From senger at ebi.ac.uk Wed Mar 1 01:57:17 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Wed, 1 Mar 2006 06:57:17 +0000 (GMT) Subject: [MOBY-dev] link to "how to get code from cvs" In-Reply-To: <5.2.1.1.2.20060228135638.01258b30@email.med.harvard.edu> Message-ID: Frank, I suggest that the "CVS Repository" link from the main biomoby.org does not go directly to the web-based cvs browser, but rather to the instructions how to get it from the CVS (unless Chris wants to put these instructions directly to the web-based CVS page). These instructions were here: http://www.biomoby.org/GettingTheCode.html (but are not anymore - BTW, where are they now? - because I have a dead link to them in jMoby), or use the one in jMoby: http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/CVS.html (this is the page that has, at the moment, the dead link mentioned above). Thanks, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger consulting for: International Rice Research Institute Biometrics and Bioinformatics Unit DAPO BOX 7777, Metro Manila Philippines, phone: +63-2-580-5600 (ext.2324) From senger at ebi.ac.uk Wed Mar 1 05:24:15 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Wed, 1 Mar 2006 10:24:15 +0000 (GMT) Subject: [MOBY-dev] policies on Biomoby registries Message-ID: You might have noticed that Mark (silently? :-)) created a new page with a list of known biomoby registries where each registry can provide its own policy (http://biomoby.org/CVS_CONTENT/moby-live/Docs/ProjectDocs/). This may not come as a surprise after his strongly expressed opinion of what he wants and does not want in "his" registry. But it may be done slightly too silently to let me feel comfortable (sorry, Mark, this is just my feeling, I cannot help it). The strength of Biomoby was always in sharing - and if we suddenly starts to have many registries this strenghts may decreased. On the other hand, I feel that we actually *need* more registries, perhaps with different purposes, and with the different level of curation. But before starting to list them we should - here my 2cs go in - think first about federation of the registries, about an API how to access more registries etc. We mentioned federation during the last developer meeting (which was, btw and so far, really the last one, at least regarding the funds available from Vancouver, as I understand it) but have not built on it yet. And we should. Can we just postpone implementation of the individual (public) registry policies and first to discuss how to make the various registries federated? Thanks in advance for your opinions. Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger consulting for: International Rice Research Institute Biometrics and Bioinformatics Unit DAPO BOX 7777, Metro Manila Philippines, phone: +63-2-580-5600 (ext.2324) From markw at illuminae.com Wed Mar 1 10:29:10 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 01 Mar 2006 07:29:10 -0800 Subject: [MOBY-dev] [moby] link to "how to get code from cvs" In-Reply-To: References: Message-ID: <1141226950.30896.2.camel@bioinfo.icapture.ubc.ca> On Wed, 2006-03-01 at 06:57 +0000, Martin Senger wrote: > I suggest that the "CVS Repository" link from the main biomoby.org does > not go directly to the web-based cvs browser, but rather to the > instructions how to get it from the CVS Done. From senger at ebi.ac.uk Wed Mar 1 10:33:00 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Wed, 1 Mar 2006 15:33:00 +0000 (GMT) Subject: [MOBY-dev] [moby] link to "how to get code from cvs" In-Reply-To: <1141226950.30896.2.camel@bioinfo.icapture.ubc.ca> Message-ID: > Done. > Thanks! Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger consulting for: International Rice Research Institute Biometrics and Bioinformatics Unit DAPO BOX 7777, Metro Manila Philippines, phone: +63-2-580-5600 (ext.2324) From markw at illuminae.com Wed Mar 1 11:30:16 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 01 Mar 2006 08:30:16 -0800 Subject: [MOBY-dev] Lengthy commentary on registry policies and my own responsibilities In-Reply-To: References: Message-ID: <1141230616.30896.64.camel@bioinfo.icapture.ubc.ca> On Wed, 2006-03-01 at 10:24 +0000, Martin Senger wrote: > You might have noticed that Mark (silently? :-)) created a new page I quote from my message of Feb 21st: "The policy of the MOBY Central registry at iCAPTURE is currently being drawn-up. A first draft is available (click on Project Docs on the right side of the moby homepage) for comment" > But it may be done slightly too silently to let me feel comfortable > (sorry, Mark, this is just my feeling, I cannot help it). Public discussion is welcome; your opinion, in particular, is **always** valued! > The strength of > Biomoby was always in sharing - and if we suddenly starts to have many > registries this strenghts may decreased. I **strongly** support this statement!!!! The reality is, unfortunately, not in line with this vision. I host a registry, you host a registry at IRRI, MIPS hosts a registry, INB hosts a registry, there is a (dead?) registry at the University of Queensland, I host a second registry here specifically for TAIR, a third for our local services here at iCAPTURE, and yet a fourth here that allows me to continue doing interoperability research, since the new RFC policies around MOBY development are not conducive to a research environment. > On the other hand, I feel that we actually *need* more registries, > perhaps with different purposes, and with the different level of curation. > But before starting to list them we should - here my 2cs go in - think > first about federation of the registries, about an API how to access more > registries etc. Absolutely! For the past year I have been slowly (yes, silently ;-) ) moving the MOBY Central Perl code to a point where we might be in a position to support multiple registries more easily once we decide how to do so. The codebase was **strongly** tied to the concept of a single registry that was aware of a single object ontology, a single service ontology, and a single namespace ontology. In many ways it still is - the ontology maintenance routines are hard-coded to prevent the modification or removal of Objects, Services, and Namespaces that are being used; however, that is only true if the registry itself KNOWS about the Service Instance that is using it - this is where the idea of multiple registries breaks down right now. This will require much more community discussion, but I think there is one possible solution that minimizes the "pain" - this is just an idea for discussion, not an RFC :-) Many years ago, largely with an eye to better supporting the PlaNet registry at MIPS - they were registering their own objects in their own ontologies - I started moving the codebase toward an LSID-based naming system for the ontology nodes; this allows secondary registries to register new ontology nodes under their own LSID authorities. This doesn't entirely solve the problem, since any registry can use any other registries Objects, Namespaces, and Services regardless of the LSID authority under which they were registered, but it does give the registry a way of detecting which Ontology nodes "belong to it", and possibly querying (through LSID resolution) other registries to retrieve information about foreign Ontology nodes. I'm not convinced that this is a "good" solution...in fact (using Phillip Lord's Name in vain - hehehhehe... funny pun in there!) Phillip would say that an Ontology is only useful if it is *shared*, and so the idea of having multiple ontologies is dangerous from the get-go. So... yes... there's a lot of discussion required around how to support multiple registries, and in particular, how to support multiple ontologies. The ontology literature would suggest that we have built, for ourselves, an unsustainable architecture as soon as we allowed the ontologies to fork... that may or may not be true, but the solution certainly isn't obvious... > (which was, btw and so far, really the last one, at least regarding the > funds available from Vancouver, as I understand it) Correct for the moment. MOBY has just received a sizable award from Genome Canada for the next 3+ years, but this is specifically for code maintenance and tooling. There is no money for meetings in that pot, though there is no reason why we can't put together a meeting that is self-funded. Traditionally I have paid for much of the expense of hosting meetings here in Canada through the MOBY Genome Canada award, but that doesn't have to be the case if there is the need for a meeting. In any case, in the next couple of months there will be another competition announcement from Genome Canada, and I will be submitting an application to that competition that includes another pot of money to support developer conferences. Fingers crossed! > Can we just postpone implementation of the > individual (public) registry policies and first to discuss how to make the > various registries federated? I am not opposed to this. Though the agent will start running in a few days, Eddie has agreed not to activate the service deregistration function for at least three months so that everyone can get used to the feeling of "being crawled". If the community feeling remains strong against the policies I have documented for "my" MOBY Central instance, the objections should be raised either to me personally, or publicly, and discussed. I do, however, have several comments with regard to my responsibilities to the MOBY community, to my granting agency, and to my own research endeavours (which is where MOBY started, and it continues to be a primary domain of *research* in my laboratory). Genome Canada funded MOBY to be developed as a platform of interoperability for other Genome Canada projects. Period. This is a responsibility that I cannot fail in, since it is the primary responsibility I undertook by accepting the award, so I am somewhat limited in my freedom. One possibility would be to support a "public" registry that was a free-for-all and largely uncurated, and to support a second, curated registry to support only the Genome Canada projects, much like the INB has done. Unfortunately, I was only awarded funds for a single server - that is the server that is currently running "my" MOBY Central - so this option makes me a bit uncomfortable. Moreover, as Paul, among others, have pointed out: "Right now in the registry if I send a generic object I get over a hundred services back, almost none of which will actually consume the object without dying a horrible death." (Gordon, Feb 17th). MOBY Central has become increasingly useless over the past couple of years as it got filled with junk, badly registered services, dead services, "localhost" services, test services, and all manner of other registration artifacts. This week, for the first time in over a year, I started up Gbrowse Moby and was (more or less) ACTUALLY ABLE TO SURF MOBY DATA!! It was heavenly! Because of the curatorial policy that I enforced - after public warnings that I was about to do so - "my" registry suddenly became a useful resource not only to Genome Canada, but also to the wider community. Some might argue about what "useful" means, but I think that "doing what it was built to do" is a pretty good measure... and, frankly, I cannot interpret the word any other way, since I have a responsibility to my funding agency to generate something useful. The curation policy I have posted does not change the API. It is only a policy, and though policies can be debated, I don't think that any of the other registry hosts would want to be told how to curate "their" registries. Granted, the registry that I host is a unique resource in that it is the only (??) public registry; I take that responsibility seriously as well! However, that responsibility (surely?!) also requires that I try to make the registry useful to the majority of the community users; we, as a community, can discuss whether the policy I proposed goes too far - though I reserve the right to make the final decision on "my" registry - however, my experience of using MOBY Central this week suggests to me that this policy only made the public resource better. That's my open-kimono. Opinions always welcome, 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 "For most of this century we have viewed communications as a conduit, a pipe between physical locations on the planet. What's happened now is that the conduit has become so big and interesting that communication has become more than a conduit, it has become a destination in its own right..." Paul Saffo - Director, Institute for the Future From duncan.hull at cs.man.ac.uk Thu Mar 2 13:27:22 2006 From: duncan.hull at cs.man.ac.uk (Duncan Hull) Date: Thu, 02 Mar 2006 18:27:22 +0000 Subject: [MOBY-dev] Printing shorthand BioMOBY RDF notation In-Reply-To: References: Message-ID: <4407390A.2090802@cs.man.ac.uk> Hello Can anyone recommend any tools for printing shorthand notation of BioMOBY RDF service descriptions, e.g. that output from http://mobycentral.icapture.ubc.ca/LSID_resolver.html ? I was thinking of N3 [1] or something similar, but maybe someone on moby-dev knows better? Fitting all that lovely RDF onto a sheet of A4 paper is a challenging task...so I could use a shorthand notation. Duncan [1] http://infomesh.net/2001/cwm/ looks very old -- Duncan Hull http://www.cs.man.ac.uk/~hulld/ Phone: +44 (0) 161 275 0677 From gss at ncgr.org Thu Mar 2 14:17:20 2006 From: gss at ncgr.org (Gary Schiltz) Date: Thu, 02 Mar 2006 12:17:20 -0700 Subject: [MOBY-dev] Printing shorthand BioMOBY RDF notation In-Reply-To: <4407390A.2090802@cs.man.ac.uk> References: <4407390A.2090802@cs.man.ac.uk> Message-ID: <440744C0.2020201@ncgr.org> If I submit the first example LSID ( urn:lsid:biomoby.org:servicetype:Retrieval) on the page, I get the following as RDF: The base retrieval type Retrieval a base Service class, never instantiated Service I can then paste that RDF into the converter at http://www.semanticmoby.org/developer/dev-tools.jsp, select RDF/XML as input format and N3 as output format, press the Convert Graph button, and get the following N3: @prefix mobyService: . @prefix mobyObject: . @prefix mobyNamespace: . @prefix serviceInstances: . @prefix moby: . @prefix rdfs: . @prefix rdf: . mobyService:Retrieval a rdfs:Class ; rdfs:comment "The base retrieval type"@en ; rdfs:label "Retrieval"@en ; rdfs:subClassOf mobyService:Service . mobyService:Service a rdfs:Class ; rdfs:comment "a base Service class, never instantiated"@en ; rdfs:label "Service"@en . Not many fewer lines, but the N3 is to my eyes more readable. // Gary Duncan Hull wrote: > Hello > > Can anyone recommend any tools for printing shorthand notation of > BioMOBY RDF service descriptions, e.g. that output from > http://mobycentral.icapture.ubc.ca/LSID_resolver.html ? > > I was thinking of N3 [1] or something similar, but maybe someone on > moby-dev knows better? > > Fitting all that lovely RDF onto a sheet of A4 paper is a challenging > task...so I could use a shorthand notation. > > Duncan > > [1] http://infomesh.net/2001/cwm/ looks very old > > From markw at illuminae.com Thu Mar 2 16:21:30 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 02 Mar 2006 13:21:30 -0800 Subject: [MOBY-dev] [moby] Printing shorthand BioMOBY RDF notation In-Reply-To: <4407390A.2090802@cs.man.ac.uk> References: <4407390A.2090802@cs.man.ac.uk> Message-ID: <1141334490.16059.0.camel@bioinfo.icapture.ubc.ca> http://www.mindswap.org/2002/rdfconvert/ M On Thu, 2006-03-02 at 18:27 +0000, Duncan Hull wrote: > Hello > > Can anyone recommend any tools for printing shorthand notation of > BioMOBY RDF service descriptions, e.g. that output from > http://mobycentral.icapture.ubc.ca/LSID_resolver.html ? > > I was thinking of N3 [1] or something similar, but maybe someone on > moby-dev knows better? > > Fitting all that lovely RDF onto a sheet of A4 paper is a challenging > task...so I could use a shorthand notation. > > Duncan > > [1] http://infomesh.net/2001/cwm/ looks very old > -- -- 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 "For most of this century we have viewed communications as a conduit, a pipe between physical locations on the planet. What's happened now is that the conduit has become so big and interesting that communication has become more than a conduit, it has become a destination in its own right..." Paul Saffo - Director, Institute for the Future From duncan.hull at cs.man.ac.uk Thu Mar 2 17:41:56 2006 From: duncan.hull at cs.man.ac.uk (Duncan Hull) Date: Thu, 02 Mar 2006 22:41:56 +0000 Subject: [MOBY-dev] [moby] Printing shorthand BioMOBY RDF notation In-Reply-To: <1141334490.16059.0.camel@bioinfo.icapture.ubc.ca> References: <4407390A.2090802@cs.man.ac.uk> <1141334490.16059.0.camel@bioinfo.icapture.ubc.ca> Message-ID: <440774B4.7090701@cs.man.ac.uk> Mark Wilkinson wrote: >http://www.mindswap.org/2002/rdfconvert/ > > great, thanks mark. I take back all the nasty things I've said about RDF :) Sesame does a pretty good job of this kind of thing too... http://www.openrdf.org/ Duncan -- Duncan Hull http://www.cs.man.ac.uk/~hulld/ Phone: +44 (0) 161 275 0677 From edward.kawas at gmail.com Thu Mar 2 18:24:03 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 2 Mar 2006 15:24:03 -0800 Subject: [MOBY-dev] RDF agent test page Message-ID: <002c01c63e50$65a11880$6500a8c0@notebook> Hi, Recently on the test registry, I have deployed the agent for, believe it or not, testing purposes. I would be very interested in having people try it out. Being a test registry, services will be removed, modified, etc as the agent encounters orphans, modifications, etc. Email is also used by the agent and so please make sure that if you are going to call the agent over that you use your email address in the contact email part of a service description. The endpoint for the registry is: http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl The URI for the registry is: http://bioinfo.icapture.ubc.ca/MOBY/Central I deployed a servlet that given a url to an RDF document that describes one or more services, parses the services into human readable formatted text and also details any errors that the agent, not the registry, has found with any particular service. This servlet is located at: http://bioinfo.icapture.ubc.ca/ekawas/agent/RDFAgent_test.html Some urls that you can use for testing the test servlet are: http://bioinfo.icapture.ubc.ca/ekawas/services/parseBlastText.rdf (contains 1 service) http://mobycentral.icapture.ubc.ca/localServices.rdf (contains >20 services?) http://bioinfo.icapture.ubc.ca/ekawas/services/blastDragon.xml http://bioinfo.icapture.ubc.ca/ekawas/services/parseBlast.xml ('valid' RDF, invalid w.r.t moby) http://biomoby.org/RESOURCES/MOBY-S/ServiceInstances (contains all of the services in the mobycentral registry - might cause browser to timeout) Feel free to use the LSID resolver to gather more examples. You can download the RDFs and modify them as you see fit. Then you can place them on a web server and call the agent to you. If you are interested in testing the correctness and validity of your RDF document strictly in terms of RDF, the w3c have an excellent resource in the RDF Validator. This validator is located at: http://www.w3.org/RDF/Validator/ Those 2 resources should take any pain out of RDF and the transition to the agent. In addition to these methods of interacting with the agent, you can perfrom registerService calls on this test registry specifying no more than a signatureURL and the agent will be called over to inspect that url. Any new services in that url will be registered, modified services will be re-registered and missing services (ones the agent thinks should be there) will be deregistered. I will have an agent html page discussing what the agent is, how to install the agent, configuring the agent, etc up soon. Thanks, Eddie From duncan.hull at cs.man.ac.uk Fri Mar 3 04:39:00 2006 From: duncan.hull at cs.man.ac.uk (Duncan Hull) Date: Fri, 03 Mar 2006 09:39:00 +0000 Subject: [MOBY-dev] Layering OWL on top of BioMOBY RDF descriptions In-Reply-To: <440744C0.2020201@ncgr.org> References: <4407390A.2090802@cs.man.ac.uk> <440744C0.2020201@ncgr.org> Message-ID: <44080EB4.3000701@cs.man.ac.uk> Gary Schiltz wrote: >I can then paste that RDF into the converter at http://www.semanticmoby.org/developer/dev-tools.jsp > > ...and thanks Gary too... Actually, while we're on the subject of RDF...BioMOBY has done a great job of demonstrating some of the strengths and limitations of using RDF to represent bioinformatics service metadata. The next layer in the semantic web cake [1] is to add OWL descriptions. Semantic MOBY, BioMOBY and myGrid have all made various moves in this direction. With OWL, we get more expressivity and the ability to reason over our services, in particular we possibly get more "bang for our buck", specifically: 1. We can distinguish between classes and instances (individuals) 2. Properties won't be able to have properties any more (something RDF/RDFS lets you do) 3. We can distinguish between language constructors and ontology vocabulary 4. We have localised range and domain constraints 5. We get existence/cardinality constraints 6. We get transitive, inverse and symmetrical properties 7. We get better reasoning support using "native" reasoners (see [2,3] for details) So, which bits of this rich service metadata are going to be a) realist to capture? b) useful for biologists and bioinformaticians describing and finding services? c) useful for registry providers to manage their services? I realise these are all very open questions, but I'd be interested to know what moby-devvers think... Duncan [1] http://www.cs.man.ac.uk/~horrocks/Publications/download/2005/HPPH05.pdf [2] http://www.cs.man.ac.uk/~horrocks/Teaching/cs646/Slides/ontologies.pdf (see problems with RDF/RDFS) [3] http://www.cs.man.ac.uk/~horrocks/Publications/download/2003/HoPH03a.pdf -- Duncan Hull http://www.cs.man.ac.uk/~hulld/ Phone: +44 (0) 161 275 0677 From Pieter.Neerincx at wur.nl Fri Mar 3 09:02:23 2006 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Fri, 3 Mar 2006 15:02:23 +0100 Subject: [MOBY-dev] Lengthy commentary on registry policies and my own responsibilities In-Reply-To: <1141230616.30896.64.camel@bioinfo.icapture.ubc.ca> References: <1141230616.30896.64.camel@bioinfo.icapture.ubc.ca> Message-ID: <6357450E-D6DF-40A9-8EC2-6DC07B77C69D@wur.nl> Hi, On 1-Mar-2006, at 5:30 PM, Mark Wilkinson wrote: > On Wed, 2006-03-01 at 10:24 +0000, Martin Senger wrote: >> You might have noticed that Mark (silently? :-)) created a new page Well it's a publicly available page and not something hidden, encoded, deeply buried inside a lot of subfolders of the CVS. I spotted the page and was actually pretty happy with it. The official registry is only useful if most of the services in it actually work. So in my opinion it should be either manually curated or the services should be frequently checked in an automated fashion to make sure they work as registered / advertised. > > > I quote from my message of Feb 21st: > > "The policy of the MOBY Central registry at iCAPTURE is currently > being drawn-up. A first draft is available (click on Project Docs on > the right side of the moby homepage) for comment" > > > >> But it may be done slightly too silently to let me feel >> comfortable >> (sorry, Mark, this is just my feeling, I cannot help it). > > Public discussion is welcome; your opinion, in particular, is > **always** valued! > > >> The strength of >> Biomoby was always in sharing - and if we suddenly starts to have >> many >> registries this strenghts may decreased. > > I **strongly** support this statement!!!! I second that. So after a lot of testing I registered my first publicly available services in the official Central 2 days ago :). On a side note: how often is that graph with the "World wide distribution of BioMOBY services" on the webside updated? I'v been refreshing that page many times a day like a little kid waiting for birthday presents, but so far nothing popped up :(. > The reality is, > unfortunately, not in line with this vision. I host a registry, you > host a registry at IRRI, MIPS hosts a registry, INB hosts a registry, > there is a (dead?) registry at the University of Queensland, I host a > second registry here specifically for TAIR, a third for our local > services here at iCAPTURE, and yet a fourth here that allows me to > continue doing interoperability research, since the new RFC policies > around MOBY development are not conducive to a research environment. I have another 2 registries here at the WUR, but exclusively for testing and debugging. I didn't want to mess up Mark's public Central with my experimental stuff. Multiple registries are fine if they have different specific functions. Having services that were meant to be publicly available from multiple registries would be good too for example for redundancy. In case one of those registries is down you can simple use another. But the tricky part is that multiple registries will easily get out of sync, both with regard to the registered services as with regard to the version of the API they are running. If that happens everybody will not trust the registries already available and create their own. In the end we'll all be licking our own lollypops and the idea of interoperability will be gone. > > >> On the other hand, I feel that we actually *need* more registries, >> perhaps with different purposes, and with the different level of >> curation. >> But before starting to list them we should - here my 2cs go in - >> think >> first about federation of the registries, about an API how to >> access more >> registries etc. > > > Absolutely! For the past year I have been slowly (yes, silently ;-) ) > moving the MOBY Central Perl code to a point where we might be in a > position to support multiple registries more easily once we decide how > to do so. The codebase was **strongly** tied to the concept of a > single > registry that was aware of a single object ontology, a single service > ontology, and a single namespace ontology. In many ways it still is - > the ontology maintenance routines are hard-coded to prevent the > modification or removal of Objects, Services, and Namespaces that are > being used; however, that is only true if the registry itself KNOWS > about the Service Instance that is using it - this is where the > idea of > multiple registries breaks down right now. > > This will require much more community discussion, but I think there is > one possible solution that minimizes the "pain" - this is just an idea > for discussion, not an RFC :-) > > Many years ago, largely with an eye to better supporting the PlaNet > registry at MIPS - they were registering their own objects in their > own > ontologies - I started moving the codebase toward an LSID-based naming > system for the ontology nodes; this allows secondary registries to > register new ontology nodes under their own LSID authorities. This > doesn't entirely solve the problem, since any registry can use any > other > registries Objects, Namespaces, and Services regardless of the LSID > authority under which they were registered, but it does give the > registry a way of detecting which Ontology nodes "belong to it", and > possibly querying (through LSID resolution) other registries to > retrieve > information about foreign Ontology nodes. > > I'm not convinced that this is a "good" solution...in fact (using > Phillip Lord's Name in vain - hehehhehe... funny pun in there!) > Phillip > would say that an Ontology is only useful if it is *shared*, and so > the > idea of having multiple ontologies is dangerous from the get-go. > > So... yes... there's a lot of discussion required around how to > support > multiple registries, and in particular, how to support multiple > ontologies. The ontology literature would suggest that we have built, > for ourselves, an unsustainable architecture as soon as we allowed the > ontologies to fork... that may or may not be true, but the solution > certainly isn't obvious... > > >> (which was, btw and so far, really the last one, at least >> regarding the >> funds available from Vancouver, as I understand it) > > Correct for the moment. MOBY has just received a sizable award from > Genome Canada for the next 3+ years, but this is specifically for code > maintenance and tooling. There is no money for meetings in that pot, > though there is no reason why we can't put together a meeting that is > self-funded. Traditionally I have paid for much of the expense of > hosting meetings here in Canada through the MOBY Genome Canada award, > but that doesn't have to be the case if there is the need for a > meeting. > In any case, in the next couple of months there will be another > competition announcement from Genome Canada, and I will be > submitting an > application to that competition that includes another pot of money to > support developer conferences. Fingers crossed! > > >> Can we just postpone implementation of the >> individual (public) registry policies and first to discuss how to >> make the >> various registries federated? > > I am not opposed to this. Though the agent will start running in a > few > days, Eddie has agreed not to activate the service deregistration > function for at least three months so that everyone can get used to > the > feeling of "being crawled". If the community feeling remains strong > against the policies I have documented for "my" MOBY Central instance, > the objections should be raised either to me personally, or publicly, > and discussed. > > I do, however, have several comments with regard to my > responsibilities > to the MOBY community, to my granting agency, and to my own research > endeavours (which is where MOBY started, and it continues to be a > primary domain of *research* in my laboratory). > > Genome Canada funded MOBY to be developed as a platform of > interoperability for other Genome Canada projects. Period. Sure! But it's in the interest of the people in Genome Canada projects to be able to use services from other service providers as well. Look at it from this side: if Genome Canada funds a good BioMOBY Central they get to use lot's of services whose development they didn't have to fund for free! > This is a > responsibility that I cannot fail in, since it is the primary > responsibility I undertook by accepting the award, so I am somewhat > limited in my freedom. One possibility would be to support a "public" > registry that was a free-for-all and largely uncurated, and to > support a > second, curated registry to support only the Genome Canada projects, > much like the INB has done. Bad idea in my point of view. The free-for-all registry will be a mess in no time, so in the end no one will use it. Then if the people in Genome Canada want to benefit from services in the INB registry, those registries will have to run the same version of the interface. Currently the registration process already differs, because at the INB they request additional info. I think it's just a matter of time before multiple Centrals will be out of sync. What we need is one big public free curated Central. Maybe it could be mirrored for load balancing and fail-over, but that will only work if those Centrals are *perfect* mirrors. If people start to host "partial" mirrors or outdated mirrors it won't work. In that case everyone will go straight to the official server, because they don't trust the mirrors. > Unfortunately, I was only awarded funds for > a single server If hardware is an issue, I think we could easily run a Central on dedicated hardware over here at the WUR. I would have to ask my boss of course, but I think we would be happy to help out with either a perfect mirror of the official public BioMOBY Central or with a public 'feel free to experiment' test Central or both. But I will never run my own 'only available to WUR users' Central or one with a custom patched interface. > - that is the server that is currently running "my" MOBY > Central - so this option makes me a bit uncomfortable. > Moreover, as > Paul, among others, have pointed out: "Right now in the registry if I > send a generic object I get over a hundred services back, almost > none of > which will actually consume the object without dying a horrible > death." (Gordon, Feb 17th). MOBY Central has become increasingly > useless > over the past couple of years as it got filled with junk, badly > registered services, dead services, "localhost" services, test > services, > and all manner of other registration artifacts. This week, for the > first time in over a year, I started up Gbrowse Moby and was (more or > less) ACTUALLY ABLE TO SURF MOBY DATA!! It was heavenly! Because of > the curatorial policy that I enforced - after public warnings that > I was > about to do so - "my" registry suddenly became a useful resource not > only to Genome Canada, but also to the wider community. Some might > argue about what "useful" means, but I think that "doing what it was > built to do" is a pretty good measure... and, frankly, I cannot > interpret the word any other way, since I have a responsibility to my > funding agency to generate something useful. > > The curation policy I have posted does not change the API. It is > only a > policy, and though policies can be debated, I don't think that any of > the other registry hosts would want to be told how to curate "their" > registries. Granted, the registry that I host is a unique resource in > that it is the only (??) public registry; I take that responsibility > seriously as well! However, that responsibility (surely?!) also > requires that I try to make the registry useful to the majority of the > community users; we, as a community, can discuss whether the policy I > proposed goes too far I think it's a fair policy and it should have been like this form the start! > - though I reserve the right to make the final > decision on "my" registry - however, my experience of using MOBY > Central > this week suggests to me that this policy only made the public > resource > better. Definitely! I'm glad the policy is there and I think Mark is doing a fine job as the guardian of the only public Central we have. Cheers, Pi > That's my open-kimono. > > Opinions always welcome, > > 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 > > "For most of this century we have viewed communications as a conduit, > a pipe between physical locations on the planet. > What's happened now is that the conduit has become so big and > interesting > that communication has become more than a conduit, > it has become a destination in its own right..." > > Paul Saffo - Director, Institute for the Future > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at biomoby.org > http://biomoby.org/mailman/listinfo/moby-dev Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 060 fax: 0317-483 584 mobile: 06-143 66 783 pieter.neerincx at wur.nl From markw at illuminae.com Fri Mar 3 11:11:20 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 03 Mar 2006 08:11:20 -0800 Subject: [MOBY-dev] [moby] Re: Lengthy commentary on registry policies and my own responsibilities In-Reply-To: <6357450E-D6DF-40A9-8EC2-6DC07B77C69D@wur.nl> References: <1141230616.30896.64.camel@bioinfo.icapture.ubc.ca> <6357450E-D6DF-40A9-8EC2-6DC07B77C69D@wur.nl> Message-ID: <1141402280.6637.40.camel@bioinfo.icapture.ubc.ca> On Fri, 2006-03-03 at 15:02 +0100, Pieter Neerincx wrote: > a side note: how often is that graph with the "World wide > distribution of BioMOBY services" on the webside updated? I'v been > refreshing that page many times a day like a little kid waiting for > birthday presents, but so far nothing popped up :(. It should be updating every few hours... I'll check the cron and see if something is broken. 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 "For most of this century we have viewed communications as a conduit, a pipe between physical locations on the planet. What's happened now is that the conduit has become so big and interesting that communication has become more than a conduit, it has become a destination in its own right..." Paul Saffo - Director, Institute for the Future From markw at illuminae.com Fri Mar 3 11:14:16 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 03 Mar 2006 08:14:16 -0800 Subject: [MOBY-dev] [moby] Re: Lengthy commentary on registry policies and my own responsibilities In-Reply-To: <6357450E-D6DF-40A9-8EC2-6DC07B77C69D@wur.nl> References: <1141230616.30896.64.camel@bioinfo.icapture.ubc.ca> <6357450E-D6DF-40A9-8EC2-6DC07B77C69D@wur.nl> Message-ID: <1141402456.6637.42.camel@bioinfo.icapture.ubc.ca> > I think it's a fair policy and it should have been like this form the > start! Thanks :-) > Definitely! I'm glad the policy is there and I think Mark is doing a > fine job as the guardian of the only public Central we have. And thanks again!! :-) 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 "For most of this century we have viewed communications as a conduit, a pipe between physical locations on the planet. What's happened now is that the conduit has become so big and interesting that communication has become more than a conduit, it has become a destination in its own right..." Paul Saffo - Director, Institute for the Future From markw at illuminae.com Fri Mar 3 11:21:30 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 03 Mar 2006 08:21:30 -0800 Subject: [MOBY-dev] [moby] Re: Lengthy commentary on registry policies and my own responsibilities In-Reply-To: <6357450E-D6DF-40A9-8EC2-6DC07B77C69D@wur.nl> References: <1141230616.30896.64.camel@bioinfo.icapture.ubc.ca> <6357450E-D6DF-40A9-8EC2-6DC07B77C69D@wur.nl> Message-ID: <1141402890.6637.51.camel@bioinfo.icapture.ubc.ca> > Sure! But it's in the interest of the people in Genome Canada > projects to be able to use services from other service providers as > well. Absolutely, and they are well aware of that! Luckily, the decisions that are best for them, are (usually, and IMO) also best for the rest of us, since we all have the same goal in mind :-) > Maybe it could be mirrored for load > balancing and fail-over, but that will only work if those Centrals > are *perfect* mirrors. If people start to host "partial" mirrors or > outdated mirrors it won't work. In that case everyone will go > straight to the official server, because they don't trust the mirrors. We discussed mirroring at the last meeting, and Phil and Pinar (@myGrid), Eddie and I discussed it at length again the last time we were in Manchester. Once we have an agent-based registration/deregistration mechanism in place, and everyone has SignatureURLs that resolve to RDF, the problem of keeping registries synchronized is (almost) trivial! Just ask one MOBY Central for all of it's signature URL's, hand those URL's to the agent of another registry, and let it crawl! Voila!! There still needs to be some hierarchy in there, and blah blah, but the crux of the problem is solved by the RDF signature... I think... we haven't DONE it yet, so there may be nefarious problems in there that aren't obvious from a superficial examination of the problem... Gotta run! Interviews to do... 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 "For most of this century we have viewed communications as a conduit, a pipe between physical locations on the planet. What's happened now is that the conduit has become so big and interesting that communication has become more than a conduit, it has become a destination in its own right..." Paul Saffo - Director, Institute for the Future From markw at illuminae.com Fri Mar 3 11:27:16 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 03 Mar 2006 08:27:16 -0800 Subject: [MOBY-dev] [moby] Layering OWL on top of BioMOBY RDF descriptions In-Reply-To: <44080EB4.3000701@cs.man.ac.uk> References: <4407390A.2090802@cs.man.ac.uk> <440744C0.2020201@ncgr.org> <44080EB4.3000701@cs.man.ac.uk> Message-ID: <1141403236.6637.57.camel@bioinfo.icapture.ubc.ca> On Fri, 2006-03-03 at 09:39 +0000, Duncan Hull wrote: > I realise these are all very open questions, but I'd be interested to > know what moby-devvers think... Outside of the public eye, I have three students right now working on OWLifying all aspects of MOBY, and making a clear separation of the models from the data and service instances. We are expecting to see some REALLY interesting behaviours in the context of tools like Ben & Clarence's Ahab/Ishmael MOBY browsers - DL-reasoned discovery of unexpected, but applicable, services after DL-reasoned *integration* and *recombination* of multiple data-types from multiple MOBY service executions into new data-types. Fun!! 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 "For most of this century we have viewed communications as a conduit, a pipe between physical locations on the planet. What's happened now is that the conduit has become so big and interesting that communication has become more than a conduit, it has become a destination in its own right..." Paul Saffo - Director, Institute for the Future From ddg at ncgr.org Fri Mar 3 12:07:30 2006 From: ddg at ncgr.org (Damian Gessler) Date: Fri, 3 Mar 2006 10:07:30 -0700 Subject: [MOBY-dev] Layering OWL on top of BioMOBY RDF descriptions References: <4407390A.2090802@cs.man.ac.uk><440744C0.2020201@ncgr.org> <44080EB4.3000701@cs.man.ac.uk> Message-ID: <00c501c63ee4$f4a04e90$674413ac@ncgr.org> Hi Duncan, > The next layer in the semantic web cake [1] is to add OWL descriptions. Totally on board with you here. To see how it's working, go to www.semanticmoby.org and type in "dna". You'll see that term retrieves, in a Google-like manner, four bioinformatic service providers. Click on the RDF icon by their name and you'll see the OWL Resource Description Graph (essentially the equivalent of a semantically-wise WSDL, though completely unrelated in implementation with WSDL). [Note: your browser may be set to any number of alternative display modes for RDF; do a View Source if it isn't easily readable). You can try the Legume Information Network to see how resources can be pipelined. For shared ontologies--the meat of the middle layer of how resources describe themselves and thus how they are discovered and engaged--a few a populating at http://ontologies.ncgr.org. We're currently lining up conversions of SO and SOFA (Sequence Ontology), POC (Plant Ontology), and TO (Trait Ontology). D. ----- Original Message ----- From: "Duncan Hull" To: "Core developer announcements" Sent: Friday, March 03, 2006 2:39 AM Subject: [MOBY-dev] Layering OWL on top of BioMOBY RDF descriptions > Gary Schiltz wrote: > >>I can then paste that RDF into the converter at >>http://www.semanticmoby.org/developer/dev-tools.jsp >> >> > ...and thanks Gary too... > > Actually, while we're on the subject of RDF...BioMOBY has done a great > job of demonstrating some of the strengths and limitations of using RDF > to represent bioinformatics service metadata. > > The next layer in the semantic web cake [1] is to add OWL descriptions. > Semantic MOBY, BioMOBY and myGrid have all made various moves in this > direction. With OWL, we get more expressivity and the ability to reason > over our services, in particular we possibly get more "bang for our > buck", specifically: > > 1. We can distinguish between classes and instances (individuals) > 2. Properties won't be able to have properties any more (something > RDF/RDFS lets you do) > 3. We can distinguish between language constructors and ontology > vocabulary > 4. We have localised range and domain constraints > 5. We get existence/cardinality constraints > 6. We get transitive, inverse and symmetrical properties > 7. We get better reasoning support using "native" reasoners > > (see [2,3] for details) > > So, which bits of this rich service metadata are going to be > a) realist to capture? > b) useful for biologists and bioinformaticians describing and finding > services? > c) useful for registry providers to manage their services? > > I realise these are all very open questions, but I'd be interested to > know what moby-devvers think... > > Duncan > > [1] > http://www.cs.man.ac.uk/~horrocks/Publications/download/2005/HPPH05.pdf > [2] > http://www.cs.man.ac.uk/~horrocks/Teaching/cs646/Slides/ontologies.pdf > (see problems with RDF/RDFS) > [3] > http://www.cs.man.ac.uk/~horrocks/Publications/download/2003/HoPH03a.pdf > > -- > Duncan Hull > http://www.cs.man.ac.uk/~hulld/ > Phone: +44 (0) 161 275 0677 > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at biomoby.org > http://biomoby.org/mailman/listinfo/moby-dev > From duncan.hull at cs.man.ac.uk Sat Mar 4 04:21:34 2006 From: duncan.hull at cs.man.ac.uk (Duncan Hull) Date: Sat, 04 Mar 2006 09:21:34 +0000 Subject: [MOBY-dev] Semantic Web Services: Blowin' in the wind In-Reply-To: <00c501c63ee4$f4a04e90$674413ac@ncgr.org> References: <4407390A.2090802@cs.man.ac.uk><440744C0.2020201@ncgr.org> <44080EB4.3000701@cs.man.ac.uk> <00c501c63ee4$f4a04e90$674413ac@ncgr.org> Message-ID: <44095C1E.4080607@cs.man.ac.uk> Thanks Damian and Mark for you replies. I suppose some of the answers are blowin' in the wind :) -- Duncan Hull http://www.cs.man.ac.uk/~hulld/ Phone: +44 (0) 161 275 0677 From senger at ebi.ac.uk Sun Mar 5 16:49:03 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Sun, 5 Mar 2006 21:49:03 +0000 (GMT) Subject: [MOBY-dev] checking services Message-ID: Hi all, Within the GCP project, I have developed a small program that can check services with testing input data. I know that we have been talking about having such inputs in metadata, and I am sure it will soon come. But we needed something running now, so I have made this small project (using libraries in jMoby). It is easy to set it up (you still need to find what input data are needed) if you wish to have it run on your set of services. The program can be run from a command-line (we use it as a cron-job to check that our services are responding), or there is a web interface (my first play with Ajax :-) ). The documentation (with links to running examples, and with instructions where you can get it) is available at http://mobycentral.icapture.ubc.ca:8090/mobyenv/ (and mirrored at http://www.iris.irri.org/mobyenv/). I will be very glad to receive any comments and suggestions for improvement. Thanks, and with regards, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger consulting for: International Rice Research Institute Biometrics and Bioinformatics Unit DAPO BOX 7777, Metro Manila Philippines, phone: +63-2-580-5600 (ext.2324) From Pieter.Neerincx at wur.nl Mon Mar 6 07:03:16 2006 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Mon, 6 Mar 2006 13:03:16 +0100 Subject: [MOBY-dev] Front page messed up? In-Reply-To: <1141403236.6637.57.camel@bioinfo.icapture.ubc.ca> References: <4407390A.2090802@cs.man.ac.uk> <440744C0.2020201@ncgr.org> <44080EB4.3000701@cs.man.ac.uk> <1141403236.6637.57.camel@bioinfo.icapture.ubc.ca> Message-ID: <5D600A84-B90E-49CF-B477-D3D498E7E3F8@wur.nl> Hi all, On my machines (both Linux and Mac OS X and several different browsers) it looks like the BioMOBY website is messed up (only the front page). Is anybody working on it or do I smell something fishy? Cheers, Pi On 3-Mar-2006, at 5:27 PM, Mark Wilkinson wrote: > On Fri, 2006-03-03 at 09:39 +0000, Duncan Hull wrote: > >> I realise these are all very open questions, but I'd be interested to >> know what moby-devvers think... > > Outside of the public eye, I have three students right now working on > OWLifying all aspects of MOBY, and making a clear separation of the > models from the data and service instances. We are expecting to see > some REALLY interesting behaviours in the context of tools like Ben & > Clarence's Ahab/Ishmael MOBY browsers - DL-reasoned discovery of > unexpected, but applicable, services after DL-reasoned > *integration* and > *recombination* of multiple data-types from multiple MOBY service > executions into new data-types. > > Fun!! > > 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 > > "For most of this century we have viewed communications as a conduit, > a pipe between physical locations on the planet. > What's happened now is that the conduit has become so big and > interesting > that communication has become more than a conduit, > it has become a destination in its own right..." > > Paul Saffo - Director, Institute for the Future > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at biomoby.org > http://biomoby.org/mailman/listinfo/moby-dev Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 060 fax: 0317-483 584 mobile: 06-143 66 783 pieter.neerincx at wur.nl From markw at illuminae.com Mon Mar 6 11:37:55 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Mon, 06 Mar 2006 08:37:55 -0800 Subject: [MOBY-dev] [moby] Front page messed up? In-Reply-To: <5D600A84-B90E-49CF-B477-D3D498E7E3F8@wur.nl> References: <4407390A.2090802@cs.man.ac.uk> <440744C0.2020201@ncgr.org> <44080EB4.3000701@cs.man.ac.uk> <1141403236.6637.57.camel@bioinfo.icapture.ubc.ca> <5D600A84-B90E-49CF-B477-D3D498E7E3F8@wur.nl> Message-ID: <1141663075.17702.24.camel@bioinfo.icapture.ubc.ca> Can anyone else confirm this? I was working on the main page last night. It renders correctly on both of my machines in both Opera and IE browsers... but that doesn't mean there isn't something wrong :-) M On Mon, 2006-03-06 at 13:03 +0100, Pieter Neerincx wrote: > Hi all, > > On my machines (both Linux and Mac OS X and several different > browsers) it looks like the BioMOBY website is messed up (only the > front page). Is anybody working on it or do I smell something fishy? > > Cheers, > > Pi > > On 3-Mar-2006, at 5:27 PM, Mark Wilkinson wrote: > > > On Fri, 2006-03-03 at 09:39 +0000, Duncan Hull wrote: > > > >> I realise these are all very open questions, but I'd be interested to > >> know what moby-devvers think... > > > > Outside of the public eye, I have three students right now working on > > OWLifying all aspects of MOBY, and making a clear separation of the > > models from the data and service instances. We are expecting to see > > some REALLY interesting behaviours in the context of tools like Ben & > > Clarence's Ahab/Ishmael MOBY browsers - DL-reasoned discovery of > > unexpected, but applicable, services after DL-reasoned > > *integration* and > > *recombination* of multiple data-types from multiple MOBY service > > executions into new data-types. > > > > Fun!! > > > > 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 > > > > "For most of this century we have viewed communications as a conduit, > > a pipe between physical locations on the planet. > > What's happened now is that the conduit has become so big and > > interesting > > that communication has become more than a conduit, > > it has become a destination in its own right..." > > > > Paul Saffo - Director, Institute for the Future > > > > _______________________________________________ > > MOBY-dev mailing list > > MOBY-dev at biomoby.org > > http://biomoby.org/mailman/listinfo/moby-dev > > > Wageningen University and Research centre (WUR) > Laboratory of Bioinformatics > Transitorium (building 312) room 1034 > Dreijenlaan 3 > 6703 HA Wageningen > The Netherlands > phone: 0317-483 060 > fax: 0317-483 584 > mobile: 06-143 66 783 > pieter.neerincx at wur.nl > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at biomoby.org > http://biomoby.org/mailman/listinfo/moby-dev -- -- 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 "For most of this century we have viewed communications as a conduit, a pipe between physical locations on the planet. What's happened now is that the conduit has become so big and interesting that communication has become more than a conduit, it has become a destination in its own right..." Paul Saffo - Director, Institute for the Future From edward.kawas at gmail.com Mon Mar 6 11:42:20 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 6 Mar 2006 08:42:20 -0800 Subject: [MOBY-dev] [moby] Front page messed up? In-Reply-To: <1141663075.17702.24.camel@bioinfo.icapture.ubc.ca> Message-ID: <000801c6413c$f1493db0$6b00a8c0@notebook> Using firefox, the page doesn't look like it used to. More specifically, the flash map is now on the upper right of the page, the search box is in the middle of the page. The menu list (archives,categories, downloads, etc) is the footer of the page. On explorer, the page is viewed correctly. Eddie > -----Original Message----- > From: moby-dev-bounces at biomoby.org > [mailto:moby-dev-bounces at biomoby.org] On Behalf Of Mark Wilkinson > Sent: Monday, March 06, 2006 8:38 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] [moby] Front page messed up? > > Can anyone else confirm this? > > I was working on the main page last night. It renders > correctly on both of my machines in both Opera and IE > browsers... but that doesn't mean there isn't something wrong :-) > > M > > > > On Mon, 2006-03-06 at 13:03 +0100, Pieter Neerincx wrote: > > Hi all, > > > > On my machines (both Linux and Mac OS X and several different > > browsers) it looks like the BioMOBY website is messed up (only the > > front page). Is anybody working on it or do I smell something fishy? > > > > Cheers, > > > > Pi > > > > On 3-Mar-2006, at 5:27 PM, Mark Wilkinson wrote: > > > > > On Fri, 2006-03-03 at 09:39 +0000, Duncan Hull wrote: > > > > > >> I realise these are all very open questions, but I'd be > interested > > >> to know what moby-devvers think... > > > > > > Outside of the public eye, I have three students right > now working > > > on OWLifying all aspects of MOBY, and making a clear > separation of > > > the models from the data and service instances. We are > expecting to > > > see some REALLY interesting behaviours in the context of > tools like > > > Ben & Clarence's Ahab/Ishmael MOBY browsers - DL-reasoned > discovery > > > of unexpected, but applicable, services after DL-reasoned > > > *integration* and > > > *recombination* of multiple data-types from multiple MOBY service > > > executions into new data-types. > > > > > > Fun!! > > > > > > 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 > > > > > > "For most of this century we have viewed communications > as a conduit, > > > a pipe between physical locations on the planet. > > > What's happened now is that the conduit has become so big and > > > interesting > > > that communication has become more than a conduit, > > > it has become a destination in its own right..." > > > > > > Paul Saffo - Director, Institute for the Future > > > > > > _______________________________________________ > > > MOBY-dev mailing list > > > MOBY-dev at biomoby.org > > > http://biomoby.org/mailman/listinfo/moby-dev > > > > > > Wageningen University and Research centre (WUR) Laboratory of > > Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 > > 6703 HA Wageningen > > The Netherlands > > phone: 0317-483 060 > > fax: 0317-483 584 > > mobile: 06-143 66 783 > > pieter.neerincx at wur.nl > > > > > > > > _______________________________________________ > > MOBY-dev mailing list > > MOBY-dev at biomoby.org > > http://biomoby.org/mailman/listinfo/moby-dev > -- > > -- > 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 > > "For most of this century we have viewed communications as a conduit, > a pipe between physical locations on the planet. > What's happened now is that the conduit has become so big and > interesting > that communication has become more than a conduit, > it has become a destination in its own right..." > > Paul Saffo - Director, Institute for the Future > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at biomoby.org > http://biomoby.org/mailman/listinfo/moby-dev From akerhornou at imim.es Mon Mar 6 12:05:25 2006 From: akerhornou at imim.es (Arnaud Kerhornou) Date: Mon, 06 Mar 2006 18:05:25 +0100 Subject: [MOBY-dev] [moby] Front page messed up? In-Reply-To: <1141663075.17702.24.camel@bioinfo.icapture.ubc.ca> References: <4407390A.2090802@cs.man.ac.uk> <440744C0.2020201@ncgr.org> <44080EB4.3000701@cs.man.ac.uk> <1141403236.6637.57.camel@bioinfo.icapture.ubc.ca> <5D600A84-B90E-49CF-B477-D3D498E7E3F8@wur.nl> <1141663075.17702.24.camel@bioinfo.icapture.ubc.ca> Message-ID: <440C6BD5.5040808@imim.es> Hi Mark, I use Firefox, and compared to Opera it looks actually different. It seems better on Opera. Arnaud Mark Wilkinson wrote: > Can anyone else confirm this? > > I was working on the main page last night. It renders correctly on both > of my machines in both Opera and IE browsers... but that doesn't mean > there isn't something wrong :-) > > M > > > > On Mon, 2006-03-06 at 13:03 +0100, Pieter Neerincx wrote: > >> Hi all, >> >> On my machines (both Linux and Mac OS X and several different >> browsers) it looks like the BioMOBY website is messed up (only the >> front page). Is anybody working on it or do I smell something fishy? >> >> Cheers, >> >> Pi >> >> >> From markw at illuminae.com Mon Mar 6 14:37:15 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Mon, 06 Mar 2006 11:37:15 -0800 Subject: [MOBY-dev] [moby] Front page messed up? In-Reply-To: <440C6BD5.5040808@imim.es> References: <4407390A.2090802@cs.man.ac.uk> <440744C0.2020201@ncgr.org> <44080EB4.3000701@cs.man.ac.uk> <1141403236.6637.57.camel@bioinfo.icapture.ubc.ca> <5D600A84-B90E-49CF-B477-D3D498E7E3F8@wur.nl> <1141663075.17702.24.camel@bioinfo.icapture.ubc.ca> <440C6BD5.5040808@imim.es> Message-ID: <1141673835.17702.50.camel@bioinfo.icapture.ubc.ca> Does it render for everyone properly now? M On Mon, 2006-03-06 at 18:05 +0100, Arnaud Kerhornou wrote: > Hi Mark, > > I use Firefox, and compared to Opera it looks actually different. It > seems better on Opera. > > Arnaud > > Mark Wilkinson wrote: > > Can anyone else confirm this? > > > > I was working on the main page last night. It renders correctly on both > > of my machines in both Opera and IE browsers... but that doesn't mean > > there isn't something wrong :-) > > > > M > > > > > > > > On Mon, 2006-03-06 at 13:03 +0100, Pieter Neerincx wrote: > > > >> Hi all, > >> > >> On my machines (both Linux and Mac OS X and several different > >> browsers) it looks like the BioMOBY website is messed up (only the > >> front page). Is anybody working on it or do I smell something fishy? > >> > >> Cheers, > >> > >> Pi > >> > >> > >> > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at biomoby.org > http://biomoby.org/mailman/listinfo/moby-dev -- -- 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 "For most of this century we have viewed communications as a conduit, a pipe between physical locations on the planet. What's happened now is that the conduit has become so big and interesting that communication has become more than a conduit, it has become a destination in its own right..." Paul Saffo - Director, Institute for the Future From spies at ipk-gatersleben.de Tue Mar 7 02:48:38 2006 From: spies at ipk-gatersleben.de (Karl Spies) Date: Tue, 07 Mar 2006 08:48:38 +0100 Subject: [MOBY-dev] [moby] Front page messed up? In-Reply-To: <1141673835.17702.50.camel@bioinfo.icapture.ubc.ca> References: <4407390A.2090802@cs.man.ac.uk> <440744C0.2020201@ncgr.org> <44080EB4.3000701@cs.man.ac.uk> <1141403236.6637.57.camel@bioinfo.icapture.ubc.ca> <5D600A84-B90E-49CF-B477-D3D498E7E3F8@wur.nl> <1141663075.17702.24.camel@bioinfo.icapture.ubc.ca> <440C6BD5.5040808@imim.es> <1141673835.17702.50.camel@bioinfo.icapture.ubc.ca> Message-ID: <440D3AD6.2030209@ipk-gatersleben.de> It looks fine! Thanks Karl -- Karl Spies presently at: Research Group Bioinformatics Dept. of Cytogenetics Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Corrensstra?e 3, D-06466 Gatersleben Germany Phone: 039482-5-765 Adress: Windthorststra?e 27 06114 Halle (Saale) Germany Phone: 0345-5237334 email: spies at ipk-gatersleben.de From edward.kawas at gmail.com Tue Mar 7 11:40:18 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 7 Mar 2006 08:40:18 -0800 Subject: [MOBY-dev] The agent Message-ID: <000401c64205$d2735000$6500a8c0@notebook> Hi, I am just curious as to why no-one has tested the agent on the 'test' registry? Did my last email go un-noticed? Thanks, Eddie From duncan.hull at cs.man.ac.uk Wed Mar 8 09:08:28 2006 From: duncan.hull at cs.man.ac.uk (Duncan Hull) Date: Wed, 08 Mar 2006 14:08:28 +0000 Subject: [MOBY-dev] BioMOBY at the Oscars In-Reply-To: <000401c64205$d2735000$6500a8c0@notebook> References: <000401c64205$d2735000$6500a8c0@notebook> Message-ID: <440EE55C.6090003@cs.man.ac.uk> Dear moby-dev Whats currently the best example a service annotation in BioMOBY? The Oscar-winning gold-standard example of how it can and should be done using the full expressive power of namespace, object and service ontologies? Is this the best example? urn:lsid:biomoby.org:serviceinstance:bioinfo.icapture.ubc.ca,getSHound3DNeighboursFromGi Or are there better ones? Duncan -- Duncan Hull http://www.cs.man.ac.uk/~hulld/ Phone: +44 (0) 161 275 0677 From markw at illuminae.com Wed Mar 8 11:25:23 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 08 Mar 2006 08:25:23 -0800 Subject: [MOBY-dev] [moby] BioMOBY at the Oscars In-Reply-To: <440EE55C.6090003@cs.man.ac.uk> References: <000401c64205$d2735000$6500a8c0@notebook> <440EE55C.6090003@cs.man.ac.uk> Message-ID: <1141835123.16213.13.camel@bioinfo.icapture.ubc.ca> I don't know about "gold standard" - there are quite a few good ones in the registry these days... this service: urn:lsid:biomoby.org:serviceinstance:org.inab.upc,runFasty:2006-03-04T08-50-58Z captures most of the features of the RDF signature... does that help? What, specifically, are you looking for in the RDF? A comprehensive use of all of the predicates, or a "gold standard" for what we consider to be a well-documented (i.e. described) service? M On Wed, 2006-03-08 at 14:08 +0000, Duncan Hull wrote: > Dear moby-dev > > Whats currently the best example a service annotation in BioMOBY? The > Oscar-winning gold-standard example of how it can and should be done > using the full expressive power of namespace, object and service ontologies? > > Is this the best example? > urn:lsid:biomoby.org:serviceinstance:bioinfo.icapture.ubc.ca,getSHound3DNeighboursFromGi > > Or are there better ones? > > Duncan > -- -- Mark Wilkinson Asst. Professor, Dept. of Medical Genetics University of British Columbia PI in Bioinformatics, iCAPTURE Centre St. Paul's Hospital, Rm. 166, 1081 Burrard St. Vancouver, BC, V6Z 1Y6 tel: 604 682 2344 x62129 fax: 604 806 9274 "For most of this century we have viewed communications as a conduit, a pipe between physical locations on the planet. What's happened now is that the conduit has become so big and interesting that communication has become more than a conduit, it has become a destination in its own right..." Paul Saffo - Director, Institute for the Future From markw at illuminae.com Wed Mar 8 12:50:47 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 08 Mar 2006 09:50:47 -0800 Subject: [MOBY-dev] [moby] BioMOBY at the Oscars In-Reply-To: References: <000401c64205$d2735000$6500a8c0@notebook> <440EE55C.6090003@cs.man.ac.uk> <1141835123.16213.13.camel@bioinfo.icapture.ubc.ca> Message-ID: <1141840247.16213.34.camel@bioinfo.icapture.ubc.ca> You should talk to Eddie - I think he already has a taverna plugin that does that... M On Wed, 2006-03-08 at 16:51 +0000, Stian Soiland wrote: > On 8. mar. 2006, at 16:25, Mark Wilkinson wrote: > > > urn:lsid:biomoby.org:serviceinstance:org.inab.upc,runFasty: > > 2006-03-04T08-50-58Z > > This seems like an OK example, but maybe not a good match for our task. > > > does that help? What, specifically, are you looking for in the > > RDF? A > > comprehensive use of all of the predicates, or a "gold standard" for > > what we consider to be a well-documented (i.e. described) service? > > More specifically we are looking for good examples of semantic > descriptions that we can use for Taverna while developing semantic > linking/browsing/searching. In particular, descriptions of inputs and > outputs that are a bit more specific than "Object", so that we can > build GUI elements in Taverna for use cases like this rough description: > > a) Add a BioMoby processor into the Taverna workflow > b) Click on the process, find that the input is a string described as > a "GCP_Phenotype" > c) Browse a list of BioMoby services that can provide the output type > "GCP_Phenotype" > d) Add one of the services to the workflow and connect it > > Of course, limiting the search by "performs task NCBI_Blast" is also > nice. > > > So a good example would be one (or a few related) services that has > this kind of information specified and that actually works. :-) > -- -- 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 "For most of this century we have viewed communications as a conduit, a pipe between physical locations on the planet. What's happened now is that the conduit has become so big and interesting that communication has become more than a conduit, it has become a destination in its own right..." Paul Saffo - Director, Institute for the Future From duncan.hull at cs.man.ac.uk Wed Mar 8 12:54:07 2006 From: duncan.hull at cs.man.ac.uk (Duncan Hull) Date: Wed, 08 Mar 2006 17:54:07 +0000 Subject: [MOBY-dev] [moby] BioMOBY at the Oscars In-Reply-To: <1141835123.16213.13.camel@bioinfo.icapture.ubc.ca> References: <000401c64205$d2735000$6500a8c0@notebook> <440EE55C.6090003@cs.man.ac.uk> <1141835123.16213.13.camel@bioinfo.icapture.ubc.ca> Message-ID: <440F1A3F.3040305@cs.man.ac.uk> Mark Wilkinson wrote: >What, specifically, are you looking for in the RDF? A >comprehensive use of all of the predicates, or a "gold standard" for >what we consider to be a well-documented (i.e. described) service? > > Well its Stian [1] whos actually after this description. Stian is a developer currently working on BioMOBY service integration in Taverna... Over to you, Stian... Duncan [1] http://www.cs.man.ac.uk/~ssoiland/ -- Duncan Hull http://www.cs.man.ac.uk/~hulld/ Phone: +44 (0) 161 275 0677 From markw at illuminae.com Wed Mar 8 12:54:19 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 08 Mar 2006 09:54:19 -0800 Subject: [MOBY-dev] [moby] BioMOBY at the Oscars In-Reply-To: <1141840247.16213.34.camel@bioinfo.icapture.ubc.ca> References: <000401c64205$d2735000$6500a8c0@notebook> <440EE55C.6090003@cs.man.ac.uk> <1141835123.16213.13.camel@bioinfo.icapture.ubc.ca> <1141840247.16213.34.camel@bioinfo.icapture.ubc.ca> Message-ID: <1141840459.16213.38.camel@bioinfo.icapture.ubc.ca> Eddie, THIS is why I keep telling you to **put these things up on the website!** :-) M On Wed, 2006-03-08 at 09:50 -0800, Mark Wilkinson wrote: > You should talk to Eddie - I think he already has a taverna plugin that > does that... > > M > > > > On Wed, 2006-03-08 at 16:51 +0000, Stian Soiland wrote: > > On 8. mar. 2006, at 16:25, Mark Wilkinson wrote: > > > > > urn:lsid:biomoby.org:serviceinstance:org.inab.upc,runFasty: > > > 2006-03-04T08-50-58Z > > > > This seems like an OK example, but maybe not a good match for our task. > > > > > does that help? What, specifically, are you looking for in the > > > RDF? A > > > comprehensive use of all of the predicates, or a "gold standard" for > > > what we consider to be a well-documented (i.e. described) service? > > > > More specifically we are looking for good examples of semantic > > descriptions that we can use for Taverna while developing semantic > > linking/browsing/searching. In particular, descriptions of inputs and > > outputs that are a bit more specific than "Object", so that we can > > build GUI elements in Taverna for use cases like this rough description: > > > > a) Add a BioMoby processor into the Taverna workflow > > b) Click on the process, find that the input is a string described as > > a "GCP_Phenotype" > > c) Browse a list of BioMoby services that can provide the output type > > "GCP_Phenotype" > > d) Add one of the services to the workflow and connect it > > > > Of course, limiting the search by "performs task NCBI_Blast" is also > > nice. > > > > > > So a good example would be one (or a few related) services that has > > this kind of information specified and that actually works. :-) > > -- -- 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 "For most of this century we have viewed communications as a conduit, a pipe between physical locations on the planet. What's happened now is that the conduit has become so big and interesting that communication has become more than a conduit, it has become a destination in its own right..." Paul Saffo - Director, Institute for the Future From markw at illuminae.com Wed Mar 8 13:02:23 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 08 Mar 2006 10:02:23 -0800 Subject: [MOBY-dev] [moby] BioMOBY at the Oscars In-Reply-To: <000701c642d9$d8aa6560$6600a8c0@notebook> References: <000701c642d9$d8aa6560$6600a8c0@notebook> Message-ID: <1141840943.16213.43.camel@bioinfo.icapture.ubc.ca> Hmmmm.... Perhaps, given that Taverna is the most widely-used client for MOBY, we need to find a more high-profile way of announcing these extensions, since they don't seem to be getting noticed, even by other Taverna developers... M On Wed, 2006-03-08 at 09:58 -0800, Edward Kawas wrote: > I did (actually martin did): > http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/taverna/guide/in > dex.html > > Eddie > > > -----Original Message----- > > From: moby-dev-bounces at biomoby.org > > [mailto:moby-dev-bounces at biomoby.org] On Behalf Of Mark Wilkinson > > Sent: Wednesday, March 08, 2006 9:54 AM > > To: Core developer announcements > > Subject: Re: [MOBY-dev] [moby] BioMOBY at the Oscars > > > > Eddie, THIS is why I keep telling you to **put these things up on the > > website!** :-) > > > > M > > > > > > > > On Wed, 2006-03-08 at 09:50 -0800, Mark Wilkinson wrote: > > > You should talk to Eddie - I think he already has a taverna plugin > > > that does that... > > > > > > M > > > > > > > > > > > > On Wed, 2006-03-08 at 16:51 +0000, Stian Soiland wrote: > > > > On 8. mar. 2006, at 16:25, Mark Wilkinson wrote: > > > > > > > > > urn:lsid:biomoby.org:serviceinstance:org.inab.upc,runFasty: > > > > > 2006-03-04T08-50-58Z > > > > > > > > This seems like an OK example, but maybe not a good match > > for our task. > > > > > > > > > does that help? What, specifically, are you looking for in the > > > > > RDF? A comprehensive use of all of the predicates, or a "gold > > > > > standard" for what we consider to be a well-documented (i.e. > > > > > described) service? > > > > > > > > More specifically we are looking for good examples of semantic > > > > descriptions that we can use for Taverna while developing > > semantic > > > > linking/browsing/searching. In particular, descriptions of inputs > > > > and outputs that are a bit more specific than "Object", > > so that we > > > > can build GUI elements in Taverna for use cases like this > > rough description: > > > > > > > > a) Add a BioMoby processor into the Taverna workflow > > > > b) Click on the process, find that the input is a string > > described > > > > as a "GCP_Phenotype" > > > > c) Browse a list of BioMoby services that can provide the output > > > > type "GCP_Phenotype" > > > > d) Add one of the services to the workflow and connect it > > > > > > > > Of course, limiting the search by "performs task > > NCBI_Blast" is also > > > > nice. > > > > > > > > > > > > So a good example would be one (or a few related) > > services that has > > > > this kind of information specified and that actually works. :-) > > > > > > -- > > > > -- > > 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 > > > > "For most of this century we have viewed communications as a conduit, > > a pipe between physical locations on the planet. > > What's happened now is that the conduit has become so big and > > interesting > > that communication has become more than a conduit, > > it has become a destination in its own right..." > > > > Paul Saffo - Director, Institute for the Future > > > > _______________________________________________ > > MOBY-dev mailing list > > MOBY-dev at biomoby.org > > http://biomoby.org/mailman/listinfo/moby-dev > -- -- 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 "For most of this century we have viewed communications as a conduit, a pipe between physical locations on the planet. What's happened now is that the conduit has become so big and interesting that communication has become more than a conduit, it has become a destination in its own right..." Paul Saffo - Director, Institute for the Future From ssoiland at cs.man.ac.uk Wed Mar 8 11:51:58 2006 From: ssoiland at cs.man.ac.uk (Stian Soiland) Date: Wed, 8 Mar 2006 16:51:58 +0000 Subject: [MOBY-dev] [moby] BioMOBY at the Oscars In-Reply-To: <1141835123.16213.13.camel@bioinfo.icapture.ubc.ca> References: <000401c64205$d2735000$6500a8c0@notebook> <440EE55C.6090003@cs.man.ac.uk> <1141835123.16213.13.camel@bioinfo.icapture.ubc.ca> Message-ID: On 8. mar. 2006, at 16:25, Mark Wilkinson wrote: > urn:lsid:biomoby.org:serviceinstance:org.inab.upc,runFasty: > 2006-03-04T08-50-58Z This seems like an OK example, but maybe not a good match for our task. > does that help? What, specifically, are you looking for in the > RDF? A > comprehensive use of all of the predicates, or a "gold standard" for > what we consider to be a well-documented (i.e. described) service? More specifically we are looking for good examples of semantic descriptions that we can use for Taverna while developing semantic linking/browsing/searching. In particular, descriptions of inputs and outputs that are a bit more specific than "Object", so that we can build GUI elements in Taverna for use cases like this rough description: a) Add a BioMoby processor into the Taverna workflow b) Click on the process, find that the input is a string described as a "GCP_Phenotype" c) Browse a list of BioMoby services that can provide the output type "GCP_Phenotype" d) Add one of the services to the workflow and connect it Of course, limiting the search by "performs task NCBI_Blast" is also nice. So a good example would be one (or a few related) services that has this kind of information specified and that actually works. :-) -- Stian Soiland School of Computer Science The University of Manchester http://www.cs.man.ac.uk/~ssoiland/ From edward.kawas at gmail.com Wed Mar 8 12:58:01 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 8 Mar 2006 09:58:01 -0800 Subject: [MOBY-dev] [moby] BioMOBY at the Oscars In-Reply-To: <1141840459.16213.38.camel@bioinfo.icapture.ubc.ca> Message-ID: <000701c642d9$d8aa6560$6600a8c0@notebook> I did (actually martin did): http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/taverna/guide/in dex.html Eddie > -----Original Message----- > From: moby-dev-bounces at biomoby.org > [mailto:moby-dev-bounces at biomoby.org] On Behalf Of Mark Wilkinson > Sent: Wednesday, March 08, 2006 9:54 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] [moby] BioMOBY at the Oscars > > Eddie, THIS is why I keep telling you to **put these things up on the > website!** :-) > > M > > > > On Wed, 2006-03-08 at 09:50 -0800, Mark Wilkinson wrote: > > You should talk to Eddie - I think he already has a taverna plugin > > that does that... > > > > M > > > > > > > > On Wed, 2006-03-08 at 16:51 +0000, Stian Soiland wrote: > > > On 8. mar. 2006, at 16:25, Mark Wilkinson wrote: > > > > > > > urn:lsid:biomoby.org:serviceinstance:org.inab.upc,runFasty: > > > > 2006-03-04T08-50-58Z > > > > > > This seems like an OK example, but maybe not a good match > for our task. > > > > > > > does that help? What, specifically, are you looking for in the > > > > RDF? A comprehensive use of all of the predicates, or a "gold > > > > standard" for what we consider to be a well-documented (i.e. > > > > described) service? > > > > > > More specifically we are looking for good examples of semantic > > > descriptions that we can use for Taverna while developing > semantic > > > linking/browsing/searching. In particular, descriptions of inputs > > > and outputs that are a bit more specific than "Object", > so that we > > > can build GUI elements in Taverna for use cases like this > rough description: > > > > > > a) Add a BioMoby processor into the Taverna workflow > > > b) Click on the process, find that the input is a string > described > > > as a "GCP_Phenotype" > > > c) Browse a list of BioMoby services that can provide the output > > > type "GCP_Phenotype" > > > d) Add one of the services to the workflow and connect it > > > > > > Of course, limiting the search by "performs task > NCBI_Blast" is also > > > nice. > > > > > > > > > So a good example would be one (or a few related) > services that has > > > this kind of information specified and that actually works. :-) > > > > -- > > -- > 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 > > "For most of this century we have viewed communications as a conduit, > a pipe between physical locations on the planet. > What's happened now is that the conduit has become so big and > interesting > that communication has become more than a conduit, > it has become a destination in its own right..." > > Paul Saffo - Director, Institute for the Future > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at biomoby.org > http://biomoby.org/mailman/listinfo/moby-dev From ssoiland at cs.man.ac.uk Thu Mar 9 04:00:00 2006 From: ssoiland at cs.man.ac.uk (Stian Soiland) Date: Thu, 9 Mar 2006 09:00:00 +0000 Subject: [MOBY-dev] BioMOBY at the Oscars In-Reply-To: <000701c642d9$d8aa6560$6600a8c0@notebook> References: <000701c642d9$d8aa6560$6600a8c0@notebook> Message-ID: <4AB8B23C-1D52-4EB6-A9C5-EB6B7774AC91@cs.man.ac.uk> On 8. mar. 2006, at 17:58, Edward Kawas wrote: > I did (actually martin did): > http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/taverna/ > guide/ Wow, yeah, that's all very cool! I should've noticed, sorry.. (I'm quite a fresh developer..) This will be a great inspiration for adding similar ontology behaviour to non-Moby-stuff! -- Stian Soiland School of Computer Science The University of Manchester http://www.cs.man.ac.uk/~ssoiland/ From simont at mcw.edu Fri Mar 10 22:44:06 2006 From: simont at mcw.edu (Twigger Simon) Date: Fri, 10 Mar 2006 21:44:06 -0600 Subject: [MOBY-dev] [moby] BioMOBY at the Oscars In-Reply-To: <000701c642d9$d8aa6560$6600a8c0@notebook> References: <000701c642d9$d8aa6560$6600a8c0@notebook> Message-ID: <5C58079B-CD65-4352-9190-8F5C35CCBDD0@mcw.edu> Actually, while I think about it. I originally thought that we might have some sort of 'workflow exchange' or repository on the site. These could also be along the lines of blog postings but with the XML files inline or attached. They could have their own post category so they would be easy to find. Sharing these workflows will make everyone's life easier but I havent seen too much of that going on I suspect people are reinventing 'how to I do a blast using MOBY' and similar things which might be made available as standard components that people could integrate into their own Taverna workflows, thereby significantly lowering the barrier to entry for new MOBY users. Simon. On Mar 8, 2006, at 11:58 AM, Edward Kawas wrote: > I did (actually martin did): > http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/taverna/ > guide/in > dex.html > > Eddie > >> -----Original Message----- >> From: moby-dev-bounces at biomoby.org >> [mailto:moby-dev-bounces at biomoby.org] On Behalf Of Mark Wilkinson >> Sent: Wednesday, March 08, 2006 9:54 AM >> To: Core developer announcements >> Subject: Re: [MOBY-dev] [moby] BioMOBY at the Oscars >> >> Eddie, THIS is why I keep telling you to **put these things up on the >> website!** :-) >> >> M >> >> >> >> On Wed, 2006-03-08 at 09:50 -0800, Mark Wilkinson wrote: >>> You should talk to Eddie - I think he already has a taverna plugin >>> that does that... >>> >>> M >>> >>> >>> >>> On Wed, 2006-03-08 at 16:51 +0000, Stian Soiland wrote: >>>> On 8. mar. 2006, at 16:25, Mark Wilkinson wrote: >>>> >>>>> urn:lsid:biomoby.org:serviceinstance:org.inab.upc,runFasty: >>>>> 2006-03-04T08-50-58Z >>>> >>>> This seems like an OK example, but maybe not a good match >> for our task. >>>> >>>>> does that help? What, specifically, are you looking for in the >>>>> RDF? A comprehensive use of all of the predicates, or a "gold >>>>> standard" for what we consider to be a well-documented (i.e. >>>>> described) service? >>>> >>>> More specifically we are looking for good examples of semantic >>>> descriptions that we can use for Taverna while developing >> semantic >>>> linking/browsing/searching. In particular, descriptions of inputs >>>> and outputs that are a bit more specific than "Object", >> so that we >>>> can build GUI elements in Taverna for use cases like this >> rough description: >>>> >>>> a) Add a BioMoby processor into the Taverna workflow >>>> b) Click on the process, find that the input is a string >> described >>>> as a "GCP_Phenotype" >>>> c) Browse a list of BioMoby services that can provide the output >>>> type "GCP_Phenotype" >>>> d) Add one of the services to the workflow and connect it >>>> >>>> Of course, limiting the search by "performs task >> NCBI_Blast" is also >>>> nice. >>>> >>>> >>>> So a good example would be one (or a few related) >> services that has >>>> this kind of information specified and that actually works. :-) >>>> >> -- >> >> -- >> 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 >> >> "For most of this century we have viewed communications as a conduit, >> a pipe between physical locations on the planet. >> What's happened now is that the conduit has become so big and >> interesting >> that communication has become more than a conduit, >> it has become a destination in its own right..." >> >> Paul Saffo - Director, Institute for the Future >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at biomoby.org >> http://biomoby.org/mailman/listinfo/moby-dev > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at biomoby.org > http://biomoby.org/mailman/listinfo/moby-dev From simont at mcw.edu Fri Mar 10 22:39:14 2006 From: simont at mcw.edu (Twigger Simon) Date: Fri, 10 Mar 2006 21:39:14 -0600 Subject: [MOBY-dev] [moby] BioMOBY at the Oscars In-Reply-To: <000701c642d9$d8aa6560$6600a8c0@notebook> References: <000701c642d9$d8aa6560$6600a8c0@notebook> Message-ID: <148D8F0D-9DD7-4675-995F-E7844ABC622F@mcw.edu> The website is a blog (and quite a few people are subscribed to it) so you could always post these types of things on there as blog postings that will appear on the front page as well as burying them in the documentation (which is a better long term place for the info but is far less likely to be seen). Simon. -- Simon N. Twigger, Ph.D. Assistant Professor, Department of Physiology Medical College of Wisconsin 8701 Watertown Plank Road, Milwaukee, WI, USA tel: 414-456-8802 fax: 414-456-6595 AIM/iChat: simontatmcw On Mar 8, 2006, at 11:58 AM, Edward Kawas wrote: > I did (actually martin did): > http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/taverna/ > guide/in > dex.html > > Eddie > >> -----Original Message----- >> From: moby-dev-bounces at biomoby.org >> [mailto:moby-dev-bounces at biomoby.org] On Behalf Of Mark Wilkinson >> Sent: Wednesday, March 08, 2006 9:54 AM >> To: Core developer announcements >> Subject: Re: [MOBY-dev] [moby] BioMOBY at the Oscars >> >> Eddie, THIS is why I keep telling you to **put these things up on the >> website!** :-) >> >> M >> >> >> >> On Wed, 2006-03-08 at 09:50 -0800, Mark Wilkinson wrote: >>> You should talk to Eddie - I think he already has a taverna plugin >>> that does that... >>> >>> M >>> >>> >>> >>> On Wed, 2006-03-08 at 16:51 +0000, Stian Soiland wrote: >>>> On 8. mar. 2006, at 16:25, Mark Wilkinson wrote: >>>> >>>>> urn:lsid:biomoby.org:serviceinstance:org.inab.upc,runFasty: >>>>> 2006-03-04T08-50-58Z >>>> >>>> This seems like an OK example, but maybe not a good match >> for our task. >>>> >>>>> does that help? What, specifically, are you looking for in the >>>>> RDF? A comprehensive use of all of the predicates, or a "gold >>>>> standard" for what we consider to be a well-documented (i.e. >>>>> described) service? >>>> >>>> More specifically we are looking for good examples of semantic >>>> descriptions that we can use for Taverna while developing >> semantic >>>> linking/browsing/searching. In particular, descriptions of inputs >>>> and outputs that are a bit more specific than "Object", >> so that we >>>> can build GUI elements in Taverna for use cases like this >> rough description: >>>> >>>> a) Add a BioMoby processor into the Taverna workflow >>>> b) Click on the process, find that the input is a string >> described >>>> as a "GCP_Phenotype" >>>> c) Browse a list of BioMoby services that can provide the output >>>> type "GCP_Phenotype" >>>> d) Add one of the services to the workflow and connect it >>>> >>>> Of course, limiting the search by "performs task >> NCBI_Blast" is also >>>> nice. >>>> >>>> >>>> So a good example would be one (or a few related) >> services that has >>>> this kind of information specified and that actually works. :-) >>>> >> -- >> >> -- >> 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 >> >> "For most of this century we have viewed communications as a conduit, >> a pipe between physical locations on the planet. >> What's happened now is that the conduit has become so big and >> interesting >> that communication has become more than a conduit, >> it has become a destination in its own right..." >> >> Paul Saffo - Director, Institute for the Future >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at biomoby.org >> http://biomoby.org/mailman/listinfo/moby-dev > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at biomoby.org > http://biomoby.org/mailman/listinfo/moby-dev From duncan.hull at cs.man.ac.uk Sat Mar 11 05:10:16 2006 From: duncan.hull at cs.man.ac.uk (Duncan Hull) Date: Sat, 11 Mar 2006 10:10:16 +0000 Subject: [MOBY-dev] Workflow repository for BioMOBY In-Reply-To: <5C58079B-CD65-4352-9190-8F5C35CCBDD0@mcw.edu> References: <000701c642d9$d8aa6560$6600a8c0@notebook> <5C58079B-CD65-4352-9190-8F5C35CCBDD0@mcw.edu> Message-ID: <4412A208.805@cs.man.ac.uk> Hi Simon Twigger Simon wrote: >Actually, while I think about it. I originally thought that we might >have some sort of 'workflow exchange' or repository on the site. > > Antoon Goderis [1] has been working on exactly this for Taverna, currently in beta version and might be of interest. http://workflows.mygrid.org.uk/repository/ Its read-only at the moment, but he's working on an upload facility. Duncan [1] http://www.cs.man.ac.uk/~goderisa/ -- Duncan Hull http://www.cs.man.ac.uk/~hulld/ Phone: +44 (0) 161 275 0677 From duncan.hull at cs.man.ac.uk Sat Mar 11 05:10:16 2006 From: duncan.hull at cs.man.ac.uk (Duncan Hull) Date: Sat, 11 Mar 2006 10:10:16 +0000 Subject: [MOBY-dev] Workflow repository for BioMOBY In-Reply-To: <5C58079B-CD65-4352-9190-8F5C35CCBDD0@mcw.edu> References: <000701c642d9$d8aa6560$6600a8c0@notebook> <5C58079B-CD65-4352-9190-8F5C35CCBDD0@mcw.edu> Message-ID: <4412A208.805@cs.man.ac.uk> Hi Simon Twigger Simon wrote: >Actually, while I think about it. I originally thought that we might >have some sort of 'workflow exchange' or repository on the site. > > Antoon Goderis [1] has been working on exactly this for Taverna, currently in beta version and might be of interest. http://workflows.mygrid.org.uk/repository/ Its read-only at the moment, but he's working on an upload facility. Duncan [1] http://www.cs.man.ac.uk/~goderisa/ -- Duncan Hull http://www.cs.man.ac.uk/~hulld/ Phone: +44 (0) 161 275 0677 From tmo at ebi.ac.uk Sat Mar 11 05:43:26 2006 From: tmo at ebi.ac.uk (Tom Oinn) Date: Sat, 11 Mar 2006 10:43:26 +0000 Subject: [MOBY-dev] Workflow repository for BioMOBY In-Reply-To: <4412A208.805@cs.man.ac.uk> References: <000701c642d9$d8aa6560$6600a8c0@notebook> <5C58079B-CD65-4352-9190-8F5C35CCBDD0@mcw.edu> <4412A208.805@cs.man.ac.uk> Message-ID: <4412A9CE.1000103@ebi.ac.uk> Duncan Hull wrote: > Hi Simon > > Twigger Simon wrote: > >> Actually, while I think about it. I originally thought that we might >> have some sort of 'workflow exchange' or repository on the site. >> >> > Antoon Goderis [1] has been working on exactly this for Taverna, > currently in beta version and might be of interest. Duncan - is there any more to this than a directory with some workflows in? The .gif files are missing the colour coding as well which makes them a bit less useful, also we should be emiting the autogenerated workflow summary HTML. I actually wrote some code to do this last year, will dig it up - it allowed workflow upload too. Tom > http://workflows.mygrid.org.uk/repository/ > > Its read-only at the moment, but he's working on an upload facility. > > Duncan > > [1] http://www.cs.man.ac.uk/~goderisa/ > From tmo at ebi.ac.uk Sat Mar 11 05:43:26 2006 From: tmo at ebi.ac.uk (Tom Oinn) Date: Sat, 11 Mar 2006 10:43:26 +0000 Subject: [MOBY-dev] Workflow repository for BioMOBY In-Reply-To: <4412A208.805@cs.man.ac.uk> References: <000701c642d9$d8aa6560$6600a8c0@notebook> <5C58079B-CD65-4352-9190-8F5C35CCBDD0@mcw.edu> <4412A208.805@cs.man.ac.uk> Message-ID: <4412A9CE.1000103@ebi.ac.uk> Duncan Hull wrote: > Hi Simon > > Twigger Simon wrote: > >> Actually, while I think about it. I originally thought that we might >> have some sort of 'workflow exchange' or repository on the site. >> >> > Antoon Goderis [1] has been working on exactly this for Taverna, > currently in beta version and might be of interest. Duncan - is there any more to this than a directory with some workflows in? The .gif files are missing the colour coding as well which makes them a bit less useful, also we should be emiting the autogenerated workflow summary HTML. I actually wrote some code to do this last year, will dig it up - it allowed workflow upload too. Tom > http://workflows.mygrid.org.uk/repository/ > > Its read-only at the moment, but he's working on an upload facility. > > Duncan > > [1] http://www.cs.man.ac.uk/~goderisa/ > From senger at ebi.ac.uk Sun Mar 12 13:29:20 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Sun, 12 Mar 2006 18:29:20 +0000 (GMT) Subject: [MOBY-dev] biomoby.org down? Message-ID: The jMoby cronjob recently started to experience problems when downloading from http://biomoby.org/jmoby-jars/jars-archive/, Now, I also cannot get the usual http://biomoby.org page (it exists, but it gives me back a very strange contents with just two links (RT and wiki)). Anybody has the same experiences, or does anybody knows the reason? Thanks, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger consulting for: International Rice Research Institute Biometrics and Bioinformatics Unit DAPO BOX 7777, Metro Manila Philippines, phone: +63-2-580-5600 (ext.2324) From haase_dirk at web.de Sun Mar 12 17:13:36 2006 From: haase_dirk at web.de (Dirk Haase) Date: Sun, 12 Mar 2006 23:13:36 +0100 Subject: [MOBY-dev] biomoby.org down? In-Reply-To: References: Message-ID: <200603122313.36929.haase_dirk@web.de> On Sunday 12 March 2006 19:29, Martin Senger wrote: > The jMoby cronjob recently started to experience problems when downloading > from http://biomoby.org/jmoby-jars/jars-archive/, Now, I also cannot get > the usual http://biomoby.org page (it exists, but it gives me back a very > strange contents with just two links (RT and wiki)). > > Anybody has the same experiences, or does anybody knows the reason? Same observation here in Cologne/Germany. I would appreciate if this could be fixed quickly, because tomorrow (Monday) we start a workshop focussing mainly on BioMOBY. It would be a pity if we could not use (and promote...) the biomoby.org site as a documentation resource. Regards, dirk From senger at ebi.ac.uk Sun Mar 12 18:14:49 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Sun, 12 Mar 2006 23:14:49 +0000 (GMT) Subject: [MOBY-dev] biomoby.org down? In-Reply-To: <200603122313.36929.haase_dirk@web.de> Message-ID: > Same observation here in Cologne/Germany. I would appreciate if this could be > fixed quickly > It is fixed now. Chris (from the open-bio) did it at once, If you still do not see the usual biomoby.org page, it will come later to you because the problem was with DNS which will take some time to be propagated throught the world (I have it right now, in UK). Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger consulting for: International Rice Research Institute Biometrics and Bioinformatics Unit DAPO BOX 7777, Metro Manila Philippines, phone: +63-2-580-5600 (ext.2324) From leire at mmb.pcb.ub.es Mon Mar 13 13:30:12 2006 From: leire at mmb.pcb.ub.es (leireZamacola) Date: Mon, 13 Mar 2006 19:30:12 +0100 Subject: [MOBY-dev] The agent References: <000401c64205$d2735000$6500a8c0@notebook> Message-ID: <002001c646cc$2a7ee5f0$0d60050a@mmb.pcb.ub.es> Hi everyone, I am developing biomoby services in Java. I compile the service and deploy it without problems but when I want to run the service I get this error. Does anyone know why? cheers 600 AN ERROR OCCURED DURING THE SERVICE EXECUTION. org.biomoby.shared.datatypes.FASTA_AA java.lang.ClassCastException: org.biomoby.shared.datatypes.FASTA_AA at PMutHotSpot.run.skeletons.RunHotSpotFromFASTASkel.get_FASTA_AA(Unknown Source) at PMutHotSpot.run.RunHotSpotFromFASTAImpl.processIt(Unknown Source) at org.biomoby.service.BaseService.processIt(BaseService.java:292) at PMutHotSpot.run.skeletons.RunHotSpotFromFASTASkel.RunHotSpotFromFASTA(Unknow n Source) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39 ) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl .java:25) at java.lang.reflect.Method.invoke(Method.java:585) at org.jboss.webservice.server.InvokerProviderJSE.invokeServiceEndpoint(Invoker ProviderJSE.java:154) at org.jboss.webservice.server.InvokerProvider.invokeMethod(InvokerProvider.jav a:305) at org.jboss.axis.providers.java.RPCProvider.invokeTarget(RPCProvider.java:176) at org.jboss.webservice.server.InvokerProviderJSE.invokeTarget(InvokerProviderJ SE.java:93) at org.jboss.axis.providers.java.RPCProvider.processMessage(RPCProvider.java:12 1) at org.jboss.axis.providers.java.JavaProvider.invoke(JavaProvider.java:358) at org.jboss.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java:7 3) at org.jboss.axis.SimpleChain.doVisiting(SimpleChain.java:160) at org.jboss.axis.SimpleChain.invoke(SimpleChain.java:123) at org.jboss.axis.handlers.soap.SOAPService.invoke(SOAPService.java:560) at org.jboss.webservice.server.ServerEngine.invokeInternal(ServerEngine.java:20 0) at org.jboss.webservice.server.ServerEngine.invoke(ServerEngine.java:89) at org.jboss.axis.transport.http.AxisServlet.doPost(AxisServlet.java:911) at javax.servlet.http.HttpServlet.service(HttpServlet.java:717) at org.jboss.axis.transport.http.AxisServletBase.service(AxisServletBase.java:3 70) at javax.servlet.http.HttpServlet.service(HttpServlet.java:810) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Application FilterChain.java:252) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterCh ain.java:173) at org.jboss.web.tomcat.filters.ReplyHeaderFilter.doFilter(ReplyHeaderFilter.ja va:81) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Application FilterChain.java:202) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterCh ain.java:173) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.ja va:213) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.ja va:178) at org.jboss.web.tomcat.security.CustomPrincipalValve.invoke(CustomPrincipalVal ve.java:39) at org.jboss.web.tomcat.security.SecurityAssociationValve.invoke(SecurityAssoci ationValve.java:159) at org.jboss.web.tomcat.security.JaccContextValve.invoke(JaccContextValve.java: 59) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:126 ) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:105 ) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java :107) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:148) at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:856) at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.processConne ction(Http11Protocol.java:744) at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.jav a:527) at org.apache.tomcat.util.net.MasterSlaveWorkerThread.run(MasterSlaveWorkerThre ad.java:112) at java.lang.Thread.run(Thread.java:595) Leire Zamacola Gandiaga Molecular Recognition Universitat de Barcelona IRBB, Parc Cientific de Barcelona C. Josep Samitier 1-5, 08028 Barcelona fax : + 34 93 403 71 57 phone: + 34 93 403 71 55 mail: leire at mmb.pcb.ub.es From senger at ebi.ac.uk Mon Mar 13 14:07:57 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Mon, 13 Mar 2006 19:07:57 +0000 (GMT) Subject: [MOBY-dev] The agent In-Reply-To: <002001c646cc$2a7ee5f0$0d60050a@mmb.pcb.ub.es> Message-ID: Hi, > Does anyone know why? > I do not know yet, but it's me who should know :-) (and fix it if needed). I wonder if you can show me the generated Java code PMutHotSpot.run.skeletons.RunHotSpotFromFASTASkel. And perhaps also the input you sent to the service. Regards, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger consulting for: International Rice Research Institute Biometrics and Bioinformatics Unit DAPO BOX 7777, Metro Manila Philippines, phone: +63-2-580-5600 (ext.2324) From edward.kawas at gmail.com Mon Mar 13 13:41:35 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 13 Mar 2006 10:41:35 -0800 Subject: [MOBY-dev] The agent In-Reply-To: <002001c646cc$2a7ee5f0$0d60050a@mmb.pcb.ub.es> Message-ID: <000101c646cd$c248d1b0$9b66a8c0@notebook> What is your service description? Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of > leireZamacola > Sent: Monday, March 13, 2006 10:30 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] The agent > > Hi everyone, > > I am developing biomoby services in Java. > > I compile the service and deploy it without problems but when > I want to run the service I get this error. > > Does anyone know why? > > cheers > > > > > > > > > > > > > 600 > > AN ERROR OCCURED DURING THE SERVICE EXECUTION. > > org.biomoby.shared.datatypes.FASTA_AA > > java.lang.ClassCastException: org.biomoby.shared.datatypes.FASTA_AA > > at > PMutHotSpot.run.skeletons.RunHotSpotFromFASTASkel.get_FASTA_AA(Unknown > Source) > > at PMutHotSpot.run.RunHotSpotFromFASTAImpl.processIt(Unknown Source) > > at org.biomoby.service.BaseService.processIt(BaseService.java:292) > > at > PMutHotSpot.run.skeletons.RunHotSpotFromFASTASkel.RunHotSpotFr > omFASTA(Unknow > n Source) > > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) > > at > sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccess > orImpl.java:39 > ) > > at > sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMeth > odAccessorImpl > .java:25) > > at java.lang.reflect.Method.invoke(Method.java:585) > > at > org.jboss.webservice.server.InvokerProviderJSE.invokeServiceEn > dpoint(Invoker > ProviderJSE.java:154) > > at > org.jboss.webservice.server.InvokerProvider.invokeMethod(Invok > erProvider.jav > a:305) > > at > org.jboss.axis.providers.java.RPCProvider.invokeTarget(RPCProv > ider.java:176) > > at > org.jboss.webservice.server.InvokerProviderJSE.invokeTarget(In > vokerProviderJ > SE.java:93) > > at > org.jboss.axis.providers.java.RPCProvider.processMessage(RPCPr > ovider.java:12 > 1) > > at > org.jboss.axis.providers.java.JavaProvider.invoke(JavaProvider > .java:358) > > at > org.jboss.axis.strategies.InvocationStrategy.visit(InvocationS > trategy.java:7 > 3) > > at org.jboss.axis.SimpleChain.doVisiting(SimpleChain.java:160) > > at org.jboss.axis.SimpleChain.invoke(SimpleChain.java:123) > > at > org.jboss.axis.handlers.soap.SOAPService.invoke(SOAPService.java:560) > > at > org.jboss.webservice.server.ServerEngine.invokeInternal(Server > Engine.java:20 > 0) > > at > org.jboss.webservice.server.ServerEngine.invoke(ServerEngine.java:89) > > at > org.jboss.axis.transport.http.AxisServlet.doPost(AxisServlet.java:911) > > at javax.servlet.http.HttpServlet.service(HttpServlet.java:717) > > at > org.jboss.axis.transport.http.AxisServletBase.service(AxisServ > letBase.java:3 > 70) > > at javax.servlet.http.HttpServlet.service(HttpServlet.java:810) > > at > org.apache.catalina.core.ApplicationFilterChain.internalDoFilt > er(Application > FilterChain.java:252) > > at > org.apache.catalina.core.ApplicationFilterChain.doFilter(Appli > cationFilterCh > ain.java:173) > > at > org.jboss.web.tomcat.filters.ReplyHeaderFilter.doFilter(ReplyH > eaderFilter.ja > va:81) > > at > org.apache.catalina.core.ApplicationFilterChain.internalDoFilt > er(Application > FilterChain.java:202) > > at > org.apache.catalina.core.ApplicationFilterChain.doFilter(Appli > cationFilterCh > ain.java:173) > > at > org.apache.catalina.core.StandardWrapperValve.invoke(StandardW > rapperValve.ja > va:213) > > at > org.apache.catalina.core.StandardContextValve.invoke(StandardC > ontextValve.ja > va:178) > > at > org.jboss.web.tomcat.security.CustomPrincipalValve.invoke(Cust > omPrincipalVal > ve.java:39) > > at > org.jboss.web.tomcat.security.SecurityAssociationValve.invoke( > SecurityAssoci > ationValve.java:159) > > at > org.jboss.web.tomcat.security.JaccContextValve.invoke(JaccCont > extValve.java: > 59) > > at > org.apache.catalina.core.StandardHostValve.invoke(StandardHost > Valve.java:126 > ) > > at > org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReport > Valve.java:105 > ) > > at > org.apache.catalina.core.StandardEngineValve.invoke(StandardEn > gineValve.java > :107) > > at > org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdap > ter.java:148) > > at > org.apache.coyote.http11.Http11Processor.process(Http11Process > or.java:856) > > at > org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandle > r.processConne > ction(Http11Protocol.java:744) > > at > org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolT > cpEndpoint.jav > a:527) > > at > org.apache.tomcat.util.net.MasterSlaveWorkerThread.run(MasterS > laveWorkerThre > ad.java:112) > > at java.lang.Thread.run(Thread.java:595) > > > > > > > > > > > > > > Leire Zamacola Gandiaga > Molecular Recognition > Universitat de Barcelona > IRBB, Parc Cientific de Barcelona > C. Josep Samitier 1-5, > 08028 Barcelona > fax : + 34 93 403 71 57 > phone: + 34 93 403 71 55 > mail: leire at mmb.pcb.ub.es > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From leire at mmb.pcb.ub.es Tue Mar 14 04:31:02 2006 From: leire at mmb.pcb.ub.es (leireZamacola) Date: Tue, 14 Mar 2006 10:31:02 +0100 Subject: [MOBY-dev] Skeleton and input for the service References: Message-ID: <001d01c6474a$02bb5020$0d60050a@mmb.pcb.ub.es> Hi, I have attached the skeleton and the input I use for that service. Many thanks Leire Zamacola Gandiaga Molecular Recognition Universitat de Barcelona IRBB, Parc Cientific de Barcelona C. Josep Samitier 1-5, 08028 Barcelona fax : + 34 93 403 71 57 phone: + 34 93 403 71 55 mail: leire at mmb.pcb.ub.es ----- Original Message ----- From: "Martin Senger" To: "leireZamacola" Cc: "Core developer announcements" Sent: Monday, March 13, 2006 8:07 PM Subject: Re: [MOBY-dev] The agent > Hi, > > > Does anyone know why? > > > I do not know yet, but it's me who should know :-) (and fix it if > needed). > I wonder if you can show me the generated Java code > PMutHotSpot.run.skeletons.RunHotSpotFromFASTASkel. And perhaps also the > input you sent to the service. > > Regards, > Martin > > -- > Martin Senger > email: martin.senger at gmail.com > skype: martinsenger > consulting for: > International Rice Research Institute > Biometrics and Bioinformatics Unit > DAPO BOX 7777, Metro Manila > Philippines, phone: +63-2-580-5600 (ext.2324) -------------- next part -------------- A non-text attachment was scrubbed... Name: RunHotSpotFromFASTASkel.java Type: application/octet-stream Size: 4114 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/moby-dev/attachments/20060314/1fc129d0/attachment.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: FASTA.xml Type: text/xml Size: 844 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/moby-dev/attachments/20060314/1fc129d0/attachment.xml From dag at sonsorol.org Tue Mar 14 09:41:34 2006 From: dag at sonsorol.org (Chris Dagdigian) Date: Tue, 14 Mar 2006 09:41:34 -0500 Subject: [MOBY-dev] help test the new open-bio anonymous source code server Message-ID: Hi folks, Apologies for the cross-post. I need some help testing out a new open- bio server The new server is http://code.open-bio.org and it has been purpose built to replace our existing anonymous CVS server (cvs.open-bio.org, etc. etc.) In addition to anonymous CVS, this new system also offers anonymous rsync mirrors of all our source code. For security reasons (the anonymous CVS pserver protocol is considered insecure) we run these anon access methods on a locked down machine that only has a read only copy of the codebase. The webserver page (except for the viewcvs CGI) actually redirects to a wiki entry on a different server so we don' have to maintain a website on the new box. The anonymous access repository is currently updated every 30 minutes from the main developer system. Things I need help with: - check out http://code.open-bio.org -- does the documentation make sense? Can it be made better? If so, change it! (it is a wiki after all...) - please experiment with anonymous CVS, confirm that you can check out code - experiment with rsync! this is a new feature for us that we could not offer on the old server (due to upstream port ACLs on a core router) - provide feedback on the "speed" and bandwidth of the anoncvs server, does it seem reasonable? Let me know what you'll think. The reason for this move is that one of our core hosting facilities (datacenter at Wyeth Research) is no longer going to be useable by us as they are changing their WAN links in such a way that our servers will not be able to directly access the internet. We are in the process of moving *every* open-bio.org service onto new hardware located in a different datacenter. Our mailing lists have already been migrated, websites are moving as well. Expect some big changes once we tackle the task of moving all the developers and the writable CVS repositories to the new datacenter - that will happen probably within the next 2 weeks. Regards, Chris Dagdigian OBF From senger at ebi.ac.uk Tue Mar 14 14:17:59 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Tue, 14 Mar 2006 19:17:59 +0000 (GMT) Subject: [MOBY-dev] Skeleton and input for the service In-Reply-To: <001d01c6474a$02bb5020$0d60050a@mmb.pcb.ub.es> Message-ID: Hi, Thanks for the input file and the skeleton. (Wow, it seems unusual, to say "thanks for the skeleton" :-)). I have tried to reproduce your error, but I failed. I found that your input data were interesing because they seem to be non-valid XML - they contain '>' in the seguence name (FASTA format). Interesting is that it does not invalidate XML (the rules about XML validity allows the '>' to be present without being escaped). So this is not the problem. Then I found that your input data were not strictly speaking compliant with the Biomoby API because the Simple should have an article name. But this also did not cause the problem because the jMoby classes are relatively forgiving on this. Then, I have written my own trivial implementation of your skeleton, and run it with your input data. Unforunately, the error that happened to you has not occured to me. This is my implementatation: --- begin --- package org.jmoby.tutorial.service; import PMutHotSpot.run.skeletons.RunHotSpotFromFASTASkel; import org.biomoby.shared.MobyException; import org.biomoby.shared.parser.MobyPackage; import org.biomoby.shared.parser.MobyJob; import org.biomoby.shared.datatypes.*; public class RunHotSpotFromFASTAImpl extends RunHotSpotFromFASTASkel { public void processIt (MobyJob request, MobyJob response, MobyPackage outputContext) throws MobyException { System.out.println (get_FASTA_AA (request)); } } --- end --- And this is how I tested: build/run/run-service -service RunHotSpotFromFASTA -xml FASTA.xml \ -class org.jmoby.tutorial.service.RunHotSpotFromFASTAImpl I have not got any errors. So, the only thing I can think about is that perhaps you do not have the latest version of jMoby (even though I have not found any concrete case where this should matter). Please cvs update again, generate your skeleton again, compile and run it. Try also my implementation class shown above. If it still gives you an error, consider to show me your own implementation class (you can remove there all sensistive pieces, of course). Sorry that I have not found yet a solution for you. But bear with me, we will find it. Regards, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger consulting for: International Rice Research Institute Biometrics and Bioinformatics Unit DAPO BOX 7777, Metro Manila Philippines, phone: +63-2-580-5600 (ext.2324) From haase_dirk at web.de Thu Mar 16 02:59:36 2006 From: haase_dirk at web.de (Dirk Haase) Date: Thu, 16 Mar 2006 08:59:36 +0100 Subject: [MOBY-dev] Test Central: not accessible by Taverna Message-ID: <200603160859.37035.haase_dirk@web.de> Hi! We just experience problems with the new test registry (http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl). When I try to create a new biomoby scavenger pointing to that registry I get an error saying "org.embl.ebi.escience.scuflui.workbench.ScavengerCreationException: Could not retrieve and or process RDF document for BioMoby Objects" So it seems there is something wrong with the RDF resolution... Eddie, can you have a look at it? Thanks and regards, dirk From edward.kawas at gmail.com Thu Mar 16 10:04:27 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 16 Mar 2006 07:04:27 -0800 Subject: [MOBY-dev] Test Central: not accessible by Taverna In-Reply-To: <200603160859.37035.haase_dirk@web.de> Message-ID: <000301c6490a$ed7f4780$6600a8c0@notebook> Hi Dirk, I committed the fix to the cvs. In addition, I placed an updated taverna-1.3.1.jar at http://bioinfo.icapture.ubc.ca/ekawas/jars/taverna-1.3.1.jar. Remember to backup your old file in /taverna-workbench-1.3.1/lib/ before replacing it. The problem is that I am updating the RDF generators so that they include LSIDs with versioning information. In addition to the versioning information, the documents include most properties contained in the registry. Having this information may prove useful in later enhancements to the plug-in. Thanks, Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dirk Haase > Sent: Thursday, March 16, 2006 12:00 AM > To: Moby Developers > Subject: [MOBY-dev] Test Central: not accessible by Taverna > > Hi! > > We just experience problems with the new test registry > (http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Centr > al.pl). When I try to create a new biomoby scavenger pointing > to that registry I get an error saying > "org.embl.ebi.escience.scuflui.workbench.ScavengerCreationExce > ption: Could not retrieve and or process RDF document for > BioMoby Objects" > > So it seems there is something wrong with the RDF > resolution... Eddie, can you have a look at it? > > Thanks and regards, > dirk > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From edward.kawas at gmail.com Thu Mar 16 10:04:27 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 16 Mar 2006 07:04:27 -0800 Subject: [MOBY-dev] Test Central: not accessible by Taverna In-Reply-To: <200603160859.37035.haase_dirk@web.de> Message-ID: <000301c6490a$ed7f4780$6600a8c0@notebook> Hi Dirk, I committed the fix to the cvs. In addition, I placed an updated taverna-1.3.1.jar at http://bioinfo.icapture.ubc.ca/ekawas/jars/taverna-1.3.1.jar. Remember to backup your old file in /taverna-workbench-1.3.1/lib/ before replacing it. The problem is that I am updating the RDF generators so that they include LSIDs with versioning information. In addition to the versioning information, the documents include most properties contained in the registry. Having this information may prove useful in later enhancements to the plug-in. Thanks, Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dirk Haase > Sent: Thursday, March 16, 2006 12:00 AM > To: Moby Developers > Subject: [MOBY-dev] Test Central: not accessible by Taverna > > Hi! > > We just experience problems with the new test registry > (http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Centr > al.pl). When I try to create a new biomoby scavenger pointing > to that registry I get an error saying > "org.embl.ebi.escience.scuflui.workbench.ScavengerCreationExce > ption: Could not retrieve and or process RDF document for > BioMoby Objects" > > So it seems there is something wrong with the RDF > resolution... Eddie, can you have a look at it? > > Thanks and regards, > dirk > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From Pieter.Neerincx at wur.nl Thu Mar 23 05:48:37 2006 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Thu, 23 Mar 2006 11:48:37 +0100 Subject: [MOBY-dev] website vanished? Message-ID: <00011E19-F7D5-4835-8F9A-C95432B45CAC@wur.nl> Hi all, Is it me or is the BioMOBY site gone? My network is Ok and I can access many other sites, but both www.biomoby.org and biomoby.open- bio.org are gone... Pi Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 060 fax: 0317-483 584 mobile: 06-143 66 783 pieter.neerincx at wur.nl From senger at ebi.ac.uk Thu Mar 23 08:32:21 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Thu, 23 Mar 2006 13:32:21 +0000 (GMT) Subject: [MOBY-dev] website vanished? In-Reply-To: <00011E19-F7D5-4835-8F9A-C95432B45CAC@wur.nl> Message-ID: > Is it me or is the BioMOBY site gone? My network is Ok and I can > access many other sites, but both www.biomoby.org and biomoby.open- > bio.org are gone... > www.biomoby.org works for me fine... Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From markw at illuminae.com Thu Mar 23 08:59:18 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 23 Mar 2006 05:59:18 -0800 Subject: [MOBY-dev] website vanished? In-Reply-To: <00011E19-F7D5-4835-8F9A-C95432B45CAC@wur.nl> References: <00011E19-F7D5-4835-8F9A-C95432B45CAC@wur.nl> Message-ID: No problems from here. M On Thu, 23 Mar 2006 02:48:37 -0800, Pieter Neerincx wrote: > Hi all, > > Is it me or is the BioMOBY site gone? My network is Ok and I can > access many other sites, but both www.biomoby.org and biomoby.open- > bio.org are gone... > > Pi > > Wageningen University and Research centre (WUR) > Laboratory of Bioinformatics > Transitorium (building 312) room 1034 > Dreijenlaan 3 > 6703 HA Wageningen > The Netherlands > phone: 0317-483 060 > fax: 0317-483 584 > mobile: 06-143 66 783 > pieter.neerincx at wur.nl > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From Pieter.Neerincx at wur.nl Thu Mar 23 10:13:56 2006 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Thu, 23 Mar 2006 16:13:56 +0100 Subject: [MOBY-dev] website vanished? In-Reply-To: References: <00011E19-F7D5-4835-8F9A-C95432B45CAC@wur.nl> Message-ID: It took a few hours, but whatever it was it's working again :). Pi On 23-Mar-2006, at 2:59 PM, Mark Wilkinson wrote: > No problems from here. > > M > > On Thu, 23 Mar 2006 02:48:37 -0800, Pieter Neerincx > wrote: > >> Hi all, >> >> Is it me or is the BioMOBY site gone? My network is Ok and I can >> access many other sites, but both www.biomoby.org and biomoby.open- >> bio.org are gone... >> >> Pi >> >> Wageningen University and Research centre (WUR) >> Laboratory of Bioinformatics >> Transitorium (building 312) room 1034 >> Dreijenlaan 3 >> 6703 HA Wageningen >> The Netherlands >> phone: 0317-483 060 >> fax: 0317-483 584 >> mobile: 06-143 66 783 >> pieter.neerincx at wur.nl >> >> >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 060 fax: 0317-483 584 mobile: 06-143 66 783 pieter.neerincx at wur.nl From francis_gibbons at hms.harvard.edu Fri Mar 24 09:38:45 2006 From: francis_gibbons at hms.harvard.edu (Frank Gibbons) Date: Fri, 24 Mar 2006 09:38:45 -0500 Subject: [MOBY-dev] [MOBY-l] missing RFC1863 support in perl CommonSubs In-Reply-To: <4423C102.3000704@mpimp-golm.mpg.de> Message-ID: <5.2.1.1.2.20060324093657.023ebc70@email.med.harvard.edu> Bj?rn, To my knowledge, nobody has yet checked in any work on integrating the new Exception mechanism into the Perl codebase. It appears that the Java codebase already has this feature, so we need it in the Perl version too, urgently. You should feel free to go ahead - anyone out there working on this? perhaps you should get together on it. -Frank At 04:50 AM 3/24/2006, you wrote: >Dear list, > >I just learned how to use Biomoby and stumbled over the problem that it >is not possible to integrate >moby Exceptions (as specified in RFC1863) into the header using the perl >method "responseHeader" from CommonSubs (latest cvs). Since everything >there which is passed in the parameter notes gets HTMLified and wrapped >into notes as well as service notes. > >Is anybody working on fixing that? >Otherwise I could try developing a version here with the additional >paramter exception (and post it on this list?) > > >Cheers, >Bj?rn > > >_______________________________________________ >moby-l mailing list >moby-l at lists.open-bio.org >http://lists.open-bio.org/mailman/listinfo/moby-l PhD, Computational Biologist, Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA 02115, USA. Tel: 617-432-3555 Fax: 617-432-3557 http://llama.med.harvard.edu/~fgibbons From darin.london at duke.edu Tue Mar 28 09:42:45 2006 From: darin.london at duke.edu (Darin London) Date: Tue, 28 Mar 2006 09:42:45 -0500 Subject: [MOBY-dev] Announcing BOSC 2006 Message-ID: <44294B65.4050207@duke.edu> MEETING ANNOUNCEMENT & CALL FOR SPEAKERS The 7th annual Bioinformatics Open Source Conference (BOSC 2006) is organized by the not-for-profit Open Bioinformatics Foundation. The meeting will take place Aug 4,5th in Fortaleza, Brasil, and is one of several Special Interest Group (SIG) meetings occurring in conjunction with the 14th International Conference on Intelligent Systems for Molecular Biology. Please consult The Official BOSC 2006 Website at http://www.open-bio.org/wiki/BOSC_2006 for details and information. In addition, a BOSC weblog has been setup to make it easier to desiminate all BOSC related announcements: http://wiki.open-bio.org/boscblog/ And if you have an ICAL compatible Calendar, there is an EventDB calendar set up with all BOSC related deadlines. http://eventful.com/groups/G0-001-000014747-0 More information about ISMB can be found at the Official ISMB 2006 Website: http://ismb2006.cbi.cnptia.embrapa.br/ Thank You, and we look forward to seeing you all, The BOSC Organizing Committee. From d.haase at gsf.de Wed Mar 29 00:51:36 2006 From: d.haase at gsf.de (Dirk Haase) Date: Wed, 29 Mar 2006 07:51:36 +0200 Subject: [MOBY-dev] Wrong links in Perl web docs Message-ID: <200603290751.36758.d.haase@gsf.de> Hi there! I'm not sure if this was topic before here, but currently the links in some of the Perl API docs on the website are wrong. Namely, in all pages http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/Perl/RegisterX.html with X in {AnObject, ServiceType, Namespace, ServiceInstance}, the links listed under 'Other parts of MOBY-S API' point to the wrong directory. The relative paths are lacking the initial dots ("../"). Regards, dirk -- ---------------------------------------------------------- Dirk Haase phone +49 89 3187 3583 http://mips.gsf.de/~haase email d.haase at gsf.de From francis_gibbons at hms.harvard.edu Wed Mar 29 10:10:05 2006 From: francis_gibbons at hms.harvard.edu (Frank Gibbons) Date: Wed, 29 Mar 2006 10:10:05 -0500 Subject: [MOBY-dev] Wrong links in Perl web docs In-Reply-To: <200603290751.36758.d.haase@gsf.de> Message-ID: <5.2.1.1.2.20060329100915.01261750@email.med.harvard.edu> Dirk. I'm waiting for my account to be reinstated on openbio.org, but feel free to go ahead and insert those little dots. The point of putting the docs under CVS control is that anyone can fix problems as they see them - enjoy ;-) -Frank At 12:51 AM 3/29/2006, you wrote: >Hi there! > >I'm not sure if this was topic before here, but currently the links in >some of >the Perl API docs on the website are wrong. Namely, in all pages > >http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/Perl/RegisterX.html > >with X in {AnObject, ServiceType, Namespace, ServiceInstance}, the links >listed under 'Other parts of MOBY-S API' point to the wrong directory. The >relative paths are lacking the initial dots ("../"). > >Regards, >dirk > >-- > >---------------------------------------------------------- >Dirk Haase phone +49 89 3187 3583 >http://mips.gsf.de/~haase email d.haase at gsf.de >_______________________________________________ >MOBY-dev mailing list >MOBY-dev at lists.open-bio.org >http://lists.open-bio.org/mailman/listinfo/moby-dev PhD, Computational Biologist, Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA 02115, USA. Tel: 617-432-3555 Fax: 617-432-3557 http://llama.med.harvard.edu/~fgibbons From d.haase at gsf.de Wed Mar 29 10:45:49 2006 From: d.haase at gsf.de (Dirk Haase) Date: Wed, 29 Mar 2006 17:45:49 +0200 Subject: [MOBY-dev] Wrong links in Perl web docs In-Reply-To: <5.2.1.1.2.20060329100915.01261750@email.med.harvard.edu> References: <5.2.1.1.2.20060329100915.01261750@email.med.harvard.edu> Message-ID: <200603291745.49568.d.haase@gsf.de> On Wednesday 29 March 2006 17:10, Frank Gibbons wrote: > Dirk. > > I'm waiting for my account to be reinstated on openbio.org, but feel free > to go ahead and insert those little dots. The point of putting the docs > under CVS control is that anyone can fix problems as they see them - enjoy > ;-) Hmm. I guess with 'anyone' you mean 'anyone with write access to CVS'... So although putting dots into docs is one of my favorite amusements, I have to step back here ;-) Regards, dirk From markw at illuminae.com Wed Mar 29 11:28:00 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 29 Mar 2006 08:28:00 -0800 Subject: [MOBY-dev] [moby] Re: Wrong links in Perl web docs In-Reply-To: <200603291745.49568.d.haase@gsf.de> References: <5.2.1.1.2.20060329100915.01261750@email.med.harvard.edu> <200603291745.49568.d.haase@gsf.de> Message-ID: <1143649680.20801.60.camel@bioinfo.icapture.ubc.ca> LOL! Yeah, not getting a CVS account is a good way to avoid the dirty work ;-) If I find time today I'll try to go in and fix them myself. Thanks for the notification! Cheers all! M On Wed, 2006-03-29 at 17:45 +0200, Dirk Haase wrote: > On Wednesday 29 March 2006 17:10, Frank Gibbons wrote: > > Dirk. > > > > I'm waiting for my account to be reinstated on openbio.org, but feel free > > to go ahead and insert those little dots. The point of putting the docs > > under CVS control is that anyone can fix problems as they see them - enjoy > > ;-) > > Hmm. I guess with 'anyone' you mean 'anyone with write access to CVS'... So > although putting dots into docs is one of my favorite amusements, I have to > step back here ;-) > > Regards, > dirk > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- -- 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 "For most of this century we have viewed communications as a conduit, a pipe between physical locations on the planet. What's happened now is that the conduit has become so big and interesting that communication has become more than a conduit, it has become a destination in its own right..." Paul Saffo - Director, Institute for the Future From senger at ebi.ac.uk Wed Mar 1 06:57:17 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Wed, 1 Mar 2006 06:57:17 +0000 (GMT) Subject: [MOBY-dev] link to "how to get code from cvs" In-Reply-To: <5.2.1.1.2.20060228135638.01258b30@email.med.harvard.edu> Message-ID: Frank, I suggest that the "CVS Repository" link from the main biomoby.org does not go directly to the web-based cvs browser, but rather to the instructions how to get it from the CVS (unless Chris wants to put these instructions directly to the web-based CVS page). These instructions were here: http://www.biomoby.org/GettingTheCode.html (but are not anymore - BTW, where are they now? - because I have a dead link to them in jMoby), or use the one in jMoby: http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/CVS.html (this is the page that has, at the moment, the dead link mentioned above). Thanks, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger consulting for: International Rice Research Institute Biometrics and Bioinformatics Unit DAPO BOX 7777, Metro Manila Philippines, phone: +63-2-580-5600 (ext.2324) From senger at ebi.ac.uk Wed Mar 1 10:24:15 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Wed, 1 Mar 2006 10:24:15 +0000 (GMT) Subject: [MOBY-dev] policies on Biomoby registries Message-ID: You might have noticed that Mark (silently? :-)) created a new page with a list of known biomoby registries where each registry can provide its own policy (http://biomoby.org/CVS_CONTENT/moby-live/Docs/ProjectDocs/). This may not come as a surprise after his strongly expressed opinion of what he wants and does not want in "his" registry. But it may be done slightly too silently to let me feel comfortable (sorry, Mark, this is just my feeling, I cannot help it). The strength of Biomoby was always in sharing - and if we suddenly starts to have many registries this strenghts may decreased. On the other hand, I feel that we actually *need* more registries, perhaps with different purposes, and with the different level of curation. But before starting to list them we should - here my 2cs go in - think first about federation of the registries, about an API how to access more registries etc. We mentioned federation during the last developer meeting (which was, btw and so far, really the last one, at least regarding the funds available from Vancouver, as I understand it) but have not built on it yet. And we should. Can we just postpone implementation of the individual (public) registry policies and first to discuss how to make the various registries federated? Thanks in advance for your opinions. Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger consulting for: International Rice Research Institute Biometrics and Bioinformatics Unit DAPO BOX 7777, Metro Manila Philippines, phone: +63-2-580-5600 (ext.2324) From markw at illuminae.com Wed Mar 1 15:29:10 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 01 Mar 2006 07:29:10 -0800 Subject: [MOBY-dev] [moby] link to "how to get code from cvs" In-Reply-To: References: Message-ID: <1141226950.30896.2.camel@bioinfo.icapture.ubc.ca> On Wed, 2006-03-01 at 06:57 +0000, Martin Senger wrote: > I suggest that the "CVS Repository" link from the main biomoby.org does > not go directly to the web-based cvs browser, but rather to the > instructions how to get it from the CVS Done. From senger at ebi.ac.uk Wed Mar 1 15:33:00 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Wed, 1 Mar 2006 15:33:00 +0000 (GMT) Subject: [MOBY-dev] [moby] link to "how to get code from cvs" In-Reply-To: <1141226950.30896.2.camel@bioinfo.icapture.ubc.ca> Message-ID: > Done. > Thanks! Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger consulting for: International Rice Research Institute Biometrics and Bioinformatics Unit DAPO BOX 7777, Metro Manila Philippines, phone: +63-2-580-5600 (ext.2324) From markw at illuminae.com Wed Mar 1 16:30:16 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 01 Mar 2006 08:30:16 -0800 Subject: [MOBY-dev] Lengthy commentary on registry policies and my own responsibilities In-Reply-To: References: Message-ID: <1141230616.30896.64.camel@bioinfo.icapture.ubc.ca> On Wed, 2006-03-01 at 10:24 +0000, Martin Senger wrote: > You might have noticed that Mark (silently? :-)) created a new page I quote from my message of Feb 21st: "The policy of the MOBY Central registry at iCAPTURE is currently being drawn-up. A first draft is available (click on Project Docs on the right side of the moby homepage) for comment" > But it may be done slightly too silently to let me feel comfortable > (sorry, Mark, this is just my feeling, I cannot help it). Public discussion is welcome; your opinion, in particular, is **always** valued! > The strength of > Biomoby was always in sharing - and if we suddenly starts to have many > registries this strenghts may decreased. I **strongly** support this statement!!!! The reality is, unfortunately, not in line with this vision. I host a registry, you host a registry at IRRI, MIPS hosts a registry, INB hosts a registry, there is a (dead?) registry at the University of Queensland, I host a second registry here specifically for TAIR, a third for our local services here at iCAPTURE, and yet a fourth here that allows me to continue doing interoperability research, since the new RFC policies around MOBY development are not conducive to a research environment. > On the other hand, I feel that we actually *need* more registries, > perhaps with different purposes, and with the different level of curation. > But before starting to list them we should - here my 2cs go in - think > first about federation of the registries, about an API how to access more > registries etc. Absolutely! For the past year I have been slowly (yes, silently ;-) ) moving the MOBY Central Perl code to a point where we might be in a position to support multiple registries more easily once we decide how to do so. The codebase was **strongly** tied to the concept of a single registry that was aware of a single object ontology, a single service ontology, and a single namespace ontology. In many ways it still is - the ontology maintenance routines are hard-coded to prevent the modification or removal of Objects, Services, and Namespaces that are being used; however, that is only true if the registry itself KNOWS about the Service Instance that is using it - this is where the idea of multiple registries breaks down right now. This will require much more community discussion, but I think there is one possible solution that minimizes the "pain" - this is just an idea for discussion, not an RFC :-) Many years ago, largely with an eye to better supporting the PlaNet registry at MIPS - they were registering their own objects in their own ontologies - I started moving the codebase toward an LSID-based naming system for the ontology nodes; this allows secondary registries to register new ontology nodes under their own LSID authorities. This doesn't entirely solve the problem, since any registry can use any other registries Objects, Namespaces, and Services regardless of the LSID authority under which they were registered, but it does give the registry a way of detecting which Ontology nodes "belong to it", and possibly querying (through LSID resolution) other registries to retrieve information about foreign Ontology nodes. I'm not convinced that this is a "good" solution...in fact (using Phillip Lord's Name in vain - hehehhehe... funny pun in there!) Phillip would say that an Ontology is only useful if it is *shared*, and so the idea of having multiple ontologies is dangerous from the get-go. So... yes... there's a lot of discussion required around how to support multiple registries, and in particular, how to support multiple ontologies. The ontology literature would suggest that we have built, for ourselves, an unsustainable architecture as soon as we allowed the ontologies to fork... that may or may not be true, but the solution certainly isn't obvious... > (which was, btw and so far, really the last one, at least regarding the > funds available from Vancouver, as I understand it) Correct for the moment. MOBY has just received a sizable award from Genome Canada for the next 3+ years, but this is specifically for code maintenance and tooling. There is no money for meetings in that pot, though there is no reason why we can't put together a meeting that is self-funded. Traditionally I have paid for much of the expense of hosting meetings here in Canada through the MOBY Genome Canada award, but that doesn't have to be the case if there is the need for a meeting. In any case, in the next couple of months there will be another competition announcement from Genome Canada, and I will be submitting an application to that competition that includes another pot of money to support developer conferences. Fingers crossed! > Can we just postpone implementation of the > individual (public) registry policies and first to discuss how to make the > various registries federated? I am not opposed to this. Though the agent will start running in a few days, Eddie has agreed not to activate the service deregistration function for at least three months so that everyone can get used to the feeling of "being crawled". If the community feeling remains strong against the policies I have documented for "my" MOBY Central instance, the objections should be raised either to me personally, or publicly, and discussed. I do, however, have several comments with regard to my responsibilities to the MOBY community, to my granting agency, and to my own research endeavours (which is where MOBY started, and it continues to be a primary domain of *research* in my laboratory). Genome Canada funded MOBY to be developed as a platform of interoperability for other Genome Canada projects. Period. This is a responsibility that I cannot fail in, since it is the primary responsibility I undertook by accepting the award, so I am somewhat limited in my freedom. One possibility would be to support a "public" registry that was a free-for-all and largely uncurated, and to support a second, curated registry to support only the Genome Canada projects, much like the INB has done. Unfortunately, I was only awarded funds for a single server - that is the server that is currently running "my" MOBY Central - so this option makes me a bit uncomfortable. Moreover, as Paul, among others, have pointed out: "Right now in the registry if I send a generic object I get over a hundred services back, almost none of which will actually consume the object without dying a horrible death." (Gordon, Feb 17th). MOBY Central has become increasingly useless over the past couple of years as it got filled with junk, badly registered services, dead services, "localhost" services, test services, and all manner of other registration artifacts. This week, for the first time in over a year, I started up Gbrowse Moby and was (more or less) ACTUALLY ABLE TO SURF MOBY DATA!! It was heavenly! Because of the curatorial policy that I enforced - after public warnings that I was about to do so - "my" registry suddenly became a useful resource not only to Genome Canada, but also to the wider community. Some might argue about what "useful" means, but I think that "doing what it was built to do" is a pretty good measure... and, frankly, I cannot interpret the word any other way, since I have a responsibility to my funding agency to generate something useful. The curation policy I have posted does not change the API. It is only a policy, and though policies can be debated, I don't think that any of the other registry hosts would want to be told how to curate "their" registries. Granted, the registry that I host is a unique resource in that it is the only (??) public registry; I take that responsibility seriously as well! However, that responsibility (surely?!) also requires that I try to make the registry useful to the majority of the community users; we, as a community, can discuss whether the policy I proposed goes too far - though I reserve the right to make the final decision on "my" registry - however, my experience of using MOBY Central this week suggests to me that this policy only made the public resource better. That's my open-kimono. Opinions always welcome, 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 "For most of this century we have viewed communications as a conduit, a pipe between physical locations on the planet. What's happened now is that the conduit has become so big and interesting that communication has become more than a conduit, it has become a destination in its own right..." Paul Saffo - Director, Institute for the Future From duncan.hull at cs.man.ac.uk Thu Mar 2 18:27:22 2006 From: duncan.hull at cs.man.ac.uk (Duncan Hull) Date: Thu, 02 Mar 2006 18:27:22 +0000 Subject: [MOBY-dev] Printing shorthand BioMOBY RDF notation In-Reply-To: References: Message-ID: <4407390A.2090802@cs.man.ac.uk> Hello Can anyone recommend any tools for printing shorthand notation of BioMOBY RDF service descriptions, e.g. that output from http://mobycentral.icapture.ubc.ca/LSID_resolver.html ? I was thinking of N3 [1] or something similar, but maybe someone on moby-dev knows better? Fitting all that lovely RDF onto a sheet of A4 paper is a challenging task...so I could use a shorthand notation. Duncan [1] http://infomesh.net/2001/cwm/ looks very old -- Duncan Hull http://www.cs.man.ac.uk/~hulld/ Phone: +44 (0) 161 275 0677 From gss at ncgr.org Thu Mar 2 19:17:20 2006 From: gss at ncgr.org (Gary Schiltz) Date: Thu, 02 Mar 2006 12:17:20 -0700 Subject: [MOBY-dev] Printing shorthand BioMOBY RDF notation In-Reply-To: <4407390A.2090802@cs.man.ac.uk> References: <4407390A.2090802@cs.man.ac.uk> Message-ID: <440744C0.2020201@ncgr.org> If I submit the first example LSID ( urn:lsid:biomoby.org:servicetype:Retrieval) on the page, I get the following as RDF: The base retrieval type Retrieval a base Service class, never instantiated Service I can then paste that RDF into the converter at http://www.semanticmoby.org/developer/dev-tools.jsp, select RDF/XML as input format and N3 as output format, press the Convert Graph button, and get the following N3: @prefix mobyService: . @prefix mobyObject: . @prefix mobyNamespace: . @prefix serviceInstances: . @prefix moby: . @prefix rdfs: . @prefix rdf: . mobyService:Retrieval a rdfs:Class ; rdfs:comment "The base retrieval type"@en ; rdfs:label "Retrieval"@en ; rdfs:subClassOf mobyService:Service . mobyService:Service a rdfs:Class ; rdfs:comment "a base Service class, never instantiated"@en ; rdfs:label "Service"@en . Not many fewer lines, but the N3 is to my eyes more readable. // Gary Duncan Hull wrote: > Hello > > Can anyone recommend any tools for printing shorthand notation of > BioMOBY RDF service descriptions, e.g. that output from > http://mobycentral.icapture.ubc.ca/LSID_resolver.html ? > > I was thinking of N3 [1] or something similar, but maybe someone on > moby-dev knows better? > > Fitting all that lovely RDF onto a sheet of A4 paper is a challenging > task...so I could use a shorthand notation. > > Duncan > > [1] http://infomesh.net/2001/cwm/ looks very old > > From markw at illuminae.com Thu Mar 2 21:21:30 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 02 Mar 2006 13:21:30 -0800 Subject: [MOBY-dev] [moby] Printing shorthand BioMOBY RDF notation In-Reply-To: <4407390A.2090802@cs.man.ac.uk> References: <4407390A.2090802@cs.man.ac.uk> Message-ID: <1141334490.16059.0.camel@bioinfo.icapture.ubc.ca> http://www.mindswap.org/2002/rdfconvert/ M On Thu, 2006-03-02 at 18:27 +0000, Duncan Hull wrote: > Hello > > Can anyone recommend any tools for printing shorthand notation of > BioMOBY RDF service descriptions, e.g. that output from > http://mobycentral.icapture.ubc.ca/LSID_resolver.html ? > > I was thinking of N3 [1] or something similar, but maybe someone on > moby-dev knows better? > > Fitting all that lovely RDF onto a sheet of A4 paper is a challenging > task...so I could use a shorthand notation. > > Duncan > > [1] http://infomesh.net/2001/cwm/ looks very old > -- -- 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 "For most of this century we have viewed communications as a conduit, a pipe between physical locations on the planet. What's happened now is that the conduit has become so big and interesting that communication has become more than a conduit, it has become a destination in its own right..." Paul Saffo - Director, Institute for the Future From duncan.hull at cs.man.ac.uk Thu Mar 2 22:41:56 2006 From: duncan.hull at cs.man.ac.uk (Duncan Hull) Date: Thu, 02 Mar 2006 22:41:56 +0000 Subject: [MOBY-dev] [moby] Printing shorthand BioMOBY RDF notation In-Reply-To: <1141334490.16059.0.camel@bioinfo.icapture.ubc.ca> References: <4407390A.2090802@cs.man.ac.uk> <1141334490.16059.0.camel@bioinfo.icapture.ubc.ca> Message-ID: <440774B4.7090701@cs.man.ac.uk> Mark Wilkinson wrote: >http://www.mindswap.org/2002/rdfconvert/ > > great, thanks mark. I take back all the nasty things I've said about RDF :) Sesame does a pretty good job of this kind of thing too... http://www.openrdf.org/ Duncan -- Duncan Hull http://www.cs.man.ac.uk/~hulld/ Phone: +44 (0) 161 275 0677 From edward.kawas at gmail.com Thu Mar 2 23:24:03 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 2 Mar 2006 15:24:03 -0800 Subject: [MOBY-dev] RDF agent test page Message-ID: <002c01c63e50$65a11880$6500a8c0@notebook> Hi, Recently on the test registry, I have deployed the agent for, believe it or not, testing purposes. I would be very interested in having people try it out. Being a test registry, services will be removed, modified, etc as the agent encounters orphans, modifications, etc. Email is also used by the agent and so please make sure that if you are going to call the agent over that you use your email address in the contact email part of a service description. The endpoint for the registry is: http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl The URI for the registry is: http://bioinfo.icapture.ubc.ca/MOBY/Central I deployed a servlet that given a url to an RDF document that describes one or more services, parses the services into human readable formatted text and also details any errors that the agent, not the registry, has found with any particular service. This servlet is located at: http://bioinfo.icapture.ubc.ca/ekawas/agent/RDFAgent_test.html Some urls that you can use for testing the test servlet are: http://bioinfo.icapture.ubc.ca/ekawas/services/parseBlastText.rdf (contains 1 service) http://mobycentral.icapture.ubc.ca/localServices.rdf (contains >20 services?) http://bioinfo.icapture.ubc.ca/ekawas/services/blastDragon.xml http://bioinfo.icapture.ubc.ca/ekawas/services/parseBlast.xml ('valid' RDF, invalid w.r.t moby) http://biomoby.org/RESOURCES/MOBY-S/ServiceInstances (contains all of the services in the mobycentral registry - might cause browser to timeout) Feel free to use the LSID resolver to gather more examples. You can download the RDFs and modify them as you see fit. Then you can place them on a web server and call the agent to you. If you are interested in testing the correctness and validity of your RDF document strictly in terms of RDF, the w3c have an excellent resource in the RDF Validator. This validator is located at: http://www.w3.org/RDF/Validator/ Those 2 resources should take any pain out of RDF and the transition to the agent. In addition to these methods of interacting with the agent, you can perfrom registerService calls on this test registry specifying no more than a signatureURL and the agent will be called over to inspect that url. Any new services in that url will be registered, modified services will be re-registered and missing services (ones the agent thinks should be there) will be deregistered. I will have an agent html page discussing what the agent is, how to install the agent, configuring the agent, etc up soon. Thanks, Eddie From duncan.hull at cs.man.ac.uk Fri Mar 3 09:39:00 2006 From: duncan.hull at cs.man.ac.uk (Duncan Hull) Date: Fri, 03 Mar 2006 09:39:00 +0000 Subject: [MOBY-dev] Layering OWL on top of BioMOBY RDF descriptions In-Reply-To: <440744C0.2020201@ncgr.org> References: <4407390A.2090802@cs.man.ac.uk> <440744C0.2020201@ncgr.org> Message-ID: <44080EB4.3000701@cs.man.ac.uk> Gary Schiltz wrote: >I can then paste that RDF into the converter at http://www.semanticmoby.org/developer/dev-tools.jsp > > ...and thanks Gary too... Actually, while we're on the subject of RDF...BioMOBY has done a great job of demonstrating some of the strengths and limitations of using RDF to represent bioinformatics service metadata. The next layer in the semantic web cake [1] is to add OWL descriptions. Semantic MOBY, BioMOBY and myGrid have all made various moves in this direction. With OWL, we get more expressivity and the ability to reason over our services, in particular we possibly get more "bang for our buck", specifically: 1. We can distinguish between classes and instances (individuals) 2. Properties won't be able to have properties any more (something RDF/RDFS lets you do) 3. We can distinguish between language constructors and ontology vocabulary 4. We have localised range and domain constraints 5. We get existence/cardinality constraints 6. We get transitive, inverse and symmetrical properties 7. We get better reasoning support using "native" reasoners (see [2,3] for details) So, which bits of this rich service metadata are going to be a) realist to capture? b) useful for biologists and bioinformaticians describing and finding services? c) useful for registry providers to manage their services? I realise these are all very open questions, but I'd be interested to know what moby-devvers think... Duncan [1] http://www.cs.man.ac.uk/~horrocks/Publications/download/2005/HPPH05.pdf [2] http://www.cs.man.ac.uk/~horrocks/Teaching/cs646/Slides/ontologies.pdf (see problems with RDF/RDFS) [3] http://www.cs.man.ac.uk/~horrocks/Publications/download/2003/HoPH03a.pdf -- Duncan Hull http://www.cs.man.ac.uk/~hulld/ Phone: +44 (0) 161 275 0677 From Pieter.Neerincx at wur.nl Fri Mar 3 14:02:23 2006 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Fri, 3 Mar 2006 15:02:23 +0100 Subject: [MOBY-dev] Lengthy commentary on registry policies and my own responsibilities In-Reply-To: <1141230616.30896.64.camel@bioinfo.icapture.ubc.ca> References: <1141230616.30896.64.camel@bioinfo.icapture.ubc.ca> Message-ID: <6357450E-D6DF-40A9-8EC2-6DC07B77C69D@wur.nl> Hi, On 1-Mar-2006, at 5:30 PM, Mark Wilkinson wrote: > On Wed, 2006-03-01 at 10:24 +0000, Martin Senger wrote: >> You might have noticed that Mark (silently? :-)) created a new page Well it's a publicly available page and not something hidden, encoded, deeply buried inside a lot of subfolders of the CVS. I spotted the page and was actually pretty happy with it. The official registry is only useful if most of the services in it actually work. So in my opinion it should be either manually curated or the services should be frequently checked in an automated fashion to make sure they work as registered / advertised. > > > I quote from my message of Feb 21st: > > "The policy of the MOBY Central registry at iCAPTURE is currently > being drawn-up. A first draft is available (click on Project Docs on > the right side of the moby homepage) for comment" > > > >> But it may be done slightly too silently to let me feel >> comfortable >> (sorry, Mark, this is just my feeling, I cannot help it). > > Public discussion is welcome; your opinion, in particular, is > **always** valued! > > >> The strength of >> Biomoby was always in sharing - and if we suddenly starts to have >> many >> registries this strenghts may decreased. > > I **strongly** support this statement!!!! I second that. So after a lot of testing I registered my first publicly available services in the official Central 2 days ago :). On a side note: how often is that graph with the "World wide distribution of BioMOBY services" on the webside updated? I'v been refreshing that page many times a day like a little kid waiting for birthday presents, but so far nothing popped up :(. > The reality is, > unfortunately, not in line with this vision. I host a registry, you > host a registry at IRRI, MIPS hosts a registry, INB hosts a registry, > there is a (dead?) registry at the University of Queensland, I host a > second registry here specifically for TAIR, a third for our local > services here at iCAPTURE, and yet a fourth here that allows me to > continue doing interoperability research, since the new RFC policies > around MOBY development are not conducive to a research environment. I have another 2 registries here at the WUR, but exclusively for testing and debugging. I didn't want to mess up Mark's public Central with my experimental stuff. Multiple registries are fine if they have different specific functions. Having services that were meant to be publicly available from multiple registries would be good too for example for redundancy. In case one of those registries is down you can simple use another. But the tricky part is that multiple registries will easily get out of sync, both with regard to the registered services as with regard to the version of the API they are running. If that happens everybody will not trust the registries already available and create their own. In the end we'll all be licking our own lollypops and the idea of interoperability will be gone. > > >> On the other hand, I feel that we actually *need* more registries, >> perhaps with different purposes, and with the different level of >> curation. >> But before starting to list them we should - here my 2cs go in - >> think >> first about federation of the registries, about an API how to >> access more >> registries etc. > > > Absolutely! For the past year I have been slowly (yes, silently ;-) ) > moving the MOBY Central Perl code to a point where we might be in a > position to support multiple registries more easily once we decide how > to do so. The codebase was **strongly** tied to the concept of a > single > registry that was aware of a single object ontology, a single service > ontology, and a single namespace ontology. In many ways it still is - > the ontology maintenance routines are hard-coded to prevent the > modification or removal of Objects, Services, and Namespaces that are > being used; however, that is only true if the registry itself KNOWS > about the Service Instance that is using it - this is where the > idea of > multiple registries breaks down right now. > > This will require much more community discussion, but I think there is > one possible solution that minimizes the "pain" - this is just an idea > for discussion, not an RFC :-) > > Many years ago, largely with an eye to better supporting the PlaNet > registry at MIPS - they were registering their own objects in their > own > ontologies - I started moving the codebase toward an LSID-based naming > system for the ontology nodes; this allows secondary registries to > register new ontology nodes under their own LSID authorities. This > doesn't entirely solve the problem, since any registry can use any > other > registries Objects, Namespaces, and Services regardless of the LSID > authority under which they were registered, but it does give the > registry a way of detecting which Ontology nodes "belong to it", and > possibly querying (through LSID resolution) other registries to > retrieve > information about foreign Ontology nodes. > > I'm not convinced that this is a "good" solution...in fact (using > Phillip Lord's Name in vain - hehehhehe... funny pun in there!) > Phillip > would say that an Ontology is only useful if it is *shared*, and so > the > idea of having multiple ontologies is dangerous from the get-go. > > So... yes... there's a lot of discussion required around how to > support > multiple registries, and in particular, how to support multiple > ontologies. The ontology literature would suggest that we have built, > for ourselves, an unsustainable architecture as soon as we allowed the > ontologies to fork... that may or may not be true, but the solution > certainly isn't obvious... > > >> (which was, btw and so far, really the last one, at least >> regarding the >> funds available from Vancouver, as I understand it) > > Correct for the moment. MOBY has just received a sizable award from > Genome Canada for the next 3+ years, but this is specifically for code > maintenance and tooling. There is no money for meetings in that pot, > though there is no reason why we can't put together a meeting that is > self-funded. Traditionally I have paid for much of the expense of > hosting meetings here in Canada through the MOBY Genome Canada award, > but that doesn't have to be the case if there is the need for a > meeting. > In any case, in the next couple of months there will be another > competition announcement from Genome Canada, and I will be > submitting an > application to that competition that includes another pot of money to > support developer conferences. Fingers crossed! > > >> Can we just postpone implementation of the >> individual (public) registry policies and first to discuss how to >> make the >> various registries federated? > > I am not opposed to this. Though the agent will start running in a > few > days, Eddie has agreed not to activate the service deregistration > function for at least three months so that everyone can get used to > the > feeling of "being crawled". If the community feeling remains strong > against the policies I have documented for "my" MOBY Central instance, > the objections should be raised either to me personally, or publicly, > and discussed. > > I do, however, have several comments with regard to my > responsibilities > to the MOBY community, to my granting agency, and to my own research > endeavours (which is where MOBY started, and it continues to be a > primary domain of *research* in my laboratory). > > Genome Canada funded MOBY to be developed as a platform of > interoperability for other Genome Canada projects. Period. Sure! But it's in the interest of the people in Genome Canada projects to be able to use services from other service providers as well. Look at it from this side: if Genome Canada funds a good BioMOBY Central they get to use lot's of services whose development they didn't have to fund for free! > This is a > responsibility that I cannot fail in, since it is the primary > responsibility I undertook by accepting the award, so I am somewhat > limited in my freedom. One possibility would be to support a "public" > registry that was a free-for-all and largely uncurated, and to > support a > second, curated registry to support only the Genome Canada projects, > much like the INB has done. Bad idea in my point of view. The free-for-all registry will be a mess in no time, so in the end no one will use it. Then if the people in Genome Canada want to benefit from services in the INB registry, those registries will have to run the same version of the interface. Currently the registration process already differs, because at the INB they request additional info. I think it's just a matter of time before multiple Centrals will be out of sync. What we need is one big public free curated Central. Maybe it could be mirrored for load balancing and fail-over, but that will only work if those Centrals are *perfect* mirrors. If people start to host "partial" mirrors or outdated mirrors it won't work. In that case everyone will go straight to the official server, because they don't trust the mirrors. > Unfortunately, I was only awarded funds for > a single server If hardware is an issue, I think we could easily run a Central on dedicated hardware over here at the WUR. I would have to ask my boss of course, but I think we would be happy to help out with either a perfect mirror of the official public BioMOBY Central or with a public 'feel free to experiment' test Central or both. But I will never run my own 'only available to WUR users' Central or one with a custom patched interface. > - that is the server that is currently running "my" MOBY > Central - so this option makes me a bit uncomfortable. > Moreover, as > Paul, among others, have pointed out: "Right now in the registry if I > send a generic object I get over a hundred services back, almost > none of > which will actually consume the object without dying a horrible > death." (Gordon, Feb 17th). MOBY Central has become increasingly > useless > over the past couple of years as it got filled with junk, badly > registered services, dead services, "localhost" services, test > services, > and all manner of other registration artifacts. This week, for the > first time in over a year, I started up Gbrowse Moby and was (more or > less) ACTUALLY ABLE TO SURF MOBY DATA!! It was heavenly! Because of > the curatorial policy that I enforced - after public warnings that > I was > about to do so - "my" registry suddenly became a useful resource not > only to Genome Canada, but also to the wider community. Some might > argue about what "useful" means, but I think that "doing what it was > built to do" is a pretty good measure... and, frankly, I cannot > interpret the word any other way, since I have a responsibility to my > funding agency to generate something useful. > > The curation policy I have posted does not change the API. It is > only a > policy, and though policies can be debated, I don't think that any of > the other registry hosts would want to be told how to curate "their" > registries. Granted, the registry that I host is a unique resource in > that it is the only (??) public registry; I take that responsibility > seriously as well! However, that responsibility (surely?!) also > requires that I try to make the registry useful to the majority of the > community users; we, as a community, can discuss whether the policy I > proposed goes too far I think it's a fair policy and it should have been like this form the start! > - though I reserve the right to make the final > decision on "my" registry - however, my experience of using MOBY > Central > this week suggests to me that this policy only made the public > resource > better. Definitely! I'm glad the policy is there and I think Mark is doing a fine job as the guardian of the only public Central we have. Cheers, Pi > That's my open-kimono. > > Opinions always welcome, > > 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 > > "For most of this century we have viewed communications as a conduit, > a pipe between physical locations on the planet. > What's happened now is that the conduit has become so big and > interesting > that communication has become more than a conduit, > it has become a destination in its own right..." > > Paul Saffo - Director, Institute for the Future > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at biomoby.org > http://biomoby.org/mailman/listinfo/moby-dev Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 060 fax: 0317-483 584 mobile: 06-143 66 783 pieter.neerincx at wur.nl From markw at illuminae.com Fri Mar 3 16:11:20 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 03 Mar 2006 08:11:20 -0800 Subject: [MOBY-dev] [moby] Re: Lengthy commentary on registry policies and my own responsibilities In-Reply-To: <6357450E-D6DF-40A9-8EC2-6DC07B77C69D@wur.nl> References: <1141230616.30896.64.camel@bioinfo.icapture.ubc.ca> <6357450E-D6DF-40A9-8EC2-6DC07B77C69D@wur.nl> Message-ID: <1141402280.6637.40.camel@bioinfo.icapture.ubc.ca> On Fri, 2006-03-03 at 15:02 +0100, Pieter Neerincx wrote: > a side note: how often is that graph with the "World wide > distribution of BioMOBY services" on the webside updated? I'v been > refreshing that page many times a day like a little kid waiting for > birthday presents, but so far nothing popped up :(. It should be updating every few hours... I'll check the cron and see if something is broken. 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 "For most of this century we have viewed communications as a conduit, a pipe between physical locations on the planet. What's happened now is that the conduit has become so big and interesting that communication has become more than a conduit, it has become a destination in its own right..." Paul Saffo - Director, Institute for the Future From markw at illuminae.com Fri Mar 3 16:14:16 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 03 Mar 2006 08:14:16 -0800 Subject: [MOBY-dev] [moby] Re: Lengthy commentary on registry policies and my own responsibilities In-Reply-To: <6357450E-D6DF-40A9-8EC2-6DC07B77C69D@wur.nl> References: <1141230616.30896.64.camel@bioinfo.icapture.ubc.ca> <6357450E-D6DF-40A9-8EC2-6DC07B77C69D@wur.nl> Message-ID: <1141402456.6637.42.camel@bioinfo.icapture.ubc.ca> > I think it's a fair policy and it should have been like this form the > start! Thanks :-) > Definitely! I'm glad the policy is there and I think Mark is doing a > fine job as the guardian of the only public Central we have. And thanks again!! :-) 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 "For most of this century we have viewed communications as a conduit, a pipe between physical locations on the planet. What's happened now is that the conduit has become so big and interesting that communication has become more than a conduit, it has become a destination in its own right..." Paul Saffo - Director, Institute for the Future From markw at illuminae.com Fri Mar 3 16:21:30 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 03 Mar 2006 08:21:30 -0800 Subject: [MOBY-dev] [moby] Re: Lengthy commentary on registry policies and my own responsibilities In-Reply-To: <6357450E-D6DF-40A9-8EC2-6DC07B77C69D@wur.nl> References: <1141230616.30896.64.camel@bioinfo.icapture.ubc.ca> <6357450E-D6DF-40A9-8EC2-6DC07B77C69D@wur.nl> Message-ID: <1141402890.6637.51.camel@bioinfo.icapture.ubc.ca> > Sure! But it's in the interest of the people in Genome Canada > projects to be able to use services from other service providers as > well. Absolutely, and they are well aware of that! Luckily, the decisions that are best for them, are (usually, and IMO) also best for the rest of us, since we all have the same goal in mind :-) > Maybe it could be mirrored for load > balancing and fail-over, but that will only work if those Centrals > are *perfect* mirrors. If people start to host "partial" mirrors or > outdated mirrors it won't work. In that case everyone will go > straight to the official server, because they don't trust the mirrors. We discussed mirroring at the last meeting, and Phil and Pinar (@myGrid), Eddie and I discussed it at length again the last time we were in Manchester. Once we have an agent-based registration/deregistration mechanism in place, and everyone has SignatureURLs that resolve to RDF, the problem of keeping registries synchronized is (almost) trivial! Just ask one MOBY Central for all of it's signature URL's, hand those URL's to the agent of another registry, and let it crawl! Voila!! There still needs to be some hierarchy in there, and blah blah, but the crux of the problem is solved by the RDF signature... I think... we haven't DONE it yet, so there may be nefarious problems in there that aren't obvious from a superficial examination of the problem... Gotta run! Interviews to do... 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 "For most of this century we have viewed communications as a conduit, a pipe between physical locations on the planet. What's happened now is that the conduit has become so big and interesting that communication has become more than a conduit, it has become a destination in its own right..." Paul Saffo - Director, Institute for the Future From markw at illuminae.com Fri Mar 3 16:27:16 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 03 Mar 2006 08:27:16 -0800 Subject: [MOBY-dev] [moby] Layering OWL on top of BioMOBY RDF descriptions In-Reply-To: <44080EB4.3000701@cs.man.ac.uk> References: <4407390A.2090802@cs.man.ac.uk> <440744C0.2020201@ncgr.org> <44080EB4.3000701@cs.man.ac.uk> Message-ID: <1141403236.6637.57.camel@bioinfo.icapture.ubc.ca> On Fri, 2006-03-03 at 09:39 +0000, Duncan Hull wrote: > I realise these are all very open questions, but I'd be interested to > know what moby-devvers think... Outside of the public eye, I have three students right now working on OWLifying all aspects of MOBY, and making a clear separation of the models from the data and service instances. We are expecting to see some REALLY interesting behaviours in the context of tools like Ben & Clarence's Ahab/Ishmael MOBY browsers - DL-reasoned discovery of unexpected, but applicable, services after DL-reasoned *integration* and *recombination* of multiple data-types from multiple MOBY service executions into new data-types. Fun!! 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 "For most of this century we have viewed communications as a conduit, a pipe between physical locations on the planet. What's happened now is that the conduit has become so big and interesting that communication has become more than a conduit, it has become a destination in its own right..." Paul Saffo - Director, Institute for the Future From ddg at ncgr.org Fri Mar 3 17:07:30 2006 From: ddg at ncgr.org (Damian Gessler) Date: Fri, 3 Mar 2006 10:07:30 -0700 Subject: [MOBY-dev] Layering OWL on top of BioMOBY RDF descriptions References: <4407390A.2090802@cs.man.ac.uk><440744C0.2020201@ncgr.org> <44080EB4.3000701@cs.man.ac.uk> Message-ID: <00c501c63ee4$f4a04e90$674413ac@ncgr.org> Hi Duncan, > The next layer in the semantic web cake [1] is to add OWL descriptions. Totally on board with you here. To see how it's working, go to www.semanticmoby.org and type in "dna". You'll see that term retrieves, in a Google-like manner, four bioinformatic service providers. Click on the RDF icon by their name and you'll see the OWL Resource Description Graph (essentially the equivalent of a semantically-wise WSDL, though completely unrelated in implementation with WSDL). [Note: your browser may be set to any number of alternative display modes for RDF; do a View Source if it isn't easily readable). You can try the Legume Information Network to see how resources can be pipelined. For shared ontologies--the meat of the middle layer of how resources describe themselves and thus how they are discovered and engaged--a few a populating at http://ontologies.ncgr.org. We're currently lining up conversions of SO and SOFA (Sequence Ontology), POC (Plant Ontology), and TO (Trait Ontology). D. ----- Original Message ----- From: "Duncan Hull" To: "Core developer announcements" Sent: Friday, March 03, 2006 2:39 AM Subject: [MOBY-dev] Layering OWL on top of BioMOBY RDF descriptions > Gary Schiltz wrote: > >>I can then paste that RDF into the converter at >>http://www.semanticmoby.org/developer/dev-tools.jsp >> >> > ...and thanks Gary too... > > Actually, while we're on the subject of RDF...BioMOBY has done a great > job of demonstrating some of the strengths and limitations of using RDF > to represent bioinformatics service metadata. > > The next layer in the semantic web cake [1] is to add OWL descriptions. > Semantic MOBY, BioMOBY and myGrid have all made various moves in this > direction. With OWL, we get more expressivity and the ability to reason > over our services, in particular we possibly get more "bang for our > buck", specifically: > > 1. We can distinguish between classes and instances (individuals) > 2. Properties won't be able to have properties any more (something > RDF/RDFS lets you do) > 3. We can distinguish between language constructors and ontology > vocabulary > 4. We have localised range and domain constraints > 5. We get existence/cardinality constraints > 6. We get transitive, inverse and symmetrical properties > 7. We get better reasoning support using "native" reasoners > > (see [2,3] for details) > > So, which bits of this rich service metadata are going to be > a) realist to capture? > b) useful for biologists and bioinformaticians describing and finding > services? > c) useful for registry providers to manage their services? > > I realise these are all very open questions, but I'd be interested to > know what moby-devvers think... > > Duncan > > [1] > http://www.cs.man.ac.uk/~horrocks/Publications/download/2005/HPPH05.pdf > [2] > http://www.cs.man.ac.uk/~horrocks/Teaching/cs646/Slides/ontologies.pdf > (see problems with RDF/RDFS) > [3] > http://www.cs.man.ac.uk/~horrocks/Publications/download/2003/HoPH03a.pdf > > -- > Duncan Hull > http://www.cs.man.ac.uk/~hulld/ > Phone: +44 (0) 161 275 0677 > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at biomoby.org > http://biomoby.org/mailman/listinfo/moby-dev > From duncan.hull at cs.man.ac.uk Sat Mar 4 09:21:34 2006 From: duncan.hull at cs.man.ac.uk (Duncan Hull) Date: Sat, 04 Mar 2006 09:21:34 +0000 Subject: [MOBY-dev] Semantic Web Services: Blowin' in the wind In-Reply-To: <00c501c63ee4$f4a04e90$674413ac@ncgr.org> References: <4407390A.2090802@cs.man.ac.uk><440744C0.2020201@ncgr.org> <44080EB4.3000701@cs.man.ac.uk> <00c501c63ee4$f4a04e90$674413ac@ncgr.org> Message-ID: <44095C1E.4080607@cs.man.ac.uk> Thanks Damian and Mark for you replies. I suppose some of the answers are blowin' in the wind :) -- Duncan Hull http://www.cs.man.ac.uk/~hulld/ Phone: +44 (0) 161 275 0677 From senger at ebi.ac.uk Sun Mar 5 21:49:03 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Sun, 5 Mar 2006 21:49:03 +0000 (GMT) Subject: [MOBY-dev] checking services Message-ID: Hi all, Within the GCP project, I have developed a small program that can check services with testing input data. I know that we have been talking about having such inputs in metadata, and I am sure it will soon come. But we needed something running now, so I have made this small project (using libraries in jMoby). It is easy to set it up (you still need to find what input data are needed) if you wish to have it run on your set of services. The program can be run from a command-line (we use it as a cron-job to check that our services are responding), or there is a web interface (my first play with Ajax :-) ). The documentation (with links to running examples, and with instructions where you can get it) is available at http://mobycentral.icapture.ubc.ca:8090/mobyenv/ (and mirrored at http://www.iris.irri.org/mobyenv/). I will be very glad to receive any comments and suggestions for improvement. Thanks, and with regards, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger consulting for: International Rice Research Institute Biometrics and Bioinformatics Unit DAPO BOX 7777, Metro Manila Philippines, phone: +63-2-580-5600 (ext.2324) From Pieter.Neerincx at wur.nl Mon Mar 6 12:03:16 2006 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Mon, 6 Mar 2006 13:03:16 +0100 Subject: [MOBY-dev] Front page messed up? In-Reply-To: <1141403236.6637.57.camel@bioinfo.icapture.ubc.ca> References: <4407390A.2090802@cs.man.ac.uk> <440744C0.2020201@ncgr.org> <44080EB4.3000701@cs.man.ac.uk> <1141403236.6637.57.camel@bioinfo.icapture.ubc.ca> Message-ID: <5D600A84-B90E-49CF-B477-D3D498E7E3F8@wur.nl> Hi all, On my machines (both Linux and Mac OS X and several different browsers) it looks like the BioMOBY website is messed up (only the front page). Is anybody working on it or do I smell something fishy? Cheers, Pi On 3-Mar-2006, at 5:27 PM, Mark Wilkinson wrote: > On Fri, 2006-03-03 at 09:39 +0000, Duncan Hull wrote: > >> I realise these are all very open questions, but I'd be interested to >> know what moby-devvers think... > > Outside of the public eye, I have three students right now working on > OWLifying all aspects of MOBY, and making a clear separation of the > models from the data and service instances. We are expecting to see > some REALLY interesting behaviours in the context of tools like Ben & > Clarence's Ahab/Ishmael MOBY browsers - DL-reasoned discovery of > unexpected, but applicable, services after DL-reasoned > *integration* and > *recombination* of multiple data-types from multiple MOBY service > executions into new data-types. > > Fun!! > > 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 > > "For most of this century we have viewed communications as a conduit, > a pipe between physical locations on the planet. > What's happened now is that the conduit has become so big and > interesting > that communication has become more than a conduit, > it has become a destination in its own right..." > > Paul Saffo - Director, Institute for the Future > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at biomoby.org > http://biomoby.org/mailman/listinfo/moby-dev Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 060 fax: 0317-483 584 mobile: 06-143 66 783 pieter.neerincx at wur.nl From markw at illuminae.com Mon Mar 6 16:37:55 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Mon, 06 Mar 2006 08:37:55 -0800 Subject: [MOBY-dev] [moby] Front page messed up? In-Reply-To: <5D600A84-B90E-49CF-B477-D3D498E7E3F8@wur.nl> References: <4407390A.2090802@cs.man.ac.uk> <440744C0.2020201@ncgr.org> <44080EB4.3000701@cs.man.ac.uk> <1141403236.6637.57.camel@bioinfo.icapture.ubc.ca> <5D600A84-B90E-49CF-B477-D3D498E7E3F8@wur.nl> Message-ID: <1141663075.17702.24.camel@bioinfo.icapture.ubc.ca> Can anyone else confirm this? I was working on the main page last night. It renders correctly on both of my machines in both Opera and IE browsers... but that doesn't mean there isn't something wrong :-) M On Mon, 2006-03-06 at 13:03 +0100, Pieter Neerincx wrote: > Hi all, > > On my machines (both Linux and Mac OS X and several different > browsers) it looks like the BioMOBY website is messed up (only the > front page). Is anybody working on it or do I smell something fishy? > > Cheers, > > Pi > > On 3-Mar-2006, at 5:27 PM, Mark Wilkinson wrote: > > > On Fri, 2006-03-03 at 09:39 +0000, Duncan Hull wrote: > > > >> I realise these are all very open questions, but I'd be interested to > >> know what moby-devvers think... > > > > Outside of the public eye, I have three students right now working on > > OWLifying all aspects of MOBY, and making a clear separation of the > > models from the data and service instances. We are expecting to see > > some REALLY interesting behaviours in the context of tools like Ben & > > Clarence's Ahab/Ishmael MOBY browsers - DL-reasoned discovery of > > unexpected, but applicable, services after DL-reasoned > > *integration* and > > *recombination* of multiple data-types from multiple MOBY service > > executions into new data-types. > > > > Fun!! > > > > 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 > > > > "For most of this century we have viewed communications as a conduit, > > a pipe between physical locations on the planet. > > What's happened now is that the conduit has become so big and > > interesting > > that communication has become more than a conduit, > > it has become a destination in its own right..." > > > > Paul Saffo - Director, Institute for the Future > > > > _______________________________________________ > > MOBY-dev mailing list > > MOBY-dev at biomoby.org > > http://biomoby.org/mailman/listinfo/moby-dev > > > Wageningen University and Research centre (WUR) > Laboratory of Bioinformatics > Transitorium (building 312) room 1034 > Dreijenlaan 3 > 6703 HA Wageningen > The Netherlands > phone: 0317-483 060 > fax: 0317-483 584 > mobile: 06-143 66 783 > pieter.neerincx at wur.nl > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at biomoby.org > http://biomoby.org/mailman/listinfo/moby-dev -- -- 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 "For most of this century we have viewed communications as a conduit, a pipe between physical locations on the planet. What's happened now is that the conduit has become so big and interesting that communication has become more than a conduit, it has become a destination in its own right..." Paul Saffo - Director, Institute for the Future From edward.kawas at gmail.com Mon Mar 6 16:42:20 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 6 Mar 2006 08:42:20 -0800 Subject: [MOBY-dev] [moby] Front page messed up? In-Reply-To: <1141663075.17702.24.camel@bioinfo.icapture.ubc.ca> Message-ID: <000801c6413c$f1493db0$6b00a8c0@notebook> Using firefox, the page doesn't look like it used to. More specifically, the flash map is now on the upper right of the page, the search box is in the middle of the page. The menu list (archives,categories, downloads, etc) is the footer of the page. On explorer, the page is viewed correctly. Eddie > -----Original Message----- > From: moby-dev-bounces at biomoby.org > [mailto:moby-dev-bounces at biomoby.org] On Behalf Of Mark Wilkinson > Sent: Monday, March 06, 2006 8:38 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] [moby] Front page messed up? > > Can anyone else confirm this? > > I was working on the main page last night. It renders > correctly on both of my machines in both Opera and IE > browsers... but that doesn't mean there isn't something wrong :-) > > M > > > > On Mon, 2006-03-06 at 13:03 +0100, Pieter Neerincx wrote: > > Hi all, > > > > On my machines (both Linux and Mac OS X and several different > > browsers) it looks like the BioMOBY website is messed up (only the > > front page). Is anybody working on it or do I smell something fishy? > > > > Cheers, > > > > Pi > > > > On 3-Mar-2006, at 5:27 PM, Mark Wilkinson wrote: > > > > > On Fri, 2006-03-03 at 09:39 +0000, Duncan Hull wrote: > > > > > >> I realise these are all very open questions, but I'd be > interested > > >> to know what moby-devvers think... > > > > > > Outside of the public eye, I have three students right > now working > > > on OWLifying all aspects of MOBY, and making a clear > separation of > > > the models from the data and service instances. We are > expecting to > > > see some REALLY interesting behaviours in the context of > tools like > > > Ben & Clarence's Ahab/Ishmael MOBY browsers - DL-reasoned > discovery > > > of unexpected, but applicable, services after DL-reasoned > > > *integration* and > > > *recombination* of multiple data-types from multiple MOBY service > > > executions into new data-types. > > > > > > Fun!! > > > > > > 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 > > > > > > "For most of this century we have viewed communications > as a conduit, > > > a pipe between physical locations on the planet. > > > What's happened now is that the conduit has become so big and > > > interesting > > > that communication has become more than a conduit, > > > it has become a destination in its own right..." > > > > > > Paul Saffo - Director, Institute for the Future > > > > > > _______________________________________________ > > > MOBY-dev mailing list > > > MOBY-dev at biomoby.org > > > http://biomoby.org/mailman/listinfo/moby-dev > > > > > > Wageningen University and Research centre (WUR) Laboratory of > > Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 > > 6703 HA Wageningen > > The Netherlands > > phone: 0317-483 060 > > fax: 0317-483 584 > > mobile: 06-143 66 783 > > pieter.neerincx at wur.nl > > > > > > > > _______________________________________________ > > MOBY-dev mailing list > > MOBY-dev at biomoby.org > > http://biomoby.org/mailman/listinfo/moby-dev > -- > > -- > 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 > > "For most of this century we have viewed communications as a conduit, > a pipe between physical locations on the planet. > What's happened now is that the conduit has become so big and > interesting > that communication has become more than a conduit, > it has become a destination in its own right..." > > Paul Saffo - Director, Institute for the Future > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at biomoby.org > http://biomoby.org/mailman/listinfo/moby-dev From akerhornou at imim.es Mon Mar 6 17:05:25 2006 From: akerhornou at imim.es (Arnaud Kerhornou) Date: Mon, 06 Mar 2006 18:05:25 +0100 Subject: [MOBY-dev] [moby] Front page messed up? In-Reply-To: <1141663075.17702.24.camel@bioinfo.icapture.ubc.ca> References: <4407390A.2090802@cs.man.ac.uk> <440744C0.2020201@ncgr.org> <44080EB4.3000701@cs.man.ac.uk> <1141403236.6637.57.camel@bioinfo.icapture.ubc.ca> <5D600A84-B90E-49CF-B477-D3D498E7E3F8@wur.nl> <1141663075.17702.24.camel@bioinfo.icapture.ubc.ca> Message-ID: <440C6BD5.5040808@imim.es> Hi Mark, I use Firefox, and compared to Opera it looks actually different. It seems better on Opera. Arnaud Mark Wilkinson wrote: > Can anyone else confirm this? > > I was working on the main page last night. It renders correctly on both > of my machines in both Opera and IE browsers... but that doesn't mean > there isn't something wrong :-) > > M > > > > On Mon, 2006-03-06 at 13:03 +0100, Pieter Neerincx wrote: > >> Hi all, >> >> On my machines (both Linux and Mac OS X and several different >> browsers) it looks like the BioMOBY website is messed up (only the >> front page). Is anybody working on it or do I smell something fishy? >> >> Cheers, >> >> Pi >> >> >> From markw at illuminae.com Mon Mar 6 19:37:15 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Mon, 06 Mar 2006 11:37:15 -0800 Subject: [MOBY-dev] [moby] Front page messed up? In-Reply-To: <440C6BD5.5040808@imim.es> References: <4407390A.2090802@cs.man.ac.uk> <440744C0.2020201@ncgr.org> <44080EB4.3000701@cs.man.ac.uk> <1141403236.6637.57.camel@bioinfo.icapture.ubc.ca> <5D600A84-B90E-49CF-B477-D3D498E7E3F8@wur.nl> <1141663075.17702.24.camel@bioinfo.icapture.ubc.ca> <440C6BD5.5040808@imim.es> Message-ID: <1141673835.17702.50.camel@bioinfo.icapture.ubc.ca> Does it render for everyone properly now? M On Mon, 2006-03-06 at 18:05 +0100, Arnaud Kerhornou wrote: > Hi Mark, > > I use Firefox, and compared to Opera it looks actually different. It > seems better on Opera. > > Arnaud > > Mark Wilkinson wrote: > > Can anyone else confirm this? > > > > I was working on the main page last night. It renders correctly on both > > of my machines in both Opera and IE browsers... but that doesn't mean > > there isn't something wrong :-) > > > > M > > > > > > > > On Mon, 2006-03-06 at 13:03 +0100, Pieter Neerincx wrote: > > > >> Hi all, > >> > >> On my machines (both Linux and Mac OS X and several different > >> browsers) it looks like the BioMOBY website is messed up (only the > >> front page). Is anybody working on it or do I smell something fishy? > >> > >> Cheers, > >> > >> Pi > >> > >> > >> > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at biomoby.org > http://biomoby.org/mailman/listinfo/moby-dev -- -- 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 "For most of this century we have viewed communications as a conduit, a pipe between physical locations on the planet. What's happened now is that the conduit has become so big and interesting that communication has become more than a conduit, it has become a destination in its own right..." Paul Saffo - Director, Institute for the Future From spies at ipk-gatersleben.de Tue Mar 7 07:48:38 2006 From: spies at ipk-gatersleben.de (Karl Spies) Date: Tue, 07 Mar 2006 08:48:38 +0100 Subject: [MOBY-dev] [moby] Front page messed up? In-Reply-To: <1141673835.17702.50.camel@bioinfo.icapture.ubc.ca> References: <4407390A.2090802@cs.man.ac.uk> <440744C0.2020201@ncgr.org> <44080EB4.3000701@cs.man.ac.uk> <1141403236.6637.57.camel@bioinfo.icapture.ubc.ca> <5D600A84-B90E-49CF-B477-D3D498E7E3F8@wur.nl> <1141663075.17702.24.camel@bioinfo.icapture.ubc.ca> <440C6BD5.5040808@imim.es> <1141673835.17702.50.camel@bioinfo.icapture.ubc.ca> Message-ID: <440D3AD6.2030209@ipk-gatersleben.de> It looks fine! Thanks Karl -- Karl Spies presently at: Research Group Bioinformatics Dept. of Cytogenetics Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Corrensstra?e 3, D-06466 Gatersleben Germany Phone: 039482-5-765 Adress: Windthorststra?e 27 06114 Halle (Saale) Germany Phone: 0345-5237334 email: spies at ipk-gatersleben.de From edward.kawas at gmail.com Tue Mar 7 16:40:18 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 7 Mar 2006 08:40:18 -0800 Subject: [MOBY-dev] The agent Message-ID: <000401c64205$d2735000$6500a8c0@notebook> Hi, I am just curious as to why no-one has tested the agent on the 'test' registry? Did my last email go un-noticed? Thanks, Eddie From duncan.hull at cs.man.ac.uk Wed Mar 8 14:08:28 2006 From: duncan.hull at cs.man.ac.uk (Duncan Hull) Date: Wed, 08 Mar 2006 14:08:28 +0000 Subject: [MOBY-dev] BioMOBY at the Oscars In-Reply-To: <000401c64205$d2735000$6500a8c0@notebook> References: <000401c64205$d2735000$6500a8c0@notebook> Message-ID: <440EE55C.6090003@cs.man.ac.uk> Dear moby-dev Whats currently the best example a service annotation in BioMOBY? The Oscar-winning gold-standard example of how it can and should be done using the full expressive power of namespace, object and service ontologies? Is this the best example? urn:lsid:biomoby.org:serviceinstance:bioinfo.icapture.ubc.ca,getSHound3DNeighboursFromGi Or are there better ones? Duncan -- Duncan Hull http://www.cs.man.ac.uk/~hulld/ Phone: +44 (0) 161 275 0677 From markw at illuminae.com Wed Mar 8 16:25:23 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 08 Mar 2006 08:25:23 -0800 Subject: [MOBY-dev] [moby] BioMOBY at the Oscars In-Reply-To: <440EE55C.6090003@cs.man.ac.uk> References: <000401c64205$d2735000$6500a8c0@notebook> <440EE55C.6090003@cs.man.ac.uk> Message-ID: <1141835123.16213.13.camel@bioinfo.icapture.ubc.ca> I don't know about "gold standard" - there are quite a few good ones in the registry these days... this service: urn:lsid:biomoby.org:serviceinstance:org.inab.upc,runFasty:2006-03-04T08-50-58Z captures most of the features of the RDF signature... does that help? What, specifically, are you looking for in the RDF? A comprehensive use of all of the predicates, or a "gold standard" for what we consider to be a well-documented (i.e. described) service? M On Wed, 2006-03-08 at 14:08 +0000, Duncan Hull wrote: > Dear moby-dev > > Whats currently the best example a service annotation in BioMOBY? The > Oscar-winning gold-standard example of how it can and should be done > using the full expressive power of namespace, object and service ontologies? > > Is this the best example? > urn:lsid:biomoby.org:serviceinstance:bioinfo.icapture.ubc.ca,getSHound3DNeighboursFromGi > > Or are there better ones? > > Duncan > -- -- Mark Wilkinson Asst. Professor, Dept. of Medical Genetics University of British Columbia PI in Bioinformatics, iCAPTURE Centre St. Paul's Hospital, Rm. 166, 1081 Burrard St. Vancouver, BC, V6Z 1Y6 tel: 604 682 2344 x62129 fax: 604 806 9274 "For most of this century we have viewed communications as a conduit, a pipe between physical locations on the planet. What's happened now is that the conduit has become so big and interesting that communication has become more than a conduit, it has become a destination in its own right..." Paul Saffo - Director, Institute for the Future From markw at illuminae.com Wed Mar 8 17:50:47 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 08 Mar 2006 09:50:47 -0800 Subject: [MOBY-dev] [moby] BioMOBY at the Oscars In-Reply-To: References: <000401c64205$d2735000$6500a8c0@notebook> <440EE55C.6090003@cs.man.ac.uk> <1141835123.16213.13.camel@bioinfo.icapture.ubc.ca> Message-ID: <1141840247.16213.34.camel@bioinfo.icapture.ubc.ca> You should talk to Eddie - I think he already has a taverna plugin that does that... M On Wed, 2006-03-08 at 16:51 +0000, Stian Soiland wrote: > On 8. mar. 2006, at 16:25, Mark Wilkinson wrote: > > > urn:lsid:biomoby.org:serviceinstance:org.inab.upc,runFasty: > > 2006-03-04T08-50-58Z > > This seems like an OK example, but maybe not a good match for our task. > > > does that help? What, specifically, are you looking for in the > > RDF? A > > comprehensive use of all of the predicates, or a "gold standard" for > > what we consider to be a well-documented (i.e. described) service? > > More specifically we are looking for good examples of semantic > descriptions that we can use for Taverna while developing semantic > linking/browsing/searching. In particular, descriptions of inputs and > outputs that are a bit more specific than "Object", so that we can > build GUI elements in Taverna for use cases like this rough description: > > a) Add a BioMoby processor into the Taverna workflow > b) Click on the process, find that the input is a string described as > a "GCP_Phenotype" > c) Browse a list of BioMoby services that can provide the output type > "GCP_Phenotype" > d) Add one of the services to the workflow and connect it > > Of course, limiting the search by "performs task NCBI_Blast" is also > nice. > > > So a good example would be one (or a few related) services that has > this kind of information specified and that actually works. :-) > -- -- 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 "For most of this century we have viewed communications as a conduit, a pipe between physical locations on the planet. What's happened now is that the conduit has become so big and interesting that communication has become more than a conduit, it has become a destination in its own right..." Paul Saffo - Director, Institute for the Future From duncan.hull at cs.man.ac.uk Wed Mar 8 17:54:07 2006 From: duncan.hull at cs.man.ac.uk (Duncan Hull) Date: Wed, 08 Mar 2006 17:54:07 +0000 Subject: [MOBY-dev] [moby] BioMOBY at the Oscars In-Reply-To: <1141835123.16213.13.camel@bioinfo.icapture.ubc.ca> References: <000401c64205$d2735000$6500a8c0@notebook> <440EE55C.6090003@cs.man.ac.uk> <1141835123.16213.13.camel@bioinfo.icapture.ubc.ca> Message-ID: <440F1A3F.3040305@cs.man.ac.uk> Mark Wilkinson wrote: >What, specifically, are you looking for in the RDF? A >comprehensive use of all of the predicates, or a "gold standard" for >what we consider to be a well-documented (i.e. described) service? > > Well its Stian [1] whos actually after this description. Stian is a developer currently working on BioMOBY service integration in Taverna... Over to you, Stian... Duncan [1] http://www.cs.man.ac.uk/~ssoiland/ -- Duncan Hull http://www.cs.man.ac.uk/~hulld/ Phone: +44 (0) 161 275 0677 From markw at illuminae.com Wed Mar 8 17:54:19 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 08 Mar 2006 09:54:19 -0800 Subject: [MOBY-dev] [moby] BioMOBY at the Oscars In-Reply-To: <1141840247.16213.34.camel@bioinfo.icapture.ubc.ca> References: <000401c64205$d2735000$6500a8c0@notebook> <440EE55C.6090003@cs.man.ac.uk> <1141835123.16213.13.camel@bioinfo.icapture.ubc.ca> <1141840247.16213.34.camel@bioinfo.icapture.ubc.ca> Message-ID: <1141840459.16213.38.camel@bioinfo.icapture.ubc.ca> Eddie, THIS is why I keep telling you to **put these things up on the website!** :-) M On Wed, 2006-03-08 at 09:50 -0800, Mark Wilkinson wrote: > You should talk to Eddie - I think he already has a taverna plugin that > does that... > > M > > > > On Wed, 2006-03-08 at 16:51 +0000, Stian Soiland wrote: > > On 8. mar. 2006, at 16:25, Mark Wilkinson wrote: > > > > > urn:lsid:biomoby.org:serviceinstance:org.inab.upc,runFasty: > > > 2006-03-04T08-50-58Z > > > > This seems like an OK example, but maybe not a good match for our task. > > > > > does that help? What, specifically, are you looking for in the > > > RDF? A > > > comprehensive use of all of the predicates, or a "gold standard" for > > > what we consider to be a well-documented (i.e. described) service? > > > > More specifically we are looking for good examples of semantic > > descriptions that we can use for Taverna while developing semantic > > linking/browsing/searching. In particular, descriptions of inputs and > > outputs that are a bit more specific than "Object", so that we can > > build GUI elements in Taverna for use cases like this rough description: > > > > a) Add a BioMoby processor into the Taverna workflow > > b) Click on the process, find that the input is a string described as > > a "GCP_Phenotype" > > c) Browse a list of BioMoby services that can provide the output type > > "GCP_Phenotype" > > d) Add one of the services to the workflow and connect it > > > > Of course, limiting the search by "performs task NCBI_Blast" is also > > nice. > > > > > > So a good example would be one (or a few related) services that has > > this kind of information specified and that actually works. :-) > > -- -- 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 "For most of this century we have viewed communications as a conduit, a pipe between physical locations on the planet. What's happened now is that the conduit has become so big and interesting that communication has become more than a conduit, it has become a destination in its own right..." Paul Saffo - Director, Institute for the Future From markw at illuminae.com Wed Mar 8 18:02:23 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 08 Mar 2006 10:02:23 -0800 Subject: [MOBY-dev] [moby] BioMOBY at the Oscars In-Reply-To: <000701c642d9$d8aa6560$6600a8c0@notebook> References: <000701c642d9$d8aa6560$6600a8c0@notebook> Message-ID: <1141840943.16213.43.camel@bioinfo.icapture.ubc.ca> Hmmmm.... Perhaps, given that Taverna is the most widely-used client for MOBY, we need to find a more high-profile way of announcing these extensions, since they don't seem to be getting noticed, even by other Taverna developers... M On Wed, 2006-03-08 at 09:58 -0800, Edward Kawas wrote: > I did (actually martin did): > http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/taverna/guide/in > dex.html > > Eddie > > > -----Original Message----- > > From: moby-dev-bounces at biomoby.org > > [mailto:moby-dev-bounces at biomoby.org] On Behalf Of Mark Wilkinson > > Sent: Wednesday, March 08, 2006 9:54 AM > > To: Core developer announcements > > Subject: Re: [MOBY-dev] [moby] BioMOBY at the Oscars > > > > Eddie, THIS is why I keep telling you to **put these things up on the > > website!** :-) > > > > M > > > > > > > > On Wed, 2006-03-08 at 09:50 -0800, Mark Wilkinson wrote: > > > You should talk to Eddie - I think he already has a taverna plugin > > > that does that... > > > > > > M > > > > > > > > > > > > On Wed, 2006-03-08 at 16:51 +0000, Stian Soiland wrote: > > > > On 8. mar. 2006, at 16:25, Mark Wilkinson wrote: > > > > > > > > > urn:lsid:biomoby.org:serviceinstance:org.inab.upc,runFasty: > > > > > 2006-03-04T08-50-58Z > > > > > > > > This seems like an OK example, but maybe not a good match > > for our task. > > > > > > > > > does that help? What, specifically, are you looking for in the > > > > > RDF? A comprehensive use of all of the predicates, or a "gold > > > > > standard" for what we consider to be a well-documented (i.e. > > > > > described) service? > > > > > > > > More specifically we are looking for good examples of semantic > > > > descriptions that we can use for Taverna while developing > > semantic > > > > linking/browsing/searching. In particular, descriptions of inputs > > > > and outputs that are a bit more specific than "Object", > > so that we > > > > can build GUI elements in Taverna for use cases like this > > rough description: > > > > > > > > a) Add a BioMoby processor into the Taverna workflow > > > > b) Click on the process, find that the input is a string > > described > > > > as a "GCP_Phenotype" > > > > c) Browse a list of BioMoby services that can provide the output > > > > type "GCP_Phenotype" > > > > d) Add one of the services to the workflow and connect it > > > > > > > > Of course, limiting the search by "performs task > > NCBI_Blast" is also > > > > nice. > > > > > > > > > > > > So a good example would be one (or a few related) > > services that has > > > > this kind of information specified and that actually works. :-) > > > > > > -- > > > > -- > > 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 > > > > "For most of this century we have viewed communications as a conduit, > > a pipe between physical locations on the planet. > > What's happened now is that the conduit has become so big and > > interesting > > that communication has become more than a conduit, > > it has become a destination in its own right..." > > > > Paul Saffo - Director, Institute for the Future > > > > _______________________________________________ > > MOBY-dev mailing list > > MOBY-dev at biomoby.org > > http://biomoby.org/mailman/listinfo/moby-dev > -- -- 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 "For most of this century we have viewed communications as a conduit, a pipe between physical locations on the planet. What's happened now is that the conduit has become so big and interesting that communication has become more than a conduit, it has become a destination in its own right..." Paul Saffo - Director, Institute for the Future From ssoiland at cs.man.ac.uk Wed Mar 8 16:51:58 2006 From: ssoiland at cs.man.ac.uk (Stian Soiland) Date: Wed, 8 Mar 2006 16:51:58 +0000 Subject: [MOBY-dev] [moby] BioMOBY at the Oscars In-Reply-To: <1141835123.16213.13.camel@bioinfo.icapture.ubc.ca> References: <000401c64205$d2735000$6500a8c0@notebook> <440EE55C.6090003@cs.man.ac.uk> <1141835123.16213.13.camel@bioinfo.icapture.ubc.ca> Message-ID: On 8. mar. 2006, at 16:25, Mark Wilkinson wrote: > urn:lsid:biomoby.org:serviceinstance:org.inab.upc,runFasty: > 2006-03-04T08-50-58Z This seems like an OK example, but maybe not a good match for our task. > does that help? What, specifically, are you looking for in the > RDF? A > comprehensive use of all of the predicates, or a "gold standard" for > what we consider to be a well-documented (i.e. described) service? More specifically we are looking for good examples of semantic descriptions that we can use for Taverna while developing semantic linking/browsing/searching. In particular, descriptions of inputs and outputs that are a bit more specific than "Object", so that we can build GUI elements in Taverna for use cases like this rough description: a) Add a BioMoby processor into the Taverna workflow b) Click on the process, find that the input is a string described as a "GCP_Phenotype" c) Browse a list of BioMoby services that can provide the output type "GCP_Phenotype" d) Add one of the services to the workflow and connect it Of course, limiting the search by "performs task NCBI_Blast" is also nice. So a good example would be one (or a few related) services that has this kind of information specified and that actually works. :-) -- Stian Soiland School of Computer Science The University of Manchester http://www.cs.man.ac.uk/~ssoiland/ From edward.kawas at gmail.com Wed Mar 8 17:58:01 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 8 Mar 2006 09:58:01 -0800 Subject: [MOBY-dev] [moby] BioMOBY at the Oscars In-Reply-To: <1141840459.16213.38.camel@bioinfo.icapture.ubc.ca> Message-ID: <000701c642d9$d8aa6560$6600a8c0@notebook> I did (actually martin did): http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/taverna/guide/in dex.html Eddie > -----Original Message----- > From: moby-dev-bounces at biomoby.org > [mailto:moby-dev-bounces at biomoby.org] On Behalf Of Mark Wilkinson > Sent: Wednesday, March 08, 2006 9:54 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] [moby] BioMOBY at the Oscars > > Eddie, THIS is why I keep telling you to **put these things up on the > website!** :-) > > M > > > > On Wed, 2006-03-08 at 09:50 -0800, Mark Wilkinson wrote: > > You should talk to Eddie - I think he already has a taverna plugin > > that does that... > > > > M > > > > > > > > On Wed, 2006-03-08 at 16:51 +0000, Stian Soiland wrote: > > > On 8. mar. 2006, at 16:25, Mark Wilkinson wrote: > > > > > > > urn:lsid:biomoby.org:serviceinstance:org.inab.upc,runFasty: > > > > 2006-03-04T08-50-58Z > > > > > > This seems like an OK example, but maybe not a good match > for our task. > > > > > > > does that help? What, specifically, are you looking for in the > > > > RDF? A comprehensive use of all of the predicates, or a "gold > > > > standard" for what we consider to be a well-documented (i.e. > > > > described) service? > > > > > > More specifically we are looking for good examples of semantic > > > descriptions that we can use for Taverna while developing > semantic > > > linking/browsing/searching. In particular, descriptions of inputs > > > and outputs that are a bit more specific than "Object", > so that we > > > can build GUI elements in Taverna for use cases like this > rough description: > > > > > > a) Add a BioMoby processor into the Taverna workflow > > > b) Click on the process, find that the input is a string > described > > > as a "GCP_Phenotype" > > > c) Browse a list of BioMoby services that can provide the output > > > type "GCP_Phenotype" > > > d) Add one of the services to the workflow and connect it > > > > > > Of course, limiting the search by "performs task > NCBI_Blast" is also > > > nice. > > > > > > > > > So a good example would be one (or a few related) > services that has > > > this kind of information specified and that actually works. :-) > > > > -- > > -- > 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 > > "For most of this century we have viewed communications as a conduit, > a pipe between physical locations on the planet. > What's happened now is that the conduit has become so big and > interesting > that communication has become more than a conduit, > it has become a destination in its own right..." > > Paul Saffo - Director, Institute for the Future > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at biomoby.org > http://biomoby.org/mailman/listinfo/moby-dev From ssoiland at cs.man.ac.uk Thu Mar 9 09:00:00 2006 From: ssoiland at cs.man.ac.uk (Stian Soiland) Date: Thu, 9 Mar 2006 09:00:00 +0000 Subject: [MOBY-dev] BioMOBY at the Oscars In-Reply-To: <000701c642d9$d8aa6560$6600a8c0@notebook> References: <000701c642d9$d8aa6560$6600a8c0@notebook> Message-ID: <4AB8B23C-1D52-4EB6-A9C5-EB6B7774AC91@cs.man.ac.uk> On 8. mar. 2006, at 17:58, Edward Kawas wrote: > I did (actually martin did): > http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/taverna/ > guide/ Wow, yeah, that's all very cool! I should've noticed, sorry.. (I'm quite a fresh developer..) This will be a great inspiration for adding similar ontology behaviour to non-Moby-stuff! -- Stian Soiland School of Computer Science The University of Manchester http://www.cs.man.ac.uk/~ssoiland/ From simont at mcw.edu Sat Mar 11 03:44:06 2006 From: simont at mcw.edu (Twigger Simon) Date: Fri, 10 Mar 2006 21:44:06 -0600 Subject: [MOBY-dev] [moby] BioMOBY at the Oscars In-Reply-To: <000701c642d9$d8aa6560$6600a8c0@notebook> References: <000701c642d9$d8aa6560$6600a8c0@notebook> Message-ID: <5C58079B-CD65-4352-9190-8F5C35CCBDD0@mcw.edu> Actually, while I think about it. I originally thought that we might have some sort of 'workflow exchange' or repository on the site. These could also be along the lines of blog postings but with the XML files inline or attached. They could have their own post category so they would be easy to find. Sharing these workflows will make everyone's life easier but I havent seen too much of that going on I suspect people are reinventing 'how to I do a blast using MOBY' and similar things which might be made available as standard components that people could integrate into their own Taverna workflows, thereby significantly lowering the barrier to entry for new MOBY users. Simon. On Mar 8, 2006, at 11:58 AM, Edward Kawas wrote: > I did (actually martin did): > http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/taverna/ > guide/in > dex.html > > Eddie > >> -----Original Message----- >> From: moby-dev-bounces at biomoby.org >> [mailto:moby-dev-bounces at biomoby.org] On Behalf Of Mark Wilkinson >> Sent: Wednesday, March 08, 2006 9:54 AM >> To: Core developer announcements >> Subject: Re: [MOBY-dev] [moby] BioMOBY at the Oscars >> >> Eddie, THIS is why I keep telling you to **put these things up on the >> website!** :-) >> >> M >> >> >> >> On Wed, 2006-03-08 at 09:50 -0800, Mark Wilkinson wrote: >>> You should talk to Eddie - I think he already has a taverna plugin >>> that does that... >>> >>> M >>> >>> >>> >>> On Wed, 2006-03-08 at 16:51 +0000, Stian Soiland wrote: >>>> On 8. mar. 2006, at 16:25, Mark Wilkinson wrote: >>>> >>>>> urn:lsid:biomoby.org:serviceinstance:org.inab.upc,runFasty: >>>>> 2006-03-04T08-50-58Z >>>> >>>> This seems like an OK example, but maybe not a good match >> for our task. >>>> >>>>> does that help? What, specifically, are you looking for in the >>>>> RDF? A comprehensive use of all of the predicates, or a "gold >>>>> standard" for what we consider to be a well-documented (i.e. >>>>> described) service? >>>> >>>> More specifically we are looking for good examples of semantic >>>> descriptions that we can use for Taverna while developing >> semantic >>>> linking/browsing/searching. In particular, descriptions of inputs >>>> and outputs that are a bit more specific than "Object", >> so that we >>>> can build GUI elements in Taverna for use cases like this >> rough description: >>>> >>>> a) Add a BioMoby processor into the Taverna workflow >>>> b) Click on the process, find that the input is a string >> described >>>> as a "GCP_Phenotype" >>>> c) Browse a list of BioMoby services that can provide the output >>>> type "GCP_Phenotype" >>>> d) Add one of the services to the workflow and connect it >>>> >>>> Of course, limiting the search by "performs task >> NCBI_Blast" is also >>>> nice. >>>> >>>> >>>> So a good example would be one (or a few related) >> services that has >>>> this kind of information specified and that actually works. :-) >>>> >> -- >> >> -- >> 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 >> >> "For most of this century we have viewed communications as a conduit, >> a pipe between physical locations on the planet. >> What's happened now is that the conduit has become so big and >> interesting >> that communication has become more than a conduit, >> it has become a destination in its own right..." >> >> Paul Saffo - Director, Institute for the Future >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at biomoby.org >> http://biomoby.org/mailman/listinfo/moby-dev > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at biomoby.org > http://biomoby.org/mailman/listinfo/moby-dev From simont at mcw.edu Sat Mar 11 03:39:14 2006 From: simont at mcw.edu (Twigger Simon) Date: Fri, 10 Mar 2006 21:39:14 -0600 Subject: [MOBY-dev] [moby] BioMOBY at the Oscars In-Reply-To: <000701c642d9$d8aa6560$6600a8c0@notebook> References: <000701c642d9$d8aa6560$6600a8c0@notebook> Message-ID: <148D8F0D-9DD7-4675-995F-E7844ABC622F@mcw.edu> The website is a blog (and quite a few people are subscribed to it) so you could always post these types of things on there as blog postings that will appear on the front page as well as burying them in the documentation (which is a better long term place for the info but is far less likely to be seen). Simon. -- Simon N. Twigger, Ph.D. Assistant Professor, Department of Physiology Medical College of Wisconsin 8701 Watertown Plank Road, Milwaukee, WI, USA tel: 414-456-8802 fax: 414-456-6595 AIM/iChat: simontatmcw On Mar 8, 2006, at 11:58 AM, Edward Kawas wrote: > I did (actually martin did): > http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/taverna/ > guide/in > dex.html > > Eddie > >> -----Original Message----- >> From: moby-dev-bounces at biomoby.org >> [mailto:moby-dev-bounces at biomoby.org] On Behalf Of Mark Wilkinson >> Sent: Wednesday, March 08, 2006 9:54 AM >> To: Core developer announcements >> Subject: Re: [MOBY-dev] [moby] BioMOBY at the Oscars >> >> Eddie, THIS is why I keep telling you to **put these things up on the >> website!** :-) >> >> M >> >> >> >> On Wed, 2006-03-08 at 09:50 -0800, Mark Wilkinson wrote: >>> You should talk to Eddie - I think he already has a taverna plugin >>> that does that... >>> >>> M >>> >>> >>> >>> On Wed, 2006-03-08 at 16:51 +0000, Stian Soiland wrote: >>>> On 8. mar. 2006, at 16:25, Mark Wilkinson wrote: >>>> >>>>> urn:lsid:biomoby.org:serviceinstance:org.inab.upc,runFasty: >>>>> 2006-03-04T08-50-58Z >>>> >>>> This seems like an OK example, but maybe not a good match >> for our task. >>>> >>>>> does that help? What, specifically, are you looking for in the >>>>> RDF? A comprehensive use of all of the predicates, or a "gold >>>>> standard" for what we consider to be a well-documented (i.e. >>>>> described) service? >>>> >>>> More specifically we are looking for good examples of semantic >>>> descriptions that we can use for Taverna while developing >> semantic >>>> linking/browsing/searching. In particular, descriptions of inputs >>>> and outputs that are a bit more specific than "Object", >> so that we >>>> can build GUI elements in Taverna for use cases like this >> rough description: >>>> >>>> a) Add a BioMoby processor into the Taverna workflow >>>> b) Click on the process, find that the input is a string >> described >>>> as a "GCP_Phenotype" >>>> c) Browse a list of BioMoby services that can provide the output >>>> type "GCP_Phenotype" >>>> d) Add one of the services to the workflow and connect it >>>> >>>> Of course, limiting the search by "performs task >> NCBI_Blast" is also >>>> nice. >>>> >>>> >>>> So a good example would be one (or a few related) >> services that has >>>> this kind of information specified and that actually works. :-) >>>> >> -- >> >> -- >> 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 >> >> "For most of this century we have viewed communications as a conduit, >> a pipe between physical locations on the planet. >> What's happened now is that the conduit has become so big and >> interesting >> that communication has become more than a conduit, >> it has become a destination in its own right..." >> >> Paul Saffo - Director, Institute for the Future >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at biomoby.org >> http://biomoby.org/mailman/listinfo/moby-dev > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at biomoby.org > http://biomoby.org/mailman/listinfo/moby-dev From duncan.hull at cs.man.ac.uk Sat Mar 11 10:10:16 2006 From: duncan.hull at cs.man.ac.uk (Duncan Hull) Date: Sat, 11 Mar 2006 10:10:16 +0000 Subject: [MOBY-dev] Workflow repository for BioMOBY In-Reply-To: <5C58079B-CD65-4352-9190-8F5C35CCBDD0@mcw.edu> References: <000701c642d9$d8aa6560$6600a8c0@notebook> <5C58079B-CD65-4352-9190-8F5C35CCBDD0@mcw.edu> Message-ID: <4412A208.805@cs.man.ac.uk> Hi Simon Twigger Simon wrote: >Actually, while I think about it. I originally thought that we might >have some sort of 'workflow exchange' or repository on the site. > > Antoon Goderis [1] has been working on exactly this for Taverna, currently in beta version and might be of interest. http://workflows.mygrid.org.uk/repository/ Its read-only at the moment, but he's working on an upload facility. Duncan [1] http://www.cs.man.ac.uk/~goderisa/ -- Duncan Hull http://www.cs.man.ac.uk/~hulld/ Phone: +44 (0) 161 275 0677 From duncan.hull at cs.man.ac.uk Sat Mar 11 10:10:16 2006 From: duncan.hull at cs.man.ac.uk (Duncan Hull) Date: Sat, 11 Mar 2006 10:10:16 +0000 Subject: [MOBY-dev] Workflow repository for BioMOBY In-Reply-To: <5C58079B-CD65-4352-9190-8F5C35CCBDD0@mcw.edu> References: <000701c642d9$d8aa6560$6600a8c0@notebook> <5C58079B-CD65-4352-9190-8F5C35CCBDD0@mcw.edu> Message-ID: <4412A208.805@cs.man.ac.uk> Hi Simon Twigger Simon wrote: >Actually, while I think about it. I originally thought that we might >have some sort of 'workflow exchange' or repository on the site. > > Antoon Goderis [1] has been working on exactly this for Taverna, currently in beta version and might be of interest. http://workflows.mygrid.org.uk/repository/ Its read-only at the moment, but he's working on an upload facility. Duncan [1] http://www.cs.man.ac.uk/~goderisa/ -- Duncan Hull http://www.cs.man.ac.uk/~hulld/ Phone: +44 (0) 161 275 0677 From tmo at ebi.ac.uk Sat Mar 11 10:43:26 2006 From: tmo at ebi.ac.uk (Tom Oinn) Date: Sat, 11 Mar 2006 10:43:26 +0000 Subject: [MOBY-dev] Workflow repository for BioMOBY In-Reply-To: <4412A208.805@cs.man.ac.uk> References: <000701c642d9$d8aa6560$6600a8c0@notebook> <5C58079B-CD65-4352-9190-8F5C35CCBDD0@mcw.edu> <4412A208.805@cs.man.ac.uk> Message-ID: <4412A9CE.1000103@ebi.ac.uk> Duncan Hull wrote: > Hi Simon > > Twigger Simon wrote: > >> Actually, while I think about it. I originally thought that we might >> have some sort of 'workflow exchange' or repository on the site. >> >> > Antoon Goderis [1] has been working on exactly this for Taverna, > currently in beta version and might be of interest. Duncan - is there any more to this than a directory with some workflows in? The .gif files are missing the colour coding as well which makes them a bit less useful, also we should be emiting the autogenerated workflow summary HTML. I actually wrote some code to do this last year, will dig it up - it allowed workflow upload too. Tom > http://workflows.mygrid.org.uk/repository/ > > Its read-only at the moment, but he's working on an upload facility. > > Duncan > > [1] http://www.cs.man.ac.uk/~goderisa/ > From tmo at ebi.ac.uk Sat Mar 11 10:43:26 2006 From: tmo at ebi.ac.uk (Tom Oinn) Date: Sat, 11 Mar 2006 10:43:26 +0000 Subject: [MOBY-dev] Workflow repository for BioMOBY In-Reply-To: <4412A208.805@cs.man.ac.uk> References: <000701c642d9$d8aa6560$6600a8c0@notebook> <5C58079B-CD65-4352-9190-8F5C35CCBDD0@mcw.edu> <4412A208.805@cs.man.ac.uk> Message-ID: <4412A9CE.1000103@ebi.ac.uk> Duncan Hull wrote: > Hi Simon > > Twigger Simon wrote: > >> Actually, while I think about it. I originally thought that we might >> have some sort of 'workflow exchange' or repository on the site. >> >> > Antoon Goderis [1] has been working on exactly this for Taverna, > currently in beta version and might be of interest. Duncan - is there any more to this than a directory with some workflows in? The .gif files are missing the colour coding as well which makes them a bit less useful, also we should be emiting the autogenerated workflow summary HTML. I actually wrote some code to do this last year, will dig it up - it allowed workflow upload too. Tom > http://workflows.mygrid.org.uk/repository/ > > Its read-only at the moment, but he's working on an upload facility. > > Duncan > > [1] http://www.cs.man.ac.uk/~goderisa/ > From senger at ebi.ac.uk Sun Mar 12 18:29:20 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Sun, 12 Mar 2006 18:29:20 +0000 (GMT) Subject: [MOBY-dev] biomoby.org down? Message-ID: The jMoby cronjob recently started to experience problems when downloading from http://biomoby.org/jmoby-jars/jars-archive/, Now, I also cannot get the usual http://biomoby.org page (it exists, but it gives me back a very strange contents with just two links (RT and wiki)). Anybody has the same experiences, or does anybody knows the reason? Thanks, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger consulting for: International Rice Research Institute Biometrics and Bioinformatics Unit DAPO BOX 7777, Metro Manila Philippines, phone: +63-2-580-5600 (ext.2324) From haase_dirk at web.de Sun Mar 12 22:13:36 2006 From: haase_dirk at web.de (Dirk Haase) Date: Sun, 12 Mar 2006 23:13:36 +0100 Subject: [MOBY-dev] biomoby.org down? In-Reply-To: References: Message-ID: <200603122313.36929.haase_dirk@web.de> On Sunday 12 March 2006 19:29, Martin Senger wrote: > The jMoby cronjob recently started to experience problems when downloading > from http://biomoby.org/jmoby-jars/jars-archive/, Now, I also cannot get > the usual http://biomoby.org page (it exists, but it gives me back a very > strange contents with just two links (RT and wiki)). > > Anybody has the same experiences, or does anybody knows the reason? Same observation here in Cologne/Germany. I would appreciate if this could be fixed quickly, because tomorrow (Monday) we start a workshop focussing mainly on BioMOBY. It would be a pity if we could not use (and promote...) the biomoby.org site as a documentation resource. Regards, dirk From senger at ebi.ac.uk Sun Mar 12 23:14:49 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Sun, 12 Mar 2006 23:14:49 +0000 (GMT) Subject: [MOBY-dev] biomoby.org down? In-Reply-To: <200603122313.36929.haase_dirk@web.de> Message-ID: > Same observation here in Cologne/Germany. I would appreciate if this could be > fixed quickly > It is fixed now. Chris (from the open-bio) did it at once, If you still do not see the usual biomoby.org page, it will come later to you because the problem was with DNS which will take some time to be propagated throught the world (I have it right now, in UK). Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger consulting for: International Rice Research Institute Biometrics and Bioinformatics Unit DAPO BOX 7777, Metro Manila Philippines, phone: +63-2-580-5600 (ext.2324) From leire at mmb.pcb.ub.es Mon Mar 13 18:30:12 2006 From: leire at mmb.pcb.ub.es (leireZamacola) Date: Mon, 13 Mar 2006 19:30:12 +0100 Subject: [MOBY-dev] The agent References: <000401c64205$d2735000$6500a8c0@notebook> Message-ID: <002001c646cc$2a7ee5f0$0d60050a@mmb.pcb.ub.es> Hi everyone, I am developing biomoby services in Java. I compile the service and deploy it without problems but when I want to run the service I get this error. Does anyone know why? cheers 600 AN ERROR OCCURED DURING THE SERVICE EXECUTION. org.biomoby.shared.datatypes.FASTA_AA java.lang.ClassCastException: org.biomoby.shared.datatypes.FASTA_AA at PMutHotSpot.run.skeletons.RunHotSpotFromFASTASkel.get_FASTA_AA(Unknown Source) at PMutHotSpot.run.RunHotSpotFromFASTAImpl.processIt(Unknown Source) at org.biomoby.service.BaseService.processIt(BaseService.java:292) at PMutHotSpot.run.skeletons.RunHotSpotFromFASTASkel.RunHotSpotFromFASTA(Unknow n Source) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39 ) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl .java:25) at java.lang.reflect.Method.invoke(Method.java:585) at org.jboss.webservice.server.InvokerProviderJSE.invokeServiceEndpoint(Invoker ProviderJSE.java:154) at org.jboss.webservice.server.InvokerProvider.invokeMethod(InvokerProvider.jav a:305) at org.jboss.axis.providers.java.RPCProvider.invokeTarget(RPCProvider.java:176) at org.jboss.webservice.server.InvokerProviderJSE.invokeTarget(InvokerProviderJ SE.java:93) at org.jboss.axis.providers.java.RPCProvider.processMessage(RPCProvider.java:12 1) at org.jboss.axis.providers.java.JavaProvider.invoke(JavaProvider.java:358) at org.jboss.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java:7 3) at org.jboss.axis.SimpleChain.doVisiting(SimpleChain.java:160) at org.jboss.axis.SimpleChain.invoke(SimpleChain.java:123) at org.jboss.axis.handlers.soap.SOAPService.invoke(SOAPService.java:560) at org.jboss.webservice.server.ServerEngine.invokeInternal(ServerEngine.java:20 0) at org.jboss.webservice.server.ServerEngine.invoke(ServerEngine.java:89) at org.jboss.axis.transport.http.AxisServlet.doPost(AxisServlet.java:911) at javax.servlet.http.HttpServlet.service(HttpServlet.java:717) at org.jboss.axis.transport.http.AxisServletBase.service(AxisServletBase.java:3 70) at javax.servlet.http.HttpServlet.service(HttpServlet.java:810) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Application FilterChain.java:252) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterCh ain.java:173) at org.jboss.web.tomcat.filters.ReplyHeaderFilter.doFilter(ReplyHeaderFilter.ja va:81) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Application FilterChain.java:202) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterCh ain.java:173) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.ja va:213) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.ja va:178) at org.jboss.web.tomcat.security.CustomPrincipalValve.invoke(CustomPrincipalVal ve.java:39) at org.jboss.web.tomcat.security.SecurityAssociationValve.invoke(SecurityAssoci ationValve.java:159) at org.jboss.web.tomcat.security.JaccContextValve.invoke(JaccContextValve.java: 59) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:126 ) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:105 ) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java :107) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:148) at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:856) at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.processConne ction(Http11Protocol.java:744) at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.jav a:527) at org.apache.tomcat.util.net.MasterSlaveWorkerThread.run(MasterSlaveWorkerThre ad.java:112) at java.lang.Thread.run(Thread.java:595) Leire Zamacola Gandiaga Molecular Recognition Universitat de Barcelona IRBB, Parc Cientific de Barcelona C. Josep Samitier 1-5, 08028 Barcelona fax : + 34 93 403 71 57 phone: + 34 93 403 71 55 mail: leire at mmb.pcb.ub.es From senger at ebi.ac.uk Mon Mar 13 19:07:57 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Mon, 13 Mar 2006 19:07:57 +0000 (GMT) Subject: [MOBY-dev] The agent In-Reply-To: <002001c646cc$2a7ee5f0$0d60050a@mmb.pcb.ub.es> Message-ID: Hi, > Does anyone know why? > I do not know yet, but it's me who should know :-) (and fix it if needed). I wonder if you can show me the generated Java code PMutHotSpot.run.skeletons.RunHotSpotFromFASTASkel. And perhaps also the input you sent to the service. Regards, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger consulting for: International Rice Research Institute Biometrics and Bioinformatics Unit DAPO BOX 7777, Metro Manila Philippines, phone: +63-2-580-5600 (ext.2324) From edward.kawas at gmail.com Mon Mar 13 18:41:35 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 13 Mar 2006 10:41:35 -0800 Subject: [MOBY-dev] The agent In-Reply-To: <002001c646cc$2a7ee5f0$0d60050a@mmb.pcb.ub.es> Message-ID: <000101c646cd$c248d1b0$9b66a8c0@notebook> What is your service description? Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of > leireZamacola > Sent: Monday, March 13, 2006 10:30 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] The agent > > Hi everyone, > > I am developing biomoby services in Java. > > I compile the service and deploy it without problems but when > I want to run the service I get this error. > > Does anyone know why? > > cheers > > > > > > > > > > > > > 600 > > AN ERROR OCCURED DURING THE SERVICE EXECUTION. > > org.biomoby.shared.datatypes.FASTA_AA > > java.lang.ClassCastException: org.biomoby.shared.datatypes.FASTA_AA > > at > PMutHotSpot.run.skeletons.RunHotSpotFromFASTASkel.get_FASTA_AA(Unknown > Source) > > at PMutHotSpot.run.RunHotSpotFromFASTAImpl.processIt(Unknown Source) > > at org.biomoby.service.BaseService.processIt(BaseService.java:292) > > at > PMutHotSpot.run.skeletons.RunHotSpotFromFASTASkel.RunHotSpotFr > omFASTA(Unknow > n Source) > > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) > > at > sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccess > orImpl.java:39 > ) > > at > sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMeth > odAccessorImpl > .java:25) > > at java.lang.reflect.Method.invoke(Method.java:585) > > at > org.jboss.webservice.server.InvokerProviderJSE.invokeServiceEn > dpoint(Invoker > ProviderJSE.java:154) > > at > org.jboss.webservice.server.InvokerProvider.invokeMethod(Invok > erProvider.jav > a:305) > > at > org.jboss.axis.providers.java.RPCProvider.invokeTarget(RPCProv > ider.java:176) > > at > org.jboss.webservice.server.InvokerProviderJSE.invokeTarget(In > vokerProviderJ > SE.java:93) > > at > org.jboss.axis.providers.java.RPCProvider.processMessage(RPCPr > ovider.java:12 > 1) > > at > org.jboss.axis.providers.java.JavaProvider.invoke(JavaProvider > .java:358) > > at > org.jboss.axis.strategies.InvocationStrategy.visit(InvocationS > trategy.java:7 > 3) > > at org.jboss.axis.SimpleChain.doVisiting(SimpleChain.java:160) > > at org.jboss.axis.SimpleChain.invoke(SimpleChain.java:123) > > at > org.jboss.axis.handlers.soap.SOAPService.invoke(SOAPService.java:560) > > at > org.jboss.webservice.server.ServerEngine.invokeInternal(Server > Engine.java:20 > 0) > > at > org.jboss.webservice.server.ServerEngine.invoke(ServerEngine.java:89) > > at > org.jboss.axis.transport.http.AxisServlet.doPost(AxisServlet.java:911) > > at javax.servlet.http.HttpServlet.service(HttpServlet.java:717) > > at > org.jboss.axis.transport.http.AxisServletBase.service(AxisServ > letBase.java:3 > 70) > > at javax.servlet.http.HttpServlet.service(HttpServlet.java:810) > > at > org.apache.catalina.core.ApplicationFilterChain.internalDoFilt > er(Application > FilterChain.java:252) > > at > org.apache.catalina.core.ApplicationFilterChain.doFilter(Appli > cationFilterCh > ain.java:173) > > at > org.jboss.web.tomcat.filters.ReplyHeaderFilter.doFilter(ReplyH > eaderFilter.ja > va:81) > > at > org.apache.catalina.core.ApplicationFilterChain.internalDoFilt > er(Application > FilterChain.java:202) > > at > org.apache.catalina.core.ApplicationFilterChain.doFilter(Appli > cationFilterCh > ain.java:173) > > at > org.apache.catalina.core.StandardWrapperValve.invoke(StandardW > rapperValve.ja > va:213) > > at > org.apache.catalina.core.StandardContextValve.invoke(StandardC > ontextValve.ja > va:178) > > at > org.jboss.web.tomcat.security.CustomPrincipalValve.invoke(Cust > omPrincipalVal > ve.java:39) > > at > org.jboss.web.tomcat.security.SecurityAssociationValve.invoke( > SecurityAssoci > ationValve.java:159) > > at > org.jboss.web.tomcat.security.JaccContextValve.invoke(JaccCont > extValve.java: > 59) > > at > org.apache.catalina.core.StandardHostValve.invoke(StandardHost > Valve.java:126 > ) > > at > org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReport > Valve.java:105 > ) > > at > org.apache.catalina.core.StandardEngineValve.invoke(StandardEn > gineValve.java > :107) > > at > org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdap > ter.java:148) > > at > org.apache.coyote.http11.Http11Processor.process(Http11Process > or.java:856) > > at > org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandle > r.processConne > ction(Http11Protocol.java:744) > > at > org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolT > cpEndpoint.jav > a:527) > > at > org.apache.tomcat.util.net.MasterSlaveWorkerThread.run(MasterS > laveWorkerThre > ad.java:112) > > at java.lang.Thread.run(Thread.java:595) > > > > > > > > > > > > > > Leire Zamacola Gandiaga > Molecular Recognition > Universitat de Barcelona > IRBB, Parc Cientific de Barcelona > C. Josep Samitier 1-5, > 08028 Barcelona > fax : + 34 93 403 71 57 > phone: + 34 93 403 71 55 > mail: leire at mmb.pcb.ub.es > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From leire at mmb.pcb.ub.es Tue Mar 14 09:31:02 2006 From: leire at mmb.pcb.ub.es (leireZamacola) Date: Tue, 14 Mar 2006 10:31:02 +0100 Subject: [MOBY-dev] Skeleton and input for the service References: Message-ID: <001d01c6474a$02bb5020$0d60050a@mmb.pcb.ub.es> Hi, I have attached the skeleton and the input I use for that service. Many thanks Leire Zamacola Gandiaga Molecular Recognition Universitat de Barcelona IRBB, Parc Cientific de Barcelona C. Josep Samitier 1-5, 08028 Barcelona fax : + 34 93 403 71 57 phone: + 34 93 403 71 55 mail: leire at mmb.pcb.ub.es ----- Original Message ----- From: "Martin Senger" To: "leireZamacola" Cc: "Core developer announcements" Sent: Monday, March 13, 2006 8:07 PM Subject: Re: [MOBY-dev] The agent > Hi, > > > Does anyone know why? > > > I do not know yet, but it's me who should know :-) (and fix it if > needed). > I wonder if you can show me the generated Java code > PMutHotSpot.run.skeletons.RunHotSpotFromFASTASkel. And perhaps also the > input you sent to the service. > > Regards, > Martin > > -- > Martin Senger > email: martin.senger at gmail.com > skype: martinsenger > consulting for: > International Rice Research Institute > Biometrics and Bioinformatics Unit > DAPO BOX 7777, Metro Manila > Philippines, phone: +63-2-580-5600 (ext.2324) -------------- next part -------------- A non-text attachment was scrubbed... Name: RunHotSpotFromFASTASkel.java Type: application/octet-stream Size: 4114 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: FASTA.xml Type: text/xml Size: 844 bytes Desc: not available URL: From dag at sonsorol.org Tue Mar 14 14:41:34 2006 From: dag at sonsorol.org (Chris Dagdigian) Date: Tue, 14 Mar 2006 09:41:34 -0500 Subject: [MOBY-dev] help test the new open-bio anonymous source code server Message-ID: Hi folks, Apologies for the cross-post. I need some help testing out a new open- bio server The new server is http://code.open-bio.org and it has been purpose built to replace our existing anonymous CVS server (cvs.open-bio.org, etc. etc.) In addition to anonymous CVS, this new system also offers anonymous rsync mirrors of all our source code. For security reasons (the anonymous CVS pserver protocol is considered insecure) we run these anon access methods on a locked down machine that only has a read only copy of the codebase. The webserver page (except for the viewcvs CGI) actually redirects to a wiki entry on a different server so we don' have to maintain a website on the new box. The anonymous access repository is currently updated every 30 minutes from the main developer system. Things I need help with: - check out http://code.open-bio.org -- does the documentation make sense? Can it be made better? If so, change it! (it is a wiki after all...) - please experiment with anonymous CVS, confirm that you can check out code - experiment with rsync! this is a new feature for us that we could not offer on the old server (due to upstream port ACLs on a core router) - provide feedback on the "speed" and bandwidth of the anoncvs server, does it seem reasonable? Let me know what you'll think. The reason for this move is that one of our core hosting facilities (datacenter at Wyeth Research) is no longer going to be useable by us as they are changing their WAN links in such a way that our servers will not be able to directly access the internet. We are in the process of moving *every* open-bio.org service onto new hardware located in a different datacenter. Our mailing lists have already been migrated, websites are moving as well. Expect some big changes once we tackle the task of moving all the developers and the writable CVS repositories to the new datacenter - that will happen probably within the next 2 weeks. Regards, Chris Dagdigian OBF From senger at ebi.ac.uk Tue Mar 14 19:17:59 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Tue, 14 Mar 2006 19:17:59 +0000 (GMT) Subject: [MOBY-dev] Skeleton and input for the service In-Reply-To: <001d01c6474a$02bb5020$0d60050a@mmb.pcb.ub.es> Message-ID: Hi, Thanks for the input file and the skeleton. (Wow, it seems unusual, to say "thanks for the skeleton" :-)). I have tried to reproduce your error, but I failed. I found that your input data were interesing because they seem to be non-valid XML - they contain '>' in the seguence name (FASTA format). Interesting is that it does not invalidate XML (the rules about XML validity allows the '>' to be present without being escaped). So this is not the problem. Then I found that your input data were not strictly speaking compliant with the Biomoby API because the Simple should have an article name. But this also did not cause the problem because the jMoby classes are relatively forgiving on this. Then, I have written my own trivial implementation of your skeleton, and run it with your input data. Unforunately, the error that happened to you has not occured to me. This is my implementatation: --- begin --- package org.jmoby.tutorial.service; import PMutHotSpot.run.skeletons.RunHotSpotFromFASTASkel; import org.biomoby.shared.MobyException; import org.biomoby.shared.parser.MobyPackage; import org.biomoby.shared.parser.MobyJob; import org.biomoby.shared.datatypes.*; public class RunHotSpotFromFASTAImpl extends RunHotSpotFromFASTASkel { public void processIt (MobyJob request, MobyJob response, MobyPackage outputContext) throws MobyException { System.out.println (get_FASTA_AA (request)); } } --- end --- And this is how I tested: build/run/run-service -service RunHotSpotFromFASTA -xml FASTA.xml \ -class org.jmoby.tutorial.service.RunHotSpotFromFASTAImpl I have not got any errors. So, the only thing I can think about is that perhaps you do not have the latest version of jMoby (even though I have not found any concrete case where this should matter). Please cvs update again, generate your skeleton again, compile and run it. Try also my implementation class shown above. If it still gives you an error, consider to show me your own implementation class (you can remove there all sensistive pieces, of course). Sorry that I have not found yet a solution for you. But bear with me, we will find it. Regards, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger consulting for: International Rice Research Institute Biometrics and Bioinformatics Unit DAPO BOX 7777, Metro Manila Philippines, phone: +63-2-580-5600 (ext.2324) From haase_dirk at web.de Thu Mar 16 07:59:36 2006 From: haase_dirk at web.de (Dirk Haase) Date: Thu, 16 Mar 2006 08:59:36 +0100 Subject: [MOBY-dev] Test Central: not accessible by Taverna Message-ID: <200603160859.37035.haase_dirk@web.de> Hi! We just experience problems with the new test registry (http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl). When I try to create a new biomoby scavenger pointing to that registry I get an error saying "org.embl.ebi.escience.scuflui.workbench.ScavengerCreationException: Could not retrieve and or process RDF document for BioMoby Objects" So it seems there is something wrong with the RDF resolution... Eddie, can you have a look at it? Thanks and regards, dirk From edward.kawas at gmail.com Thu Mar 16 15:04:27 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 16 Mar 2006 07:04:27 -0800 Subject: [MOBY-dev] Test Central: not accessible by Taverna In-Reply-To: <200603160859.37035.haase_dirk@web.de> Message-ID: <000301c6490a$ed7f4780$6600a8c0@notebook> Hi Dirk, I committed the fix to the cvs. In addition, I placed an updated taverna-1.3.1.jar at http://bioinfo.icapture.ubc.ca/ekawas/jars/taverna-1.3.1.jar. Remember to backup your old file in /taverna-workbench-1.3.1/lib/ before replacing it. The problem is that I am updating the RDF generators so that they include LSIDs with versioning information. In addition to the versioning information, the documents include most properties contained in the registry. Having this information may prove useful in later enhancements to the plug-in. Thanks, Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dirk Haase > Sent: Thursday, March 16, 2006 12:00 AM > To: Moby Developers > Subject: [MOBY-dev] Test Central: not accessible by Taverna > > Hi! > > We just experience problems with the new test registry > (http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Centr > al.pl). When I try to create a new biomoby scavenger pointing > to that registry I get an error saying > "org.embl.ebi.escience.scuflui.workbench.ScavengerCreationExce > ption: Could not retrieve and or process RDF document for > BioMoby Objects" > > So it seems there is something wrong with the RDF > resolution... Eddie, can you have a look at it? > > Thanks and regards, > dirk > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From edward.kawas at gmail.com Thu Mar 16 15:04:27 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 16 Mar 2006 07:04:27 -0800 Subject: [MOBY-dev] Test Central: not accessible by Taverna In-Reply-To: <200603160859.37035.haase_dirk@web.de> Message-ID: <000301c6490a$ed7f4780$6600a8c0@notebook> Hi Dirk, I committed the fix to the cvs. In addition, I placed an updated taverna-1.3.1.jar at http://bioinfo.icapture.ubc.ca/ekawas/jars/taverna-1.3.1.jar. Remember to backup your old file in /taverna-workbench-1.3.1/lib/ before replacing it. The problem is that I am updating the RDF generators so that they include LSIDs with versioning information. In addition to the versioning information, the documents include most properties contained in the registry. Having this information may prove useful in later enhancements to the plug-in. Thanks, Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dirk Haase > Sent: Thursday, March 16, 2006 12:00 AM > To: Moby Developers > Subject: [MOBY-dev] Test Central: not accessible by Taverna > > Hi! > > We just experience problems with the new test registry > (http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Centr > al.pl). When I try to create a new biomoby scavenger pointing > to that registry I get an error saying > "org.embl.ebi.escience.scuflui.workbench.ScavengerCreationExce > ption: Could not retrieve and or process RDF document for > BioMoby Objects" > > So it seems there is something wrong with the RDF > resolution... Eddie, can you have a look at it? > > Thanks and regards, > dirk > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From Pieter.Neerincx at wur.nl Thu Mar 23 10:48:37 2006 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Thu, 23 Mar 2006 11:48:37 +0100 Subject: [MOBY-dev] website vanished? Message-ID: <00011E19-F7D5-4835-8F9A-C95432B45CAC@wur.nl> Hi all, Is it me or is the BioMOBY site gone? My network is Ok and I can access many other sites, but both www.biomoby.org and biomoby.open- bio.org are gone... Pi Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 060 fax: 0317-483 584 mobile: 06-143 66 783 pieter.neerincx at wur.nl From senger at ebi.ac.uk Thu Mar 23 13:32:21 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Thu, 23 Mar 2006 13:32:21 +0000 (GMT) Subject: [MOBY-dev] website vanished? In-Reply-To: <00011E19-F7D5-4835-8F9A-C95432B45CAC@wur.nl> Message-ID: > Is it me or is the BioMOBY site gone? My network is Ok and I can > access many other sites, but both www.biomoby.org and biomoby.open- > bio.org are gone... > www.biomoby.org works for me fine... Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From markw at illuminae.com Thu Mar 23 13:59:18 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 23 Mar 2006 05:59:18 -0800 Subject: [MOBY-dev] website vanished? In-Reply-To: <00011E19-F7D5-4835-8F9A-C95432B45CAC@wur.nl> References: <00011E19-F7D5-4835-8F9A-C95432B45CAC@wur.nl> Message-ID: No problems from here. M On Thu, 23 Mar 2006 02:48:37 -0800, Pieter Neerincx wrote: > Hi all, > > Is it me or is the BioMOBY site gone? My network is Ok and I can > access many other sites, but both www.biomoby.org and biomoby.open- > bio.org are gone... > > Pi > > Wageningen University and Research centre (WUR) > Laboratory of Bioinformatics > Transitorium (building 312) room 1034 > Dreijenlaan 3 > 6703 HA Wageningen > The Netherlands > phone: 0317-483 060 > fax: 0317-483 584 > mobile: 06-143 66 783 > pieter.neerincx at wur.nl > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From Pieter.Neerincx at wur.nl Thu Mar 23 15:13:56 2006 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Thu, 23 Mar 2006 16:13:56 +0100 Subject: [MOBY-dev] website vanished? In-Reply-To: References: <00011E19-F7D5-4835-8F9A-C95432B45CAC@wur.nl> Message-ID: It took a few hours, but whatever it was it's working again :). Pi On 23-Mar-2006, at 2:59 PM, Mark Wilkinson wrote: > No problems from here. > > M > > On Thu, 23 Mar 2006 02:48:37 -0800, Pieter Neerincx > wrote: > >> Hi all, >> >> Is it me or is the BioMOBY site gone? My network is Ok and I can >> access many other sites, but both www.biomoby.org and biomoby.open- >> bio.org are gone... >> >> Pi >> >> Wageningen University and Research centre (WUR) >> Laboratory of Bioinformatics >> Transitorium (building 312) room 1034 >> Dreijenlaan 3 >> 6703 HA Wageningen >> The Netherlands >> phone: 0317-483 060 >> fax: 0317-483 584 >> mobile: 06-143 66 783 >> pieter.neerincx at wur.nl >> >> >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 060 fax: 0317-483 584 mobile: 06-143 66 783 pieter.neerincx at wur.nl From francis_gibbons at hms.harvard.edu Fri Mar 24 14:38:45 2006 From: francis_gibbons at hms.harvard.edu (Frank Gibbons) Date: Fri, 24 Mar 2006 09:38:45 -0500 Subject: [MOBY-dev] [MOBY-l] missing RFC1863 support in perl CommonSubs In-Reply-To: <4423C102.3000704@mpimp-golm.mpg.de> Message-ID: <5.2.1.1.2.20060324093657.023ebc70@email.med.harvard.edu> Bj?rn, To my knowledge, nobody has yet checked in any work on integrating the new Exception mechanism into the Perl codebase. It appears that the Java codebase already has this feature, so we need it in the Perl version too, urgently. You should feel free to go ahead - anyone out there working on this? perhaps you should get together on it. -Frank At 04:50 AM 3/24/2006, you wrote: >Dear list, > >I just learned how to use Biomoby and stumbled over the problem that it >is not possible to integrate >moby Exceptions (as specified in RFC1863) into the header using the perl >method "responseHeader" from CommonSubs (latest cvs). Since everything >there which is passed in the parameter notes gets HTMLified and wrapped >into notes as well as service notes. > >Is anybody working on fixing that? >Otherwise I could try developing a version here with the additional >paramter exception (and post it on this list?) > > >Cheers, >Bj?rn > > >_______________________________________________ >moby-l mailing list >moby-l at lists.open-bio.org >http://lists.open-bio.org/mailman/listinfo/moby-l PhD, Computational Biologist, Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA 02115, USA. Tel: 617-432-3555 Fax: 617-432-3557 http://llama.med.harvard.edu/~fgibbons From darin.london at duke.edu Tue Mar 28 14:42:45 2006 From: darin.london at duke.edu (Darin London) Date: Tue, 28 Mar 2006 09:42:45 -0500 Subject: [MOBY-dev] Announcing BOSC 2006 Message-ID: <44294B65.4050207@duke.edu> MEETING ANNOUNCEMENT & CALL FOR SPEAKERS The 7th annual Bioinformatics Open Source Conference (BOSC 2006) is organized by the not-for-profit Open Bioinformatics Foundation. The meeting will take place Aug 4,5th in Fortaleza, Brasil, and is one of several Special Interest Group (SIG) meetings occurring in conjunction with the 14th International Conference on Intelligent Systems for Molecular Biology. Please consult The Official BOSC 2006 Website at http://www.open-bio.org/wiki/BOSC_2006 for details and information. In addition, a BOSC weblog has been setup to make it easier to desiminate all BOSC related announcements: http://wiki.open-bio.org/boscblog/ And if you have an ICAL compatible Calendar, there is an EventDB calendar set up with all BOSC related deadlines. http://eventful.com/groups/G0-001-000014747-0 More information about ISMB can be found at the Official ISMB 2006 Website: http://ismb2006.cbi.cnptia.embrapa.br/ Thank You, and we look forward to seeing you all, The BOSC Organizing Committee. From d.haase at gsf.de Wed Mar 29 05:51:36 2006 From: d.haase at gsf.de (Dirk Haase) Date: Wed, 29 Mar 2006 07:51:36 +0200 Subject: [MOBY-dev] Wrong links in Perl web docs Message-ID: <200603290751.36758.d.haase@gsf.de> Hi there! I'm not sure if this was topic before here, but currently the links in some of the Perl API docs on the website are wrong. Namely, in all pages http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/Perl/RegisterX.html with X in {AnObject, ServiceType, Namespace, ServiceInstance}, the links listed under 'Other parts of MOBY-S API' point to the wrong directory. The relative paths are lacking the initial dots ("../"). Regards, dirk -- ---------------------------------------------------------- Dirk Haase phone +49 89 3187 3583 http://mips.gsf.de/~haase email d.haase at gsf.de From francis_gibbons at hms.harvard.edu Wed Mar 29 15:10:05 2006 From: francis_gibbons at hms.harvard.edu (Frank Gibbons) Date: Wed, 29 Mar 2006 10:10:05 -0500 Subject: [MOBY-dev] Wrong links in Perl web docs In-Reply-To: <200603290751.36758.d.haase@gsf.de> Message-ID: <5.2.1.1.2.20060329100915.01261750@email.med.harvard.edu> Dirk. I'm waiting for my account to be reinstated on openbio.org, but feel free to go ahead and insert those little dots. The point of putting the docs under CVS control is that anyone can fix problems as they see them - enjoy ;-) -Frank At 12:51 AM 3/29/2006, you wrote: >Hi there! > >I'm not sure if this was topic before here, but currently the links in >some of >the Perl API docs on the website are wrong. Namely, in all pages > >http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/Perl/RegisterX.html > >with X in {AnObject, ServiceType, Namespace, ServiceInstance}, the links >listed under 'Other parts of MOBY-S API' point to the wrong directory. The >relative paths are lacking the initial dots ("../"). > >Regards, >dirk > >-- > >---------------------------------------------------------- >Dirk Haase phone +49 89 3187 3583 >http://mips.gsf.de/~haase email d.haase at gsf.de >_______________________________________________ >MOBY-dev mailing list >MOBY-dev at lists.open-bio.org >http://lists.open-bio.org/mailman/listinfo/moby-dev PhD, Computational Biologist, Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA 02115, USA. Tel: 617-432-3555 Fax: 617-432-3557 http://llama.med.harvard.edu/~fgibbons From d.haase at gsf.de Wed Mar 29 15:45:49 2006 From: d.haase at gsf.de (Dirk Haase) Date: Wed, 29 Mar 2006 17:45:49 +0200 Subject: [MOBY-dev] Wrong links in Perl web docs In-Reply-To: <5.2.1.1.2.20060329100915.01261750@email.med.harvard.edu> References: <5.2.1.1.2.20060329100915.01261750@email.med.harvard.edu> Message-ID: <200603291745.49568.d.haase@gsf.de> On Wednesday 29 March 2006 17:10, Frank Gibbons wrote: > Dirk. > > I'm waiting for my account to be reinstated on openbio.org, but feel free > to go ahead and insert those little dots. The point of putting the docs > under CVS control is that anyone can fix problems as they see them - enjoy > ;-) Hmm. I guess with 'anyone' you mean 'anyone with write access to CVS'... So although putting dots into docs is one of my favorite amusements, I have to step back here ;-) Regards, dirk From markw at illuminae.com Wed Mar 29 16:28:00 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 29 Mar 2006 08:28:00 -0800 Subject: [MOBY-dev] [moby] Re: Wrong links in Perl web docs In-Reply-To: <200603291745.49568.d.haase@gsf.de> References: <5.2.1.1.2.20060329100915.01261750@email.med.harvard.edu> <200603291745.49568.d.haase@gsf.de> Message-ID: <1143649680.20801.60.camel@bioinfo.icapture.ubc.ca> LOL! Yeah, not getting a CVS account is a good way to avoid the dirty work ;-) If I find time today I'll try to go in and fix them myself. Thanks for the notification! Cheers all! M On Wed, 2006-03-29 at 17:45 +0200, Dirk Haase wrote: > On Wednesday 29 March 2006 17:10, Frank Gibbons wrote: > > Dirk. > > > > I'm waiting for my account to be reinstated on openbio.org, but feel free > > to go ahead and insert those little dots. The point of putting the docs > > under CVS control is that anyone can fix problems as they see them - enjoy > > ;-) > > Hmm. I guess with 'anyone' you mean 'anyone with write access to CVS'... So > although putting dots into docs is one of my favorite amusements, I have to > step back here ;-) > > Regards, > dirk > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- -- 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 "For most of this century we have viewed communications as a conduit, a pipe between physical locations on the planet. What's happened now is that the conduit has become so big and interesting that communication has become more than a conduit, it has become a destination in its own right..." Paul Saffo - Director, Institute for the Future