncgr.org> Simon Twigger wrote: [...] > I managed to get the S-MOBY reference implementation up and running on > my PowerBook this morning. It wasn't completely plain sailing though the > install docs are great. It's great (and a little scary :-) to see someone looking at Semantic MOBY! I'm glad to see that you got it running on OS X - I have assumed that it would work, but haven't had the chance (or hardware) to try it out. [...] > Gary/Damian: I can add these notes to the S-MOBY/ref-impl/INSTALL.html > file and commit to the CVS repository if you would like, or I can leave > it to you to add in as appropriate. > > Simon. I would be quite happy for you to modify INSTALL.html to include the notes that you wrote up (perhaps in a separate "OS-X-NOTES.html" file linked to from INSTALL.html; you make the call). I would be very happy to see someone else get involved with S-MOBY, since NCGR/CSHL funding for the project is winding down. I'm making quite a few changes that haven't been checked in yet, in order to bring the www.semanticmoby.org web site online. The site will include more examples and keyword-based search. Now I have incentive to make sure my changes don't break anyone else's installation when I do check them in :-) // Gary From simont at aa9pw.com Mon Jul 12 11:14:22 2004 From: simont at aa9pw.com (Simon Twigger) Date: Mon, 12 Jul 2004 10:14:22 -0500 Subject: [MOBY-dev] S-MOBY install on OS X Message-ID: <276F663C-D416-11D8-96F3-000A959D1D82@aa9pw.com> I managed to get the S-MOBY reference implementation up and running on my PowerBook this morning. It wasn't completely plain sailing though the install docs are great. Notes from the OS X Install: Tested using Tomcat 5.0.25, Ant 1.6.1, Java 1.4.2 on Mac OSX 10.3.4 When Editing /etc/hosts: /etc/hosts on 10.3.4 claims that it is not used in the hostname lookup process except for single-user mode. Apparently this is incorrect (at least with the current versions) so this file can be modified as detailed for unix/linux. You may also need to modify the lookup order for the lookupd so it checks the flat file /etc/hosts first, before using DNS, etc. Otherwise trying to find www.s-moby.org:8080 ends up searching DNS rather than using localhost. I followed the advice on the web page listed below, modifying to search the Flat File first rather than DNS which is how it is described in the article. I found this was necessary as once I had everything installed and restarted Tomcat5, localhost:8080 wasnt working as expected and was pointing to some site at MIT (!) sudo mkdir /etc/lookupd sudo echo LookupOrder FF Cache NI DNS DS > /etc/lookupd/hosts sudo kill -1 `cat /var/run/lookupd.pid` See www.aplawrence.com/MacOSX/macosxlookupd.html for more information. Running the Ant Build: In the ant build process, you might need to add appropriate entries in ~/.cvspass if it fails when trying to access CVS servers. Presumably this will only happen if you havent had reason to do any previous anon checkouts from these cvs repositories. :pserver:anoncvs at cvs.apache.org:/home/cvspublic A :pserver:anonymous at cvs.sourceforge.net:/cvsroot/jena A Other than these noted issues, the build ran fine and so far seems to work as advertised though I havent really tried to do much yet. Im trying to get some experience with Jena and how it works with OWL, etc. and having a working application that uses this will be very handy. Gary/Damian: I can add these notes to the S-MOBY/ref-impl/INSTALL.html file and commit to the CVS repository if you would like, or I can leave it to you to add in as appropriate. 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 yanwong at ebgm.jussieu.fr Thu Jul 22 04:55:09 2004 From: yanwong at ebgm.jussieu.fr (Yan Wong) Date: 22 Jul 2004 10:55:09 +0200 Subject: [MOBY-dev] Are there people in the biomoby list who are working on structures? Message-ID: <1090486509.27675.21.camel@prot1.rpbs.jussieu.fr> I would like to have some points of view of people who are working on protein structures. From mwilkinson at mrl.ubc.ca Thu Jul 29 21:08:08 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Thu, 29 Jul 2004 18:08:08 -0700 Subject: [MOBY-dev] API finally RDF-ized to what we decided on at the last MOBY meeting Message-ID: <1091149688.22146.155.camel@myhost.mydomain> Hi all, between Nina and I we have now come fairly close to a working ~distributed model for service registration/deregistration/updates, as we had decided at the CSHL MOBY Meeting. Here's the way it works: There is a new optional parameter in the registerService call - signatureURL. In that parameter, you enter the URL that the MOBY Central agent should look to for an RDF describing your service. If your registration was successful, you will receive a Registration object, as usual, but the registration object now contains an extra element that contains the RDF describing your service signature. You should place that RDF at the location you indicated in your signatureURL. Nina's agent will come around occasionally and check that document for any updates/additions, etc. If the document is removed, your service will be deregistered. Any RDF tags present in that document that are not familiar to MOBY will be ignored - thus you can annotate your service as much as you wish without affecting the registry agent. Services registered with a signatureURL **cannot be deleted by the deregisterService call!!**, only by the agent. You can temporarily register a service by registering it without a signatureURL - the next time the agent goes exploring, it will delete your service (i.e. it deletes services if it finds no RDF at the URL, or if there is no URL to look to) Once MOBY Central knows your URL, you can add new services without using the MOBY Central API at all! Simply add a new signature to the RDF document, and the agent will register your new service next time it explores your site. Of course, if you don't want to write the RDF yourself (and who would?!?) you can simply use the registerService call of MOBY Central as usual, and it will return the RDF to you. In the next few days, I will be setting up a temporary method call to be used by all existing service providers that will allow you to send a signautureURL to MOBY Central and retrieve an RDF document for all of the services you currently have registered, so you will NOT have to re-register them all! :-) This will bring the database up to date with a URL for everyone. NOTE TO THOSE WITH THEIR OWN MOBY CENTRAL INSTALLATIONS There is now an extra field in the service_instances table: signatureURL varchar(255) null is allowed. You will need to alter your database the next time you cvs update. Shortly - probably this weekend - I will be sending messages only to those who have services registered with information on how to retrieve your RDF signatures. At the moment, all tests pass, so I think it should be a ~painless transition. Lete me know if you experience difficulties. Best wishes all! Mark -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre From gss at ncgr.org Thu Jul 1 00:30:43 2004 From: gss at ncgr.org (Gary Schiltz) Date: Wed, 30 Jun 2004 18:30:43 -0600 Subject: [MOBY-dev] Sesame? Message-ID: <40E35B33.7070206@ncgr.org> I looked at Sesame when I was trying to decide on the best architecture on top of which to implement S-MOBY (about 6 months ago). While it looked like a good tool, it didn't seem to be very actively maintained at the time. I just looked at the Sesame web site (www.openrdf.org), and it looks like the user forums have had a bit of traffic, so maybe it's more active than before. In the end, I settled on Jena (jena.sourceforge.net) as the underlying framework for working with RDF. It is quite actively supported by HP, and also seems to have an active user community. At least, its mailing list gets a large number of messages every day. // Gary From simont at mcw.edu Tue Jul 13 17:29:49 2004 From: simont at mcw.edu (Simon Twigger) Date: Tue, 13 Jul 2004 12:29:49 -0500 Subject: [MOBY-dev] S-MOBY Install on OS X Message-ID: <3E13688F-D4F2-11D8-8910-000A959D1D82@mcw.edu> (I posted this from a different email a/c and the post got held up pending review so I thought I'd repost from my normal account - apologies if you end up getting this twice) I managed to get the S-MOBY reference implementation up and running on my PowerBook this morning. It wasn't completely plain sailing though the install docs are great. Notes from the OS X Install: Tested using Tomcat 5.0.25, Ant 1.6.1, Java 1.4.2 on Mac OSX 10.3.4 When Editing /etc/hosts: /etc/hosts on 10.3.4 claims that it is not used in the hostname lookup process except for single-user mode. Apparently this is incorrect (at least with the current versions) so this file can be modified as detailed for unix/linux. You may also need to modify the lookup order for the lookupd so it checks the flat file /etc/hosts first, before using DNS, etc. Otherwise trying to find www.s-moby.org:8080 ends up searching DNS rather than using localhost. I followed the advice on the web page listed below, modifying to search the Flat File first rather than DNS which is how it is described in the article. I found this was necessary as once I had everything installed and restarted Tomcat5, localhost:8080 wasnt working as expected and was pointing to some site at MIT (!) sudo mkdir /etc/lookupd sudo echo LookupOrder FF Cache NI DNS DS > /etc/lookupd/hosts sudo kill -1 `cat /var/run/lookupd.pid` See www.aplawrence.com/MacOSX/macosxlookupd.html for more information. Running the Ant Build: In the ant build process, you might need to add appropriate entries in ~/.cvspass if it fails when trying to access CVS servers. Presumably this will only happen if you havent had reason to do any previous anon checkouts from these cvs repositories. :pserver:anoncvs at cvs.apache.org:/home/cvspublic A :pserver:anonymous at cvs.sourceforge.net:/cvsroot/jena A Other than these noted issues, the build ran fine and so far seems to work as advertised though I havent really tried to do much yet. Im trying to get some experience with Jena and how it works with OWL, etc. and having a working application that uses this will be very handy. Gary/Damian: I can add these notes to the S-MOBY/ref-impl/INSTALL.html file and commit to the CVS repository if you would like, or I can leave it to you to add in as appropriate. 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 gss at ncgr.org Tue Jul 13 17:51:54 2004 From: gss at ncgr.org (Gary Schiltz) Date: Tue, 13 Jul 2004 11:51:54 -0600 Subject: [MOBY-dev] S-MOBY Install on OS X In-Reply-To: <3E13688F-D4F2-11D8-8910-000A959D1D82@mcw.edu> References: <3E13688F-D4F2-11D8-8910-000A959D1D82@mcw.edu> Message-ID: <40F4213A.7060307@ncgr.org> Simon Twigger wrote: [...] > I managed to get the S-MOBY reference implementation up and running on > my PowerBook this morning. It wasn't completely plain sailing though the > install docs are great. It's great (and a little scary :-) to see someone looking at Semantic MOBY! I'm glad to see that you got it running on OS X - I have assumed that it would work, but haven't had the chance (or hardware) to try it out. [...] > Gary/Damian: I can add these notes to the S-MOBY/ref-impl/INSTALL.html > file and commit to the CVS repository if you would like, or I can leave > it to you to add in as appropriate. > > Simon. I would be quite happy for you to modify INSTALL.html to include the notes that you wrote up (perhaps in a separate "OS-X-NOTES.html" file linked to from INSTALL.html; you make the call). I would be very happy to see someone else get involved with S-MOBY, since NCGR/CSHL funding for the project is winding down. I'm making quite a few changes that haven't been checked in yet, in order to bring the www.semanticmoby.org web site online. The site will include more examples and keyword-based search. Now I have incentive to make sure my changes don't break anyone else's installation when I do check them in :-) // Gary From simont at aa9pw.com Mon Jul 12 15:14:22 2004 From: simont at aa9pw.com (Simon Twigger) Date: Mon, 12 Jul 2004 10:14:22 -0500 Subject: [MOBY-dev] S-MOBY install on OS X Message-ID: <276F663C-D416-11D8-96F3-000A959D1D82@aa9pw.com> I managed to get the S-MOBY reference implementation up and running on my PowerBook this morning. It wasn't completely plain sailing though the install docs are great. Notes from the OS X Install: Tested using Tomcat 5.0.25, Ant 1.6.1, Java 1.4.2 on Mac OSX 10.3.4 When Editing /etc/hosts: /etc/hosts on 10.3.4 claims that it is not used in the hostname lookup process except for single-user mode. Apparently this is incorrect (at least with the current versions) so this file can be modified as detailed for unix/linux. You may also need to modify the lookup order for the lookupd so it checks the flat file /etc/hosts first, before using DNS, etc. Otherwise trying to find www.s-moby.org:8080 ends up searching DNS rather than using localhost. I followed the advice on the web page listed below, modifying to search the Flat File first rather than DNS which is how it is described in the article. I found this was necessary as once I had everything installed and restarted Tomcat5, localhost:8080 wasnt working as expected and was pointing to some site at MIT (!) sudo mkdir /etc/lookupd sudo echo LookupOrder FF Cache NI DNS DS > /etc/lookupd/hosts sudo kill -1 `cat /var/run/lookupd.pid` See www.aplawrence.com/MacOSX/macosxlookupd.html for more information. Running the Ant Build: In the ant build process, you might need to add appropriate entries in ~/.cvspass if it fails when trying to access CVS servers. Presumably this will only happen if you havent had reason to do any previous anon checkouts from these cvs repositories. :pserver:anoncvs at cvs.apache.org:/home/cvspublic A :pserver:anonymous at cvs.sourceforge.net:/cvsroot/jena A Other than these noted issues, the build ran fine and so far seems to work as advertised though I havent really tried to do much yet. Im trying to get some experience with Jena and how it works with OWL, etc. and having a working application that uses this will be very handy. Gary/Damian: I can add these notes to the S-MOBY/ref-impl/INSTALL.html file and commit to the CVS repository if you would like, or I can leave it to you to add in as appropriate. 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 yanwong at ebgm.jussieu.fr Thu Jul 22 08:55:09 2004 From: yanwong at ebgm.jussieu.fr (Yan Wong) Date: 22 Jul 2004 10:55:09 +0200 Subject: [MOBY-dev] Are there people in the biomoby list who are working on structures? Message-ID: <1090486509.27675.21.camel@prot1.rpbs.jussieu.fr> I would like to have some points of view of people who are working on protein structures. From mwilkinson at mrl.ubc.ca Fri Jul 30 01:08:08 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Thu, 29 Jul 2004 18:08:08 -0700 Subject: [MOBY-dev] API finally RDF-ized to what we decided on at the last MOBY meeting Message-ID: <1091149688.22146.155.camel@myhost.mydomain> Hi all, between Nina and I we have now come fairly close to a working ~distributed model for service registration/deregistration/updates, as we had decided at the CSHL MOBY Meeting. Here's the way it works: There is a new optional parameter in the registerService call - signatureURL. In that parameter, you enter the URL that the MOBY Central agent should look to for an RDF describing your service. If your registration was successful, you will receive a Registration object, as usual, but the registration object now contains an extra element that contains the RDF describing your service signature. You should place that RDF at the location you indicated in your signatureURL. Nina's agent will come around occasionally and check that document for any updates/additions, etc. If the document is removed, your service will be deregistered. Any RDF tags present in that document that are not familiar to MOBY will be ignored - thus you can annotate your service as much as you wish without affecting the registry agent. Services registered with a signatureURL **cannot be deleted by the deregisterService call!!**, only by the agent. You can temporarily register a service by registering it without a signatureURL - the next time the agent goes exploring, it will delete your service (i.e. it deletes services if it finds no RDF at the URL, or if there is no URL to look to) Once MOBY Central knows your URL, you can add new services without using the MOBY Central API at all! Simply add a new signature to the RDF document, and the agent will register your new service next time it explores your site. Of course, if you don't want to write the RDF yourself (and who would?!?) you can simply use the registerService call of MOBY Central as usual, and it will return the RDF to you. In the next few days, I will be setting up a temporary method call to be used by all existing service providers that will allow you to send a signautureURL to MOBY Central and retrieve an RDF document for all of the services you currently have registered, so you will NOT have to re-register them all! :-) This will bring the database up to date with a URL for everyone. NOTE TO THOSE WITH THEIR OWN MOBY CENTRAL INSTALLATIONS There is now an extra field in the service_instances table: signatureURL varchar(255) null is allowed. You will need to alter your database the next time you cvs update. Shortly - probably this weekend - I will be sending messages only to those who have services registered with information on how to retrieve your RDF signatures. At the moment, all tests pass, so I think it should be a ~painless transition. Lete me know if you experience difficulties. Best wishes all! Mark -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre