From lstein at cshl.edu Mon Mar 8 15:16:22 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Mon Mar 8 15:22:12 2004 Subject: [MOBY-dev] Re: URGENT - Re: [MISC] April 3-4 meeting In-Reply-To: <1078596500.1901.54.camel@localilluminae.com> References: <1077758193.1916.43.camel@localilluminae.com> <200402271740.49773.lstein@cshl.edu> <1078596500.1901.54.camel@localilluminae.com> Message-ID: <200403081516.22753.lstein@cshl.edu> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 HI Folks, If you are planning to attend the April 3-4 MOBY meeting at CSHL, please contact Sandra Michelsen for assistance arranging housing and transportation from the airport. Lincoln On Saturday 06 March 2004 01:08 pm, Mark Wilkinson wrote: > Hi Lincoln, > > can you confirm this now? there hasn't been a "clear" public > announcement of this meeting yet, and it's getting close! > > M > > On Fri, 2004-02-27 at 07:40, Lincoln Stein wrote: > > -----BEGIN PGP SIGNED MESSAGE----- > > Hash: SHA1 > > > > I am waiting for CSHL to get back to me on the availability of > > housing and rooms, but should know early next week whether I can > > confirm the April 3-4 dates. > > > > Lincoln > > > > - -- > > Lincoln D. Stein > > Cold Spring Harbor Laboratory > > 1 Bungtown Road > > Cold Spring Harbor, NY 11724 > > -----BEGIN PGP SIGNATURE----- > > Version: GnuPG v1.2.1 (GNU/Linux) > > > > iD8DBQFAP2UB0CIvUP7P+AkRAoN3AJ0TkJBdreyQX4wH6PvlGiUVoX+CSACfb180 > > gbFv0o1B6DxN8GHZVLqr5dY= > > =ZEuI > > -----END PGP SIGNATURE----- - -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.1 (GNU/Linux) iD8DBQFATNSW0CIvUP7P+AkRAur7AJ9D0JeoO5dtSfsUvuXlWX4UKeaJ+QCcCCI4 hnZWxgtKlpp2ZRD4g5OY+aQ= =i33i -----END PGP SIGNATURE----- From senger at ebi.ac.uk Mon Mar 8 15:29:21 2004 From: senger at ebi.ac.uk (Martin Senger) Date: Mon Mar 8 15:35:06 2004 Subject: [MOBY-dev] what is correct "Service List Response Object"? In-Reply-To: <200403081516.22753.lstein@cshl.edu> Message-ID: Mark, I am trying to fix a bug discovered today by Viji in jMoby and I found some inconsistencies. Please advise what I should expect: 1) The API documentation on the web says: Service_Ontology_Term moby http://service.endpoint.here/scriptname your@email.addy.here 1 ... ... ... ... 2) The value returned from your BioMoby server is (see that some tags are different, and also the tag order is slightly different): Retrieval 1 moby ... viji@gsf.de http://146.107.217.144/axis/services/RetrieveElements-MobyService ... ... ... 3) And, just pro-forma, this is the version which was so far used by jMoby (which is now obviously obsolete and I am going to fix it): Service_Ontology_Term moby 1 ... ... ... Thanks, Martin -- Martin Senger EMBL Outstation - Hinxton Senger@EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From markw at illuminae.com Wed Mar 10 20:02:18 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Wed Mar 10 20:07:54 2004 Subject: [MOBY-dev] screen-scraping MOBY Message-ID: <1078966938.1717.345.camel@localilluminae.com> Hi MOBYers! In an effort to make your lives easier (and especially those at PlaNet who are currently displaying the raw XML of the MOBY Objects in their portal :-P ) I have just made it easier to ask the MOBY CGI client program at mobycentral to do what you want it to do, and then screen-scrape the result. The client program accepts the following CGI GET parameters: namespace - a namespace id - an id servicename - the name of the service you wish to execute authority - the authority providing that service object - this is a URL-encoded MOBY object (object, no message struct) What comes out of it is HTML, but I have made the HTML scrape-easy! Each object is surrounded by a pair of HTML comments: between those comment tags is a .... containing the rendering of a single MOBY response object into HTML. Thus you can simply do a wget or an LWP GET from inside of your own web pages, do a regexp on the result, and stick it into a on your own web page in whatever format you like. Ta Daaaaaa! Who loves you more than I do ;-) These small changes have not yet been migrated into the CVS copy of the browser (@Gbrowse) because they are aiming for a release soon and I don't want to bugger that up. If you want a copy of this code, let me know and I'll mail it to you. Mark -- Mark Wilkinson (mwilkinson@mrl.ubc.ca) University of British Columbia iCAPTURE Centre From a.garcia at imb.uq.edu.au Wed Mar 24 07:43:53 2004 From: a.garcia at imb.uq.edu.au (a.garcia@imb.uq.edu.au) Date: Wed Mar 24 07:49:17 2004 Subject: [MOBY-dev] inquiry/ontology Message-ID: I would like to know if there is an ontology for bioinformatic services available? Is that part of BioMoby? Who is working on that ontology? Cheers. From markw at illuminae.com Wed Mar 24 11:34:03 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Wed Mar 24 11:39:36 2004 Subject: [MOBY] [MOBY-dev] inquiry/ontology In-Reply-To: References: Message-ID: <1080146042.1950.89.camel@localilluminae.com> On Wed, 2004-03-24 at 04:43, a.garcia@imb.uq.edu.au wrote: > Who is working on that ontology? Cheers. Apparently, you are ;-) We currently have a *horrible* ontology for MOBY Services, and in fact this is quite a timely message as there is a conversation going on another list (the OBO list) about exactly this topic. Our ontology should soon get a lot better... I still haven't had time to find the original proposal for the MOBY Service ontology, but I know that we have not yet built it. If I find it, I will post it to the list and we can re-evaluate it as a group. the myGrid project also has a (much richer) ontology for bioinformatics services. You might want to talk to them. M > _______________________________________________ > MOBY-dev mailing list > MOBY-dev@biomoby.org > http://www.biomoby.org/mailman/listinfo/moby-dev -- Mark Wilkinson (mwilkinson@mrl.ubc.ca) University of British Columbia iCAPTURE Centre From markw at illuminae.com Wed Mar 24 11:34:03 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Wed Mar 24 11:39:37 2004 Subject: [MOBY] [MOBY-dev] inquiry/ontology In-Reply-To: References: Message-ID: <1080146042.1950.89.camel@localilluminae.com> On Wed, 2004-03-24 at 04:43, a.garcia@imb.uq.edu.au wrote: > Who is working on that ontology? Cheers. Apparently, you are ;-) We currently have a *horrible* ontology for MOBY Services, and in fact this is quite a timely message as there is a conversation going on another list (the OBO list) about exactly this topic. Our ontology should soon get a lot better... I still haven't had time to find the original proposal for the MOBY Service ontology, but I know that we have not yet built it. If I find it, I will post it to the list and we can re-evaluate it as a group. the myGrid project also has a (much richer) ontology for bioinformatics services. You might want to talk to them. M > _______________________________________________ > MOBY-dev mailing list > MOBY-dev@biomoby.org > http://www.biomoby.org/mailman/listinfo/moby-dev -- Mark Wilkinson (mwilkinson@mrl.ubc.ca) University of British Columbia iCAPTURE Centre From markw at illuminae.com Wed Mar 24 17:21:42 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Wed Mar 24 17:27:04 2004 Subject: [MOBY-dev] Forwarded message from Lincoln Message-ID: <1080166902.1950.151.camel@localilluminae.com> Sorry Lincoln, your messages are being filtered out. I've just weakened the content filtering rules - can you post something just to test this? -----Forwarded Message----- > From: Lincoln Stein > To: mobydev > Subject: Handouts > Date: Wed, 24 Mar 2004 17:00:29 -0500 > > Hi, > > For people who are giving presentations at the upcoming MOBY meeting, > please send me your presentations or handouts by April 1 so that I > can have them printed out to distribute on April 3. > > Lincoln -- Mark Wilkinson (mwilkinson@mrl.ubc.ca) University of British Columbia iCAPTURE Centre From markw at illuminae.com Wed Mar 24 17:22:06 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Wed Mar 24 17:27:25 2004 Subject: [MOBY-dev] Forwarded message from Lincoln Message-ID: <1080166926.10956.153.camel@localilluminae.com> > From: Lincoln Stein > To: mobydev > Subject: Draft agenda for CSHL MOBY meeting. > Date: Wed, 24 Mar 2004 16:57:24 -0500 > > Draft agenda for CSHL MOBY meeting. > > This was developed in today's conference call. Please comment. > Additions are most welcome! > > Lincoln > > Saturday April 3: > > 9:00 Welcome & Introductions - Lincoln Stein > 9:05 Recapping goals of project & major milestones - Damian Gessler > 9:30 MOBY-S: status report - Mark Wilkinson > 10:30 break > 11:00 S-MOBY: status report I - Gary Schiltz > 12:00 lunch > 1:30 S-MOBY: status report II - Gary Schiltz > 2:30 Discussion > 3:00 break > 3:30 HapMap services in MOBY-S: Ardavan Kanani > 4:00 Visualization tools for MOBY-S: Martin Senger > 4:30 Bioferret in MOBY-S: Mike Niemi > 5:00 Towards DAS/2 - Lincoln Stein > 5:30 Discussion > 6:30 Dinner > > Sunday April 4: > 9:00 SMOBY/MOBYS/DAS interoperability > Security Models > Replication > > 11:00 Publications > Future grant opportunities > Milestones to meet > > Lincoln -- Mark Wilkinson (mwilkinson@mrl.ubc.ca) University of British Columbia iCAPTURE Centre From natural at facedoctor.ca Fri Mar 26 17:18:24 2004 From: natural at facedoctor.ca (natural@facedoctor.ca) Date: Fri Mar 26 17:12:15 2004 Subject: [MOBY-dev] Bad Skin ?????? Message-ID: From simont at mcw.edu Tue Mar 30 13:07:17 2004 From: simont at mcw.edu (Simon Twigger) Date: Tue Mar 30 13:12:28 2004 Subject: [MOBY-dev] MOBY Mtg: Security model agenda Message-ID: <14D6A70C-8275-11D8-B25A-000A959D1D82@mcw.edu> Hi there, I was wondering if anyone could expand very briefly on what might be covered at the meeting this weekend under 'Security Models'? Will this have anything to do with Authentication of services, digital signatures and algorithms, perhaps even encryption/anonymization of service traffic via MOBY? I've been doing some reading on the subject but there's a lot out there so I wanted to get some idea of what might be covered so I can concentrate on the right things. Cheers, Simon. -- Simon N. Twigger, Ph.D. Assistant Professor, Department of Physiology Medical College of Wisconsin 8701 Watertown Plank Road, Milwaukee, WI, USA tel: 414-456-8802 fax: 414-456-6595 From 21CFR11 at biozak.com Tue Mar 30 16:50:41 2004 From: 21CFR11 at biozak.com (21CFR11@biozak.com) Date: Tue Mar 30 16:29:51 2004 Subject: [MOBY-dev] We have emails of thousands of your prospective customers - life science executives Message-ID: <200403302150.NAA12920@main.biozak.com> Our CD-ROM databases contain detailed contact information on 34,000+ life science executives worldwide. Limited time offer: Contact us now to get 15% off the regular price - mention promotion code int_service_providers_gen when you order. More Details at http://main.biozak.com/cgi-bin/BIOZAK/sublinks.pl?type=CD Sincerely, -- Ekaterina Kalygina, Marketing Director, BioZak InfoBase, Inc. - business intelligence for life science markets! ----- Every effort is made to ensure that this message is received only by interested parties. If this message was sent to you in error, please reply with 'remove' in the subject line - you will get no further email from us. From M.BATE.ALANN at netscape.net Tue Mar 30 22:41:50 2004 From: M.BATE.ALANN at netscape.net (M.BATE.ALANN@netscape.net) Date: Tue Mar 30 22:41:54 2004 Subject: [MOBY-dev] REPLY BACK Message-ID: <200403310341.i2V3fng2030665@portal.open-bio.org> Dear Friend, As you read this, I don't want you to feel sorry for me, because, I believe everyone will die someday. My name is BATES ALAN a merchant in Dubai, in the U.A.E.I have been diagnosed with Esophageal cancer. It has defiled all forms of medical treatment, and right now I have only about a few months to live, according to medical experts. I have not particularly lived my life so well, as I never really cared for anyone(not even myself)but my business. Though I am very rich, I was never generous, I was always hostile to people and only focused on my business as that was the only thing I cared for. But now I regret all this as I now know that there is more to life than just wanting to have or make all the money in the world. I believe when God gives me a second chance to come to this world I would live my life a different way from how I have lived it. Now that God has called me, I have willed and given most of my property and assets to my immediate and extended family members as well as a few close friends. I want God to be merciful to me and accept my soul so, I have decided to give alms to charity organizations, as I want this to be one of the last good deeds I do on earth. So far, I have distributed money to some charity organizations in the U.A.E, Algeria and Malaysia. Now that my health has deteriorated so badly, I cannot do this myself anymore. I once asked members of my family to close one of my accounts and distribute the money which I have there to charity organization in Bulgaria and Pakistan, they refused and kept the money to themselves. Hence, I do not trust them anymore, as they seem not to be contended with what I have left for them. The last of my money which no one knows of is the huge cash deposit of eighteen million dollars $18,000,000,00 that I have with a finance/Security Company abroad. I will want you to help me collect this deposit and dispatched it to charity organizations. I have set aside 10% for you and for your time. God be with you. BATES ALAN From dwprlzrmc at dra.forthnet.gr Wed Mar 31 04:27:12 2004 From: dwprlzrmc at dra.forthnet.gr (Daniel Everett) Date: Wed Mar 31 04:33:22 2004 Subject: [MOBY-dev] Make profit with google - no website required Message-ID: From lstein at cshl.edu Mon Mar 8 15:16:22 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Mon, 08 Mar 2004 15:16:22 -0500 Subject: [MOBY-dev] Re: URGENT - Re: [MISC] April 3-4 meeting In-Reply-To: <1078596500.1901.54.camel@localilluminae.com> References: <1077758193.1916.43.camel@localilluminae.com> <200402271740.49773.lstein@cshl.edu> <1078596500.1901.54.camel@localilluminae.com> Message-ID: <200403081516.22753.lstein@cshl.edu> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 HI Folks, If you are planning to attend the April 3-4 MOBY meeting at CSHL, please contact Sandra Michelsen for assistance arranging housing and transportation from the airport. Lincoln On Saturday 06 March 2004 01:08 pm, Mark Wilkinson wrote: > Hi Lincoln, > > can you confirm this now? there hasn't been a "clear" public > announcement of this meeting yet, and it's getting close! > > M > > On Fri, 2004-02-27 at 07:40, Lincoln Stein wrote: > > -----BEGIN PGP SIGNED MESSAGE----- > > Hash: SHA1 > > > > I am waiting for CSHL to get back to me on the availability of > > housing and rooms, but should know early next week whether I can > > confirm the April 3-4 dates. > > > > Lincoln > > > > - -- > > Lincoln D. Stein > > Cold Spring Harbor Laboratory > > 1 Bungtown Road > > Cold Spring Harbor, NY 11724 > > -----BEGIN PGP SIGNATURE----- > > Version: GnuPG v1.2.1 (GNU/Linux) > > > > iD8DBQFAP2UB0CIvUP7P+AkRAoN3AJ0TkJBdreyQX4wH6PvlGiUVoX+CSACfb180 > > gbFv0o1B6DxN8GHZVLqr5dY= > > =ZEuI > > -----END PGP SIGNATURE----- - -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.1 (GNU/Linux) iD8DBQFATNSW0CIvUP7P+AkRAur7AJ9D0JeoO5dtSfsUvuXlWX4UKeaJ+QCcCCI4 hnZWxgtKlpp2ZRD4g5OY+aQ= =i33i -----END PGP SIGNATURE----- From senger at ebi.ac.uk Mon Mar 8 15:29:21 2004 From: senger at ebi.ac.uk (Martin Senger) Date: Mon, 8 Mar 2004 20:29:21 +0000 (GMT) Subject: [MOBY-dev] what is correct "Service List Response Object"? In-Reply-To: <200403081516.22753.lstein@cshl.edu> Message-ID: Mark, I am trying to fix a bug discovered today by Viji in jMoby and I found some inconsistencies. Please advise what I should expect: 1) The API documentation on the web says: Service_Ontology_Term moby http://service.endpoint.here/scriptname your at email.addy.here 1 ... ... ... ... 2) The value returned from your BioMoby server is (see that some tags are different, and also the tag order is slightly different): Retrieval 1 moby ... viji at gsf.de http://146.107.217.144/axis/services/RetrieveElements-MobyService ... ... ... 3) And, just pro-forma, this is the version which was so far used by jMoby (which is now obviously obsolete and I am going to fix it): Service_Ontology_Term moby 1 ... ... ... Thanks, Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From markw at illuminae.com Wed Mar 10 20:02:18 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 10 Mar 2004 17:02:18 -0800 Subject: [MOBY-dev] screen-scraping MOBY Message-ID: <1078966938.1717.345.camel@localilluminae.com> Hi MOBYers! In an effort to make your lives easier (and especially those at PlaNet who are currently displaying the raw XML of the MOBY Objects in their portal :-P ) I have just made it easier to ask the MOBY CGI client program at mobycentral to do what you want it to do, and then screen-scrape the result. The client program accepts the following CGI GET parameters: namespace - a namespace id - an id servicename - the name of the service you wish to execute authority - the authority providing that service object - this is a URL-encoded MOBY object (object, no message struct) What comes out of it is HTML, but I have made the HTML scrape-easy! Each object is surrounded by a pair of HTML comments: between those comment tags is a .... containing the rendering of a single MOBY response object into HTML. Thus you can simply do a wget or an LWP GET from inside of your own web pages, do a regexp on the result, and stick it into a
on your own web page in whatever format you like. Ta Daaaaaa! Who loves you more than I do ;-) These small changes have not yet been migrated into the CVS copy of the browser (@Gbrowse) because they are aiming for a release soon and I don't want to bugger that up. If you want a copy of this code, let me know and I'll mail it to you. Mark -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre From a.garcia at imb.uq.edu.au Wed Mar 24 07:43:53 2004 From: a.garcia at imb.uq.edu.au (a.garcia@imb.uq.edu.au) Date: Wed, 24 Mar 2004 22:43:53 +1000 Subject: [MOBY-dev] inquiry/ontology Message-ID: I would like to know if there is an ontology for bioinformatic services available? Is that part of BioMoby? Who is working on that ontology? Cheers. From markw at illuminae.com Wed Mar 24 11:34:03 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 24 Mar 2004 08:34:03 -0800 Subject: [MOBY] [MOBY-dev] inquiry/ontology In-Reply-To: References: Message-ID: <1080146042.1950.89.camel@localilluminae.com> On Wed, 2004-03-24 at 04:43, a.garcia at imb.uq.edu.au wrote: > Who is working on that ontology? Cheers. Apparently, you are ;-) We currently have a *horrible* ontology for MOBY Services, and in fact this is quite a timely message as there is a conversation going on another list (the OBO list) about exactly this topic. Our ontology should soon get a lot better... I still haven't had time to find the original proposal for the MOBY Service ontology, but I know that we have not yet built it. If I find it, I will post it to the list and we can re-evaluate it as a group. the myGrid project also has a (much richer) ontology for bioinformatics services. You might want to talk to them. M > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at biomoby.org > http://www.biomoby.org/mailman/listinfo/moby-dev -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre From markw at illuminae.com Wed Mar 24 11:34:03 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 24 Mar 2004 08:34:03 -0800 Subject: [MOBY] [MOBY-dev] inquiry/ontology In-Reply-To: References: Message-ID: <1080146042.1950.89.camel@localilluminae.com> On Wed, 2004-03-24 at 04:43, a.garcia at imb.uq.edu.au wrote: > Who is working on that ontology? Cheers. Apparently, you are ;-) We currently have a *horrible* ontology for MOBY Services, and in fact this is quite a timely message as there is a conversation going on another list (the OBO list) about exactly this topic. Our ontology should soon get a lot better... I still haven't had time to find the original proposal for the MOBY Service ontology, but I know that we have not yet built it. If I find it, I will post it to the list and we can re-evaluate it as a group. the myGrid project also has a (much richer) ontology for bioinformatics services. You might want to talk to them. M > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at biomoby.org > http://www.biomoby.org/mailman/listinfo/moby-dev -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre From markw at illuminae.com Wed Mar 24 17:21:42 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 24 Mar 2004 14:21:42 -0800 Subject: [MOBY-dev] Forwarded message from Lincoln Message-ID: <1080166902.1950.151.camel@localilluminae.com> Sorry Lincoln, your messages are being filtered out. I've just weakened the content filtering rules - can you post something just to test this? -----Forwarded Message----- > From: Lincoln Stein > To: mobydev > Subject: Handouts > Date: Wed, 24 Mar 2004 17:00:29 -0500 > > Hi, > > For people who are giving presentations at the upcoming MOBY meeting, > please send me your presentations or handouts by April 1 so that I > can have them printed out to distribute on April 3. > > Lincoln -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre From markw at illuminae.com Wed Mar 24 17:22:06 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 24 Mar 2004 14:22:06 -0800 Subject: [MOBY-dev] Forwarded message from Lincoln Message-ID: <1080166926.10956.153.camel@localilluminae.com> > From: Lincoln Stein > To: mobydev > Subject: Draft agenda for CSHL MOBY meeting. > Date: Wed, 24 Mar 2004 16:57:24 -0500 > > Draft agenda for CSHL MOBY meeting. > > This was developed in today's conference call. Please comment. > Additions are most welcome! > > Lincoln > > Saturday April 3: > > 9:00 Welcome & Introductions - Lincoln Stein > 9:05 Recapping goals of project & major milestones - Damian Gessler > 9:30 MOBY-S: status report - Mark Wilkinson > 10:30 break > 11:00 S-MOBY: status report I - Gary Schiltz > 12:00 lunch > 1:30 S-MOBY: status report II - Gary Schiltz > 2:30 Discussion > 3:00 break > 3:30 HapMap services in MOBY-S: Ardavan Kanani > 4:00 Visualization tools for MOBY-S: Martin Senger > 4:30 Bioferret in MOBY-S: Mike Niemi > 5:00 Towards DAS/2 - Lincoln Stein > 5:30 Discussion > 6:30 Dinner > > Sunday April 4: > 9:00 SMOBY/MOBYS/DAS interoperability > Security Models > Replication > > 11:00 Publications > Future grant opportunities > Milestones to meet > > Lincoln -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre From natural at facedoctor.ca Fri Mar 26 17:18:24 2004 From: natural at facedoctor.ca (natural@facedoctor.ca) Date: Fri, 26 Mar 2004 17:18:24 -0500 Subject: [MOBY-dev] Bad Skin ?????? Message-ID: From simont at mcw.edu Tue Mar 30 13:07:17 2004 From: simont at mcw.edu (Simon Twigger) Date: Tue, 30 Mar 2004 12:07:17 -0600 Subject: [MOBY-dev] MOBY Mtg: Security model agenda Message-ID: <14D6A70C-8275-11D8-B25A-000A959D1D82@mcw.edu> Hi there, I was wondering if anyone could expand very briefly on what might be covered at the meeting this weekend under 'Security Models'? Will this have anything to do with Authentication of services, digital signatures and algorithms, perhaps even encryption/anonymization of service traffic via MOBY? I've been doing some reading on the subject but there's a lot out there so I wanted to get some idea of what might be covered so I can concentrate on the right things. Cheers, Simon. -- Simon N. Twigger, Ph.D. Assistant Professor, Department of Physiology Medical College of Wisconsin 8701 Watertown Plank Road, Milwaukee, WI, USA tel: 414-456-8802 fax: 414-456-6595 From 21CFR11 at biozak.com Tue Mar 30 16:50:41 2004 From: 21CFR11 at biozak.com (21CFR11@biozak.com) Date: Tue, 30 Mar 2004 21:50:41 UT Subject: [MOBY-dev] We have emails of thousands of your prospective customers - life science executives Message-ID: <200403302150.NAA12920@main.biozak.com> An embedded and charset-unspecified text was scrubbed... Name: not available Url: http://www.biomoby.org/pipermail/moby-dev/attachments/20040330/26026234/attachment.pl From M.BATE.ALANN at netscape.net Tue Mar 30 22:41:50 2004 From: M.BATE.ALANN at netscape.net (M.BATE.ALANN@netscape.net) Date: Tue, 30 Mar 2004 22:41:50 -0500 Subject: [MOBY-dev] REPLY BACK Message-ID: <200403310341.i2V3fng2030665@portal.open-bio.org> Dear Friend, As you read this, I don't want you to feel sorry for me, because, I believe everyone will die someday. My name is BATES ALAN a merchant in Dubai, in the U.A.E.I have been diagnosed with Esophageal cancer. It has defiled all forms of medical treatment, and right now I have only about a few months to live, according to medical experts. I have not particularly lived my life so well, as I never really cared for anyone(not even myself)but my business. Though I am very rich, I was never generous, I was always hostile to people and only focused on my business as that was the only thing I cared for. But now I regret all this as I now know that there is more to life than just wanting to have or make all the money in the world. I believe when God gives me a second chance to come to this world I would live my life a different way from how I have lived it. Now that God has called me, I have willed and given most of my property and assets to my immediate and extended family members as well as a few close friends. I want God to be merciful to me and accept my soul so, I have decided to give alms to charity organizations, as I want this to be one of the last good deeds I do on earth. So far, I have distributed money to some charity organizations in the U.A.E, Algeria and Malaysia. Now that my health has deteriorated so badly, I cannot do this myself anymore. I once asked members of my family to close one of my accounts and distribute the money which I have there to charity organization in Bulgaria and Pakistan, they refused and kept the money to themselves. Hence, I do not trust them anymore, as they seem not to be contended with what I have left for them. The last of my money which no one knows of is the huge cash deposit of eighteen million dollars $18,000,000,00 that I have with a finance/Security Company abroad. I will want you to help me collect this deposit and dispatched it to charity organizations. I have set aside 10% for you and for your time. God be with you. BATES ALAN From dwprlzrmc at dra.forthnet.gr Wed Mar 31 04:27:12 2004 From: dwprlzrmc at dra.forthnet.gr (Daniel Everett) Date: Wed, 31 Mar 2004 15:27:12 +0600 Subject: [MOBY-dev] Make profit with google - no website required Message-ID: From lstein at cshl.edu Mon Mar 8 20:16:22 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Mon, 08 Mar 2004 15:16:22 -0500 Subject: [MOBY-dev] Re: URGENT - Re: [MISC] April 3-4 meeting In-Reply-To: <1078596500.1901.54.camel@localilluminae.com> References: <1077758193.1916.43.camel@localilluminae.com> <200402271740.49773.lstein@cshl.edu> <1078596500.1901.54.camel@localilluminae.com> Message-ID: <200403081516.22753.lstein@cshl.edu> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 HI Folks, If you are planning to attend the April 3-4 MOBY meeting at CSHL, please contact Sandra Michelsen for assistance arranging housing and transportation from the airport. Lincoln On Saturday 06 March 2004 01:08 pm, Mark Wilkinson wrote: > Hi Lincoln, > > can you confirm this now? there hasn't been a "clear" public > announcement of this meeting yet, and it's getting close! > > M > > On Fri, 2004-02-27 at 07:40, Lincoln Stein wrote: > > -----BEGIN PGP SIGNED MESSAGE----- > > Hash: SHA1 > > > > I am waiting for CSHL to get back to me on the availability of > > housing and rooms, but should know early next week whether I can > > confirm the April 3-4 dates. > > > > Lincoln > > > > - -- > > Lincoln D. Stein > > Cold Spring Harbor Laboratory > > 1 Bungtown Road > > Cold Spring Harbor, NY 11724 > > -----BEGIN PGP SIGNATURE----- > > Version: GnuPG v1.2.1 (GNU/Linux) > > > > iD8DBQFAP2UB0CIvUP7P+AkRAoN3AJ0TkJBdreyQX4wH6PvlGiUVoX+CSACfb180 > > gbFv0o1B6DxN8GHZVLqr5dY= > > =ZEuI > > -----END PGP SIGNATURE----- - -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.1 (GNU/Linux) iD8DBQFATNSW0CIvUP7P+AkRAur7AJ9D0JeoO5dtSfsUvuXlWX4UKeaJ+QCcCCI4 hnZWxgtKlpp2ZRD4g5OY+aQ= =i33i -----END PGP SIGNATURE----- From senger at ebi.ac.uk Mon Mar 8 20:29:21 2004 From: senger at ebi.ac.uk (Martin Senger) Date: Mon, 8 Mar 2004 20:29:21 +0000 (GMT) Subject: [MOBY-dev] what is correct "Service List Response Object"? In-Reply-To: <200403081516.22753.lstein@cshl.edu> Message-ID: Mark, I am trying to fix a bug discovered today by Viji in jMoby and I found some inconsistencies. Please advise what I should expect: 1) The API documentation on the web says: Service_Ontology_Term moby http://service.endpoint.here/scriptname your at email.addy.here 1 ... ... ... ... 2) The value returned from your BioMoby server is (see that some tags are different, and also the tag order is slightly different): Retrieval 1 moby ... viji at gsf.de http://146.107.217.144/axis/services/RetrieveElements-MobyService ... ... ... 3) And, just pro-forma, this is the version which was so far used by jMoby (which is now obviously obsolete and I am going to fix it): Service_Ontology_Term moby 1 ... ... ... Thanks, Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From markw at illuminae.com Thu Mar 11 01:02:18 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 10 Mar 2004 17:02:18 -0800 Subject: [MOBY-dev] screen-scraping MOBY Message-ID: <1078966938.1717.345.camel@localilluminae.com> Hi MOBYers! In an effort to make your lives easier (and especially those at PlaNet who are currently displaying the raw XML of the MOBY Objects in their portal :-P ) I have just made it easier to ask the MOBY CGI client program at mobycentral to do what you want it to do, and then screen-scrape the result. The client program accepts the following CGI GET parameters: namespace - a namespace id - an id servicename - the name of the service you wish to execute authority - the authority providing that service object - this is a URL-encoded MOBY object (object, no message struct) What comes out of it is HTML, but I have made the HTML scrape-easy! Each object is surrounded by a pair of HTML comments: between those comment tags is a .... containing the rendering of a single MOBY response object into HTML. Thus you can simply do a wget or an LWP GET from inside of your own web pages, do a regexp on the result, and stick it into a
on your own web page in whatever format you like. Ta Daaaaaa! Who loves you more than I do ;-) These small changes have not yet been migrated into the CVS copy of the browser (@Gbrowse) because they are aiming for a release soon and I don't want to bugger that up. If you want a copy of this code, let me know and I'll mail it to you. Mark -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre From a.garcia at imb.uq.edu.au Wed Mar 24 12:43:53 2004 From: a.garcia at imb.uq.edu.au (a.garcia at imb.uq.edu.au) Date: Wed, 24 Mar 2004 22:43:53 +1000 Subject: [MOBY-dev] inquiry/ontology Message-ID: I would like to know if there is an ontology for bioinformatic services available? Is that part of BioMoby? Who is working on that ontology? Cheers. From markw at illuminae.com Wed Mar 24 16:34:03 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 24 Mar 2004 08:34:03 -0800 Subject: [MOBY] [MOBY-dev] inquiry/ontology In-Reply-To: References: Message-ID: <1080146042.1950.89.camel@localilluminae.com> On Wed, 2004-03-24 at 04:43, a.garcia at imb.uq.edu.au wrote: > Who is working on that ontology? Cheers. Apparently, you are ;-) We currently have a *horrible* ontology for MOBY Services, and in fact this is quite a timely message as there is a conversation going on another list (the OBO list) about exactly this topic. Our ontology should soon get a lot better... I still haven't had time to find the original proposal for the MOBY Service ontology, but I know that we have not yet built it. If I find it, I will post it to the list and we can re-evaluate it as a group. the myGrid project also has a (much richer) ontology for bioinformatics services. You might want to talk to them. M > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at biomoby.org > http://www.biomoby.org/mailman/listinfo/moby-dev -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre From markw at illuminae.com Wed Mar 24 16:34:03 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 24 Mar 2004 08:34:03 -0800 Subject: [MOBY] [MOBY-dev] inquiry/ontology In-Reply-To: References: Message-ID: <1080146042.1950.89.camel@localilluminae.com> On Wed, 2004-03-24 at 04:43, a.garcia at imb.uq.edu.au wrote: > Who is working on that ontology? Cheers. Apparently, you are ;-) We currently have a *horrible* ontology for MOBY Services, and in fact this is quite a timely message as there is a conversation going on another list (the OBO list) about exactly this topic. Our ontology should soon get a lot better... I still haven't had time to find the original proposal for the MOBY Service ontology, but I know that we have not yet built it. If I find it, I will post it to the list and we can re-evaluate it as a group. the myGrid project also has a (much richer) ontology for bioinformatics services. You might want to talk to them. M > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at biomoby.org > http://www.biomoby.org/mailman/listinfo/moby-dev -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre From markw at illuminae.com Wed Mar 24 22:21:42 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 24 Mar 2004 14:21:42 -0800 Subject: [MOBY-dev] Forwarded message from Lincoln Message-ID: <1080166902.1950.151.camel@localilluminae.com> Sorry Lincoln, your messages are being filtered out. I've just weakened the content filtering rules - can you post something just to test this? -----Forwarded Message----- > From: Lincoln Stein > To: mobydev > Subject: Handouts > Date: Wed, 24 Mar 2004 17:00:29 -0500 > > Hi, > > For people who are giving presentations at the upcoming MOBY meeting, > please send me your presentations or handouts by April 1 so that I > can have them printed out to distribute on April 3. > > Lincoln -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre From markw at illuminae.com Wed Mar 24 22:22:06 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 24 Mar 2004 14:22:06 -0800 Subject: [MOBY-dev] Forwarded message from Lincoln Message-ID: <1080166926.10956.153.camel@localilluminae.com> > From: Lincoln Stein > To: mobydev > Subject: Draft agenda for CSHL MOBY meeting. > Date: Wed, 24 Mar 2004 16:57:24 -0500 > > Draft agenda for CSHL MOBY meeting. > > This was developed in today's conference call. Please comment. > Additions are most welcome! > > Lincoln > > Saturday April 3: > > 9:00 Welcome & Introductions - Lincoln Stein > 9:05 Recapping goals of project & major milestones - Damian Gessler > 9:30 MOBY-S: status report - Mark Wilkinson > 10:30 break > 11:00 S-MOBY: status report I - Gary Schiltz > 12:00 lunch > 1:30 S-MOBY: status report II - Gary Schiltz > 2:30 Discussion > 3:00 break > 3:30 HapMap services in MOBY-S: Ardavan Kanani > 4:00 Visualization tools for MOBY-S: Martin Senger > 4:30 Bioferret in MOBY-S: Mike Niemi > 5:00 Towards DAS/2 - Lincoln Stein > 5:30 Discussion > 6:30 Dinner > > Sunday April 4: > 9:00 SMOBY/MOBYS/DAS interoperability > Security Models > Replication > > 11:00 Publications > Future grant opportunities > Milestones to meet > > Lincoln -- Mark Wilkinson (mwilkinson at mrl.ubc.ca) University of British Columbia iCAPTURE Centre From natural at facedoctor.ca Fri Mar 26 22:18:24 2004 From: natural at facedoctor.ca (natural at facedoctor.ca) Date: Fri, 26 Mar 2004 17:18:24 -0500 Subject: [MOBY-dev] Bad Skin ?????? Message-ID: From simont at mcw.edu Tue Mar 30 18:07:17 2004 From: simont at mcw.edu (Simon Twigger) Date: Tue, 30 Mar 2004 12:07:17 -0600 Subject: [MOBY-dev] MOBY Mtg: Security model agenda Message-ID: <14D6A70C-8275-11D8-B25A-000A959D1D82@mcw.edu> Hi there, I was wondering if anyone could expand very briefly on what might be covered at the meeting this weekend under 'Security Models'? Will this have anything to do with Authentication of services, digital signatures and algorithms, perhaps even encryption/anonymization of service traffic via MOBY? I've been doing some reading on the subject but there's a lot out there so I wanted to get some idea of what might be covered so I can concentrate on the right things. Cheers, Simon. -- Simon N. Twigger, Ph.D. Assistant Professor, Department of Physiology Medical College of Wisconsin 8701 Watertown Plank Road, Milwaukee, WI, USA tel: 414-456-8802 fax: 414-456-6595 From 21CFR11 at biozak.com Tue Mar 30 21:50:41 2004 From: 21CFR11 at biozak.com (21CFR11 at biozak.com) Date: Tue, 30 Mar 2004 21:50:41 UT Subject: [MOBY-dev] We have emails of thousands of your prospective customers - life science executives Message-ID: <200403302150.NAA12920@main.biozak.com> An embedded and charset-unspecified text was scrubbed... Name: not available URL: From M.BATE.ALANN at netscape.net Wed Mar 31 03:41:50 2004 From: M.BATE.ALANN at netscape.net (M.BATE.ALANN at netscape.net) Date: Tue, 30 Mar 2004 22:41:50 -0500 Subject: [MOBY-dev] REPLY BACK Message-ID: <200403310341.i2V3fng2030665@portal.open-bio.org> Dear Friend, As you read this, I don't want you to feel sorry for me, because, I believe everyone will die someday. My name is BATES ALAN a merchant in Dubai, in the U.A.E.I have been diagnosed with Esophageal cancer. It has defiled all forms of medical treatment, and right now I have only about a few months to live, according to medical experts. I have not particularly lived my life so well, as I never really cared for anyone(not even myself)but my business. Though I am very rich, I was never generous, I was always hostile to people and only focused on my business as that was the only thing I cared for. But now I regret all this as I now know that there is more to life than just wanting to have or make all the money in the world. I believe when God gives me a second chance to come to this world I would live my life a different way from how I have lived it. Now that God has called me, I have willed and given most of my property and assets to my immediate and extended family members as well as a few close friends. I want God to be merciful to me and accept my soul so, I have decided to give alms to charity organizations, as I want this to be one of the last good deeds I do on earth. So far, I have distributed money to some charity organizations in the U.A.E, Algeria and Malaysia. Now that my health has deteriorated so badly, I cannot do this myself anymore. I once asked members of my family to close one of my accounts and distribute the money which I have there to charity organization in Bulgaria and Pakistan, they refused and kept the money to themselves. Hence, I do not trust them anymore, as they seem not to be contended with what I have left for them. The last of my money which no one knows of is the huge cash deposit of eighteen million dollars $18,000,000,00 that I have with a finance/Security Company abroad. I will want you to help me collect this deposit and dispatched it to charity organizations. I have set aside 10% for you and for your time. God be with you. BATES ALAN From dwprlzrmc at dra.forthnet.gr Wed Mar 31 09:27:12 2004 From: dwprlzrmc at dra.forthnet.gr (Daniel Everett) Date: Wed, 31 Mar 2004 15:27:12 +0600 Subject: [MOBY-dev] Make profit with google - no website required Message-ID: