From yuying at vbi.vt.edu Wed Sep 13 12:19:59 2006 From: yuying at vbi.vt.edu (yuying at vbi.vt.edu) Date: Wed, 13 Sep 2006 12:19:59 -0400 (EDT) Subject: [MOBY-l] please help - using Dashboard Message-ID: <36309.67.38.19.157.1158164399.squirrel@webmail.vbi.vt.edu> Hi: I am new to the BioMoby project. I am trying to set up everything on my local computer and I am trying to do a testing for an Echo web service. I am following the guide for Java from biomoby.tigr.org. And my current step is to register this testing service using Dashboard. The Dashboard documentation did not tell me how to find out the namespace, service type, data types and necessary fields for registering the service. My guess is that the service type is testing. Could anyone tell me how to find such information? And if I want to use RDF, how to find out the signature URL? Thank you! Yuying Tian Virginia Bioinformatics Institute From d.haase at gsf.de Thu Sep 14 07:13:31 2006 From: d.haase at gsf.de (Dirk Haase) Date: Thu, 14 Sep 2006 13:13:31 +0200 Subject: [MOBY-l] please help - using Dashboard In-Reply-To: <36309.67.38.19.157.1158164399.squirrel@webmail.vbi.vt.edu> References: <36309.67.38.19.157.1158164399.squirrel@webmail.vbi.vt.edu> Message-ID: <200609141313.32217.d.haase@gsf.de> Hi Yuying, On Wednesday 13 September 2006 18:19, yuying at vbi.vt.edu wrote: > Hi: > > I am new to the BioMoby project. Welcome to the club! > I am trying to set up everything on my > local computer and I am trying to do a testing for an Echo web service. I > am following the guide for Java from biomoby.tigr.org. And my current step > is to register this testing service using Dashboard. The Dashboard > documentation did not tell me how to find out the namespace, service type, > data types and necessary fields for registering the service. Generally speaking, these are the things which are specific for each new service, so it's hard for a general guide to help you there... All these things have to be fixed at the very beginning, it only makes sense to register a service when you are sure about its 'signature' (ie. input and output datatypes/namespaces/service type). In order to get an idea of these concepts which are very basic for the whole biomoby thing, I would recommend the general documentation on biomoby.org->'For Developers'. Data types: http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/DataClassOntology.html Namespaces: http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/ObjectStructure.html Service types are not very well described, but the ones which already exist have quite speaking names, just browse the hierarchy and select whatever fits best. For the special case of an Echo service we can of course offer you advice. To be a real echo, it should be able to deal with any sort of object, so it would be wrong to rely on any 'special feature' of an input. Thus, the input data type has to be just 'Object'. Same for the output, otherwise it's not an echo ;-) You also wouldn't want to restrict the service to objects of a specific namespace, so leave it blank. Consequently, the output namespace is also not specifyable (ie. blank). Regarding the service type 'Testing' is the best choice as you guessed correctly. > My guess is > that the service type is testing. Could anyone tell me how to find such > information? And if I want to use RDF, how to find out the signature URL? The signature URL can not be 'found out', you have to specify it. Remember that it must be a link to a place where a) it can be accessed from everywhere (i.e. on your publicly accessible webserver) b) you have write permissions, because you have to put the RDF document to the place which is referenced by the signature URL You might also have a look at http://bioinfo.mpiz-koeln.mpg.de/araws/documentation/help/rdf-faq/ which answers the most important question concerning RDF. The parent folder contains more documentary stuff which could also be helpful. > Thank you! Hope this helps, dirk -- ---------------------------------------------------------- Dirk Haase phone +49 89 3187 3583 http://mips.gsf.de/~haase email d.haase at gsf.de From yuying at vbi.vt.edu Thu Sep 14 11:01:34 2006 From: yuying at vbi.vt.edu (yuying at vbi.vt.edu) Date: Thu, 14 Sep 2006 11:01:34 -0400 (EDT) Subject: [MOBY-l] thank you and more question In-Reply-To: <200609141313.32217.d.haase@gsf.de> References: <36309.67.38.19.157.1158164399.squirrel@webmail.vbi.vt.edu> <200609141313.32217.d.haase@gsf.de> Message-ID: <52596.67.38.19.157.1158246094.squirrel@webmail.vbi.vt.edu> Hi moby-members: Thank you all for youe reply. That was very helpful. I read about the Class Ontology and Object Structure. Now I have two questions: 1. Why some classes such as ABI_Encoded, alignment, and SimpleAnnotatedJPEGImage, are in the Ontology document on-line, but not in the Dashboard DataType tree? Why Object itself is not in the Object Ontology list? 2. Do I need to register every panel (namespace, service type, datatype, service) when I want to register a service? If I can leave the namespace blank, do I have to use the namespace register panel? How do I find about the article name? 3. My situation is that I am working on my local computer (Linux) and I will deploy on a remote server. What is different between service endpoint and RDF endpoint? Yuying On Thu, September 14, 2006 7:13 am, Dirk Haase wrote: > Hi Yuying, > > > On Wednesday 13 September 2006 18:19, yuying at vbi.vt.edu wrote: > >> Hi: >> >> >> I am new to the BioMoby project. >> > > Welcome to the club! > > >> I am trying to set up everything on my >> local computer and I am trying to do a testing for an Echo web service. >> I >> am following the guide for Java from biomoby.tigr.org. And my current >> step is to register this testing service using Dashboard. The Dashboard >> documentation did not tell me how to find out the namespace, service >> type, data types and necessary fields for registering the service. > > Generally speaking, these are the things which are specific for each new > service, so it's hard for a general guide to help you there... All these > things have to be fixed at the very beginning, it only makes sense to > register a service when you are sure about its 'signature' (ie. input and > output datatypes/namespaces/service type). In order to get an idea of > these concepts which are very basic for the whole biomoby thing, I would > recommend the general documentation on biomoby.org->'For Developers'. Data > types: > http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/DataClas > sOntology.html Namespaces: > http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/ObjectSt > ructure.html Service types are not very well described, but the ones which > already exist have quite speaking names, just browse the hierarchy and > select whatever fits best. > > For the special case of an Echo service we can of course offer you > advice. To be a real echo, it should be able to deal with any sort of > object, so it would be wrong to rely on any 'special feature' of an input. > Thus, the input > data type has to be just 'Object'. Same for the output, otherwise it's not > an echo ;-) You also wouldn't want to restrict the service to objects of a > specific namespace, so leave it blank. Consequently, the output > namespace is also not specifyable (ie. blank). Regarding the service type > 'Testing' is the > best choice as you guessed correctly. > >> My guess is >> that the service type is testing. Could anyone tell me how to find such >> information? And if I want to use RDF, how to find out the signature >> URL? >> > > The signature URL can not be 'found out', you have to specify it. > Remember > that it must be a link to a place where a) it can be accessed from > everywhere (i.e. on your publicly accessible webserver) b) you have write > permissions, because you have to put the RDF document to the place which > is referenced by the signature URL > > You might also have a look at > http://bioinfo.mpiz-koeln.mpg.de/araws/documentation/help/rdf-faq/ > which answers the most important question concerning RDF. The parent > folder contains more documentary stuff which could also be helpful. > >> Thank you! >> > > Hope this helps, > dirk > > -- > > > ---------------------------------------------------------- > Dirk Haase phone +49 89 3187 3583 > http://mips.gsf.de/~haase email d.haase at gsf.de > _______________________________________________ > moby-l mailing list moby-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-l > > From edward.kawas at gmail.com Thu Sep 14 11:31:51 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 14 Sep 2006 08:31:51 -0700 Subject: [MOBY-l] thank you and more question In-Reply-To: <52596.67.38.19.157.1158246094.squirrel@webmail.vbi.vt.edu> Message-ID: <004301c6d812$e7717060$6400a8c0@notebook> Hi, > Hi moby-members: > > Thank you all for youe reply. That was very helpful. I read > about the Class Ontology and Object Structure. Now I have two > questions: > > 1. Why some classes such as ABI_Encoded, alignment, and > SimpleAnnotatedJPEGImage, are in the Ontology document > on-line, but not in the Dashboard DataType tree? Why Object > itself is not in the Object Ontology list? They should be ... Especially Object, since it is the root of the ontology! > > 2. Do I need to register every panel (namespace, service > type, datatype, > service) when I want to register a service? If I can leave > the namespace blank, do I have to use the namespace register > panel? How do I find about the article name? To register a service, you only need the register service instance panel, unless you would like to introduce a new namespace/service type/datatype. The article name is the name that you give the datatype when you register your service. For instance, if I register a service that consumes a DNASequence, I might give it an articlename of 'sequence'. The name is entirely up to you when you register the service. > > 3. My situation is that I am working on my local computer > (Linux) and I will deploy on a remote server. What is > different between service endpoint and RDF endpoint? > The rdf endpoint is the url that if I use a browser and point to the url, I can view the full description of the service. The service endpoint is the url that a client calls with the appropriate parameters to invoke your service. Eddie > Yuying > > > On Thu, September 14, 2006 7:13 am, Dirk Haase wrote: > > Hi Yuying, > > > > > > On Wednesday 13 September 2006 18:19, yuying at vbi.vt.edu wrote: > > > >> Hi: > >> > >> > >> I am new to the BioMoby project. > >> > > > > Welcome to the club! > > > > > >> I am trying to set up everything on my local computer and > I am trying > >> to do a testing for an Echo web service. > >> I > >> am following the guide for Java from biomoby.tigr.org. And > my current > >> step is to register this testing service using Dashboard. The > >> Dashboard documentation did not tell me how to find out the > >> namespace, service type, data types and necessary fields > for registering the service. > > > > Generally speaking, these are the things which are specific > for each > > new service, so it's hard for a general guide to help you there... > > All these things have to be fixed at the very beginning, it > only makes > > sense to register a service when you are sure about its 'signature' > > (ie. input and output datatypes/namespaces/service type). > In order to > > get an idea of these concepts which are very basic for the whole > > biomoby thing, I would recommend the general documentation on > > biomoby.org->'For Developers'. Data > > types: > > > http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/Data > > Clas > > sOntology.html Namespaces: > > > http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/Obje > > ctSt ructure.html Service types are not very well > described, but the > > ones which already exist have quite speaking names, just browse the > > hierarchy and select whatever fits best. > > > > For the special case of an Echo service we can of course offer you > > advice. To be a real echo, it should be able to deal with > any sort of > > object, so it would be wrong to rely on any 'special > feature' of an input. > > Thus, the input > > data type has to be just 'Object'. Same for the output, > otherwise it's > > not an echo ;-) You also wouldn't want to restrict the service to > > objects of a specific namespace, so leave it blank. > Consequently, the > > output namespace is also not specifyable (ie. blank). Regarding the > > service type 'Testing' is the best choice as you guessed correctly. > > > >> My guess is > >> that the service type is testing. Could anyone tell me how to find > >> such information? And if I want to use RDF, how to find out the > >> signature URL? > >> > > > > The signature URL can not be 'found out', you have to specify it. > > Remember > > that it must be a link to a place where a) it can be accessed from > > everywhere (i.e. on your publicly accessible webserver) b) you have > > write permissions, because you have to put the RDF document to the > > place which is referenced by the signature URL > > > > You might also have a look at > > http://bioinfo.mpiz-koeln.mpg.de/araws/documentation/help/rdf-faq/ > > which answers the most important question concerning RDF. > The parent > > folder contains more documentary stuff which could also be helpful. > > > >> Thank you! > >> > > > > Hope this helps, > > dirk > > > > -- > > > > > > ---------------------------------------------------------- > > Dirk Haase phone +49 89 3187 3583 > > http://mips.gsf.de/~haase email d.haase at gsf.de > > _______________________________________________ > > moby-l mailing list moby-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/moby-l > > > > > > > _______________________________________________ > moby-l mailing list > moby-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-l From markw at illuminae.com Mon Sep 18 14:10:02 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Mon, 18 Sep 2006 11:10:02 -0700 Subject: [MOBY-l] MOBY Central going down for 15 minutes for a RAM upgrade Message-ID: <1158603002.18578.20.camel@bioinfo.icapture.ubc.ca> Hi all, In one hour we're going to shut-down MOBY Central for just long enough to stick another 2Gig of RAM in it. Shouldn't be more than 15 minutes. Please scream if this is a problem for you! M -- 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 "Since the point of a definition is to explain the meaning of a term to someone who is unfamiliar with its proper application, the use of language that doesn't help such a person learn how to apply the term is pointless. Thus, "happiness is a warm puppy" may be a lovely thought, but it is a lousy definition." K?hler et al, 2006