From a.garcia at imb.uq.edu.au Fri Jul 1 12:35:46 2005 From: a.garcia at imb.uq.edu.au (a.garcia@imb.uq.edu.au) Date: Fri Jul 1 12:27:13 2005 Subject: [MOBY-l] Object ontology browser In-Reply-To: <1293586438-1119967038-cardhu_blackberry.rim.net-3291-@engine10-cell01> References: <1293586438-1119967038-cardhu_blackberry.rim.net-3291-@engine10-cell01> Message-ID: the url asks for user name and passwd. how can we get the tool? On Tue, 28 Jun 2005 13:52:36 +0000 GMT "mark wilkinson" wrote: > Do you want me to add this to the "cool tools" page? > > M > > > -----Original Message----- >From: Yan Wong > Date: Tue, 28 Jun 2005 11:50:03 > To:Dirk Haase > Cc:moby-l@biomoby.org > Subject: Re: [MOBY-l] Object ontology browser > > Dirk Haase wrote: > >>Hi Yan, >> >>On Thursday 16 June 2005 20:05, ywong@infobiogen.fr >>wrote: >> >> >>>Hello, >>> >>>I've Built a ontology object browser in Java. It has the >>>same >>>functionalities than the Python version. >>> >>>For people using unix and windows: >>> http://yan.wong.free.fr/Public/jMOBrowser.zip >>> >>>unzip the file and launch the objectBrowser script >>> >>> >> >>I just tried your object ontology browser and it works >>nice on our Linux >>boxes. Just one remark: in the dialog which opens after >>selecting 'Browse a >>Moby directory', I found the labels for the input fields >>very confusing. I >>would prefer "Moby Central URL" instead of just "URL" and >>- even more >>important - "Moby Central URI" instead of 'Namespace'. I >>first tried to >>insert namespaces like "Global_Keyword" in the latter >>one and got obscure >>error messages... >> >>Clicking the Root node always leads to a NPE - which does >>no harm besides >>spoiling the start shell with ugly java errors... >> >>But the rest of it is very nice! >> >>Regards, >>dirk >>_______________________________________________ >>moby-l mailing list >>moby-l@biomoby.org >>http://biomoby.org/mailman/listinfo/moby-l >> >> >> > OK I posted the modifications this morning... If I have >time, I'll > implement some search functionalities... > _______________________________________________ > moby-l mailing list > moby-l@biomoby.org > http://biomoby.org/mailman/listinfo/moby-l > > -- > Mark Wilkinson > ...on the road! > _______________________________________________ > moby-l mailing list > moby-l@biomoby.org > http://biomoby.org/mailman/listinfo/moby-l Alexander Garcia From Pieter.Neerincx at wur.nl Sat Jul 2 04:23:28 2005 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Sat Jul 2 04:45:54 2005 Subject: [MOBY-l] Object ontology browser In-Reply-To: References: <1293586438-1119967038-cardhu_blackberry.rim.net-3291-@engine10-cell01> Message-ID: <92600E01-EBCB-4B0C-ADCD-0A5CC93B9B2C@wur.nl> On 01Jul2005, at 18:35, wrote: > the url asks for user name and passwd. how can we get the tool? User and Pass were listed in one of the previous emails and on the BioMOBY website as well: http://www.biomoby.org/toolstoys.html > > > On Tue, 28 Jun 2005 13:52:36 +0000 GMT > "mark wilkinson" wrote: > >> Do you want me to add this to the "cool tools" page? >> M >> -----Original Message----- >> From: Yan Wong >> Date: Tue, 28 Jun 2005 11:50:03 To:Dirk Haase >> Cc:moby-l@biomoby.org >> Subject: Re: [MOBY-l] Object ontology browser >> Dirk Haase wrote: >> >>> Hi Yan, >>> >>> On Thursday 16 June 2005 20:05, ywong@infobiogen.fr wrote: >>> >>> >>>> Hello, >>>> >>>> I've Built a ontology object browser in Java. It has the same >>>> functionalities than the Python version. >>>> >>>> For people using unix and windows: >>>> http://yan.wong.free.fr/Public/jMOBrowser.zip >>>> >>>> unzip the file and launch the objectBrowser script >>>> >>>> >>> >>> I just tried your object ontology browser and it works nice on >>> our Linux boxes. Just one remark: in the dialog which opens after >>> selecting 'Browse a Moby directory', I found the labels for the >>> input fields very confusing. I would prefer "Moby Central URL" >>> instead of just "URL" and - even more important - "Moby Central >>> URI" instead of 'Namespace'. I first tried to insert namespaces >>> like "Global_Keyword" in the latter one and got obscure error >>> messages... >>> >>> Clicking the Root node always leads to a NPE - which does no harm >>> besides spoiling the start shell with ugly java errors... >>> >>> But the rest of it is very nice! >>> >>> Regards, >>> dirk >>> _______________________________________________ >>> moby-l mailing list >>> moby-l@biomoby.org >>> http://biomoby.org/mailman/listinfo/moby-l >>> >>> >>> >> OK I posted the modifications this morning... If I have time, I'll >> implement some search functionalities... >> _______________________________________________ >> moby-l mailing list >> moby-l@biomoby.org >> http://biomoby.org/mailman/listinfo/moby-l >> -- >> Mark Wilkinson >> ...on the road! >> _______________________________________________ >> moby-l mailing list >> moby-l@biomoby.org >> http://biomoby.org/mailman/listinfo/moby-l >> > > Alexander Garcia > _______________________________________________ > moby-l mailing list > moby-l@biomoby.org > http://biomoby.org/mailman/listinfo/moby-l > From ismael at lcc.uma.es Wed Jul 6 05:55:19 2005 From: ismael at lcc.uma.es (Ismael Navas) Date: Wed Jul 6 05:46:29 2005 Subject: [MOBY-l] Freefluo In-Reply-To: <200507020846.j628kQPD025302@portal.open-bio.org> Message-ID: <20050706095044.5493738CE5@sol10.lcc.uma.es> Hello all, I'm trying to use Freefluo, and I've tried with some workflows but it does not work. Could somebody send me an example (an its input file) which works on Freefluo. Thanks in advance, Ismael Navas. From markw at illuminae.com Wed Jul 6 10:41:49 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Wed Jul 6 10:32:58 2005 Subject: [moby] [MOBY-l] Freefluo In-Reply-To: <20050706095044.5493738CE5@sol10.lcc.uma.es> References: <20050706095044.5493738CE5@sol10.lcc.uma.es> Message-ID: <1120660909.8869.13.camel@mobycentral.mrl.ubc.ca> Hi Ismael, I don't know if you really mean Freefluo, or if you mean Taverna... ?? M On Wed, 2005-07-06 at 11:55 +0200, Ismael Navas wrote: > Hello all, > > I'm trying to use Freefluo, and I've tried with some workflows but it does > not work. Could somebody send me an example (an its input file) which works > on Freefluo. > > Thanks in advance, > Ismael Navas. > > > _______________________________________________ > moby-l mailing list > moby-l@biomoby.org > http://biomoby.org/mailman/listinfo/moby-l -- Mark Wilkinson Asst. Professor Dept. of Medical Genetics University of British Columbia PI in Bioinformatics iCAPTURE Centre St. Paul's Hospital Vancouver, BC From markw at illuminae.com Wed Jul 6 17:44:14 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Wed Jul 6 17:35:15 2005 Subject: [MOBY-l] everything should be functional again now... touch wood Message-ID: <1120686254.8869.242.camel@mobycentral.mrl.ubc.ca> Hi all, Well, everything should be functional again now. I've updated the links on the tools page to point to their new installations and everything seems to be alive. Taverna users: You need to edit the location of mobycentral in the /taverna-wrokbench/conf/mygrid.properties file - it's about 50 lines down. It should be: taverna.defaultbiomoby = http://mobycentral.icapture.ubc.ca/cgi- bin/MOBY05/mobycentral.pl Most of my own services are back up again - there's still a firewall issue with one or two of them that I hope to sort out soon. Let me know if you see any weirdness. Thankfully, we are moving toward a mirroring architecture, so this wont happen again once we get there... M -- Mark Wilkinson Asst. Professor Dept. of Medical Genetics University of British Columbia PI in Bioinformatics iCAPTURE Centre St. Paul's Hospital Vancouver, BC From edward.kawas at gmail.com Wed Jul 6 18:58:02 2005 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed Jul 6 18:49:07 2005 Subject: [MOBY-l] everything should be functional again now... touch wood In-Reply-To: <1120686254.8869.242.camel@mobycentral.mrl.ubc.ca> Message-ID: <42cc61fd.1c5266ed.3a3c.ffff805f@mx.gmail.com> Also, you will need to change the endpoints in your workflows to this same address! Eddie > -----Original Message----- > From: moby-l-bounces@portal.open-bio.org [mailto:moby-l- > bounces@portal.open-bio.org] On Behalf Of Mark Wilkinson > Sent: Wednesday, July 06, 2005 2:44 PM > To: mobyl > Subject: [MOBY-l] everything should be functional again > now... touch wood > > Hi all, > > Well, everything should be functional again now. I've > updated the links > on the tools page to point to their new installations and > everything > seems to be alive. > > Taverna users: You need to edit the location of > mobycentral in > the /taverna-wrokbench/conf/mygrid.properties file - it's > about 50 lines > down. It should be: > > taverna.defaultbiomoby = > http://mobycentral.icapture.ubc.ca/cgi- > bin/MOBY05/mobycentral.pl > > > Most of my own services are back up again - there's still > a firewall > issue with one or two of them that I hope to sort out soon. > Let me know > if you see any weirdness. > > Thankfully, we are moving toward a mirroring architecture, > so this wont > happen again once we get there... > > M > > > -- > Mark Wilkinson > Asst. Professor > Dept. of Medical Genetics > University of British Columbia > PI in Bioinformatics > iCAPTURE Centre > St. Paul's Hospital > Vancouver, BC > > > _______________________________________________ > moby-l mailing list > moby-l@biomoby.org > http://biomoby.org/mailman/listinfo/moby-l From Pieter.Neerincx at wur.nl Thu Jul 7 08:59:35 2005 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Thu Jul 7 08:50:50 2005 Subject: [MOBY-l] everything should be functional again now... touch wood In-Reply-To: <1120686254.8869.242.camel@mobycentral.mrl.ubc.ca> References: <1120686254.8869.242.camel@mobycentral.mrl.ubc.ca> Message-ID: <946363AC-A5EE-442D-BF00-3EC97E986816@wur.nl> Hi, On 6-Jul-2005, at 11:44 PM, Mark Wilkinson wrote: > Hi all, > > Well, everything should be functional again now. I've updated the > links > on the tools page to point to their new installations and everything > seems to be alive. > <-- snip --> > > Thankfully, we are moving toward a mirroring architecture, so this > wont > happen again once we get there... For those of you who are interested in having a local BioMOBY Central: I've just added moby-live/Perl/scripts/CloneCentralDatabases.pl to the CVS. Might be especially handy when you want to test scripts to register stuff. If you are not satisfied with the result you can simply use this script to nuke your existing MOBY Central clone and create a fresh one. If you put something like this in a crontab you might have quick and dirty mirroring system. But won't take care of load balancing, automaic failover etc. Moreover it won't scale well when MOBY gets big, but for the moment being it does the job for me :). It replaces the steps from the manual listed below. Cheers, Pieter ---------------------------------------------------- SET UP ALL MOBY CENTRAL DATABASES start mysql as root create databases: mobycentral mobyobject mobynamespace mobyservice mobyrelationship CREATE A USER FOR THE MOBYCENTRAL DATABASES (must have write access to all). GRANT ALL PRIVILEGES ON [each database] TO moby_central@localhost identified by "*********"; exit mysql foreach (databasename) you need to load a mysql DUMP. Either a bootstrap dump from the /Database folder of the CVS, or a dump from the public MOBY Central registry. mysql -u moby_central -p databasename< ~/moby-live/Database/ databasename.mysql NOTE: The database dumps in the /Database folder of the CVS contain the bootstrap objects and services (primitives, base objects, base services, relationship types, etc) so you should be ready to roll right away. If you prefer a full dump of the existing MOBY Central database, call the method $C->DUMP on MOBY::Client:Central, or call the procedure "DUMP" on the public MOBY Central's SOAP interface. ---------------------------------------------------- > > M > > > -- > Mark Wilkinson > Asst. Professor > Dept. of Medical Genetics > University of British Columbia > PI in Bioinformatics > iCAPTURE Centre > St. Paul's Hospital > Vancouver, BC > > > _______________________________________________ > moby-l mailing list > moby-l@biomoby.org > http://biomoby.org/mailman/listinfo/moby-l > Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1038 Dreijenlaan 3 6703 HA Wageningen phone: 0317-484 706 fax: 0317-483 584 mobile: 06-143 66 783 pieter.neerincx@wur.nl From markw at illuminae.com Fri Jul 8 18:08:47 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Fri Jul 8 17:59:38 2005 Subject: [MOBY-l] New release of MOBY Perl code Message-ID: <1120860527.3721.16.camel@bioinfo.icapture.ubc.ca> Hi all, There's a new release of the Perl libraries at http://biomoby.org/releases v0.8.2 It has the various little improvements that we have added over the past month, but more importantly, I want everyone to know it is there because the code in the CVS is likely to become pretty flakey over the next couple of months as we start to commit our major changes and move toward LSID compliance (and dependence...). This will be the last release of the code that does not require you to install the LSID libraries, and people hosting MOBY Central will also have to install and set-up an LSID resolver (we will provide the code for that too). So, hold on to your hats, and if you need a functional copy of the code, you better get it from this release 'cause the codebase is about to get ugly ;-) It will all be worth it - we are getting VERY excited about the 1.0 release!! Mark P.S. I have also updated the online install docs to explain how to set up the OntologyServer to serve from a local database. However, the problem of keeping your ontology synchronized with the main one is entirely yours... it is one of the things we will be addressing first in the next codebase. -- Mark Wilkinson Asst. Professor Dept. of Medical Genetics University of British Columbia PI in Bioinformatics iCAPTURE Centre St. Paul's Hospital Vancouver, BC From harttig at mail.dife.de Tue Jul 19 11:00:26 2005 From: harttig at mail.dife.de (Ulrich Harttig) Date: Tue Jul 19 10:48:57 2005 Subject: [MOBY-l] Connecting to BIOMOBY Central using Taverna 1.2 Message-ID: <42DD158A.8050201@mail.dife.de> Hello all There seems to be a problem connecting to the standard BioMOBY repository at http://mobycentral.icapture.ubc.ca/ using Taverna version 1.2. In contrast to version 1.1 that connects w/o problem, the new 'add Biomoby scavenger' dialog asks now for an URL for a BioMOBY Object RDF document with the default pointing to "http://biomoby.org/RESOURCES/MOBY-S/Objects". But this seems to be no longer a valid URL (and the RESOURCES script has also disappeared from the BioMOBY CVS repository) Does anyone know what the correct entry would be ? (leavin it empty doesn't work) And where one could find documentation explaining the RDF business that is also used for describing Moby services. Thanks for your help Ulrich -- Dr. Ulrich Harttig German Institute of Human Nutrition Potsdam-Rehbruecke Dept. of Epidemiology Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany phone: +49 (0)33200 88-729, fax: +49 (0)33200 88-721 From markw at illuminae.com Tue Jul 19 11:16:22 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Tue Jul 19 11:08:25 2005 Subject: [moby] [MOBY-l] Connecting to BIOMOBY Central using Taverna 1.2 In-Reply-To: <42DD158A.8050201@mail.dife.de> References: <42DD158A.8050201@mail.dife.de> Message-ID: <1121786182.21968.31.camel@bioinfo.icapture.ubc.ca> The URL works for me... HOWEVER it is retrieving over port 8090 from a Tomcat applet instead of from the Perl script that (as you point out) is now deprecated. As such, if your firewall is preventing access on 8090 this will be the source of the problem. I am trying to set up ProxyPass in Apache such that we can serve this same information over port 80. I'll let you know if we succeed. Otherwise, you will need to open port 8090 in the interim. >>sigh<< Thousands of things to do, and only two hands :-/ M On Tue, 2005-07-19 at 17:00 +0200, Ulrich Harttig wrote: > Hello all > > There seems to be a problem connecting to the standard BioMOBY > repository at http://mobycentral.icapture.ubc.ca/ > using Taverna version 1.2. In contrast to version 1.1 that connects w/o > problem, the new 'add Biomoby scavenger' dialog asks now for an URL for > a BioMOBY Object RDF document with the default pointing to > "http://biomoby.org/RESOURCES/MOBY-S/Objects". > But this seems to be no longer a valid URL (and the RESOURCES script has > also disappeared from the BioMOBY CVS repository) > Does anyone know what the correct entry would be ? (leavin it empty > doesn't work) And where one could find documentation explaining the RDF > business that is also used for describing Moby services. > > Thanks for your help > Ulrich > -- "Ontologists do it with the edges!" Mark Wilkinson Asst. Professor Dept. of Medical Genetics University of British Columbia PI in Bioinformatics iCAPTURE Centre St. Paul's Hospital Rm. 166, 1081 Burrard St. Vancouver, BC, V6Z 1Y6 tel: 604 682 2344 x62129 fax: 604 806 9274 From gordonp at ucalgary.ca Tue Jul 19 12:45:51 2005 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue Jul 19 12:36:26 2005 Subject: [MOBY-l] Reuest for small change to MOBY API Wiki In-Reply-To: <1121786182.21968.31.camel@bioinfo.icapture.ubc.ca> References: <42DD158A.8050201@mail.dife.de> <1121786182.21968.31.camel@bioinfo.icapture.ubc.ca> Message-ID: <42DD2E3F.30606@ucalgary.ca> The API currently says for the mobyData tag: "The value if queryID is arbitrary, and is up to the Client program to fill in. It should be unique to each mobyData in the message..." It should probably say " The value *of* queryID is arbitrary...It *must* be unique to each mobyData in the message..." then "...or missing or blank, in which case the message recipient can assign consecutive base-10 numerical IDs that can be used in responses" Right now, if you don't have queryIDs in a request with multiple invocations, the only thing a server can do is return responses in the same order as the input. Also, the API wording allows multiple invocations with the same name, which would make the responses impossible to differentiate automatically. Hopefully this change isn't a big deal for anyone... From bgulden at purdue.edu Fri Jul 22 12:20:19 2005 From: bgulden at purdue.edu (bgulden@purdue.edu) Date: Fri Jul 22 12:11:22 2005 Subject: [MOBY-l] Dynamically discovering service parameters Message-ID: <1122049219.42e11cc3649ee@webmail.purdue.edu> Is there any way to dynamically discover the secondary input for each service? Perhaps something akin to $ServiceInstance->input? Thanks -Brian Gulden From markw at illuminae.com Fri Jul 22 13:11:37 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Fri Jul 22 13:03:07 2005 Subject: [moby] [MOBY-l] Dynamically discovering service parameters In-Reply-To: <1122049219.42e11cc3649ee@webmail.purdue.edu> References: <1122049219.42e11cc3649ee@webmail.purdue.edu> Message-ID: <1122052297.30191.4.camel@bioinfo.icapture.ubc.ca> Hi Brian, Thanks for the heads-up! The documentation for MOBY::Client::ServiceInstance hasn't been updated properly. You should be able to get what you want as follows: my $outputs $ServiceInstance->output; # returns MOBY::Cient::SimpleArticle, CollectionArticle, # and/or SecondaryArticle objects foreach (@$outputs){ if ($_->isSecondary){ print $_->articleName; print $_->min; print $_->max; print $_->default; print $_->datatype; } } Hope that helps! M On Fri, 2005-07-22 at 11:20 -0500, bgulden@purdue.edu wrote: > Is there any way to dynamically discover the secondary input for each > service? Perhaps something akin to $ServiceInstance->input? > > Thanks > -Brian Gulden > > > _______________________________________________ > moby-l mailing list > moby-l@biomoby.org > http://biomoby.org/mailman/listinfo/moby-l -- "Ontologists do it with the edges!" Mark Wilkinson Asst. Professor Dept. of Medical Genetics University of British Columbia PI in Bioinformatics iCAPTURE Centre St. Paul's Hospital Rm. 166, 1081 Burrard St. Vancouver, BC, V6Z 1Y6 tel: 604 682 2344 x62129 fax: 604 806 9274 From bgulden at purdue.edu Fri Jul 22 14:47:13 2005 From: bgulden at purdue.edu (bgulden@purdue.edu) Date: Fri Jul 22 14:38:04 2005 Subject: [moby] [MOBY-l] Dynamically discovering service parameters In-Reply-To: <1122052297.30191.4.camel@bioinfo.icapture.ubc.ca> References: <1122049219.42e11cc3649ee@webmail.purdue.edu> <1122052297.30191.4.camel@bioinfo.icapture.ubc.ca> Message-ID: <1122058033.42e13f319299f@webmail.purdue.edu> According to the API, the function $ServiceInstance->input/output will only return SimpleArticles or a CollectionArticles. I have tried using these functions on services where I know there are secondary inputs and the only articles that appear are Simple or Collection. If this was recently changed in the MOBY code, that would explain my problems (I have an older release of the code Sept '04 I believe). Thanks again, -Brian Quoting Mark Wilkinson : > Hi Brian, > > Thanks for the heads-up! The documentation for > MOBY::Client::ServiceInstance hasn't been updated properly. > > You should be able to get what you want as follows: > > my $outputs $ServiceInstance->output; > # returns MOBY::Cient::SimpleArticle, CollectionArticle, > # and/or SecondaryArticle objects > > foreach (@$outputs){ > if ($_->isSecondary){ > print $_->articleName; > print $_->min; > print $_->max; > print $_->default; > print $_->datatype; > } > } > > > Hope that helps! > > M > > > On Fri, 2005-07-22 at 11:20 -0500, bgulden@purdue.edu wrote: > > Is there any way to dynamically discover the secondary input for each > > service? Perhaps something akin to $ServiceInstance->input? > > > > Thanks > > -Brian Gulden > > > > > > _______________________________________________ > > moby-l mailing list > > moby-l@biomoby.org > > http://biomoby.org/mailman/listinfo/moby-l > -- > "Ontologists do it with the edges!" > > Mark Wilkinson > Asst. Professor > Dept. of Medical Genetics > University of British Columbia > PI in Bioinformatics > iCAPTURE Centre > St. Paul's Hospital > Rm. 166, 1081 Burrard St. > Vancouver, BC, V6Z 1Y6 > tel: 604 682 2344 x62129 > fax: 604 806 9274 > > From markw at illuminae.com Fri Jul 22 15:37:34 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Fri Jul 22 15:57:45 2005 Subject: [moby] [MOBY-l] Dynamically discovering service parameters In-Reply-To: <1122058033.42e13f319299f@webmail.purdue.edu> References: <1122049219.42e11cc3649ee@webmail.purdue.edu> <1122052297.30191.4.camel@bioinfo.icapture.ubc.ca> <1122058033.42e13f319299f@webmail.purdue.edu> Message-ID: <1122061054.30191.30.camel@bioinfo.icapture.ubc.ca> Hmmm... it *should* return secondary articles as, but there may be a bug. You might want to try the new release of the codebase and see if that solves your problems. M On Fri, 2005-07-22 at 13:47 -0500, bgulden@purdue.edu wrote: > According to the API, the function $ServiceInstance->input/output will only > return SimpleArticles or a CollectionArticles. I have tried using these > functions on services where I know there are secondary inputs and the only > articles that appear are Simple or Collection. If this was recently changed > in the MOBY code, that would explain my problems (I have an older release of > the code Sept '04 I believe). > > Thanks again, > -Brian > > Quoting Mark Wilkinson : > > > Hi Brian, > > > > Thanks for the heads-up! The documentation for > > MOBY::Client::ServiceInstance hasn't been updated properly. > > > > You should be able to get what you want as follows: > > > > my $outputs $ServiceInstance->output; > > # returns MOBY::Cient::SimpleArticle, CollectionArticle, > > # and/or SecondaryArticle objects > > > > foreach (@$outputs){ > > if ($_->isSecondary){ > > print $_->articleName; > > print $_->min; > > print $_->max; > > print $_->default; > > print $_->datatype; > > } > > } > > > > > > Hope that helps! > > > > M > > > > > > On Fri, 2005-07-22 at 11:20 -0500, bgulden@purdue.edu wrote: > > > Is there any way to dynamically discover the secondary input for each > > > service? Perhaps something akin to $ServiceInstance->input? > > > > > > Thanks > > > -Brian Gulden > > > > > > > > > _______________________________________________ > > > moby-l mailing list > > > moby-l@biomoby.org > > > http://biomoby.org/mailman/listinfo/moby-l > > -- > > "Ontologists do it with the edges!" > > > > Mark Wilkinson > > Asst. Professor > > Dept. of Medical Genetics > > University of British Columbia > > PI in Bioinformatics > > iCAPTURE Centre > > St. Paul's Hospital > > Rm. 166, 1081 Burrard St. > > Vancouver, BC, V6Z 1Y6 > > tel: 604 682 2344 x62129 > > fax: 604 806 9274 > > > > > > > -- "Ontologists do it with the edges!" Mark Wilkinson Asst. Professor Dept. of Medical Genetics University of British Columbia PI in Bioinformatics iCAPTURE Centre St. Paul's Hospital Rm. 166, 1081 Burrard St. Vancouver, BC, V6Z 1Y6 tel: 604 682 2344 x62129 fax: 604 806 9274 From markw at illuminae.com Fri Jul 22 18:56:58 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Fri Jul 22 18:47:26 2005 Subject: [moby] [MOBY-l] Dynamically discovering service parameters In-Reply-To: <1122061054.30191.30.camel@bioinfo.icapture.ubc.ca> References: <1122049219.42e11cc3649ee@webmail.purdue.edu> <1122052297.30191.4.camel@bioinfo.icapture.ubc.ca> <1122058033.42e13f319299f@webmail.purdue.edu> <1122061054.30191.30.camel@bioinfo.icapture.ubc.ca> Message-ID: <1122073018.30191.46.camel@bioinfo.icapture.ubc.ca> Doh! I meant $ServiceInstance->secondary, not $ServiceInstance->output Sorry about that! M On Fri, 2005-07-22 at 12:37 -0700, Mark Wilkinson wrote: > Hmmm... it *should* return secondary articles as, but there may be a > bug. You might want to try the new release of the codebase and see if > that solves your problems. > > M > > On Fri, 2005-07-22 at 13:47 -0500, bgulden@purdue.edu wrote: > > According to the API, the function $ServiceInstance->input/output will only > > return SimpleArticles or a CollectionArticles. I have tried using these > > functions on services where I know there are secondary inputs and the only > > articles that appear are Simple or Collection. If this was recently changed > > in the MOBY code, that would explain my problems (I have an older release of > > the code Sept '04 I believe). > > > > Thanks again, > > -Brian > > > > Quoting Mark Wilkinson : > > > > > Hi Brian, > > > > > > Thanks for the heads-up! The documentation for > > > MOBY::Client::ServiceInstance hasn't been updated properly. > > > > > > You should be able to get what you want as follows: > > > > > > my $outputs $ServiceInstance->output; > > > # returns MOBY::Cient::SimpleArticle, CollectionArticle, > > > # and/or SecondaryArticle objects > > > > > > foreach (@$outputs){ > > > if ($_->isSecondary){ > > > print $_->articleName; > > > print $_->min; > > > print $_->max; > > > print $_->default; > > > print $_->datatype; > > > } > > > } > > > > > > > > > Hope that helps! > > > > > > M > > > > > > > > > On Fri, 2005-07-22 at 11:20 -0500, bgulden@purdue.edu wrote: > > > > Is there any way to dynamically discover the secondary input for each > > > > service? Perhaps something akin to $ServiceInstance->input? > > > > > > > > Thanks > > > > -Brian Gulden > > > > > > > > > > > > _______________________________________________ > > > > moby-l mailing list > > > > moby-l@biomoby.org > > > > http://biomoby.org/mailman/listinfo/moby-l > > > -- > > > "Ontologists do it with the edges!" > > > > > > Mark Wilkinson > > > Asst. Professor > > > Dept. of Medical Genetics > > > University of British Columbia > > > PI in Bioinformatics > > > iCAPTURE Centre > > > St. Paul's Hospital > > > Rm. 166, 1081 Burrard St. > > > Vancouver, BC, V6Z 1Y6 > > > tel: 604 682 2344 x62129 > > > fax: 604 806 9274 > > > > > > > > > > > > -- "Ontologists do it with the edges!" Mark Wilkinson Asst. Professor Dept. of Medical Genetics University of British Columbia PI in Bioinformatics iCAPTURE Centre St. Paul's Hospital Rm. 166, 1081 Burrard St. Vancouver, BC, V6Z 1Y6 tel: 604 682 2344 x62129 fax: 604 806 9274 From robert.stevens at manchester.ac.uk Mon Jul 4 14:02:22 2005 From: robert.stevens at manchester.ac.uk (Robert Stevens) Date: Mon Aug 15 11:29:04 2005 Subject: [MOBY-l] Reminder Re: CFP: Semantic Webs for the Life Sciences -- PSB06 Message-ID: <6.1.2.0.2.20050704191017.01e9b5b0@mailhost.cs.man.ac.uk> >_______________________________________________________________________ > > This message is posted to several lists. > We apologize if you receive multiple copies. > Please forward it to everyone who might be interested. >_______________________________________________________________________ > > > Call for Papers and Posters > > Semantic Webs for Life Sciences > > at the Pacific Symposium on Biocomputing 2006 > http://psb.stanford.edu/ > January 3-7, 2006 > Grand Wailea Resort, Wailea, Maui, Hawaii > >_______________________________________________________________________ > >Biology is evolving from a science of organisms and molecules to one >that increasingly relies on processing data. These data range from raw >sequences represented in a reasonably computational form, to the vast >body of annotation of these data that are less amenable to computational >processing. The shift from hypothesis-driven experiments to data-driven >experiments relies on having computational access to all these data and >the tools that manipulate those data. > >The Semantic Web is a vision that moves the Web from a form that is only >really usable by humans, to one where the data and services are open to >autonomous computational agents. This vision relies on the semantics of >both the content and services on the Web being accessible to computers. >Semantic markup through ontologies developed in OWl or RDF are meant to >provide this semantic markup -- OWL is, after all, the web Ontology >Language. As the recent biomedical ontology sessions at PSB have >revealed, there is much activity within bioinformatics in the field of >semantic markup of data. The discipline is well poised to build >Semantic Webs for Life Sciences that will afford bioinformatics >applications deeper computational access to the knowledge element of >bioinformatics resources. > >This session on Semantic Webs for Life Sciences would therefore welcome >papers that discuss: > > * The creation and use of Semantic Web applications > * Reasoning about the biomedical domain based on Semantic Web > technologies to make scientific insights > * Intelligent agent technologies and associated ontologies > * Use of Semantic Web technologies to bridge between heterogeneous > information resources (e.g., to connect genotype to gene > expression and ultimately to clinical medicine, drug discoveries, > etc.) > * Use of Semantic Web technologies to make biomedical applications > interoperable > * The use of OWL, RDF, etc. to describe and use knowledge in the > biomedical arena > * Advances in Semantic Web related technologies as applied to > bioinformatics and biomedical problems > * Other research associated with Semantic Webs for Life Sciences > >_______________________________________________________________________ > > > Session co-chairs > > * Robert Stevens (Contact Person) > University of Manchester, UK > robert.stevens@manchester.ac.uk > > * Olivier Bodenreider > National Library of Medicine > olivier@nlm.nih.gov > > * Yves A. Lussier > Columbia University, NY, USA > yves.lussier@dbmi.columbia.edu > >_______________________________________________________________________ > > > Submission information > > > Papers and Posters > >The core of the conference consists of rigorously peer-reviewed >full-length papers reporting on original work. Accepted papers will be >published in a hard-bound archival proceedings, and the best of these >will be presented orally to the entire conference. Researchers wishing >to present their research without official publication are encouraged to >submit a one page abstract by November 1, 2005 to present their work in >the poster sessions. > > > Important dates > > * Paper submissions due: July 18, 2005 > * Notification of paper acceptance: September 6, 2005 > * Final paper deadline: September 23, 2005 > * Abstract deadline: November 1, 2005 > * Meeting: January 3-7, 2006 > > > Paper format > >All papers must be submitted to russ.altman@stanford.edu in electronic >format. The file formats we accept are: postscript (*.ps), Adobe Acrobat >(*.pdf) and Microsoft Word documents (*.doc). Attached files should be >named with the last name of the first author (e.g. altman.ps, altman.pdf, >or altman.doc). >Hardcopy submissions or unprocessed TEX or LATEX files will be rejected >without review. > >Each paper must be accompanied by a cover letter. The *cover letter must >state* the following: > > * The email address of the corresponding author > * The specific PSB session that should review the paper or abstract > * The submitted paper contains original, unpublished results, and > is not currently under consideration elsewhere. > * All co-authors concur with the contents of the paper. > > >Submitted papers are limited to twelve (12) pages in our publication >format. Please format your paper according to instructions found at >http://psb.stanford.edu/psb-online/psb-submit/. If figures can not be >easily resized and placed precisely in the text, then it should be clear >that with appropriate modifications, the total manuscript length would >be within the page limit. > >Color pictures can be printed at the expense of the authors. The fee is >$500 per page of color pictures, payable at the time of camera ready >submission. > >Contact Russ Altman (russ.altman@stanford.edu) for additional information >about paper submission requirements. From a.garcia at imb.uq.edu.au Fri Jul 1 12:35:46 2005 From: a.garcia at imb.uq.edu.au (a.garcia@imb.uq.edu.au) Date: Sat, 02 Jul 2005 02:35:46 +1000 Subject: [MOBY-l] Object ontology browser In-Reply-To: <1293586438-1119967038-cardhu_blackberry.rim.net-3291-@engine10-cell01> References: <1293586438-1119967038-cardhu_blackberry.rim.net-3291-@engine10-cell01> Message-ID: the url asks for user name and passwd. how can we get the tool? On Tue, 28 Jun 2005 13:52:36 +0000 GMT "mark wilkinson" wrote: > Do you want me to add this to the "cool tools" page? > > M > > > -----Original Message----- >From: Yan Wong > Date: Tue, 28 Jun 2005 11:50:03 > To:Dirk Haase > Cc:moby-l at biomoby.org > Subject: Re: [MOBY-l] Object ontology browser > > Dirk Haase wrote: > >>Hi Yan, >> >>On Thursday 16 June 2005 20:05, ywong at infobiogen.fr >>wrote: >> >> >>>Hello, >>> >>>I've Built a ontology object browser in Java. It has the >>>same >>>functionalities than the Python version. >>> >>>For people using unix and windows: >>> http://yan.wong.free.fr/Public/jMOBrowser.zip >>> >>>unzip the file and launch the objectBrowser script >>> >>> >> >>I just tried your object ontology browser and it works >>nice on our Linux >>boxes. Just one remark: in the dialog which opens after >>selecting 'Browse a >>Moby directory', I found the labels for the input fields >>very confusing. I >>would prefer "Moby Central URL" instead of just "URL" and >>- even more >>important - "Moby Central URI" instead of 'Namespace'. I >>first tried to >>insert namespaces like "Global_Keyword" in the latter >>one and got obscure >>error messages... >> >>Clicking the Root node always leads to a NPE - which does >>no harm besides >>spoiling the start shell with ugly java errors... >> >>But the rest of it is very nice! >> >>Regards, >>dirk >>_______________________________________________ >>moby-l mailing list >>moby-l at biomoby.org >>http://biomoby.org/mailman/listinfo/moby-l >> >> >> > OK I posted the modifications this morning... If I have >time, I'll > implement some search functionalities... > _______________________________________________ > moby-l mailing list > moby-l at biomoby.org > http://biomoby.org/mailman/listinfo/moby-l > > -- > Mark Wilkinson > ...on the road! > _______________________________________________ > moby-l mailing list > moby-l at biomoby.org > http://biomoby.org/mailman/listinfo/moby-l Alexander Garcia From Pieter.Neerincx at wur.nl Sat Jul 2 04:23:28 2005 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Sat, 2 Jul 2005 10:23:28 +0200 Subject: [MOBY-l] Object ontology browser In-Reply-To: References: <1293586438-1119967038-cardhu_blackberry.rim.net-3291-@engine10-cell01> Message-ID: <92600E01-EBCB-4B0C-ADCD-0A5CC93B9B2C@wur.nl> On 01Jul2005, at 18:35, wrote: > the url asks for user name and passwd. how can we get the tool? User and Pass were listed in one of the previous emails and on the BioMOBY website as well: http://www.biomoby.org/toolstoys.html > > > On Tue, 28 Jun 2005 13:52:36 +0000 GMT > "mark wilkinson" wrote: > >> Do you want me to add this to the "cool tools" page? >> M >> -----Original Message----- >> From: Yan Wong >> Date: Tue, 28 Jun 2005 11:50:03 To:Dirk Haase >> Cc:moby-l at biomoby.org >> Subject: Re: [MOBY-l] Object ontology browser >> Dirk Haase wrote: >> >>> Hi Yan, >>> >>> On Thursday 16 June 2005 20:05, ywong at infobiogen.fr wrote: >>> >>> >>>> Hello, >>>> >>>> I've Built a ontology object browser in Java. It has the same >>>> functionalities than the Python version. >>>> >>>> For people using unix and windows: >>>> http://yan.wong.free.fr/Public/jMOBrowser.zip >>>> >>>> unzip the file and launch the objectBrowser script >>>> >>>> >>> >>> I just tried your object ontology browser and it works nice on >>> our Linux boxes. Just one remark: in the dialog which opens after >>> selecting 'Browse a Moby directory', I found the labels for the >>> input fields very confusing. I would prefer "Moby Central URL" >>> instead of just "URL" and - even more important - "Moby Central >>> URI" instead of 'Namespace'. I first tried to insert namespaces >>> like "Global_Keyword" in the latter one and got obscure error >>> messages... >>> >>> Clicking the Root node always leads to a NPE - which does no harm >>> besides spoiling the start shell with ugly java errors... >>> >>> But the rest of it is very nice! >>> >>> Regards, >>> dirk >>> _______________________________________________ >>> moby-l mailing list >>> moby-l at biomoby.org >>> http://biomoby.org/mailman/listinfo/moby-l >>> >>> >>> >> OK I posted the modifications this morning... If I have time, I'll >> implement some search functionalities... >> _______________________________________________ >> moby-l mailing list >> moby-l at biomoby.org >> http://biomoby.org/mailman/listinfo/moby-l >> -- >> Mark Wilkinson >> ...on the road! >> _______________________________________________ >> moby-l mailing list >> moby-l at biomoby.org >> http://biomoby.org/mailman/listinfo/moby-l >> > > Alexander Garcia > _______________________________________________ > moby-l mailing list > moby-l at biomoby.org > http://biomoby.org/mailman/listinfo/moby-l > From ismael at lcc.uma.es Wed Jul 6 05:55:19 2005 From: ismael at lcc.uma.es (Ismael Navas) Date: Wed, 6 Jul 2005 11:55:19 +0200 Subject: [MOBY-l] Freefluo In-Reply-To: <200507020846.j628kQPD025302@portal.open-bio.org> Message-ID: <20050706095044.5493738CE5@sol10.lcc.uma.es> Hello all, I'm trying to use Freefluo, and I've tried with some workflows but it does not work. Could somebody send me an example (an its input file) which works on Freefluo. Thanks in advance, Ismael Navas. From markw at illuminae.com Wed Jul 6 10:41:49 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 06 Jul 2005 07:41:49 -0700 Subject: [moby] [MOBY-l] Freefluo In-Reply-To: <20050706095044.5493738CE5@sol10.lcc.uma.es> References: <20050706095044.5493738CE5@sol10.lcc.uma.es> Message-ID: <1120660909.8869.13.camel@mobycentral.mrl.ubc.ca> Hi Ismael, I don't know if you really mean Freefluo, or if you mean Taverna... ?? M On Wed, 2005-07-06 at 11:55 +0200, Ismael Navas wrote: > Hello all, > > I'm trying to use Freefluo, and I've tried with some workflows but it does > not work. Could somebody send me an example (an its input file) which works > on Freefluo. > > Thanks in advance, > Ismael Navas. > > > _______________________________________________ > moby-l mailing list > moby-l at biomoby.org > http://biomoby.org/mailman/listinfo/moby-l -- Mark Wilkinson Asst. Professor Dept. of Medical Genetics University of British Columbia PI in Bioinformatics iCAPTURE Centre St. Paul's Hospital Vancouver, BC From markw at illuminae.com Wed Jul 6 17:44:14 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 06 Jul 2005 14:44:14 -0700 Subject: [MOBY-l] everything should be functional again now... touch wood Message-ID: <1120686254.8869.242.camel@mobycentral.mrl.ubc.ca> Hi all, Well, everything should be functional again now. I've updated the links on the tools page to point to their new installations and everything seems to be alive. Taverna users: You need to edit the location of mobycentral in the /taverna-wrokbench/conf/mygrid.properties file - it's about 50 lines down. It should be: taverna.defaultbiomoby = http://mobycentral.icapture.ubc.ca/cgi- bin/MOBY05/mobycentral.pl Most of my own services are back up again - there's still a firewall issue with one or two of them that I hope to sort out soon. Let me know if you see any weirdness. Thankfully, we are moving toward a mirroring architecture, so this wont happen again once we get there... M -- Mark Wilkinson Asst. Professor Dept. of Medical Genetics University of British Columbia PI in Bioinformatics iCAPTURE Centre St. Paul's Hospital Vancouver, BC From edward.kawas at gmail.com Wed Jul 6 18:58:02 2005 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 6 Jul 2005 15:58:02 -0700 Subject: [MOBY-l] everything should be functional again now... touch wood In-Reply-To: <1120686254.8869.242.camel@mobycentral.mrl.ubc.ca> Message-ID: <42cc61fd.1c5266ed.3a3c.ffff805f@mx.gmail.com> Also, you will need to change the endpoints in your workflows to this same address! Eddie > -----Original Message----- > From: moby-l-bounces at portal.open-bio.org [mailto:moby-l- > bounces at portal.open-bio.org] On Behalf Of Mark Wilkinson > Sent: Wednesday, July 06, 2005 2:44 PM > To: mobyl > Subject: [MOBY-l] everything should be functional again > now... touch wood > > Hi all, > > Well, everything should be functional again now. I've > updated the links > on the tools page to point to their new installations and > everything > seems to be alive. > > Taverna users: You need to edit the location of > mobycentral in > the /taverna-wrokbench/conf/mygrid.properties file - it's > about 50 lines > down. It should be: > > taverna.defaultbiomoby = > http://mobycentral.icapture.ubc.ca/cgi- > bin/MOBY05/mobycentral.pl > > > Most of my own services are back up again - there's still > a firewall > issue with one or two of them that I hope to sort out soon. > Let me know > if you see any weirdness. > > Thankfully, we are moving toward a mirroring architecture, > so this wont > happen again once we get there... > > M > > > -- > Mark Wilkinson > Asst. Professor > Dept. of Medical Genetics > University of British Columbia > PI in Bioinformatics > iCAPTURE Centre > St. Paul's Hospital > Vancouver, BC > > > _______________________________________________ > moby-l mailing list > moby-l at biomoby.org > http://biomoby.org/mailman/listinfo/moby-l From Pieter.Neerincx at wur.nl Thu Jul 7 08:59:35 2005 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Thu, 7 Jul 2005 14:59:35 +0200 Subject: [MOBY-l] everything should be functional again now... touch wood In-Reply-To: <1120686254.8869.242.camel@mobycentral.mrl.ubc.ca> References: <1120686254.8869.242.camel@mobycentral.mrl.ubc.ca> Message-ID: <946363AC-A5EE-442D-BF00-3EC97E986816@wur.nl> Hi, On 6-Jul-2005, at 11:44 PM, Mark Wilkinson wrote: > Hi all, > > Well, everything should be functional again now. I've updated the > links > on the tools page to point to their new installations and everything > seems to be alive. > <-- snip --> > > Thankfully, we are moving toward a mirroring architecture, so this > wont > happen again once we get there... For those of you who are interested in having a local BioMOBY Central: I've just added moby-live/Perl/scripts/CloneCentralDatabases.pl to the CVS. Might be especially handy when you want to test scripts to register stuff. If you are not satisfied with the result you can simply use this script to nuke your existing MOBY Central clone and create a fresh one. If you put something like this in a crontab you might have quick and dirty mirroring system. But won't take care of load balancing, automaic failover etc. Moreover it won't scale well when MOBY gets big, but for the moment being it does the job for me :). It replaces the steps from the manual listed below. Cheers, Pieter ---------------------------------------------------- SET UP ALL MOBY CENTRAL DATABASES start mysql as root create databases: mobycentral mobyobject mobynamespace mobyservice mobyrelationship CREATE A USER FOR THE MOBYCENTRAL DATABASES (must have write access to all). GRANT ALL PRIVILEGES ON [each database] TO moby_central at localhost identified by "*********"; exit mysql foreach (databasename) you need to load a mysql DUMP. Either a bootstrap dump from the /Database folder of the CVS, or a dump from the public MOBY Central registry. mysql -u moby_central -p databasename< ~/moby-live/Database/ databasename.mysql NOTE: The database dumps in the /Database folder of the CVS contain the bootstrap objects and services (primitives, base objects, base services, relationship types, etc) so you should be ready to roll right away. If you prefer a full dump of the existing MOBY Central database, call the method $C->DUMP on MOBY::Client:Central, or call the procedure "DUMP" on the public MOBY Central's SOAP interface. ---------------------------------------------------- > > M > > > -- > Mark Wilkinson > Asst. Professor > Dept. of Medical Genetics > University of British Columbia > PI in Bioinformatics > iCAPTURE Centre > St. Paul's Hospital > Vancouver, BC > > > _______________________________________________ > moby-l mailing list > moby-l at biomoby.org > http://biomoby.org/mailman/listinfo/moby-l > Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1038 Dreijenlaan 3 6703 HA Wageningen phone: 0317-484 706 fax: 0317-483 584 mobile: 06-143 66 783 pieter.neerincx at wur.nl From markw at illuminae.com Fri Jul 8 18:08:47 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 08 Jul 2005 15:08:47 -0700 Subject: [MOBY-l] New release of MOBY Perl code Message-ID: <1120860527.3721.16.camel@bioinfo.icapture.ubc.ca> Hi all, There's a new release of the Perl libraries at http://biomoby.org/releases v0.8.2 It has the various little improvements that we have added over the past month, but more importantly, I want everyone to know it is there because the code in the CVS is likely to become pretty flakey over the next couple of months as we start to commit our major changes and move toward LSID compliance (and dependence...). This will be the last release of the code that does not require you to install the LSID libraries, and people hosting MOBY Central will also have to install and set-up an LSID resolver (we will provide the code for that too). So, hold on to your hats, and if you need a functional copy of the code, you better get it from this release 'cause the codebase is about to get ugly ;-) It will all be worth it - we are getting VERY excited about the 1.0 release!! Mark P.S. I have also updated the online install docs to explain how to set up the OntologyServer to serve from a local database. However, the problem of keeping your ontology synchronized with the main one is entirely yours... it is one of the things we will be addressing first in the next codebase. -- Mark Wilkinson Asst. Professor Dept. of Medical Genetics University of British Columbia PI in Bioinformatics iCAPTURE Centre St. Paul's Hospital Vancouver, BC From harttig at mail.dife.de Tue Jul 19 11:00:26 2005 From: harttig at mail.dife.de (Ulrich Harttig) Date: Tue, 19 Jul 2005 17:00:26 +0200 Subject: [MOBY-l] Connecting to BIOMOBY Central using Taverna 1.2 Message-ID: <42DD158A.8050201@mail.dife.de> Hello all There seems to be a problem connecting to the standard BioMOBY repository at http://mobycentral.icapture.ubc.ca/ using Taverna version 1.2. In contrast to version 1.1 that connects w/o problem, the new 'add Biomoby scavenger' dialog asks now for an URL for a BioMOBY Object RDF document with the default pointing to "http://biomoby.org/RESOURCES/MOBY-S/Objects". But this seems to be no longer a valid URL (and the RESOURCES script has also disappeared from the BioMOBY CVS repository) Does anyone know what the correct entry would be ? (leavin it empty doesn't work) And where one could find documentation explaining the RDF business that is also used for describing Moby services. Thanks for your help Ulrich -- Dr. Ulrich Harttig German Institute of Human Nutrition Potsdam-Rehbruecke Dept. of Epidemiology Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany phone: +49 (0)33200 88-729, fax: +49 (0)33200 88-721 From markw at illuminae.com Tue Jul 19 11:16:22 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 19 Jul 2005 08:16:22 -0700 Subject: [moby] [MOBY-l] Connecting to BIOMOBY Central using Taverna 1.2 In-Reply-To: <42DD158A.8050201@mail.dife.de> References: <42DD158A.8050201@mail.dife.de> Message-ID: <1121786182.21968.31.camel@bioinfo.icapture.ubc.ca> The URL works for me... HOWEVER it is retrieving over port 8090 from a Tomcat applet instead of from the Perl script that (as you point out) is now deprecated. As such, if your firewall is preventing access on 8090 this will be the source of the problem. I am trying to set up ProxyPass in Apache such that we can serve this same information over port 80. I'll let you know if we succeed. Otherwise, you will need to open port 8090 in the interim. >>sigh<< Thousands of things to do, and only two hands :-/ M On Tue, 2005-07-19 at 17:00 +0200, Ulrich Harttig wrote: > Hello all > > There seems to be a problem connecting to the standard BioMOBY > repository at http://mobycentral.icapture.ubc.ca/ > using Taverna version 1.2. In contrast to version 1.1 that connects w/o > problem, the new 'add Biomoby scavenger' dialog asks now for an URL for > a BioMOBY Object RDF document with the default pointing to > "http://biomoby.org/RESOURCES/MOBY-S/Objects". > But this seems to be no longer a valid URL (and the RESOURCES script has > also disappeared from the BioMOBY CVS repository) > Does anyone know what the correct entry would be ? (leavin it empty > doesn't work) And where one could find documentation explaining the RDF > business that is also used for describing Moby services. > > Thanks for your help > Ulrich > -- "Ontologists do it with the edges!" Mark Wilkinson Asst. Professor Dept. of Medical Genetics University of British Columbia PI in Bioinformatics iCAPTURE Centre St. Paul's Hospital Rm. 166, 1081 Burrard St. Vancouver, BC, V6Z 1Y6 tel: 604 682 2344 x62129 fax: 604 806 9274 From gordonp at ucalgary.ca Tue Jul 19 12:45:51 2005 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue, 19 Jul 2005 10:45:51 -0600 Subject: [MOBY-l] Reuest for small change to MOBY API Wiki In-Reply-To: <1121786182.21968.31.camel@bioinfo.icapture.ubc.ca> References: <42DD158A.8050201@mail.dife.de> <1121786182.21968.31.camel@bioinfo.icapture.ubc.ca> Message-ID: <42DD2E3F.30606@ucalgary.ca> The API currently says for the mobyData tag: "The value if queryID is arbitrary, and is up to the Client program to fill in. It should be unique to each mobyData in the message..." It should probably say " The value *of* queryID is arbitrary...It *must* be unique to each mobyData in the message..." then "...or missing or blank, in which case the message recipient can assign consecutive base-10 numerical IDs that can be used in responses" Right now, if you don't have queryIDs in a request with multiple invocations, the only thing a server can do is return responses in the same order as the input. Also, the API wording allows multiple invocations with the same name, which would make the responses impossible to differentiate automatically. Hopefully this change isn't a big deal for anyone... From bgulden at purdue.edu Fri Jul 22 12:20:19 2005 From: bgulden at purdue.edu (bgulden@purdue.edu) Date: Fri, 22 Jul 2005 11:20:19 -0500 Subject: [MOBY-l] Dynamically discovering service parameters Message-ID: <1122049219.42e11cc3649ee@webmail.purdue.edu> Is there any way to dynamically discover the secondary input for each service? Perhaps something akin to $ServiceInstance->input? Thanks -Brian Gulden From markw at illuminae.com Fri Jul 22 13:11:37 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 22 Jul 2005 10:11:37 -0700 Subject: [moby] [MOBY-l] Dynamically discovering service parameters In-Reply-To: <1122049219.42e11cc3649ee@webmail.purdue.edu> References: <1122049219.42e11cc3649ee@webmail.purdue.edu> Message-ID: <1122052297.30191.4.camel@bioinfo.icapture.ubc.ca> Hi Brian, Thanks for the heads-up! The documentation for MOBY::Client::ServiceInstance hasn't been updated properly. You should be able to get what you want as follows: my $outputs $ServiceInstance->output; # returns MOBY::Cient::SimpleArticle, CollectionArticle, # and/or SecondaryArticle objects foreach (@$outputs){ if ($_->isSecondary){ print $_->articleName; print $_->min; print $_->max; print $_->default; print $_->datatype; } } Hope that helps! M On Fri, 2005-07-22 at 11:20 -0500, bgulden at purdue.edu wrote: > Is there any way to dynamically discover the secondary input for each > service? Perhaps something akin to $ServiceInstance->input? > > Thanks > -Brian Gulden > > > _______________________________________________ > moby-l mailing list > moby-l at biomoby.org > http://biomoby.org/mailman/listinfo/moby-l -- "Ontologists do it with the edges!" Mark Wilkinson Asst. Professor Dept. of Medical Genetics University of British Columbia PI in Bioinformatics iCAPTURE Centre St. Paul's Hospital Rm. 166, 1081 Burrard St. Vancouver, BC, V6Z 1Y6 tel: 604 682 2344 x62129 fax: 604 806 9274 From bgulden at purdue.edu Fri Jul 22 14:47:13 2005 From: bgulden at purdue.edu (bgulden@purdue.edu) Date: Fri, 22 Jul 2005 13:47:13 -0500 Subject: [moby] [MOBY-l] Dynamically discovering service parameters In-Reply-To: <1122052297.30191.4.camel@bioinfo.icapture.ubc.ca> References: <1122049219.42e11cc3649ee@webmail.purdue.edu> <1122052297.30191.4.camel@bioinfo.icapture.ubc.ca> Message-ID: <1122058033.42e13f319299f@webmail.purdue.edu> According to the API, the function $ServiceInstance->input/output will only return SimpleArticles or a CollectionArticles. I have tried using these functions on services where I know there are secondary inputs and the only articles that appear are Simple or Collection. If this was recently changed in the MOBY code, that would explain my problems (I have an older release of the code Sept '04 I believe). Thanks again, -Brian Quoting Mark Wilkinson : > Hi Brian, > > Thanks for the heads-up! The documentation for > MOBY::Client::ServiceInstance hasn't been updated properly. > > You should be able to get what you want as follows: > > my $outputs $ServiceInstance->output; > # returns MOBY::Cient::SimpleArticle, CollectionArticle, > # and/or SecondaryArticle objects > > foreach (@$outputs){ > if ($_->isSecondary){ > print $_->articleName; > print $_->min; > print $_->max; > print $_->default; > print $_->datatype; > } > } > > > Hope that helps! > > M > > > On Fri, 2005-07-22 at 11:20 -0500, bgulden at purdue.edu wrote: > > Is there any way to dynamically discover the secondary input for each > > service? Perhaps something akin to $ServiceInstance->input? > > > > Thanks > > -Brian Gulden > > > > > > _______________________________________________ > > moby-l mailing list > > moby-l at biomoby.org > > http://biomoby.org/mailman/listinfo/moby-l > -- > "Ontologists do it with the edges!" > > Mark Wilkinson > Asst. Professor > Dept. of Medical Genetics > University of British Columbia > PI in Bioinformatics > iCAPTURE Centre > St. Paul's Hospital > Rm. 166, 1081 Burrard St. > Vancouver, BC, V6Z 1Y6 > tel: 604 682 2344 x62129 > fax: 604 806 9274 > > From markw at illuminae.com Fri Jul 22 15:37:34 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 22 Jul 2005 12:37:34 -0700 Subject: [moby] [MOBY-l] Dynamically discovering service parameters In-Reply-To: <1122058033.42e13f319299f@webmail.purdue.edu> References: <1122049219.42e11cc3649ee@webmail.purdue.edu> <1122052297.30191.4.camel@bioinfo.icapture.ubc.ca> <1122058033.42e13f319299f@webmail.purdue.edu> Message-ID: <1122061054.30191.30.camel@bioinfo.icapture.ubc.ca> Hmmm... it *should* return secondary articles as, but there may be a bug. You might want to try the new release of the codebase and see if that solves your problems. M On Fri, 2005-07-22 at 13:47 -0500, bgulden at purdue.edu wrote: > According to the API, the function $ServiceInstance->input/output will only > return SimpleArticles or a CollectionArticles. I have tried using these > functions on services where I know there are secondary inputs and the only > articles that appear are Simple or Collection. If this was recently changed > in the MOBY code, that would explain my problems (I have an older release of > the code Sept '04 I believe). > > Thanks again, > -Brian > > Quoting Mark Wilkinson : > > > Hi Brian, > > > > Thanks for the heads-up! The documentation for > > MOBY::Client::ServiceInstance hasn't been updated properly. > > > > You should be able to get what you want as follows: > > > > my $outputs $ServiceInstance->output; > > # returns MOBY::Cient::SimpleArticle, CollectionArticle, > > # and/or SecondaryArticle objects > > > > foreach (@$outputs){ > > if ($_->isSecondary){ > > print $_->articleName; > > print $_->min; > > print $_->max; > > print $_->default; > > print $_->datatype; > > } > > } > > > > > > Hope that helps! > > > > M > > > > > > On Fri, 2005-07-22 at 11:20 -0500, bgulden at purdue.edu wrote: > > > Is there any way to dynamically discover the secondary input for each > > > service? Perhaps something akin to $ServiceInstance->input? > > > > > > Thanks > > > -Brian Gulden > > > > > > > > > _______________________________________________ > > > moby-l mailing list > > > moby-l at biomoby.org > > > http://biomoby.org/mailman/listinfo/moby-l > > -- > > "Ontologists do it with the edges!" > > > > Mark Wilkinson > > Asst. Professor > > Dept. of Medical Genetics > > University of British Columbia > > PI in Bioinformatics > > iCAPTURE Centre > > St. Paul's Hospital > > Rm. 166, 1081 Burrard St. > > Vancouver, BC, V6Z 1Y6 > > tel: 604 682 2344 x62129 > > fax: 604 806 9274 > > > > > > > -- "Ontologists do it with the edges!" Mark Wilkinson Asst. Professor Dept. of Medical Genetics University of British Columbia PI in Bioinformatics iCAPTURE Centre St. Paul's Hospital Rm. 166, 1081 Burrard St. Vancouver, BC, V6Z 1Y6 tel: 604 682 2344 x62129 fax: 604 806 9274 From markw at illuminae.com Fri Jul 22 18:56:58 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 22 Jul 2005 15:56:58 -0700 Subject: [moby] [MOBY-l] Dynamically discovering service parameters In-Reply-To: <1122061054.30191.30.camel@bioinfo.icapture.ubc.ca> References: <1122049219.42e11cc3649ee@webmail.purdue.edu> <1122052297.30191.4.camel@bioinfo.icapture.ubc.ca> <1122058033.42e13f319299f@webmail.purdue.edu> <1122061054.30191.30.camel@bioinfo.icapture.ubc.ca> Message-ID: <1122073018.30191.46.camel@bioinfo.icapture.ubc.ca> Doh! I meant $ServiceInstance->secondary, not $ServiceInstance->output Sorry about that! M On Fri, 2005-07-22 at 12:37 -0700, Mark Wilkinson wrote: > Hmmm... it *should* return secondary articles as, but there may be a > bug. You might want to try the new release of the codebase and see if > that solves your problems. > > M > > On Fri, 2005-07-22 at 13:47 -0500, bgulden at purdue.edu wrote: > > According to the API, the function $ServiceInstance->input/output will only > > return SimpleArticles or a CollectionArticles. I have tried using these > > functions on services where I know there are secondary inputs and the only > > articles that appear are Simple or Collection. If this was recently changed > > in the MOBY code, that would explain my problems (I have an older release of > > the code Sept '04 I believe). > > > > Thanks again, > > -Brian > > > > Quoting Mark Wilkinson : > > > > > Hi Brian, > > > > > > Thanks for the heads-up! The documentation for > > > MOBY::Client::ServiceInstance hasn't been updated properly. > > > > > > You should be able to get what you want as follows: > > > > > > my $outputs $ServiceInstance->output; > > > # returns MOBY::Cient::SimpleArticle, CollectionArticle, > > > # and/or SecondaryArticle objects > > > > > > foreach (@$outputs){ > > > if ($_->isSecondary){ > > > print $_->articleName; > > > print $_->min; > > > print $_->max; > > > print $_->default; > > > print $_->datatype; > > > } > > > } > > > > > > > > > Hope that helps! > > > > > > M > > > > > > > > > On Fri, 2005-07-22 at 11:20 -0500, bgulden at purdue.edu wrote: > > > > Is there any way to dynamically discover the secondary input for each > > > > service? Perhaps something akin to $ServiceInstance->input? > > > > > > > > Thanks > > > > -Brian Gulden > > > > > > > > > > > > _______________________________________________ > > > > moby-l mailing list > > > > moby-l at biomoby.org > > > > http://biomoby.org/mailman/listinfo/moby-l > > > -- > > > "Ontologists do it with the edges!" > > > > > > Mark Wilkinson > > > Asst. Professor > > > Dept. of Medical Genetics > > > University of British Columbia > > > PI in Bioinformatics > > > iCAPTURE Centre > > > St. Paul's Hospital > > > Rm. 166, 1081 Burrard St. > > > Vancouver, BC, V6Z 1Y6 > > > tel: 604 682 2344 x62129 > > > fax: 604 806 9274 > > > > > > > > > > > > -- "Ontologists do it with the edges!" Mark Wilkinson Asst. Professor Dept. of Medical Genetics University of British Columbia PI in Bioinformatics iCAPTURE Centre St. Paul's Hospital Rm. 166, 1081 Burrard St. Vancouver, BC, V6Z 1Y6 tel: 604 682 2344 x62129 fax: 604 806 9274 From robert.stevens at manchester.ac.uk Mon Jul 4 14:02:22 2005 From: robert.stevens at manchester.ac.uk (Robert Stevens) Date: Mon, 04 Jul 2005 18:02:22 -0000 Subject: [MOBY-l] Reminder Re: CFP: Semantic Webs for the Life Sciences -- PSB06 Message-ID: <6.1.2.0.2.20050704191017.01e9b5b0@mailhost.cs.man.ac.uk> >_______________________________________________________________________ > > This message is posted to several lists. > We apologize if you receive multiple copies. > Please forward it to everyone who might be interested. >_______________________________________________________________________ > > > Call for Papers and Posters > > Semantic Webs for Life Sciences > > at the Pacific Symposium on Biocomputing 2006 > http://psb.stanford.edu/ > January 3-7, 2006 > Grand Wailea Resort, Wailea, Maui, Hawaii > >_______________________________________________________________________ > >Biology is evolving from a science of organisms and molecules to one >that increasingly relies on processing data. These data range from raw >sequences represented in a reasonably computational form, to the vast >body of annotation of these data that are less amenable to computational >processing. The shift from hypothesis-driven experiments to data-driven >experiments relies on having computational access to all these data and >the tools that manipulate those data. > >The Semantic Web is a vision that moves the Web from a form that is only >really usable by humans, to one where the data and services are open to >autonomous computational agents. This vision relies on the semantics of >both the content and services on the Web being accessible to computers. >Semantic markup through ontologies developed in OWl or RDF are meant to >provide this semantic markup -- OWL is, after all, the web Ontology >Language. As the recent biomedical ontology sessions at PSB have >revealed, there is much activity within bioinformatics in the field of >semantic markup of data. The discipline is well poised to build >Semantic Webs for Life Sciences that will afford bioinformatics >applications deeper computational access to the knowledge element of >bioinformatics resources. > >This session on Semantic Webs for Life Sciences would therefore welcome >papers that discuss: > > * The creation and use of Semantic Web applications > * Reasoning about the biomedical domain based on Semantic Web > technologies to make scientific insights > * Intelligent agent technologies and associated ontologies > * Use of Semantic Web technologies to bridge between heterogeneous > information resources (e.g., to connect genotype to gene > expression and ultimately to clinical medicine, drug discoveries, > etc.) > * Use of Semantic Web technologies to make biomedical applications > interoperable > * The use of OWL, RDF, etc. to describe and use knowledge in the > biomedical arena > * Advances in Semantic Web related technologies as applied to > bioinformatics and biomedical problems > * Other research associated with Semantic Webs for Life Sciences > >_______________________________________________________________________ > > > Session co-chairs > > * Robert Stevens (Contact Person) > University of Manchester, UK > robert.stevens at manchester.ac.uk > > * Olivier Bodenreider > National Library of Medicine > olivier at nlm.nih.gov > > * Yves A. Lussier > Columbia University, NY, USA > yves.lussier at dbmi.columbia.edu > >_______________________________________________________________________ > > > Submission information > > > Papers and Posters > >The core of the conference consists of rigorously peer-reviewed >full-length papers reporting on original work. Accepted papers will be >published in a hard-bound archival proceedings, and the best of these >will be presented orally to the entire conference. Researchers wishing >to present their research without official publication are encouraged to >submit a one page abstract by November 1, 2005 to present their work in >the poster sessions. > > > Important dates > > * Paper submissions due: July 18, 2005 > * Notification of paper acceptance: September 6, 2005 > * Final paper deadline: September 23, 2005 > * Abstract deadline: November 1, 2005 > * Meeting: January 3-7, 2006 > > > Paper format > >All papers must be submitted to russ.altman at stanford.edu in electronic >format. The file formats we accept are: postscript (*.ps), Adobe Acrobat >(*.pdf) and Microsoft Word documents (*.doc). Attached files should be >named with the last name of the first author (e.g. altman.ps, altman.pdf, >or altman.doc). >Hardcopy submissions or unprocessed TEX or LATEX files will be rejected >without review. > >Each paper must be accompanied by a cover letter. The *cover letter must >state* the following: > > * The email address of the corresponding author > * The specific PSB session that should review the paper or abstract > * The submitted paper contains original, unpublished results, and > is not currently under consideration elsewhere. > * All co-authors concur with the contents of the paper. > > >Submitted papers are limited to twelve (12) pages in our publication >format. Please format your paper according to instructions found at >http://psb.stanford.edu/psb-online/psb-submit/. If figures can not be >easily resized and placed precisely in the text, then it should be clear >that with appropriate modifications, the total manuscript length would >be within the page limit. > >Color pictures can be printed at the expense of the authors. The fee is >$500 per page of color pictures, payable at the time of camera ready >submission. > >Contact Russ Altman (russ.altman at stanford.edu) for additional information >about paper submission requirements.