From letondal at pasteur.fr Fri Jan 2 07:35:14 2004 From: letondal at pasteur.fr (Catherine Letondal) Date: Fri Jan 2 07:42:27 2004 Subject: [MOBY-dev] Re: [MISC] Re: [MOBY-l] People's experience with perl-based GUI libraries In-Reply-To: Your message of "Mon, 29 Dec 2003 10:56:06 CST." <1072716966.1724.72.camel@localhost.localdomain> Message-ID: <200401021235.i02CZEa0322286@electre.pasteur.fr> Hi, Happy new year! ... speaking of users(-interfaces), does someone in the Biomoby/myGrid community participate to this workshop in Edimburgh: http://www.nesc.ac.uk/esi/events/320/ where topics include user-centred aspects for the deployment of Grid technologies? I ask because myGrid is referenced as one of the NESC projects: http://www.nesc.ac.uk/action/projects/project_action.cfm?Title=7 Best, -- Catherine Letondal -- Pasteur Institute Computing Center From markw at illuminae.com Fri Jan 2 10:51:32 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Fri Jan 2 10:58:48 2004 Subject: [MOBY-l] "up"grade of Apache/mod-perl on mobycentral Message-ID: <1073058692.1730.20.camel@localhost.localdomain> Hi all, Over the new year's holiday I "up"graded the webserver on mobycentral to an older version of Apache/mod-perl. The reason was that the Apache2/mod-perl2 installation was breaking so frequently that I had it on an hourly cron to restart it! This isn't surprising since Apache2 is still not "production quality", however after weeks of trying to compile Apache/mod-perl on that SUN machine I had to give up and install Apache2 (which surprisingly installed completely effortlessly!). I finally built up the patience to try again, and after searching the net extensively for assistance I found a message from a SUN administrator indicating that the problem is with the "strip" program. Renaming that executable at least allowed the server to start up, but there may still be other problems (make test still fails on many tests). I've been running it through its paces for the past couple of days and I haven't noticed any obvious problems. I haven't had to restart it, and it actually seems to run faster than before, so... things look good! Please let me know ASAP if you notice any 'flakyness'. I'm just giving everyone a heads-up that if you notice anything strange you should possibly consider the server as a potential source of problems before you go banging your heads looking for bugs in your code. Cheers! Mark -- Mark Wilkinson Illuminae From markw at illuminae.com Thu Jan 8 14:27:53 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Thu Jan 8 14:34:54 2004 Subject: [MOBY-l] Release 0.6.0 available Message-ID: <1073590073.5067.8.camel@localhost.localdomain> Hi all, I just made a release of the code to coincide with the release of the latest Gbrowse. Gbrowse now ships with both a MOBY-S client as well as ~10 MOBY Services that auto-install/register to serve data out of the underlying Gbrowse database. It was necessary to make an "official" release in order to build the RPM packages for installation. Please let me know if you try this and find any bugs! ... wow... our first release :-) We're growing up! Mark -- Mark Wilkinson Illuminae From scott at scientificminds.com Fri Jan 9 08:39:10 2004 From: scott at scientificminds.com (Validation) Date: Fri Jan 9 08:46:01 2004 Subject: [MOBY-l] Validation Message-ID: <200401091345.i09DjwNQ031279@portal.open-bio.org> I have several new consulting and permanent 21 CFR Part 11 requirements: Europe: LIMS, SampleManager, Millenium32, Empower New England: Empower, Millenium32, Gap Analysis NY-NJ-PA: Procedural Remediations, Consent Decree, FDA Audit, LIMS (all types), SAP, MRP San Francisco: Equipment, Cleaning, Instrument, HPLC, LIMS, MRP, Network Security. LAX/San Diego: ERP, LIMS, Instrumentation, Manufacturing Systems. I manage all sourcing and prequalification of Validation Compliance candidates for a substantial number of US Pharmaceuticals and select Consulting Groups. Please forward a resume to me by replying to this message. My website is intentionally simple and straightforward. You may submit your resume from it if you wish: www.scientificminds.com Linda Scott Scientificminds Note: We are not an "agency." We work similarly to "contract recruiters" filling permanent and consulting positions for direct clients. From markw at illuminae.com Wed Jan 14 08:59:49 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Wed Jan 14 09:06:36 2004 Subject: [MOBY-l] quick (but important) poll on pervasiveness Message-ID: <1074088789.1729.21.camel@localhost.localdomain> Hi all, We are rapidly approaching the mid-term review of the Genome Canada grant to the BioMOBY project. I'm doing the write-up on our successes (we have no failures ;-) ), and I'd like to get a straw-poll on the impact of what we are doing in "the real world". Can I get an "aye" from everyone who is seriously planning to set up MOBY-S services in the next 6 months. You can reply on-list, or personally. This is also a good opportunity to say THANKS to all of you for your interest and enthusiasm in the past year! You will be able to tell your grandchildren that you were there at the beginning ;-) Happy new year everyone! Mark -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. of Medical Genetics University of British Columbia's iCAPTURE Centre Vancouver, BC, Canada ------------------------------------------------------------------------ It just goes to show you that SOAP::Lite is more intuitive than you might think, if you know enough Perl and have the patience to dive into the source code. -Byrne Reese -http://builder.com.com/5100-6389_14-1045078-2.html ------------------------------------------------------------------------ From steube at sdsc.edu Sat Jan 17 10:31:58 2004 From: steube at sdsc.edu (Ken Steube) Date: Sat Jan 17 10:38:42 2004 Subject: [MOBY-l] MOBY Workshop In-Reply-To: <1074088789.1729.21.camel@localhost.localdomain> Message-ID: Another MOBY workshop completed! Nine more people introduced to writing web services with MOBY. Each has registered at least one simple service and executed it. They also know how to install my FASTA service once they get home so they're ready to start writing useful services. Woohoo! Ken -- -- Ken Steube San Diego Supercomputer Center University of California, San Diego Mail code 0537, CRB room 207 9500 Gilman Drive San Diego, California, 92093-0537 USA FAX (858) 822-3610 From markw at illuminae.com Sat Jan 17 10:58:41 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Sat Jan 17 11:05:32 2004 Subject: [MOBY] [MOBY-l] MOBY Workshop In-Reply-To: References: Message-ID: <1074355120.1728.90.camel@localilluminae.com> That's fantastic! thanks for all your hard work, Ken! Mark On Sat, 2004-01-17 at 09:31, Ken Steube wrote: > Another MOBY workshop completed! Nine more people introduced to writing > web services with MOBY. Each has registered at least one simple service > and executed it. They also know how to install my FASTA service once they > get home so they're ready to start writing useful services. > > Woohoo! > > Ken > > -- > -- > Ken Steube > San Diego Supercomputer Center > University of California, San Diego > Mail code 0537, CRB room 207 > 9500 Gilman Drive > San Diego, California, 92093-0537 USA > FAX (858) 822-3610 > > _______________________________________________ > moby-l mailing list > moby-l@biomoby.org > http://biomoby.org/mailman/listinfo/moby-l -- Mark Wilkinson Illuminae From markw at illuminae.com Sat Jan 17 15:52:43 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Sat Jan 17 15:59:27 2004 Subject: [MOBY-l] Suggestion from Ken implemented Message-ID: <1074372763.3580.7.camel@localilluminae.com> Hi all, Ken Steube just made a suggestion that I thought was fantastic, so I just implemented it in the browser. He suggested that there be some clickable examples of a variety of initialization parameters that lead to interesting services. This was surprisingly easy to do, since the new client program uses the gbrowse configuration file, which can include HTML for the header/footer of the cgi page :-) (thanks Lincoln!) If any of you want to showcase your services, please send me an example namespace/id and service name and I'll add it to the list on the browser homepage. Mark -- Mark Wilkinson Illuminae From avraham at cshl.edu Sat Jan 17 18:12:39 2004 From: avraham at cshl.edu (Shuly Avraham) Date: Sat Jan 17 18:19:29 2004 Subject: [MOBY-l] MOBY Workshop In-Reply-To: Message-ID: Thanks, Ken! The workshop was very good and helpful(and fun too!), as well as the tutorials you wrote. Shuly. On Sat, 17 Jan 2004, Ken Steube wrote: > Another MOBY workshop completed! Nine more people introduced to writing > web services with MOBY. Each has registered at least one simple service > and executed it. They also know how to install my FASTA service once they > get home so they're ready to start writing useful services. > > Woohoo! > > Ken > > -- > -- > Ken Steube > San Diego Supercomputer Center > University of California, San Diego > Mail code 0537, CRB room 207 > 9500 Gilman Drive > San Diego, California, 92093-0537 USA > FAX (858) 822-3610 > > _______________________________________________ > moby-l mailing list > moby-l@biomoby.org > http://biomoby.org/mailman/listinfo/moby-l > From lstein at cshl.edu Mon Jan 19 09:31:43 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Mon Jan 19 09:38:33 2004 Subject: [MOBY-l] MOBY conference calls Message-ID: <200401191631.43495.lstein@cshl.edu> Hello, As some of you know I am doing a mini-sabbatical in Capetown South Africa until March 2. Unfortunately this means I am in the GMT+2 timezone, which is 7 hours ahead of the east coast, and 10 hours ahead of the west coast. This means that in order for me to participate in the conference calls, we will have to move them to early in the morning for you west-coast people, and mid-morning for you New Mexico people. Needless to say, I'm doing this for other scheduled conference calls too! Friday mornings are good for me. How about others? Lincoln -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 From dtb24 at cornell.edu Thu Jan 22 13:18:44 2004 From: dtb24 at cornell.edu (David Bogaty) Date: Thu Jan 22 13:25:19 2004 Subject: [MOBY-l] MOBY Workshop In-Reply-To: References: Message-ID: <5.2.1.1.2.20040122131526.00b3a4e0@postoffice6.mail.cornell.edu> I second the motion... thanks Ken, a job well done! Aside from MOBY, I also learned a thing or two about barbecue potato chips and the importance of remembering one's age at a restaurant. Look for some services from SGN soon =) Dave Bogaty http://sgn.cornell.edu PS - does anyone have those pictures? At 06:12 PM 1/17/2004 -0500, Shuly Avraham wrote: >Thanks, Ken! >The workshop was very good and helpful(and fun too!), >as well as the tutorials you wrote. >Shuly. From markw at illuminae.com Fri Jan 23 09:59:22 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Fri Jan 23 10:06:01 2004 Subject: [MOBY-l] Moving on up! Message-ID: <1074869962.1621.6.camel@localilluminae.com> Hi all MOBY'ers! Just a quick note to say that I will be out of contact for the next ~2 weeks as I am moving to Vancouver. My email address will not change, so I will get your mails, but they will be badly stacked by the time I get a chance to login again, so I might not get to them very quickly. I'll see you all on the other side! Best wishes! Mark P.S. For anyone who has never lived in Canada before, here is the weather forecast for moving day. Eat your heart out, Lincoln, and think of me as you sip your MaiTai on the beach! Tuesday - A mix of sun and clouds High: -25?C Low: -33?C Wind 10 km/h W POP: 30% Wednesday - Cloudy with sunny breaks High: -33?C Low: -37?C Wind 5 km/h NW POP: 20% -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. of Medical Genetics University of British Columbia's iCAPTURE Centre Vancouver, BC, Canada ------------------------------------------------------------------------ It just goes to show you that SOAP::Lite is more intuitive than you might think, if you know enough Perl and have the patience to dive into the source code. -Byrne Reese -http://builder.com.com/5100-6389_14-1045078-2.html ------------------------------------------------------------------------ From steube at sdsc.edu Wed Jan 28 12:07:36 2004 From: steube at sdsc.edu (Ken Steube) Date: Wed Jan 28 12:14:05 2004 Subject: [MOBY-l] Re: namespace In-Reply-To: <92012141-51B2-11D8-8DDC-000A9591E2C8@cshl.org> Message-ID: I'm not sure I understand the question...I'll try to answer and you can reply for more info. An object belongs to a particular namespace belongs to AGI_LocusCode. Sometimes you might see the namespace might being left blank if it's not important (such as for the Integer object inside a GenericSequence). I wouldn't really say a service belongs to a namespace, rather we say it accepts objects from particular namespaces. Or a service might accept objects of a certain type from any namespace if the namespace isn't important (such as BLAST: can accept a DNA seq from any namespace so the namespace isn't generally critical info for BLAST). Ken On Wed, 28 Jan 2004, Ardavan Kanani wrote: > Ken, > > Thanks for responding to my question. My question is more about an > object belonging to a namespace or services belonging to a namespace > and not accepting or outputting objects from a particular namespace. > Do objects belong to particular namespaces? If that's the case where > in the object registration should I declare its namespace? Since > services are, sort of, objects too, where do I specify what namespace > they belong to. I am trying to create all my objects and services > under a namespace called "haplotyping_study" I might be totally > confused as how the namespaces work on MOBY. I am coming from an > object oriented world. So when I see the disjoint between objects and > services in MOBY I get confused. > > Thanks, Ardavan Kanani > > On Jan 28, 2004, at 11:36 AM, Ken Steube wrote: > > > On Wed, 28 Jan 2004, Ardavan Kanani wrote: > >> Mark, > >> How would I register an object or a service under a particular > >> namespace? I looked at the API doc and the signature for > >> registerObjectClass and registerServiceName/Type does not include a > >> namespace parameter. > > > > Here is the script that registers my plantspGetProtein service to > > accept an Object from any of the namespaces > > ['AGI_LocusCode', 'NCBI_gi', 'SDSC_fg']. > > > > Ken > > > > > > > > > > > > #!/usr/local/bin/perl5.6.1 > > use warnings 'all'; # Issue warnings about suspicious programming > > use strict; # Must declare and initialize all variables > > > > ####################################################################### > > ## > > # This script will register the plantspGetProtein MOBY service > > ####################################################################### > > ## > > > > use MOBY::Client::Central; > > use MOBY::Client::Service; > > > > my $Central = MOBY::Client::Central->new(); > > > > my $reg = $Central->registerService( > > serviceName => 'plantspGetProtein', > > authURI => 'www.sdsc.edu', > > contactEmail => 'steube@sdsc.edu', > > description => "Retrieves a protein sequence from the PlantsP > > database (proteins related to phosphorylation, transporters and > > ubiquitin)", > > URL => > > 'http://plantsp.sdsc.edu/cgi-bin/MOBY/PlantsP_dispatcher.cgi', > > input => [ ['', ["Object" => ['AGI_LocusCode', 'NCBI_gi', > > 'SDSC_fg']]], ], > > output => [ ['', ["AminoAcidSequence" => []]], ], > > category => "moby", > > serviceType => "Retrieval", > > ); > > die "Bad return value from registerService" unless $reg; > > if ($reg->success == 1){ > > print "Registration successful\n\n"; > > } > > else { > > print "Registration failed: ", $reg->message, "\n"; > > } > > > > > > -- > > -- > > -- > > Ken Steube > > San Diego Supercomputer Center > > University of California, San Diego > > Mail code 0537, CRB room 207 > > 9500 Gilman Drive > > San Diego, California, 92093-0537 USA > > FAX (858) 822-3610 > > > -- -- -- Ken Steube San Diego Supercomputer Center University of California, San Diego Mail code 0537, CRB room 207 9500 Gilman Drive San Diego, California, 92093-0537 USA FAX (858) 822-3610 From beatrice at arabidopsis.info Thu Jan 29 11:58:01 2004 From: beatrice at arabidopsis.info (Beatrice Schildknecht) Date: Thu Jan 29 12:04:45 2004 Subject: [MOBY-l] Proxies... Message-ID: <40193B99.4070207@arabidopsis.info> Help note/patch for those using proxy servers. This is how I got MOBY to use my proxy server: 1) In: /MOBY/Client/OntologyServer.pm /MOBY/Client/Central.pm Change all occurences of: my $ua = LWP::UserAgent->new; to: my $ua = LWP::UserAgent->new(env_proxy=>1); 2) In your httpd.conf file, set environmental variables to use your proxy server. e.g.: setenv HTTP_proxy http://wwwcache.nottingham.ac.uk:3128 setenv CGI_HTTP_PROXY http://wwwcache.nottingham.ac.uk:3128 3) Restart http. [4) Set your environmental variables again. How I did it in my .bashrc config file: export CGI_HTTP_proxy=http://wwwcache.nottingham.ac.uk:3128 export HTTP_proxy=http://wwwcache.nottingham.ac.uk:3128 ] See www.cpan.org for more. (This may not be the best way of doing it....Any other ideas welcome....Mark, would it be possible for this be fixed in the next update?) Thanks, Beatrice -- Nottingham Arabidopsis Stock Centre School of Biosciences Plant Science Division University of Nottingham Sutton Bonington Campus Loughborough LE12 5RD Tel: +44 115 951 3091 http://arabidopsis.info From letondal at pasteur.fr Fri Jan 2 07:35:14 2004 From: letondal at pasteur.fr (Catherine Letondal) Date: Fri, 02 Jan 2004 13:35:14 +0100 Subject: [MOBY-dev] Re: [MISC] Re: [MOBY-l] People's experience with perl-based GUI libraries In-Reply-To: Your message of "Mon, 29 Dec 2003 10:56:06 CST." <1072716966.1724.72.camel@localhost.localdomain> Message-ID: <200401021235.i02CZEa0322286@electre.pasteur.fr> Hi, Happy new year! ... speaking of users(-interfaces), does someone in the Biomoby/myGrid community participate to this workshop in Edimburgh: http://www.nesc.ac.uk/esi/events/320/ where topics include user-centred aspects for the deployment of Grid technologies? I ask because myGrid is referenced as one of the NESC projects: http://www.nesc.ac.uk/action/projects/project_action.cfm?Title=7 Best, -- Catherine Letondal -- Pasteur Institute Computing Center From markw at illuminae.com Fri Jan 2 10:51:32 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 02 Jan 2004 09:51:32 -0600 Subject: [MOBY-l] "up"grade of Apache/mod-perl on mobycentral Message-ID: <1073058692.1730.20.camel@localhost.localdomain> Hi all, Over the new year's holiday I "up"graded the webserver on mobycentral to an older version of Apache/mod-perl. The reason was that the Apache2/mod-perl2 installation was breaking so frequently that I had it on an hourly cron to restart it! This isn't surprising since Apache2 is still not "production quality", however after weeks of trying to compile Apache/mod-perl on that SUN machine I had to give up and install Apache2 (which surprisingly installed completely effortlessly!). I finally built up the patience to try again, and after searching the net extensively for assistance I found a message from a SUN administrator indicating that the problem is with the "strip" program. Renaming that executable at least allowed the server to start up, but there may still be other problems (make test still fails on many tests). I've been running it through its paces for the past couple of days and I haven't noticed any obvious problems. I haven't had to restart it, and it actually seems to run faster than before, so... things look good! Please let me know ASAP if you notice any 'flakyness'. I'm just giving everyone a heads-up that if you notice anything strange you should possibly consider the server as a potential source of problems before you go banging your heads looking for bugs in your code. Cheers! Mark -- Mark Wilkinson Illuminae From markw at illuminae.com Thu Jan 8 14:27:53 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 08 Jan 2004 13:27:53 -0600 Subject: [MOBY-l] Release 0.6.0 available Message-ID: <1073590073.5067.8.camel@localhost.localdomain> Hi all, I just made a release of the code to coincide with the release of the latest Gbrowse. Gbrowse now ships with both a MOBY-S client as well as ~10 MOBY Services that auto-install/register to serve data out of the underlying Gbrowse database. It was necessary to make an "official" release in order to build the RPM packages for installation. Please let me know if you try this and find any bugs! ... wow... our first release :-) We're growing up! Mark -- Mark Wilkinson Illuminae From scott at scientificminds.com Fri Jan 9 08:39:10 2004 From: scott at scientificminds.com (Validation) Date: Fri, 9 Jan 2004 08:39:10 -0500 Subject: [MOBY-l] Validation Message-ID: <200401091345.i09DjwNQ031279@portal.open-bio.org> I have several new consulting and permanent 21 CFR Part 11 requirements: Europe: LIMS, SampleManager, Millenium32, Empower New England: Empower, Millenium32, Gap Analysis NY-NJ-PA: Procedural Remediations, Consent Decree, FDA Audit, LIMS (all types), SAP, MRP San Francisco: Equipment, Cleaning, Instrument, HPLC, LIMS, MRP, Network Security. LAX/San Diego: ERP, LIMS, Instrumentation, Manufacturing Systems. I manage all sourcing and prequalification of Validation Compliance candidates for a substantial number of US Pharmaceuticals and select Consulting Groups. Please forward a resume to me by replying to this message. My website is intentionally simple and straightforward. You may submit your resume from it if you wish: www.scientificminds.com Linda Scott Scientificminds Note: We are not an "agency." We work similarly to "contract recruiters" filling permanent and consulting positions for direct clients. From markw at illuminae.com Wed Jan 14 08:59:49 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 14 Jan 2004 07:59:49 -0600 Subject: [MOBY-l] quick (but important) poll on pervasiveness Message-ID: <1074088789.1729.21.camel@localhost.localdomain> Hi all, We are rapidly approaching the mid-term review of the Genome Canada grant to the BioMOBY project. I'm doing the write-up on our successes (we have no failures ;-) ), and I'd like to get a straw-poll on the impact of what we are doing in "the real world". Can I get an "aye" from everyone who is seriously planning to set up MOBY-S services in the next 6 months. You can reply on-list, or personally. This is also a good opportunity to say THANKS to all of you for your interest and enthusiasm in the past year! You will be able to tell your grandchildren that you were there at the beginning ;-) Happy new year everyone! Mark -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. of Medical Genetics University of British Columbia's iCAPTURE Centre Vancouver, BC, Canada ------------------------------------------------------------------------ It just goes to show you that SOAP::Lite is more intuitive than you might think, if you know enough Perl and have the patience to dive into the source code. -Byrne Reese -http://builder.com.com/5100-6389_14-1045078-2.html ------------------------------------------------------------------------ From steube at sdsc.edu Sat Jan 17 10:31:58 2004 From: steube at sdsc.edu (Ken Steube) Date: Sat, 17 Jan 2004 07:31:58 -0800 (PST) Subject: [MOBY-l] MOBY Workshop In-Reply-To: <1074088789.1729.21.camel@localhost.localdomain> Message-ID: Another MOBY workshop completed! Nine more people introduced to writing web services with MOBY. Each has registered at least one simple service and executed it. They also know how to install my FASTA service once they get home so they're ready to start writing useful services. Woohoo! Ken -- -- Ken Steube San Diego Supercomputer Center University of California, San Diego Mail code 0537, CRB room 207 9500 Gilman Drive San Diego, California, 92093-0537 USA FAX (858) 822-3610 From markw at illuminae.com Sat Jan 17 10:58:41 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Sat, 17 Jan 2004 09:58:41 -0600 Subject: [MOBY] [MOBY-l] MOBY Workshop In-Reply-To: References: Message-ID: <1074355120.1728.90.camel@localilluminae.com> That's fantastic! thanks for all your hard work, Ken! Mark On Sat, 2004-01-17 at 09:31, Ken Steube wrote: > Another MOBY workshop completed! Nine more people introduced to writing > web services with MOBY. Each has registered at least one simple service > and executed it. They also know how to install my FASTA service once they > get home so they're ready to start writing useful services. > > Woohoo! > > Ken > > -- > -- > Ken Steube > San Diego Supercomputer Center > University of California, San Diego > Mail code 0537, CRB room 207 > 9500 Gilman Drive > San Diego, California, 92093-0537 USA > FAX (858) 822-3610 > > _______________________________________________ > moby-l mailing list > moby-l at biomoby.org > http://biomoby.org/mailman/listinfo/moby-l -- Mark Wilkinson Illuminae From markw at illuminae.com Sat Jan 17 15:52:43 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Sat, 17 Jan 2004 14:52:43 -0600 Subject: [MOBY-l] Suggestion from Ken implemented Message-ID: <1074372763.3580.7.camel@localilluminae.com> Hi all, Ken Steube just made a suggestion that I thought was fantastic, so I just implemented it in the browser. He suggested that there be some clickable examples of a variety of initialization parameters that lead to interesting services. This was surprisingly easy to do, since the new client program uses the gbrowse configuration file, which can include HTML for the header/footer of the cgi page :-) (thanks Lincoln!) If any of you want to showcase your services, please send me an example namespace/id and service name and I'll add it to the list on the browser homepage. Mark -- Mark Wilkinson Illuminae From avraham at cshl.edu Sat Jan 17 18:12:39 2004 From: avraham at cshl.edu (Shuly Avraham) Date: Sat, 17 Jan 2004 18:12:39 -0500 (EST) Subject: [MOBY-l] MOBY Workshop In-Reply-To: Message-ID: Thanks, Ken! The workshop was very good and helpful(and fun too!), as well as the tutorials you wrote. Shuly. On Sat, 17 Jan 2004, Ken Steube wrote: > Another MOBY workshop completed! Nine more people introduced to writing > web services with MOBY. Each has registered at least one simple service > and executed it. They also know how to install my FASTA service once they > get home so they're ready to start writing useful services. > > Woohoo! > > Ken > > -- > -- > Ken Steube > San Diego Supercomputer Center > University of California, San Diego > Mail code 0537, CRB room 207 > 9500 Gilman Drive > San Diego, California, 92093-0537 USA > FAX (858) 822-3610 > > _______________________________________________ > moby-l mailing list > moby-l at biomoby.org > http://biomoby.org/mailman/listinfo/moby-l > From lstein at cshl.edu Mon Jan 19 09:31:43 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Mon, 19 Jan 2004 16:31:43 +0200 Subject: [MOBY-l] MOBY conference calls Message-ID: <200401191631.43495.lstein@cshl.edu> Hello, As some of you know I am doing a mini-sabbatical in Capetown South Africa until March 2. Unfortunately this means I am in the GMT+2 timezone, which is 7 hours ahead of the east coast, and 10 hours ahead of the west coast. This means that in order for me to participate in the conference calls, we will have to move them to early in the morning for you west-coast people, and mid-morning for you New Mexico people. Needless to say, I'm doing this for other scheduled conference calls too! Friday mornings are good for me. How about others? Lincoln -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 From dtb24 at cornell.edu Thu Jan 22 13:18:44 2004 From: dtb24 at cornell.edu (David Bogaty) Date: Thu, 22 Jan 2004 13:18:44 -0500 Subject: [MOBY-l] MOBY Workshop In-Reply-To: References: Message-ID: <5.2.1.1.2.20040122131526.00b3a4e0@postoffice6.mail.cornell.edu> I second the motion... thanks Ken, a job well done! Aside from MOBY, I also learned a thing or two about barbecue potato chips and the importance of remembering one's age at a restaurant. Look for some services from SGN soon =) Dave Bogaty http://sgn.cornell.edu PS - does anyone have those pictures? At 06:12 PM 1/17/2004 -0500, Shuly Avraham wrote: >Thanks, Ken! >The workshop was very good and helpful(and fun too!), >as well as the tutorials you wrote. >Shuly. From markw at illuminae.com Fri Jan 23 09:59:22 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 23 Jan 2004 08:59:22 -0600 Subject: [MOBY-l] Moving on up! Message-ID: <1074869962.1621.6.camel@localilluminae.com> Hi all MOBY'ers! Just a quick note to say that I will be out of contact for the next ~2 weeks as I am moving to Vancouver. My email address will not change, so I will get your mails, but they will be badly stacked by the time I get a chance to login again, so I might not get to them very quickly. I'll see you all on the other side! Best wishes! Mark P.S. For anyone who has never lived in Canada before, here is the weather forecast for moving day. Eat your heart out, Lincoln, and think of me as you sip your MaiTai on the beach! Tuesday - A mix of sun and clouds High: -25?C Low: -33?C Wind 10 km/h W POP: 30% Wednesday - Cloudy with sunny breaks High: -33?C Low: -37?C Wind 5 km/h NW POP: 20% -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. of Medical Genetics University of British Columbia's iCAPTURE Centre Vancouver, BC, Canada ------------------------------------------------------------------------ It just goes to show you that SOAP::Lite is more intuitive than you might think, if you know enough Perl and have the patience to dive into the source code. -Byrne Reese -http://builder.com.com/5100-6389_14-1045078-2.html ------------------------------------------------------------------------ From steube at sdsc.edu Wed Jan 28 12:07:36 2004 From: steube at sdsc.edu (Ken Steube) Date: Wed, 28 Jan 2004 09:07:36 -0800 (PST) Subject: [MOBY-l] Re: namespace In-Reply-To: <92012141-51B2-11D8-8DDC-000A9591E2C8@cshl.org> Message-ID: I'm not sure I understand the question...I'll try to answer and you can reply for more info. An object belongs to a particular namespace belongs to AGI_LocusCode. Sometimes you might see the namespace might being left blank if it's not important (such as for the Integer object inside a GenericSequence). I wouldn't really say a service belongs to a namespace, rather we say it accepts objects from particular namespaces. Or a service might accept objects of a certain type from any namespace if the namespace isn't important (such as BLAST: can accept a DNA seq from any namespace so the namespace isn't generally critical info for BLAST). Ken On Wed, 28 Jan 2004, Ardavan Kanani wrote: > Ken, > > Thanks for responding to my question. My question is more about an > object belonging to a namespace or services belonging to a namespace > and not accepting or outputting objects from a particular namespace. > Do objects belong to particular namespaces? If that's the case where > in the object registration should I declare its namespace? Since > services are, sort of, objects too, where do I specify what namespace > they belong to. I am trying to create all my objects and services > under a namespace called "haplotyping_study" I might be totally > confused as how the namespaces work on MOBY. I am coming from an > object oriented world. So when I see the disjoint between objects and > services in MOBY I get confused. > > Thanks, Ardavan Kanani > > On Jan 28, 2004, at 11:36 AM, Ken Steube wrote: > > > On Wed, 28 Jan 2004, Ardavan Kanani wrote: > >> Mark, > >> How would I register an object or a service under a particular > >> namespace? I looked at the API doc and the signature for > >> registerObjectClass and registerServiceName/Type does not include a > >> namespace parameter. > > > > Here is the script that registers my plantspGetProtein service to > > accept an Object from any of the namespaces > > ['AGI_LocusCode', 'NCBI_gi', 'SDSC_fg']. > > > > Ken > > > > > > > > > > > > #!/usr/local/bin/perl5.6.1 > > use warnings 'all'; # Issue warnings about suspicious programming > > use strict; # Must declare and initialize all variables > > > > ####################################################################### > > ## > > # This script will register the plantspGetProtein MOBY service > > ####################################################################### > > ## > > > > use MOBY::Client::Central; > > use MOBY::Client::Service; > > > > my $Central = MOBY::Client::Central->new(); > > > > my $reg = $Central->registerService( > > serviceName => 'plantspGetProtein', > > authURI => 'www.sdsc.edu', > > contactEmail => 'steube at sdsc.edu', > > description => "Retrieves a protein sequence from the PlantsP > > database (proteins related to phosphorylation, transporters and > > ubiquitin)", > > URL => > > 'http://plantsp.sdsc.edu/cgi-bin/MOBY/PlantsP_dispatcher.cgi', > > input => [ ['', ["Object" => ['AGI_LocusCode', 'NCBI_gi', > > 'SDSC_fg']]], ], > > output => [ ['', ["AminoAcidSequence" => []]], ], > > category => "moby", > > serviceType => "Retrieval", > > ); > > die "Bad return value from registerService" unless $reg; > > if ($reg->success == 1){ > > print "Registration successful\n\n"; > > } > > else { > > print "Registration failed: ", $reg->message, "\n"; > > } > > > > > > -- > > -- > > -- > > Ken Steube > > San Diego Supercomputer Center > > University of California, San Diego > > Mail code 0537, CRB room 207 > > 9500 Gilman Drive > > San Diego, California, 92093-0537 USA > > FAX (858) 822-3610 > > > -- -- -- Ken Steube San Diego Supercomputer Center University of California, San Diego Mail code 0537, CRB room 207 9500 Gilman Drive San Diego, California, 92093-0537 USA FAX (858) 822-3610 From beatrice at arabidopsis.info Thu Jan 29 11:58:01 2004 From: beatrice at arabidopsis.info (Beatrice Schildknecht) Date: Thu, 29 Jan 2004 16:58:01 +0000 Subject: [MOBY-l] Proxies... Message-ID: <40193B99.4070207@arabidopsis.info> Help note/patch for those using proxy servers. This is how I got MOBY to use my proxy server: 1) In: /MOBY/Client/OntologyServer.pm /MOBY/Client/Central.pm Change all occurences of: my $ua = LWP::UserAgent->new; to: my $ua = LWP::UserAgent->new(env_proxy=>1); 2) In your httpd.conf file, set environmental variables to use your proxy server. e.g.: setenv HTTP_proxy http://wwwcache.nottingham.ac.uk:3128 setenv CGI_HTTP_PROXY http://wwwcache.nottingham.ac.uk:3128 3) Restart http. [4) Set your environmental variables again. How I did it in my .bashrc config file: export CGI_HTTP_proxy=http://wwwcache.nottingham.ac.uk:3128 export HTTP_proxy=http://wwwcache.nottingham.ac.uk:3128 ] See www.cpan.org for more. (This may not be the best way of doing it....Any other ideas welcome....Mark, would it be possible for this be fixed in the next update?) Thanks, Beatrice -- Nottingham Arabidopsis Stock Centre School of Biosciences Plant Science Division University of Nottingham Sutton Bonington Campus Loughborough LE12 5RD Tel: +44 115 951 3091 http://arabidopsis.info