From gss at ncgr.org Tue Nov 9 17:39:11 2004 From: gss at ncgr.org (Gary Schiltz) Date: Tue Nov 9 17:41:24 2004 Subject: [MOBY-l] MOBY Meeting: Reminder & Details Message-ID: <4191470F.9010001@ncgr.org> This is a reminder that the MOBY autumn 2004 meeting is approaching quickly (11 days from now) - see www.semanticmoby.org/meeting for details, www.semanticmoby.org/meeting/registration-form.html to register: Date : November 20-21 (Saturday & Sunday) Location : Santa Fe, New Mexico USA Venue : National Center for Genome Resources (www.ncgr.org) Fee : $50 USD/person (covers lunch and transportation between hotels and NCGR) The tentative agenda is as follows; please post any suggestions to the moby-l or moby-dev lists: Saturday, November 20, 2004: 8:30 am Bagels and coffee 9:00 am Semantic MOBY (Damian Gessler) 10:00 am Taverna (Martin Senger) 10:45 am Break 11:00 am MOBY Services (Mark Wilkinson) 12:00 pm Lunch provided 1:00 pm: Virtual Plant Network (Bill Beavis, discussion leader) 2:00 pm: Conceptual ways to merge S-MOBY, MOBY-S, and MyGrid in a real-world application (joined by Phil Lord via telecon [Manchester is seven hours ahead of Santa Fe]) 6:00pm Dinner Sunday, November 21, 2004 9:00 am Bagels and coffee 9:30 am Technical challenges to merging S-MOBY, MOBY-S, and MyGrid 11:30 am Next steps From p.lord at cs.man.ac.uk Wed Nov 10 19:28:38 2004 From: p.lord at cs.man.ac.uk (Phillip Lord) Date: Wed Nov 10 19:28:55 2004 Subject: [MOBY-l] Re: [MOBY-dev] Semantic Moby and Web Services <-> Semantic Web integration efforts? In-Reply-To: <24F7236E-3338-11D9-94D7-000D93B0BD32@pasteur.fr> References: <24F7236E-3338-11D9-94D7-000D93B0BD32@pasteur.fr> Message-ID: >>>>> "Catherine" == Catherine Letondal writes: Catherine> Hi, Catherine> I would have a question: how is the Moby-S branch of Catherine> Biomoby connected to other efforts that seek to integrate Catherine> Web services and Semantic Web? I mean groups, systems or Catherine> forums such as: Catherine> http://www.w3.org/2002/ws/swsig/ http://www.wsmo.org Catherine> (Web service modelling Ontology) Catherine> http://www.wsmo.org/wsml (Web Service Modeling Catherine> Language) http://www.daml.org/services/owl-s Catherine> (OWL-based Web service ontology) Catherine> ...? Catherine> BTW, I have just heard of this book: Developing Semantic Catherine> Web Services (A. K. Peters) : Catherine> http://www.akpeters.com/product.asp?ProdCode=2124 It isn't really. There is some similarity between the OWL-S profile, and moby-s data model. OWL-S/WSMO are trying to do a different thing to moby-s. The main aim for these technologies is to use highly expressive logics to enable automated composition and choreography of web services. This is a nice idea, but, my own suspicion is that most biologists, or bioinformatics service providers are not going to go to the effort to describe their services logically. Moby-s on the other hand takes a more constrained view of semantics. It's trying to produce semantic descriptions which are good enough to reduce the problem for the biologist to selecting from one or a short list, rather than then 500. There is a paper in this years ISWC (currently going on now!), which you can get from here... http://www.cs.man.ac.uk/~phillord/download/publications/biomoby-comparison-iswc2004.pdf Cheers Phil From gasalazar at parquesoft.com Thu Nov 11 12:31:59 2004 From: gasalazar at parquesoft.com (Gustavo Adolfo Salazar Orejuela) Date: Thu Nov 11 12:30:18 2004 Subject: [MOBY-l] (no subject) Message-ID: <32981.192.168.2.173.1100194319.squirrel@192.168.2.173> Hi everybody, I don't know if this is the right place to send my question, if i'm wrong please let me know where is it... I'm interested in learn how to use MOBY, that's why i did the next things: 1 I download movy-live of CVS like anonymous user and download too the separate distribution of jMoby 2 I install without problems the perl client 3 I did some test(ask for services and call a service) with this client, and all work fine 4 I Wanted to test the Java's Client, then I compile that, and so far so good 5 I used the script run-cmdline-client asking for services and everything was right 6 When i tryed to use that script with something like that: =========== /run-cmdline-client -call MOBYSHoundGetGenBankff objeto.xml =========== where objeto.xml is a file with just this line: i got this error: ===ERROR=== org.biomoby.shared.MobyException: ===ERROR=== Fault details: [stackTrace: null] Fault string: org.xml.sax.SAXException: SimpleDeserializer encountered a child element, which is NOT expected, in something it was trying to deserialize. Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException Fault actor: null When calling: http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY05/mobycentral.pl =========== at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:172) at org.biomoby.client.CentralImpl.call(CentralImpl.java:1176) at MobyCmdLineClient.main(MobyCmdLineClient.java:512) =========== What did I wrong?? later... 7 I used the source code downladed of CVS and compile that... and everithing OK 8 I found some example called MobyServiceInvocationExample.java, but when i try to complile, i had the next error: ========== Finding services that correspond to input data: Invoking service MOBYSHoundGetGenBankff Exception in thread "main" java.lang.NullPointerException at org.apache.crimson.tree.ElementNode2.getAttributeNodeNS(ElementNode2.java:432) at org.apache.crimson.tree.ElementNode2.getAttributeNS(ElementNode2.java:409) at org.biomoby.shared.MobyPrefixResolver.getAttr(Unknown Source) at org.biomoby.shared.MobyDataSimpleInstance.(Unknown Source) at org.biomoby.client.MobyRequest.convertMOBYResponseToMOBYData(Unknown Source) at org.biomoby.client.MobyRequest.invokeService(Unknown Source) at MobyServiceInvocationExample.main(MobyServiceInvocationExample.java:66) ========== I used that line to compile java -classpath ../build/classes/:axis.jar:jaxrpc.jar:commons-logging.jar:commons-discovery.jar:saaj.jar:../build/Clients/ MobyServiceInvocationExample and again... wath did i wrong?? I know that maybe all that questions looks like the begginers, but really i'm I will apreciate wathever kind of help. Bye Gustavo Adolfo From markw at illuminae.com Thu Nov 11 13:02:17 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Thu Nov 11 13:00:29 2004 Subject: [MOBY-l] (no subject) In-Reply-To: <32981.192.168.2.173.1100194319.squirrel@192.168.2.173> References: <32981.192.168.2.173.1100194319.squirrel@192.168.2.173> Message-ID: <4193A929.5070506@illuminae.com> Gustavo Adolfo Salazar Orejuela wrote: >where objeto.xml is a file with just this line: > >i got this error: > > I'm assuming that this is a typo in your message - please double-check that your namespace is NCBI_gi, rather than NCBI_ig Otherwise, I'll bounce this question on to Martin or Nina... M > > From senger at ebi.ac.uk Thu Nov 11 13:32:39 2004 From: senger at ebi.ac.uk (Martin Senger) Date: Thu Nov 11 13:31:00 2004 Subject: [MOBY-l] (no subject) In-Reply-To: <32981.192.168.2.173.1100194319.squirrel@192.168.2.173> Message-ID: > 6 When i tryed to use that script with something like that: > =========== > /run-cmdline-client -call MOBYSHoundGetGenBankff objeto.xml > =========== > where objeto.xml is a file with just this line: > > i got this error: > The main problem is that you are using a command-line client that talks to Moby Central registry, not to a service you want to call. You can, however, use this command-line client to call a service, but you need to add two more parameters: 1) -e The URL of a service you either know, or you can get it by a separate call from Moby registry: run-cmdline-client -fn MOBYSHoundGetGenBankff (This will give you this URL: http://mobycentral.cbr.nrc.ca/cgi-bin/Services/Services.cgi) 2) -uri http://biomoby.org/ This is a mandatory namespace for moby services (I hope I have it right). Additionally to that, it's recommended that you put your XML input in a file (let's say bankff.xml). The whole command then look like this: run-cmdline-client \ -e http://mobycentral.cbr.nrc.ca/cgi-bin/Services/Services.cgi \ -uri http://biomoby.org/ \ -call MOBYSHoundGetGenBankff bankff.xml Which still does not do what you want because your input needs a moby envelope (the line above gets back an empty result). The correct full input is this: Put it in bankff.xml and run the line above again and you get a response from this service (I have just tried). > 7 I used the source code downladed of CVS and compile that... and > everithing OK > 8 I found some example called MobyServiceInvocationExample.java, but > when i try to complile, i had the next error: (I assume that by "try to compile" you mean "try to run", right?) Let's wait for Paul Gordon to answer this part - he is the author of this class. Paul, arer you around? With regard, Martin -- Martin Senger EMBL Outstation - Hinxton Senger@EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From gordonp at cbr.nrc.ca Thu Nov 11 14:01:27 2004 From: gordonp at cbr.nrc.ca (Paul Gordon) Date: Thu Nov 11 14:03:05 2004 Subject: [MOBY-l] (no subject) In-Reply-To: <32981.192.168.2.173.1100194319.squirrel@192.168.2.173> References: <32981.192.168.2.173.1100194319.squirrel@192.168.2.173> Message-ID: <4193B707.6000303@cbr.nrc.ca> Hi Gustavo, >7 I used the source code downladed of CVS and compile that... and >everithing OK >8 I found some example called MobyServiceInvocationExample.java, but when >i try to complile, i had the next error: > > Indeed, this is the correct class to use invoke a service. The problem you encountered below is that unfortunately Crimson does not handle null namespaces as per the XML Namespaces spec (as Crimson is no longer being actively maintained). I suggest you use Apache Xerces as your XML parser, and the appliucation should not fail. As Mark pointed out though, you'll get an empty response, if that NCBI_ig typo from your e-mail in the input, though it looks like your actual input is okay from the message below. If you don't have Xerces, it can be downloaded as a jar from http://xml.apache.org/. If you do have it, but it's not your default XML parser, you can make it the default with any number of techniques as described at that site, or define a rather verbose system property on the command line Java invocation: "-Djavax.xml.parsers.DocumentBuilderFactory=org.apache.*xerces*.*jaxp*.DocumentBuilderFactoryImpl" Good Luck! >========== >Finding services that correspond to input data: namespace="NCBI_gi" id="431260"/> >Invoking service MOBYSHoundGetGenBankff >Exception in thread "main" java.lang.NullPointerException > at >org.apache.crimson.tree.ElementNode2.getAttributeNodeNS(ElementNode2.java:432) > at >org.apache.crimson.tree.ElementNode2.getAttributeNS(ElementNode2.java:409) > at org.biomoby.shared.MobyPrefixResolver.getAttr(Unknown Source) > at org.biomoby.shared.MobyDataSimpleInstance.(Unknown Source) > at >org.biomoby.client.MobyRequest.convertMOBYResponseToMOBYData(Unknown >Source) > at org.biomoby.client.MobyRequest.invokeService(Unknown Source) > at >MobyServiceInvocationExample.main(MobyServiceInvocationExample.java:66) >========== > >I used that line to compile >java -classpath >../build/classes/:axis.jar:jaxrpc.jar:commons-logging.jar:commons-discovery.jar:saaj.jar:../build/Clients/ >MobyServiceInvocationExample > > From markw at illuminae.com Thu Nov 11 14:03:26 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Thu Nov 11 14:03:05 2004 Subject: [MOBY-l] (no subject) In-Reply-To: References: Message-ID: <4193B77E.5070808@illuminae.com> Ugh... as simple as it is, even MOBY-S is pretty complicated! I wonder if we should write a quick command-line tool that executes one of the more stable MOBY services (like one of the wrapped SeqHound functions) for cases like this where people just want to be sure that the whole thing is working. All I can say is "thank heavens we have tools like Taverna!" :-) M Martin Senger wrote: >>6 When i tryed to use that script with something like that: >>=========== >> /run-cmdline-client -call MOBYSHoundGetGenBankff objeto.xml >>=========== >>where objeto.xml is a file with just this line: >> >>i got this error: >> >> >> > The main problem is that you are using a command-line client that >talks to Moby Central registry, not to a service you want to call. You >can, however, use this command-line client to call a service, but you need >to add two more parameters: > > 1) -e > >The URL of a service you either know, or you can get it by a separate call >from Moby registry: > > run-cmdline-client -fn MOBYSHoundGetGenBankff > >(This will give you this URL: > http://mobycentral.cbr.nrc.ca/cgi-bin/Services/Services.cgi) > > 2) -uri http://biomoby.org/ > >This is a mandatory namespace for moby services (I hope I have it right). > >Additionally to that, it's recommended that you put your XML input in a >file (let's say bankff.xml). The whole command then look like this: > >run-cmdline-client \ > -e http://mobycentral.cbr.nrc.ca/cgi-bin/Services/Services.cgi \ > -uri http://biomoby.org/ \ > -call MOBYSHoundGetGenBankff bankff.xml > > >Which still does not do what you want because your input needs a moby >envelope (the line above gets back an empty result). > >The correct full input is this: > > > > > > > > > > > > >Put it in bankff.xml and run the line above again and you get a response >from this service (I have just tried). > > > >>7 I used the source code downladed of CVS and compile that... and >>everithing OK >>8 I found some example called MobyServiceInvocationExample.java, but >>when i try to complile, i had the next error: >> >> > >(I assume that by "try to compile" you mean "try to run", right?) >Let's wait for Paul Gordon to answer this part - he is the author of this >class. Paul, arer you around? > > > With regard, > Martin > > > From senger at ebi.ac.uk Thu Nov 11 14:10:17 2004 From: senger at ebi.ac.uk (Martin Senger) Date: Thu Nov 11 14:08:33 2004 Subject: [MOBY-l] (no subject) In-Reply-To: <4193B77E.5070808@illuminae.com> Message-ID: > I wonder if we should write a quick command-line tool that executes one > of the more stable MOBY services (like one of the wrapped SeqHound > functions) for cases like this where people just want to be sure that > the whole thing is working. > I agree. Anyway, the first step will be to improve jMoby documentation, it needs update. I hope to finish it before Santa Fe. But writing such client for one or more particular services could be question of an hour. Mark, if you pick up few such services and send me their names and their corresponding inputs, I will write it as well still before Santa Fe. Cheers, Martin -- Martin Senger EMBL Outstation - Hinxton Senger@EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From gordonp at cbr.nrc.ca Thu Nov 11 14:50:13 2004 From: gordonp at cbr.nrc.ca (Paul Gordon) Date: Thu Nov 11 14:49:35 2004 Subject: [MOBY-l] (no subject) In-Reply-To: References: Message-ID: <4193C275.1090807@cbr.nrc.ca> Well, if you have a fully functional XML parser around (which unfortunately Java does not come with by default, it uses Crimson), MobyServiceInvocationExample is supposed to be simple :-) I'll see if I can fix it up a bit to find Xerces automatically... Martin Senger wrote: >>I wonder if we should write a quick command-line tool that executes one >>of the more stable MOBY services (like one of the wrapped SeqHound >>functions) for cases like this where people just want to be sure that >>the whole thing is working. >> >> >> > I agree. Anyway, the first step will be to improve jMoby documentation, >it needs update. I hope to finish it before Santa Fe. But writing such >client for one or more particular services could be question of an hour. >Mark, if you pick up few such services and send me their names and their >corresponding inputs, I will write it as well still before Santa Fe. > > Cheers, > Martin > > > From gasalazar at parquesoft.com Thu Nov 11 15:40:13 2004 From: gasalazar at parquesoft.com (Gustavo Adolfo Salazar Orejuela) Date: Thu Nov 11 15:38:27 2004 Subject: [MOBY-l] (no subject) In-Reply-To: <4193C275.1090807@cbr.nrc.ca> References: <4193C275.1090807@cbr.nrc.ca> Message-ID: <33245.192.168.2.173.1100205613.squirrel@192.168.2.173> Hello... I am working now with the run-cmdline-client, thanks a lot. Right now I am trying to work with the Java classes, Like Paul Gordon suggested me(Xerces downloading...). I noticed when i tryed to compile the class Example with jMOBY.jar provided by the separated version that this jar is not updated with respect to classes on the CVS just like the documentation... Well... i have another question... what if I want to call another service with the answer recently got with previous service? In that case, i need to use some API like JDOM(or similar in PERL) to get the interesting information to build another XML or exist another way to connect the output of the first service with the input of the second? Somebody has a sample file(Java or Perl) that do some near to my question. And again, Thanks for your help. -- Gustavo Adolfo > Well, if you have a fully functional XML parser around (which > unfortunately Java does not come with by default, it uses Crimson), > MobyServiceInvocationExample is supposed to be simple :-) I'll see if I > can fix it up a bit to find Xerces automatically... > > Martin Senger wrote: > >>>I wonder if we should write a quick command-line tool that executes one >>>of the more stable MOBY services (like one of the wrapped SeqHound >>>functions) for cases like this where people just want to be sure that >>>the whole thing is working. >>> >>> >>> >> I agree. Anyway, the first step will be to improve jMoby >> documentation, >>it needs update. I hope to finish it before Santa Fe. But writing such >>client for one or more particular services could be question of an hour. >>Mark, if you pick up few such services and send me their names and their >>corresponding inputs, I will write it as well still before Santa Fe. >> >> Cheers, >> Martin >> >> >> > > _______________________________________________ > moby-l mailing list > moby-l@biomoby.org > http://biomoby.org/mailman/listinfo/moby-l > From markw at illuminae.com Thu Nov 11 15:49:39 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Thu Nov 11 15:47:50 2004 Subject: [MOBY-l] (no subject) In-Reply-To: <33245.192.168.2.173.1100205613.squirrel@192.168.2.173> References: <4193C275.1090807@cbr.nrc.ca> <33245.192.168.2.173.1100205613.squirrel@192.168.2.173> Message-ID: <4193D063.6000501@illuminae.com> >Well... i have another question... >what if I want to call another service with the answer recently got with >previous service? In that case, i need to use some API like JDOM(or >similar in PERL) to get the interesting information to build another XML >or exist another way to connect the output of the first service with the >input of the second? >Somebody has a sample file(Java or Perl) that do some near to my question. > > This is basically what the CGI client does (http://mobycentral.cbr.nrc.ca). The (perl) code for that client is distributed as part of the Gbrowse package. If you prefer, I can grab a copy of just the client code and mail it to you directly. (gbrowse: http://www.gmod.org/ggb/) In addition, Taverna (http://taverna.sourceforge.net) will do that for you through a pretty GUI :-) Unless you really need to build your own client, you might find it more useful to use one of the existing tools, or tweak them to suit your situation. M >And again, Thanks for your help. > > > > From senger at ebi.ac.uk Thu Nov 11 16:30:32 2004 From: senger at ebi.ac.uk (Martin Senger) Date: Thu Nov 11 16:29:02 2004 Subject: [MOBY-l] (no subject) In-Reply-To: <33245.192.168.2.173.1100205613.squirrel@192.168.2.173> Message-ID: > Right now I am trying to work with the Java classes, Like Paul Gordon > suggested me(Xerces downloading...). > Xerces is part of the CVS (once you bild everything). If the version there does not work, we need to find why and replace it. (I have still one unanswered email from Ninan about perhaps something similar.) If you start using a different xerces, you will never stay compatible with jMoby CVS. So my suggestion is: do not download xerces but find what wrong with the existing one. (This is a suggestion for Paul, as the class author, not for you, Gustavo.) > I noticed when i tryed to compile the class Example with jMOBY.jar > provided by the separated version that this jar is not updated with > respect to classes on the CVS just like the documentation... > If you use CVS, it always use the latest classes. Do not use any jMOBY.jar taken from somewhere else. But perhaps I did not fully understand this point. > Well... i have another question... > what if I want to call another service with the answer recently got with > previous service? In that case, i need to use some API like JDOM(or > similar in PERL) to get the interesting information to build another XML > or exist another way to connect the output of the first service with the > input of the second? > Yes, you need an XML parser - and jdom.jar is part of CVS (again, once you build there everything). Remember, however, that both input and output moby data are wrapped in the same envelope - so, unless you want to extract information from this envelope, such as crosss-references, you can just pass the output of one services directly as an input to another service without even looking into it. Cheers, Martin -- Martin Senger EMBL Outstation - Hinxton Senger@EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From gordonp at cbr.nrc.ca Thu Nov 11 16:46:26 2004 From: gordonp at cbr.nrc.ca (Paul Gordon) Date: Thu Nov 11 16:44:33 2004 Subject: [MOBY-l] (no subject) In-Reply-To: References: Message-ID: <4193DDB2.8060204@cbr.nrc.ca> Actually, the problem that he is using Crimson. MobyServiceInvocationExample uses JAXP's DocumentBuilder interface, so it uses whatever XML parser implementation is the user's default. To help the user, I'll have the client check if Xerces is in the classpath (hopefully from the jMOBY CVS), and force it as the default if available, since Crimson is so crappy. > So my suggestion is: do not download xerces but find what wrong with >the existing one. (This is a suggestion for Paul, as the class author, not >for you, Gustavo.) > > From gss at ncgr.org Fri Nov 12 16:57:05 2004 From: gss at ncgr.org (Gary Schiltz) Date: Fri Nov 12 16:59:13 2004 Subject: [MOBY-l] MOBY Meeting: Reminder & Updates In-Reply-To: <4191470F.9010001@ncgr.org> References: <4191470F.9010001@ncgr.org> Message-ID: <419531B1.20208@ncgr.org> This is another reminder that the MOBY autumn 2004 meeting is quickly approaching (8 days from now) - see www.semanticmoby.org/meeting for details, www.semanticmoby.org/meeting/registration-form.html to register. The meeting pages on semanticmoby.org have been updated. I look forward to seeing you there! ---- Gary Schiltz Principal Software Engineer National Center for Genome Resources Santa Fe, New Mexico USA From senger at ebi.ac.uk Fri Nov 12 18:16:25 2004 From: senger at ebi.ac.uk (Martin Senger) Date: Fri Nov 12 18:14:52 2004 Subject: [MOBY-l] (no subject) In-Reply-To: Message-ID: Hi all, Motivated by the previous conversation in this thread, and recognizing that more and more people are actually using jMoby command-line client for calling services (even though its original intent was to call Moby registry), I have added there a new command-line option that makes this a bit easier. Easier in a sense that you do not need to fins the URL of a servic yourselv, and that you do not need to specify service uri (which is constant for all services) - so it is not easier in a sense to support you with the XML input, not yet. The new option -scall is documented in the help file, including an example. Please CVS update and you can try. Cheers, Martin -- Martin Senger EMBL Outstation - Hinxton Senger@EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From mwilkinson at mobile.rogers.com Fri Nov 12 18:16:39 2004 From: mwilkinson at mobile.rogers.com (mwilkinson) Date: Fri Nov 12 18:18:15 2004 Subject: [MOBY-l] (no subject) Message-ID: <200411122317.iACNHvKr006864@portal.open-bio.org> What was I saying about 24 hour turnaround times with Martin... More like 2 hours! ...who says Martin works for myGrid!! ;-) M -----Original Message----- From: Martin Senger Date: Fri, 12 Nov 2004 23:16:25 To:Gustavo Adolfo Salazar Orejuela Cc:moby-l@biomoby.org Subject: Re: [MOBY-l] (no subject) Hi all, Motivated by the previous conversation in this thread, and recognizing that more and more people are actually using jMoby command-line client for calling services (even though its original intent was to call Moby registry), I have added there a new command-line option that makes this a bit easier. Easier in a sense that you do not need to fins the URL of a servic yourselv, and that you do not need to specify service uri (which is constant for all services) - so it is not easier in a sense to support you with the XML input, not yet. The new option -scall is documented in the help file, including an example. Please CVS update and you can try. Cheers, Martin -- Martin Senger EMBL Outstation - Hinxton Senger@EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger _______________________________________________ moby-l mailing list moby-l@biomoby.org http://biomoby.org/mailman/listinfo/moby-l !!!!!!!!!!!!!!!! To respond to this message you MUST send your response to (note new address!) markw_mobile2 at illuminae dot com Responses to the reply-to address go directly to trash! !!!!!!!!!!!!!!!!!!!!!!!!!!!! From senger at ebi.ac.uk Fri Nov 12 18:20:23 2004 From: senger at ebi.ac.uk (Martin Senger) Date: Fri Nov 12 18:18:44 2004 Subject: [MOBY-l] small change in Taverna (in BioMoby services) Message-ID: Hi all, I have slightly improved the error messages in Taverna generating by Moby services. It also better copes now when a service returns an empty result. I also replaced jmoby.jar for the latest one. If you want to have this, CVS update Taverna please. Cheers, Martin -- Martin Senger EMBL Outstation - Hinxton Senger@EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From senger at ebi.ac.uk Fri Nov 12 18:24:38 2004 From: senger at ebi.ac.uk (Martin Senger) Date: Fri Nov 12 18:22:58 2004 Subject: [MOBY-l] (no subject) In-Reply-To: <200411122319.iACNJkvO004798@madeiro.ebi.ac.uk> Message-ID: > What was I saying about 24 hour turnaround times with Martin... > Mark, thanks, but you are too polite. I still feel guilty that the stuff I have started with Ben in IRRI is still not yet done... (talking about full XSD returned by registry, which will lead to a better support for Java client and service provider for complex data types). Cheers, Martin -- Martin Senger EMBL Outstation - Hinxton Senger@EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From p.lord at cs.man.ac.uk Sun Nov 14 09:04:16 2004 From: p.lord at cs.man.ac.uk (Phillip Lord) Date: Mon Nov 15 05:06:20 2004 Subject: [MOBY-l] Re: [MOBY-dev] Semantic Moby and Web Services <-> Semantic Web integration efforts? In-Reply-To: References: <24F7236E-3338-11D9-94D7-000D93B0BD32@pasteur.fr> Message-ID: >>>>> "Catherine" == Catherine Letondal writes: >> OWL-S/WSMO are trying to do a different thing to moby-s. The main >> aim for these technologies is to use highly expressive logics to >> enable automated composition and choreography of web >> services. >> >> Moby-s on the other hand takes a more constrained view of >> semantics. It's trying to produce semantic descriptions which are >> good enough to reduce the problem for the biologist to selecting >> from one or a short list, rather than then 500. >> Catherine> I meant S-Moby in fact, not Moby-S, sorry for this Catherine> mistake. Ah, well, this makes quite a difference! >> There is a paper in this years ISWC (currently going on now!), >> which you can get from here... >> >> http://www.cs.man.ac.uk/~phillord/download/publications/biomoby- >> comparison-iswc2004.pdf >> Catherine> Thanks a lot for this information. I have read the paper, Catherine> which indeed helped a lot to understand your underlying Catherine> choices (BTW, I would be interested to know about the Catherine> feedback it had at the ISCW conference - generally, Catherine> bioinformatics is considered as a "very specific" area, Catherine> and since the differences between "generial" applications Catherine> such as e-commerce and e-science are very well explained Catherine> in your paper, I'm curious to know whether the audience Catherine> reacted). It's difficult to say at the moment. I got some interest immediately after the talk. The paper was written to be slightly provocative, and, indeed, some people asked about my statement that "automated service composition is (largely) inappropriate in a scientific domain". Sadly, I seem to have picked up a illness at the conference, and was in bed for most of the social events and poster sessions. This meant that a) I didn't get a chance to talk to more people and get better feedback and b) I missed some free beer, good food and Japanese drumming. Those who of you who know me, will realise how irked I was at this. So, I'll have to wait a while for people to read the paper, before I am sure of the reaction. Catherine> I still have a question about the comparison to OWL-S. In Catherine> section 7 of your paper (Service provision and Service Catherine> interfaces), you explain that OWL-S defines a grounding Catherine> ontology, and that the 3 approaches (moby-s, s-moby and Catherine> myGrid) have chosen a simpler approach. The "grounding" in OWL-S is specifically that part of the ontology which relates between the domain concepts describing the functionality of the service (in the "process" and "profile" subontologies) and the specific invocation interface, which for web services pretty much means the WSDL document. Catherine> I understand that the problem that is addressed here is Catherine> to have a high description not only of domain concepts, Catherine> but also on their relations, and that this is not Catherine> required in the 3 approaches, for different reasons. Catherine> But I don't understand your explanations: How is the Catherine> S-Moby interface defined by its "upper" ontology? I have Catherine> carefully read the S-moby design document Catherine> (http://www.biomoby.org/S-MOBY/doc/Design/S-MOBY_Design_Overview.html), Catherine> what do you call an upper ontology there - the set of RDF Catherine> graphs submitted by providers? S-moby is basically a REST architecture, with RDF and OWL messages. Strictly, it's service interfaces are all very simple, and all identical; it's HTTP, post, get, and the other three commands that I (and most people) can never remember. The response to these is, again, always the same for an s-moby service, and defined in the spec. So you don't need an ontology to describe this. There is no heterogeneity. Alternatively, you could consider the service interface to be specific RDF graphs that an s-moby service returns. Perhaps this is the better analogy, as this defines the specific functionality of the service. In this case, the graph defines the functionality totally. If you have the graph, you know how to address the service, what queries to send to it, and how to interpret the result coming back. So, again, you do not need to ground a s-moby service to an underlying WSDL. k Catherine> You also mention that moby-s interfaces are not Catherine> heterogeneous (and thus does not need an ontology to Catherine> interconnect concepts). What is not heterogeneous and Catherine> why? All moby-s services are the same. They have a single method, which you can invoke. Again, if you have the ontological description, you can understand what data you should send to a service, and how to interpret the data that comes back. So, again, no grounding is required. MyGrid is most like moby-s, in this context, except that instead of having a single defined service interface, we have a couple, and a pluggability layer within the other components to cope with the difference. This is why taverna and freefluo can cope with, for example, moby-s services. I hope this makes sense. It's quite hard to describe, particularly as s-moby's REST interface breaks (my use of) the standard web services terminology somewhat. Let me know if things are unclear. Cheers Phil From fgibbons at hms.harvard.edu Mon Nov 15 17:58:16 2004 From: fgibbons at hms.harvard.edu (Frank Gibbons) Date: Mon Nov 15 17:50:40 2004 Subject: [MOBY-l] Changes to registry? Signatures lost? Message-ID: <5.2.1.1.2.20041115174048.019d0008@email.med.harvard.edu> Hi MOBYers, I've been away from the MOBY world for a while (apart from bumping into Martin and Gary at the Semantic Web for Life Sciences Workshop in Cambridge), so perhaps I've missed out on some changes. Today I noticed that while my older services are still around, they seem to have lost their namespace information - whereas before they reported consuming information in specific namespaces, now they report that they do not support any particular namespace. I have a number of newly registered services (as of this morning), which correctly report namespaces. So, I'm wondering if perhaps the namespace information was accidentally dropped recently (was there a DB migration?) Or is it something more planned, where namespace info is no longer being reliably supplied, and I shouldn't rely on it (if this is the case, I'm in trouble!). Appended below is the code I use to determine this (originally provided by Mark, I suspect) - might help someone determine what's going on, or whether it's my problem. The services Ito/Uetz/Tong are the new ones, others are older. Strangely, YAService has been up for a month or two, yet still reports supporting namespace SGD. All services were registered by the old method, with no RDF generated. I believe I generated RDF for the older (non-namespace-supporting) ones, after having registered them, using Mark's script. Is this related to that? Sorry I can't make it out to Santa Fe, look forward to reading about the latest MOBY developments here. Thanks for help, -Frank ------------------------------- appended Perl script to see function/namespaces ----------------------------- #!/usr/bin/perl use lib qw(/share/local/share/perl/5.6.1 /share/lib/perl5/site_perl/5.8.3); # Use latest MOBY use MOBY::Client::Central; use MOBY::Client::Service; $m = MOBY::Client::Central->new(); my ($auth, $name) = ('llama.med.harvard.edu', 'YAService'); ($ss, $r) = $m->findService(authURI => $auth); #, serviceName => $name); my $i = 0; my %Count = (authority => (), type => (), input => ()); foreach my $service (sort { lc $a->name cmp lc $b->name } @{$ss} ) { $i++; $Count{authority}{$service->authority}++; $Count{type}{$service->type}++; $Count{input}{$service->input}++; print "$i: Service ", $service->name, " from ", $service->authority, " is of type ", $service->type, "\n"; print "It consumes: \n"; $inputs = $service->input; foreach $in ( @{$inputs} ) { eval {print "\t", $in->objectType, "\n"; }; print "\t\tin namespace(s)\n"; eval { my $namespaces = $in->namespaces; foreach $ns ( @{$namespaces} ) { print "\t\t\t\t$ns\n"; } }; } print "It generates "; $outputs = $service->output; foreach $out ( @{$outputs} ) { # Check for isCollection, each element of the collection should have an objectType if ($out->isCollection) { print "a collection of outputs:\n"; foreach my $simple (@{$out->Simples}) { print "\t", $simple->objectType, "\n"; print "\t\tin namespace(s)\n"; foreach $ns ( @{$simple->namespaces} ) { print "\t\t\t\t$ns\n"; } } } else { print "a single output:\n"; print "\t", $out->objectType, "\n"; print "\t\tin namespace(s)\n"; foreach $ns ( @{$out->namespaces} ) { print "\t\t\t\t$ns\n"; } } } print "\n", '-'x80, "\n"; } print "Services by authority:\n"; #while (my ($k, $v) = each $Count{authority}) { for my $s (sort {lc $a cmp lc $b} keys %{$Count{authority}}) { print "$Count{authority}{$s} $s\n"; } 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 mwilkinson at mrl.ubc.ca Mon Nov 15 19:00:19 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Mon Nov 15 18:37:35 2004 Subject: [spam] [MOBY-l] Changes to registry? Signatures lost? In-Reply-To: <5.2.1.1.2.20041115174048.019d0008@email.med.harvard.edu> References: <5.2.1.1.2.20041115174048.019d0008@email.med.harvard.edu> Message-ID: <1100563219.13798.198.camel@mobycentral.icapture.ubc.ca> Try again now... should be fixed. It was a miscommunication between Nina and I last week that led to a small and easily repaired change to the database. All should be back to normal now. M On Mon, 2004-11-15 at 14:58, Frank Gibbons wrote: > Hi MOBYers, > > I've been away from the MOBY world for a while (apart from bumping into > Martin and Gary at the Semantic Web for Life Sciences Workshop in > Cambridge), so perhaps I've missed out on some changes. > > Today I noticed that while my older services are still around, they seem to > have lost their namespace information - whereas before they reported > consuming information in specific namespaces, now they report that they do > not support any particular namespace. > > I have a number of newly registered services (as of this morning), which > correctly report namespaces. So, I'm wondering if perhaps the namespace > information was accidentally dropped recently (was there a DB migration?) > Or is it something more planned, where namespace info is no longer being > reliably supplied, and I shouldn't rely on it (if this is the case, I'm in > trouble!). > > Appended below is the code I use to determine this (originally provided by > Mark, I suspect) - might help someone determine what's going on, or whether > it's my problem. The services Ito/Uetz/Tong are the new ones, others are > older. Strangely, YAService has been up for a month or two, yet still > reports supporting namespace SGD. > > All services were registered by the old method, with no RDF generated. I > believe I generated RDF for the older (non-namespace-supporting) ones, > after having registered them, using Mark's script. Is this related to that? > > Sorry I can't make it out to Santa Fe, look forward to reading about the > latest MOBY developments here. > > Thanks for help, > > -Frank > > ------------------------------- appended Perl script to see > function/namespaces ----------------------------- > #!/usr/bin/perl > > use lib qw(/share/local/share/perl/5.6.1 > /share/lib/perl5/site_perl/5.8.3); # Use latest MOBY > use MOBY::Client::Central; > use MOBY::Client::Service; > $m = MOBY::Client::Central->new(); > my ($auth, $name) = ('llama.med.harvard.edu', 'YAService'); > ($ss, $r) = $m->findService(authURI => $auth); #, serviceName => $name); > my $i = 0; > my %Count = (authority => (), type => (), input => ()); > foreach my $service (sort { lc $a->name cmp lc $b->name } @{$ss} ) { > $i++; > $Count{authority}{$service->authority}++; > $Count{type}{$service->type}++; > $Count{input}{$service->input}++; > print "$i: Service ", $service->name, " from ", > $service->authority, " is of type ", $service->type, "\n"; > print "It consumes: \n"; > $inputs = $service->input; > foreach $in ( @{$inputs} ) { > eval {print "\t", $in->objectType, "\n"; }; > print "\t\tin namespace(s)\n"; > eval { > my $namespaces = $in->namespaces; > foreach $ns ( @{$namespaces} ) { > print "\t\t\t\t$ns\n"; > } > }; > } > > print "It generates "; > $outputs = $service->output; > foreach $out ( @{$outputs} ) { > # Check for isCollection, each element of the collection should have > an objectType > if ($out->isCollection) { > print "a collection of outputs:\n"; > foreach my $simple (@{$out->Simples}) { > print "\t", $simple->objectType, "\n"; > print "\t\tin namespace(s)\n"; > foreach $ns ( @{$simple->namespaces} ) { print "\t\t\t\t$ns\n"; } > } > } > else { > print "a single output:\n"; > print "\t", $out->objectType, "\n"; > print "\t\tin namespace(s)\n"; > foreach $ns ( @{$out->namespaces} ) { print "\t\t\t\t$ns\n"; } > } > } > print "\n", '-'x80, "\n"; > } > > print "Services by authority:\n"; > #while (my ($k, $v) = each $Count{authority}) { > for my $s (sort {lc $a cmp lc $b} keys %{$Count{authority}}) { > print "$Count{authority}{$s} $s\n"; > } > > > 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 > > _______________________________________________ > moby-l mailing list > moby-l@biomoby.org > http://biomoby.org/mailman/listinfo/moby-l -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From gss at ncgr.org Tue Nov 16 12:39:01 2004 From: gss at ncgr.org (Gary Schiltz) Date: Tue Nov 16 12:41:07 2004 Subject: [MOBY-l] MOBY Meeting: LAST CALL In-Reply-To: <419531B1.20208@ncgr.org> References: <4191470F.9010001@ncgr.org> <419531B1.20208@ncgr.org> Message-ID: <419A3B35.4020400@ncgr.org> This is a final reminder that the MOBY autumn 2004 meeting is next Saturday and Sunday, November 20 & 21 at NCGR in Santa Fe, New Mexico (four days from now) - see www.semanticmoby.org/meeting for details, www.semanticmoby.org/meeting/registration-form.html to register. If you plan to attend, please register as soon as possible. The list of people I have recorded as registering are the following; please let me know if you are planning to attend and your name is not on the list: Andrew Farmer (NCGR) Bill Beavis (NCGR) Damian Gessler (NCGR) Dirk Haase (MIPS) Fernando Rojas (CIAT) Gary Schiltz (NCGR) Guy Davenport (CIMMYT) Manuel Ruiz (CIRAD) Mark Wilkinson (UBC) Martin Senger (EBI) Milko Skofic (IPGRI) Rex Nelson (USDA-ARS CICGR) Richard Bruskiewich (IRRI) Thomas Hazekamp (IPGRI) ---- Gary Schiltz Principal Software Engineer National Center for Genome Resources Santa Fe, New Mexico USA From gss at ncgr.org Tue Nov 16 17:37:36 2004 From: gss at ncgr.org (Gary Schiltz) Date: Tue Nov 16 17:39:38 2004 Subject: [MOBY-l] [Fwd: an application for MOBY developers to consider] Message-ID: <419A8130.6010103@ncgr.org> Bill Beavis of NCGR asked that I pass this along to the list. Since I seem to remember the Listsrv software sometimes not liking attachments, I have put the attachments from Bill's email at www.semanticmoby.org/meeting/vpn instead of leaving them attached. The white paper Bill refers to is the file An_app_for_MOBY.pdf // Gary -------- Original Message -------- Subject: an application for MOBY developers to consider Date: Tue, 16 Nov 2004 14:55:23 -0700 From: Bill Beavis Greetings from Santa Fe, As many of you are aware, we'd like to visit about an application for the BioMOBY projects during our meeting this weekend. Because many of us work with Plant Information Resources we'd like to discuss the potential of using BioMOBY for development of a Virtual Plant Network (we may have to name it something else so that the acronym is not confused with another VPN). After visiting with the cognizant program officers, Stinger Guala and Manfred Zorn, I believe that we would have a reasonably good chance of obtaining support from the NSF-BDI for such a proposal. In order to stimulate discussion of the idea, please find attached a white paper utlining the concept and specific aims that might be included in such a proposal. Note that yellow highlights indicate areas that need clarification. Also, please find attached a couple of references that are germane to the discussion. For those of you who have been interested in utilizing MOBY for the CGIAR - Grand Challenge Program, there is a mechanism to obtain supplemental funding in this proposal for development of international collaborations. Thus, for those of you from non-US institutions, participation in this proposal could bring in some funding to support your efforts to utilize MOBY. For those of you who are not able to attend the MOBY meeting, you can join the discussion, which will begin at 1:00 pm MST, through a teleconference. Instructions for joining us: Date : Saturday, Nov. 20, 2004 Time : 1 pm Mountain Standard Time Discussion : Integrating Semantic MOBY and MOBY Services in a real world, distributed application: The Virtual Plant Network. Instructions to join: 1 - Dial the toll-free On-Demand Plus Number: 1-888-387-8686 (For international users, dial the international dial-out plus the country code (1) followed by 303-928-3281) 2 - Enter the Room number: 4139056, and press # 3 - You will be placed directly into the meeting if the moderator has already joined. If the moderator hasn't joined, you will be placed on hold for up to 10 minutes. Best regards, Bill Beavis From rebecca.ernst at gsf.de Wed Nov 17 05:10:20 2004 From: rebecca.ernst at gsf.de (Rebecca Ernst) Date: Wed Nov 17 05:08:52 2004 Subject: [MOBY-l] python services Message-ID: <419B238C.5020100@gsf.de> Hi Yan! within the PlaNet consortium there are currently two people that would like to use the Python API. Obviously it is not perfectly clear how a python service should be implemented. (does it work with a cgi and a dispatch like in perl?) Are there any examples available? E.g. a simple 'hello world' service which can be used to establish the system? Thanks a lot for your help! Rebecca -- Rebecca Ernst MIPS, Inst. for Bioinformatics GSF Research Center for Environment and Health Ingolstaedter Landstr. 1 85764 Neuherberg fon: +49 89 3187 3583 email: Rebecca.Ernst@gsf.de From lstein at cshl.edu Wed Nov 17 15:55:42 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Wed Nov 17 15:53:55 2004 Subject: [MOBY-l] MOBY Meeting: Reminder & Details In-Reply-To: <4191470F.9010001@ncgr.org> References: <4191470F.9010001@ncgr.org> Message-ID: <200411171555.42826.lstein@cshl.edu> You'll provide me with a dial-in number, right? Lincoln On Tuesday 09 November 2004 05:39 pm, Gary Schiltz wrote: > This is a reminder that the MOBY autumn 2004 meeting is approaching > quickly (11 days from now) - see www.semanticmoby.org/meeting for > details, www.semanticmoby.org/meeting/registration-form.html to > register: > > Date : November 20-21 (Saturday & Sunday) > Location : Santa Fe, New Mexico USA > Venue : National Center for Genome Resources (www.ncgr.org) > Fee : $50 USD/person (covers lunch and transportation > between hotels and NCGR) > > The tentative agenda is as follows; please post any suggestions to > the moby-l or moby-dev lists: > > Saturday, November 20, 2004: > 8:30 am Bagels and coffee > 9:00 am Semantic MOBY (Damian Gessler) > 10:00 am Taverna (Martin Senger) > 10:45 am Break > 11:00 am MOBY Services (Mark Wilkinson) > 12:00 pm Lunch provided > 1:00 pm: Virtual Plant Network (Bill Beavis, discussion > leader) 2:00 pm: Conceptual ways to merge S-MOBY, MOBY-S, and > MyGrid in a real-world application (joined by Phil Lord via telecon > [Manchester is seven hours ahead of Santa Fe]) 6:00pm Dinner > > Sunday, November 21, 2004 > 9:00 am Bagels and coffee > 9:30 am Technical challenges to merging S-MOBY, MOBY-S, > and MyGrid > 11:30 am Next steps > > > > > > _______________________________________________ > moby-l mailing list > moby-l@biomoby.org > http://biomoby.org/mailman/listinfo/moby-l -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 NOTE: Please copy Sandra Michelsen on all emails regarding scheduling and other time-critical topics. From markw at illuminae.com Sat Nov 20 12:26:42 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Sat Nov 20 12:24:41 2004 Subject: [MOBY-l] Santa Fe developers Meeting Blog Message-ID: <419F7E52.6070806@illuminae.com> Link on the biomoby.org homepage. Updated every few minutes. Cheers all! M From markw at illuminae.com Sat Nov 20 12:51:23 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Sat Nov 20 12:49:16 2004 Subject: [MOBY-l] we were just hacked...?? Message-ID: <419F841B.5090003@illuminae.com> In the past 10 minutes, it appears that someone hacked the biomoby.org website. It seems so far that only the index.html file was affected... I will try to get it back up ASAP. In the meantime, interested people can find the blog of the ongoing developers meeting at: http://biomoby.org/twiki/bin//view/Moby/MobyDevelopersMeetingSantaFe M From michael at acutrans.net Mon Nov 29 12:40:40 2004 From: michael at acutrans.net (Michael Jensen) Date: Mon Nov 29 12:38:24 2004 Subject: [MOBY-l] we were just hacked...?? In-Reply-To: <419F841B.5090003@illuminae.com> References: <419F841B.5090003@illuminae.com> Message-ID: Where's the meeting blog? Didn't see a link on biomoby.org and the URL below gives me a 403 error. -Michael Jensen michael@inblosam.com On Nov 20, 2004, at 11:51 AM, Mark Wilkinson wrote: > In the past 10 minutes, it appears that someone hacked the biomoby.org > website. It seems so far that only the index.html file was > affected... > > I will try to get it back up ASAP. > > In the meantime, interested people can find the blog of the ongoing > developers meeting at: > http://biomoby.org/twiki/bin//view/Moby/MobyDevelopersMeetingSantaFe > > M > > > _______________________________________________ > moby-l mailing list > moby-l@biomoby.org > http://biomoby.org/mailman/listinfo/moby-l > From gss at ncgr.org Tue Nov 9 17:39:11 2004 From: gss at ncgr.org (Gary Schiltz) Date: Tue, 09 Nov 2004 15:39:11 -0700 Subject: [MOBY-l] MOBY Meeting: Reminder & Details Message-ID: <4191470F.9010001@ncgr.org> This is a reminder that the MOBY autumn 2004 meeting is approaching quickly (11 days from now) - see www.semanticmoby.org/meeting for details, www.semanticmoby.org/meeting/registration-form.html to register: Date : November 20-21 (Saturday & Sunday) Location : Santa Fe, New Mexico USA Venue : National Center for Genome Resources (www.ncgr.org) Fee : $50 USD/person (covers lunch and transportation between hotels and NCGR) The tentative agenda is as follows; please post any suggestions to the moby-l or moby-dev lists: Saturday, November 20, 2004: 8:30 am Bagels and coffee 9:00 am Semantic MOBY (Damian Gessler) 10:00 am Taverna (Martin Senger) 10:45 am Break 11:00 am MOBY Services (Mark Wilkinson) 12:00 pm Lunch provided 1:00 pm: Virtual Plant Network (Bill Beavis, discussion leader) 2:00 pm: Conceptual ways to merge S-MOBY, MOBY-S, and MyGrid in a real-world application (joined by Phil Lord via telecon [Manchester is seven hours ahead of Santa Fe]) 6:00pm Dinner Sunday, November 21, 2004 9:00 am Bagels and coffee 9:30 am Technical challenges to merging S-MOBY, MOBY-S, and MyGrid 11:30 am Next steps From p.lord at cs.man.ac.uk Wed Nov 10 19:28:38 2004 From: p.lord at cs.man.ac.uk (Phillip Lord) Date: 11 Nov 2004 00:28:38 +0000 Subject: [MOBY-l] Re: [MOBY-dev] Semantic Moby and Web Services <-> Semantic Web integration efforts? In-Reply-To: <24F7236E-3338-11D9-94D7-000D93B0BD32@pasteur.fr> References: <24F7236E-3338-11D9-94D7-000D93B0BD32@pasteur.fr> Message-ID: >>>>> "Catherine" == Catherine Letondal writes: Catherine> Hi, Catherine> I would have a question: how is the Moby-S branch of Catherine> Biomoby connected to other efforts that seek to integrate Catherine> Web services and Semantic Web? I mean groups, systems or Catherine> forums such as: Catherine> http://www.w3.org/2002/ws/swsig/ http://www.wsmo.org Catherine> (Web service modelling Ontology) Catherine> http://www.wsmo.org/wsml (Web Service Modeling Catherine> Language) http://www.daml.org/services/owl-s Catherine> (OWL-based Web service ontology) Catherine> ...? Catherine> BTW, I have just heard of this book: Developing Semantic Catherine> Web Services (A. K. Peters) : Catherine> http://www.akpeters.com/product.asp?ProdCode=2124 It isn't really. There is some similarity between the OWL-S profile, and moby-s data model. OWL-S/WSMO are trying to do a different thing to moby-s. The main aim for these technologies is to use highly expressive logics to enable automated composition and choreography of web services. This is a nice idea, but, my own suspicion is that most biologists, or bioinformatics service providers are not going to go to the effort to describe their services logically. Moby-s on the other hand takes a more constrained view of semantics. It's trying to produce semantic descriptions which are good enough to reduce the problem for the biologist to selecting from one or a short list, rather than then 500. There is a paper in this years ISWC (currently going on now!), which you can get from here... http://www.cs.man.ac.uk/~phillord/download/publications/biomoby-comparison-iswc2004.pdf Cheers Phil From gasalazar at parquesoft.com Thu Nov 11 12:31:59 2004 From: gasalazar at parquesoft.com (Gustavo Adolfo Salazar Orejuela) Date: Thu, 11 Nov 2004 12:31:59 -0500 (COT) Subject: [MOBY-l] (no subject) Message-ID: <32981.192.168.2.173.1100194319.squirrel@192.168.2.173> Hi everybody, I don't know if this is the right place to send my question, if i'm wrong please let me know where is it... I'm interested in learn how to use MOBY, that's why i did the next things: 1 I download movy-live of CVS like anonymous user and download too the separate distribution of jMoby 2 I install without problems the perl client 3 I did some test(ask for services and call a service) with this client, and all work fine 4 I Wanted to test the Java's Client, then I compile that, and so far so good 5 I used the script run-cmdline-client asking for services and everything was right 6 When i tryed to use that script with something like that: =========== /run-cmdline-client -call MOBYSHoundGetGenBankff objeto.xml =========== where objeto.xml is a file with just this line: i got this error: ===ERROR=== org.biomoby.shared.MobyException: ===ERROR=== Fault details: [stackTrace: null] Fault string: org.xml.sax.SAXException: SimpleDeserializer encountered a child element, which is NOT expected, in something it was trying to deserialize. Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException Fault actor: null When calling: http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY05/mobycentral.pl =========== at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:172) at org.biomoby.client.CentralImpl.call(CentralImpl.java:1176) at MobyCmdLineClient.main(MobyCmdLineClient.java:512) =========== What did I wrong?? later... 7 I used the source code downladed of CVS and compile that... and everithing OK 8 I found some example called MobyServiceInvocationExample.java, but when i try to complile, i had the next error: ========== Finding services that correspond to input data: Invoking service MOBYSHoundGetGenBankff Exception in thread "main" java.lang.NullPointerException at org.apache.crimson.tree.ElementNode2.getAttributeNodeNS(ElementNode2.java:432) at org.apache.crimson.tree.ElementNode2.getAttributeNS(ElementNode2.java:409) at org.biomoby.shared.MobyPrefixResolver.getAttr(Unknown Source) at org.biomoby.shared.MobyDataSimpleInstance.(Unknown Source) at org.biomoby.client.MobyRequest.convertMOBYResponseToMOBYData(Unknown Source) at org.biomoby.client.MobyRequest.invokeService(Unknown Source) at MobyServiceInvocationExample.main(MobyServiceInvocationExample.java:66) ========== I used that line to compile java -classpath ../build/classes/:axis.jar:jaxrpc.jar:commons-logging.jar:commons-discovery.jar:saaj.jar:../build/Clients/ MobyServiceInvocationExample and again... wath did i wrong?? I know that maybe all that questions looks like the begginers, but really i'm I will apreciate wathever kind of help. Bye Gustavo Adolfo From markw at illuminae.com Thu Nov 11 13:02:17 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 11 Nov 2004 10:02:17 -0800 Subject: [MOBY-l] (no subject) In-Reply-To: <32981.192.168.2.173.1100194319.squirrel@192.168.2.173> References: <32981.192.168.2.173.1100194319.squirrel@192.168.2.173> Message-ID: <4193A929.5070506@illuminae.com> Gustavo Adolfo Salazar Orejuela wrote: >where objeto.xml is a file with just this line: > >i got this error: > > I'm assuming that this is a typo in your message - please double-check that your namespace is NCBI_gi, rather than NCBI_ig Otherwise, I'll bounce this question on to Martin or Nina... M > > From senger at ebi.ac.uk Thu Nov 11 13:32:39 2004 From: senger at ebi.ac.uk (Martin Senger) Date: Thu, 11 Nov 2004 18:32:39 +0000 (GMT) Subject: [MOBY-l] (no subject) In-Reply-To: <32981.192.168.2.173.1100194319.squirrel@192.168.2.173> Message-ID: > 6 When i tryed to use that script with something like that: > =========== > /run-cmdline-client -call MOBYSHoundGetGenBankff objeto.xml > =========== > where objeto.xml is a file with just this line: > > i got this error: > The main problem is that you are using a command-line client that talks to Moby Central registry, not to a service you want to call. You can, however, use this command-line client to call a service, but you need to add two more parameters: 1) -e The URL of a service you either know, or you can get it by a separate call from Moby registry: run-cmdline-client -fn MOBYSHoundGetGenBankff (This will give you this URL: http://mobycentral.cbr.nrc.ca/cgi-bin/Services/Services.cgi) 2) -uri http://biomoby.org/ This is a mandatory namespace for moby services (I hope I have it right). Additionally to that, it's recommended that you put your XML input in a file (let's say bankff.xml). The whole command then look like this: run-cmdline-client \ -e http://mobycentral.cbr.nrc.ca/cgi-bin/Services/Services.cgi \ -uri http://biomoby.org/ \ -call MOBYSHoundGetGenBankff bankff.xml Which still does not do what you want because your input needs a moby envelope (the line above gets back an empty result). The correct full input is this: Put it in bankff.xml and run the line above again and you get a response from this service (I have just tried). > 7 I used the source code downladed of CVS and compile that... and > everithing OK > 8 I found some example called MobyServiceInvocationExample.java, but > when i try to complile, i had the next error: (I assume that by "try to compile" you mean "try to run", right?) Let's wait for Paul Gordon to answer this part - he is the author of this class. Paul, arer you around? With regard, Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From gordonp at cbr.nrc.ca Thu Nov 11 14:01:27 2004 From: gordonp at cbr.nrc.ca (Paul Gordon) Date: Thu, 11 Nov 2004 12:01:27 -0700 Subject: [MOBY-l] (no subject) In-Reply-To: <32981.192.168.2.173.1100194319.squirrel@192.168.2.173> References: <32981.192.168.2.173.1100194319.squirrel@192.168.2.173> Message-ID: <4193B707.6000303@cbr.nrc.ca> Hi Gustavo, >7 I used the source code downladed of CVS and compile that... and >everithing OK >8 I found some example called MobyServiceInvocationExample.java, but when >i try to complile, i had the next error: > > Indeed, this is the correct class to use invoke a service. The problem you encountered below is that unfortunately Crimson does not handle null namespaces as per the XML Namespaces spec (as Crimson is no longer being actively maintained). I suggest you use Apache Xerces as your XML parser, and the appliucation should not fail. As Mark pointed out though, you'll get an empty response, if that NCBI_ig typo from your e-mail in the input, though it looks like your actual input is okay from the message below. If you don't have Xerces, it can be downloaded as a jar from http://xml.apache.org/. If you do have it, but it's not your default XML parser, you can make it the default with any number of techniques as described at that site, or define a rather verbose system property on the command line Java invocation: "-Djavax.xml.parsers.DocumentBuilderFactory=org.apache.*xerces*.*jaxp*.DocumentBuilderFactoryImpl" Good Luck! >========== >Finding services that correspond to input data: namespace="NCBI_gi" id="431260"/> >Invoking service MOBYSHoundGetGenBankff >Exception in thread "main" java.lang.NullPointerException > at >org.apache.crimson.tree.ElementNode2.getAttributeNodeNS(ElementNode2.java:432) > at >org.apache.crimson.tree.ElementNode2.getAttributeNS(ElementNode2.java:409) > at org.biomoby.shared.MobyPrefixResolver.getAttr(Unknown Source) > at org.biomoby.shared.MobyDataSimpleInstance.(Unknown Source) > at >org.biomoby.client.MobyRequest.convertMOBYResponseToMOBYData(Unknown >Source) > at org.biomoby.client.MobyRequest.invokeService(Unknown Source) > at >MobyServiceInvocationExample.main(MobyServiceInvocationExample.java:66) >========== > >I used that line to compile >java -classpath >../build/classes/:axis.jar:jaxrpc.jar:commons-logging.jar:commons-discovery.jar:saaj.jar:../build/Clients/ >MobyServiceInvocationExample > > From markw at illuminae.com Thu Nov 11 14:03:26 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 11 Nov 2004 11:03:26 -0800 Subject: [MOBY-l] (no subject) In-Reply-To: References: Message-ID: <4193B77E.5070808@illuminae.com> Ugh... as simple as it is, even MOBY-S is pretty complicated! I wonder if we should write a quick command-line tool that executes one of the more stable MOBY services (like one of the wrapped SeqHound functions) for cases like this where people just want to be sure that the whole thing is working. All I can say is "thank heavens we have tools like Taverna!" :-) M Martin Senger wrote: >>6 When i tryed to use that script with something like that: >>=========== >> /run-cmdline-client -call MOBYSHoundGetGenBankff objeto.xml >>=========== >>where objeto.xml is a file with just this line: >> >>i got this error: >> >> >> > The main problem is that you are using a command-line client that >talks to Moby Central registry, not to a service you want to call. You >can, however, use this command-line client to call a service, but you need >to add two more parameters: > > 1) -e > >The URL of a service you either know, or you can get it by a separate call >from Moby registry: > > run-cmdline-client -fn MOBYSHoundGetGenBankff > >(This will give you this URL: > http://mobycentral.cbr.nrc.ca/cgi-bin/Services/Services.cgi) > > 2) -uri http://biomoby.org/ > >This is a mandatory namespace for moby services (I hope I have it right). > >Additionally to that, it's recommended that you put your XML input in a >file (let's say bankff.xml). The whole command then look like this: > >run-cmdline-client \ > -e http://mobycentral.cbr.nrc.ca/cgi-bin/Services/Services.cgi \ > -uri http://biomoby.org/ \ > -call MOBYSHoundGetGenBankff bankff.xml > > >Which still does not do what you want because your input needs a moby >envelope (the line above gets back an empty result). > >The correct full input is this: > > > > > > > > > > > > >Put it in bankff.xml and run the line above again and you get a response >from this service (I have just tried). > > > >>7 I used the source code downladed of CVS and compile that... and >>everithing OK >>8 I found some example called MobyServiceInvocationExample.java, but >>when i try to complile, i had the next error: >> >> > >(I assume that by "try to compile" you mean "try to run", right?) >Let's wait for Paul Gordon to answer this part - he is the author of this >class. Paul, arer you around? > > > With regard, > Martin > > > From senger at ebi.ac.uk Thu Nov 11 14:10:17 2004 From: senger at ebi.ac.uk (Martin Senger) Date: Thu, 11 Nov 2004 19:10:17 +0000 (GMT) Subject: [MOBY-l] (no subject) In-Reply-To: <4193B77E.5070808@illuminae.com> Message-ID: > I wonder if we should write a quick command-line tool that executes one > of the more stable MOBY services (like one of the wrapped SeqHound > functions) for cases like this where people just want to be sure that > the whole thing is working. > I agree. Anyway, the first step will be to improve jMoby documentation, it needs update. I hope to finish it before Santa Fe. But writing such client for one or more particular services could be question of an hour. Mark, if you pick up few such services and send me their names and their corresponding inputs, I will write it as well still before Santa Fe. Cheers, Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From gordonp at cbr.nrc.ca Thu Nov 11 14:50:13 2004 From: gordonp at cbr.nrc.ca (Paul Gordon) Date: Thu, 11 Nov 2004 12:50:13 -0700 Subject: [MOBY-l] (no subject) In-Reply-To: References: Message-ID: <4193C275.1090807@cbr.nrc.ca> Well, if you have a fully functional XML parser around (which unfortunately Java does not come with by default, it uses Crimson), MobyServiceInvocationExample is supposed to be simple :-) I'll see if I can fix it up a bit to find Xerces automatically... Martin Senger wrote: >>I wonder if we should write a quick command-line tool that executes one >>of the more stable MOBY services (like one of the wrapped SeqHound >>functions) for cases like this where people just want to be sure that >>the whole thing is working. >> >> >> > I agree. Anyway, the first step will be to improve jMoby documentation, >it needs update. I hope to finish it before Santa Fe. But writing such >client for one or more particular services could be question of an hour. >Mark, if you pick up few such services and send me their names and their >corresponding inputs, I will write it as well still before Santa Fe. > > Cheers, > Martin > > > From gasalazar at parquesoft.com Thu Nov 11 15:40:13 2004 From: gasalazar at parquesoft.com (Gustavo Adolfo Salazar Orejuela) Date: Thu, 11 Nov 2004 15:40:13 -0500 (COT) Subject: [MOBY-l] (no subject) In-Reply-To: <4193C275.1090807@cbr.nrc.ca> References: <4193C275.1090807@cbr.nrc.ca> Message-ID: <33245.192.168.2.173.1100205613.squirrel@192.168.2.173> Hello... I am working now with the run-cmdline-client, thanks a lot. Right now I am trying to work with the Java classes, Like Paul Gordon suggested me(Xerces downloading...). I noticed when i tryed to compile the class Example with jMOBY.jar provided by the separated version that this jar is not updated with respect to classes on the CVS just like the documentation... Well... i have another question... what if I want to call another service with the answer recently got with previous service? In that case, i need to use some API like JDOM(or similar in PERL) to get the interesting information to build another XML or exist another way to connect the output of the first service with the input of the second? Somebody has a sample file(Java or Perl) that do some near to my question. And again, Thanks for your help. -- Gustavo Adolfo > Well, if you have a fully functional XML parser around (which > unfortunately Java does not come with by default, it uses Crimson), > MobyServiceInvocationExample is supposed to be simple :-) I'll see if I > can fix it up a bit to find Xerces automatically... > > Martin Senger wrote: > >>>I wonder if we should write a quick command-line tool that executes one >>>of the more stable MOBY services (like one of the wrapped SeqHound >>>functions) for cases like this where people just want to be sure that >>>the whole thing is working. >>> >>> >>> >> I agree. Anyway, the first step will be to improve jMoby >> documentation, >>it needs update. I hope to finish it before Santa Fe. But writing such >>client for one or more particular services could be question of an hour. >>Mark, if you pick up few such services and send me their names and their >>corresponding inputs, I will write it as well still before Santa Fe. >> >> Cheers, >> Martin >> >> >> > > _______________________________________________ > moby-l mailing list > moby-l at biomoby.org > http://biomoby.org/mailman/listinfo/moby-l > From markw at illuminae.com Thu Nov 11 15:49:39 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 11 Nov 2004 12:49:39 -0800 Subject: [MOBY-l] (no subject) In-Reply-To: <33245.192.168.2.173.1100205613.squirrel@192.168.2.173> References: <4193C275.1090807@cbr.nrc.ca> <33245.192.168.2.173.1100205613.squirrel@192.168.2.173> Message-ID: <4193D063.6000501@illuminae.com> >Well... i have another question... >what if I want to call another service with the answer recently got with >previous service? In that case, i need to use some API like JDOM(or >similar in PERL) to get the interesting information to build another XML >or exist another way to connect the output of the first service with the >input of the second? >Somebody has a sample file(Java or Perl) that do some near to my question. > > This is basically what the CGI client does (http://mobycentral.cbr.nrc.ca). The (perl) code for that client is distributed as part of the Gbrowse package. If you prefer, I can grab a copy of just the client code and mail it to you directly. (gbrowse: http://www.gmod.org/ggb/) In addition, Taverna (http://taverna.sourceforge.net) will do that for you through a pretty GUI :-) Unless you really need to build your own client, you might find it more useful to use one of the existing tools, or tweak them to suit your situation. M >And again, Thanks for your help. > > > > From senger at ebi.ac.uk Thu Nov 11 16:30:32 2004 From: senger at ebi.ac.uk (Martin Senger) Date: Thu, 11 Nov 2004 21:30:32 +0000 (GMT) Subject: [MOBY-l] (no subject) In-Reply-To: <33245.192.168.2.173.1100205613.squirrel@192.168.2.173> Message-ID: > Right now I am trying to work with the Java classes, Like Paul Gordon > suggested me(Xerces downloading...). > Xerces is part of the CVS (once you bild everything). If the version there does not work, we need to find why and replace it. (I have still one unanswered email from Ninan about perhaps something similar.) If you start using a different xerces, you will never stay compatible with jMoby CVS. So my suggestion is: do not download xerces but find what wrong with the existing one. (This is a suggestion for Paul, as the class author, not for you, Gustavo.) > I noticed when i tryed to compile the class Example with jMOBY.jar > provided by the separated version that this jar is not updated with > respect to classes on the CVS just like the documentation... > If you use CVS, it always use the latest classes. Do not use any jMOBY.jar taken from somewhere else. But perhaps I did not fully understand this point. > Well... i have another question... > what if I want to call another service with the answer recently got with > previous service? In that case, i need to use some API like JDOM(or > similar in PERL) to get the interesting information to build another XML > or exist another way to connect the output of the first service with the > input of the second? > Yes, you need an XML parser - and jdom.jar is part of CVS (again, once you build there everything). Remember, however, that both input and output moby data are wrapped in the same envelope - so, unless you want to extract information from this envelope, such as crosss-references, you can just pass the output of one services directly as an input to another service without even looking into it. Cheers, Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From gordonp at cbr.nrc.ca Thu Nov 11 16:46:26 2004 From: gordonp at cbr.nrc.ca (Paul Gordon) Date: Thu, 11 Nov 2004 14:46:26 -0700 Subject: [MOBY-l] (no subject) In-Reply-To: References: Message-ID: <4193DDB2.8060204@cbr.nrc.ca> Actually, the problem that he is using Crimson. MobyServiceInvocationExample uses JAXP's DocumentBuilder interface, so it uses whatever XML parser implementation is the user's default. To help the user, I'll have the client check if Xerces is in the classpath (hopefully from the jMOBY CVS), and force it as the default if available, since Crimson is so crappy. > So my suggestion is: do not download xerces but find what wrong with >the existing one. (This is a suggestion for Paul, as the class author, not >for you, Gustavo.) > > From gss at ncgr.org Fri Nov 12 16:57:05 2004 From: gss at ncgr.org (Gary Schiltz) Date: Fri, 12 Nov 2004 14:57:05 -0700 Subject: [MOBY-l] MOBY Meeting: Reminder & Updates In-Reply-To: <4191470F.9010001@ncgr.org> References: <4191470F.9010001@ncgr.org> Message-ID: <419531B1.20208@ncgr.org> This is another reminder that the MOBY autumn 2004 meeting is quickly approaching (8 days from now) - see www.semanticmoby.org/meeting for details, www.semanticmoby.org/meeting/registration-form.html to register. The meeting pages on semanticmoby.org have been updated. I look forward to seeing you there! ---- Gary Schiltz Principal Software Engineer National Center for Genome Resources Santa Fe, New Mexico USA From senger at ebi.ac.uk Fri Nov 12 18:16:25 2004 From: senger at ebi.ac.uk (Martin Senger) Date: Fri, 12 Nov 2004 23:16:25 +0000 (GMT) Subject: [MOBY-l] (no subject) In-Reply-To: Message-ID: Hi all, Motivated by the previous conversation in this thread, and recognizing that more and more people are actually using jMoby command-line client for calling services (even though its original intent was to call Moby registry), I have added there a new command-line option that makes this a bit easier. Easier in a sense that you do not need to fins the URL of a servic yourselv, and that you do not need to specify service uri (which is constant for all services) - so it is not easier in a sense to support you with the XML input, not yet. The new option -scall is documented in the help file, including an example. Please CVS update and you can try. Cheers, Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From mwilkinson at mobile.rogers.com Fri Nov 12 18:16:39 2004 From: mwilkinson at mobile.rogers.com (mwilkinson) Date: Fri, 12 Nov 2004 18:16:39 -0500 Subject: [MOBY-l] (no subject) Message-ID: <200411122317.iACNHvKr006864@portal.open-bio.org> What was I saying about 24 hour turnaround times with Martin... More like 2 hours! ...who says Martin works for myGrid!! ;-) M -----Original Message----- From: Martin Senger Date: Fri, 12 Nov 2004 23:16:25 To:Gustavo Adolfo Salazar Orejuela Cc:moby-l at biomoby.org Subject: Re: [MOBY-l] (no subject) Hi all, Motivated by the previous conversation in this thread, and recognizing that more and more people are actually using jMoby command-line client for calling services (even though its original intent was to call Moby registry), I have added there a new command-line option that makes this a bit easier. Easier in a sense that you do not need to fins the URL of a servic yourselv, and that you do not need to specify service uri (which is constant for all services) - so it is not easier in a sense to support you with the XML input, not yet. The new option -scall is documented in the help file, including an example. Please CVS update and you can try. Cheers, Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger _______________________________________________ moby-l mailing list moby-l at biomoby.org http://biomoby.org/mailman/listinfo/moby-l !!!!!!!!!!!!!!!! To respond to this message you MUST send your response to (note new address!) markw_mobile2 at illuminae dot com Responses to the reply-to address go directly to trash! !!!!!!!!!!!!!!!!!!!!!!!!!!!! From senger at ebi.ac.uk Fri Nov 12 18:20:23 2004 From: senger at ebi.ac.uk (Martin Senger) Date: Fri, 12 Nov 2004 23:20:23 +0000 (GMT) Subject: [MOBY-l] small change in Taverna (in BioMoby services) Message-ID: Hi all, I have slightly improved the error messages in Taverna generating by Moby services. It also better copes now when a service returns an empty result. I also replaced jmoby.jar for the latest one. If you want to have this, CVS update Taverna please. Cheers, Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From senger at ebi.ac.uk Fri Nov 12 18:24:38 2004 From: senger at ebi.ac.uk (Martin Senger) Date: Fri, 12 Nov 2004 23:24:38 +0000 (GMT) Subject: [MOBY-l] (no subject) In-Reply-To: <200411122319.iACNJkvO004798@madeiro.ebi.ac.uk> Message-ID: > What was I saying about 24 hour turnaround times with Martin... > Mark, thanks, but you are too polite. I still feel guilty that the stuff I have started with Ben in IRRI is still not yet done... (talking about full XSD returned by registry, which will lead to a better support for Java client and service provider for complex data types). Cheers, Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger From p.lord at cs.man.ac.uk Sun Nov 14 09:04:16 2004 From: p.lord at cs.man.ac.uk (Phillip Lord) Date: 14 Nov 2004 14:04:16 +0000 Subject: [MOBY-l] Re: [MOBY-dev] Semantic Moby and Web Services <-> Semantic Web integration efforts? In-Reply-To: References: <24F7236E-3338-11D9-94D7-000D93B0BD32@pasteur.fr> Message-ID: >>>>> "Catherine" == Catherine Letondal writes: >> OWL-S/WSMO are trying to do a different thing to moby-s. The main >> aim for these technologies is to use highly expressive logics to >> enable automated composition and choreography of web >> services. >> >> Moby-s on the other hand takes a more constrained view of >> semantics. It's trying to produce semantic descriptions which are >> good enough to reduce the problem for the biologist to selecting >> from one or a short list, rather than then 500. >> Catherine> I meant S-Moby in fact, not Moby-S, sorry for this Catherine> mistake. Ah, well, this makes quite a difference! >> There is a paper in this years ISWC (currently going on now!), >> which you can get from here... >> >> http://www.cs.man.ac.uk/~phillord/download/publications/biomoby- >> comparison-iswc2004.pdf >> Catherine> Thanks a lot for this information. I have read the paper, Catherine> which indeed helped a lot to understand your underlying Catherine> choices (BTW, I would be interested to know about the Catherine> feedback it had at the ISCW conference - generally, Catherine> bioinformatics is considered as a "very specific" area, Catherine> and since the differences between "generial" applications Catherine> such as e-commerce and e-science are very well explained Catherine> in your paper, I'm curious to know whether the audience Catherine> reacted). It's difficult to say at the moment. I got some interest immediately after the talk. The paper was written to be slightly provocative, and, indeed, some people asked about my statement that "automated service composition is (largely) inappropriate in a scientific domain". Sadly, I seem to have picked up a illness at the conference, and was in bed for most of the social events and poster sessions. This meant that a) I didn't get a chance to talk to more people and get better feedback and b) I missed some free beer, good food and Japanese drumming. Those who of you who know me, will realise how irked I was at this. So, I'll have to wait a while for people to read the paper, before I am sure of the reaction. Catherine> I still have a question about the comparison to OWL-S. In Catherine> section 7 of your paper (Service provision and Service Catherine> interfaces), you explain that OWL-S defines a grounding Catherine> ontology, and that the 3 approaches (moby-s, s-moby and Catherine> myGrid) have chosen a simpler approach. The "grounding" in OWL-S is specifically that part of the ontology which relates between the domain concepts describing the functionality of the service (in the "process" and "profile" subontologies) and the specific invocation interface, which for web services pretty much means the WSDL document. Catherine> I understand that the problem that is addressed here is Catherine> to have a high description not only of domain concepts, Catherine> but also on their relations, and that this is not Catherine> required in the 3 approaches, for different reasons. Catherine> But I don't understand your explanations: How is the Catherine> S-Moby interface defined by its "upper" ontology? I have Catherine> carefully read the S-moby design document Catherine> (http://www.biomoby.org/S-MOBY/doc/Design/S-MOBY_Design_Overview.html), Catherine> what do you call an upper ontology there - the set of RDF Catherine> graphs submitted by providers? S-moby is basically a REST architecture, with RDF and OWL messages. Strictly, it's service interfaces are all very simple, and all identical; it's HTTP, post, get, and the other three commands that I (and most people) can never remember. The response to these is, again, always the same for an s-moby service, and defined in the spec. So you don't need an ontology to describe this. There is no heterogeneity. Alternatively, you could consider the service interface to be specific RDF graphs that an s-moby service returns. Perhaps this is the better analogy, as this defines the specific functionality of the service. In this case, the graph defines the functionality totally. If you have the graph, you know how to address the service, what queries to send to it, and how to interpret the result coming back. So, again, you do not need to ground a s-moby service to an underlying WSDL. k Catherine> You also mention that moby-s interfaces are not Catherine> heterogeneous (and thus does not need an ontology to Catherine> interconnect concepts). What is not heterogeneous and Catherine> why? All moby-s services are the same. They have a single method, which you can invoke. Again, if you have the ontological description, you can understand what data you should send to a service, and how to interpret the data that comes back. So, again, no grounding is required. MyGrid is most like moby-s, in this context, except that instead of having a single defined service interface, we have a couple, and a pluggability layer within the other components to cope with the difference. This is why taverna and freefluo can cope with, for example, moby-s services. I hope this makes sense. It's quite hard to describe, particularly as s-moby's REST interface breaks (my use of) the standard web services terminology somewhat. Let me know if things are unclear. Cheers Phil From fgibbons at hms.harvard.edu Mon Nov 15 17:58:16 2004 From: fgibbons at hms.harvard.edu (Frank Gibbons) Date: Mon, 15 Nov 2004 17:58:16 -0500 Subject: [MOBY-l] Changes to registry? Signatures lost? Message-ID: <5.2.1.1.2.20041115174048.019d0008@email.med.harvard.edu> Hi MOBYers, I've been away from the MOBY world for a while (apart from bumping into Martin and Gary at the Semantic Web for Life Sciences Workshop in Cambridge), so perhaps I've missed out on some changes. Today I noticed that while my older services are still around, they seem to have lost their namespace information - whereas before they reported consuming information in specific namespaces, now they report that they do not support any particular namespace. I have a number of newly registered services (as of this morning), which correctly report namespaces. So, I'm wondering if perhaps the namespace information was accidentally dropped recently (was there a DB migration?) Or is it something more planned, where namespace info is no longer being reliably supplied, and I shouldn't rely on it (if this is the case, I'm in trouble!). Appended below is the code I use to determine this (originally provided by Mark, I suspect) - might help someone determine what's going on, or whether it's my problem. The services Ito/Uetz/Tong are the new ones, others are older. Strangely, YAService has been up for a month or two, yet still reports supporting namespace SGD. All services were registered by the old method, with no RDF generated. I believe I generated RDF for the older (non-namespace-supporting) ones, after having registered them, using Mark's script. Is this related to that? Sorry I can't make it out to Santa Fe, look forward to reading about the latest MOBY developments here. Thanks for help, -Frank ------------------------------- appended Perl script to see function/namespaces ----------------------------- #!/usr/bin/perl use lib qw(/share/local/share/perl/5.6.1 /share/lib/perl5/site_perl/5.8.3); # Use latest MOBY use MOBY::Client::Central; use MOBY::Client::Service; $m = MOBY::Client::Central->new(); my ($auth, $name) = ('llama.med.harvard.edu', 'YAService'); ($ss, $r) = $m->findService(authURI => $auth); #, serviceName => $name); my $i = 0; my %Count = (authority => (), type => (), input => ()); foreach my $service (sort { lc $a->name cmp lc $b->name } @{$ss} ) { $i++; $Count{authority}{$service->authority}++; $Count{type}{$service->type}++; $Count{input}{$service->input}++; print "$i: Service ", $service->name, " from ", $service->authority, " is of type ", $service->type, "\n"; print "It consumes: \n"; $inputs = $service->input; foreach $in ( @{$inputs} ) { eval {print "\t", $in->objectType, "\n"; }; print "\t\tin namespace(s)\n"; eval { my $namespaces = $in->namespaces; foreach $ns ( @{$namespaces} ) { print "\t\t\t\t$ns\n"; } }; } print "It generates "; $outputs = $service->output; foreach $out ( @{$outputs} ) { # Check for isCollection, each element of the collection should have an objectType if ($out->isCollection) { print "a collection of outputs:\n"; foreach my $simple (@{$out->Simples}) { print "\t", $simple->objectType, "\n"; print "\t\tin namespace(s)\n"; foreach $ns ( @{$simple->namespaces} ) { print "\t\t\t\t$ns\n"; } } } else { print "a single output:\n"; print "\t", $out->objectType, "\n"; print "\t\tin namespace(s)\n"; foreach $ns ( @{$out->namespaces} ) { print "\t\t\t\t$ns\n"; } } } print "\n", '-'x80, "\n"; } print "Services by authority:\n"; #while (my ($k, $v) = each $Count{authority}) { for my $s (sort {lc $a cmp lc $b} keys %{$Count{authority}}) { print "$Count{authority}{$s} $s\n"; } 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 mwilkinson at mrl.ubc.ca Mon Nov 15 19:00:19 2004 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Mon, 15 Nov 2004 16:00:19 -0800 Subject: [spam] [MOBY-l] Changes to registry? Signatures lost? In-Reply-To: <5.2.1.1.2.20041115174048.019d0008@email.med.harvard.edu> References: <5.2.1.1.2.20041115174048.019d0008@email.med.harvard.edu> Message-ID: <1100563219.13798.198.camel@mobycentral.icapture.ubc.ca> Try again now... should be fixed. It was a miscommunication between Nina and I last week that led to a small and easily repaired change to the database. All should be back to normal now. M On Mon, 2004-11-15 at 14:58, Frank Gibbons wrote: > Hi MOBYers, > > I've been away from the MOBY world for a while (apart from bumping into > Martin and Gary at the Semantic Web for Life Sciences Workshop in > Cambridge), so perhaps I've missed out on some changes. > > Today I noticed that while my older services are still around, they seem to > have lost their namespace information - whereas before they reported > consuming information in specific namespaces, now they report that they do > not support any particular namespace. > > I have a number of newly registered services (as of this morning), which > correctly report namespaces. So, I'm wondering if perhaps the namespace > information was accidentally dropped recently (was there a DB migration?) > Or is it something more planned, where namespace info is no longer being > reliably supplied, and I shouldn't rely on it (if this is the case, I'm in > trouble!). > > Appended below is the code I use to determine this (originally provided by > Mark, I suspect) - might help someone determine what's going on, or whether > it's my problem. The services Ito/Uetz/Tong are the new ones, others are > older. Strangely, YAService has been up for a month or two, yet still > reports supporting namespace SGD. > > All services were registered by the old method, with no RDF generated. I > believe I generated RDF for the older (non-namespace-supporting) ones, > after having registered them, using Mark's script. Is this related to that? > > Sorry I can't make it out to Santa Fe, look forward to reading about the > latest MOBY developments here. > > Thanks for help, > > -Frank > > ------------------------------- appended Perl script to see > function/namespaces ----------------------------- > #!/usr/bin/perl > > use lib qw(/share/local/share/perl/5.6.1 > /share/lib/perl5/site_perl/5.8.3); # Use latest MOBY > use MOBY::Client::Central; > use MOBY::Client::Service; > $m = MOBY::Client::Central->new(); > my ($auth, $name) = ('llama.med.harvard.edu', 'YAService'); > ($ss, $r) = $m->findService(authURI => $auth); #, serviceName => $name); > my $i = 0; > my %Count = (authority => (), type => (), input => ()); > foreach my $service (sort { lc $a->name cmp lc $b->name } @{$ss} ) { > $i++; > $Count{authority}{$service->authority}++; > $Count{type}{$service->type}++; > $Count{input}{$service->input}++; > print "$i: Service ", $service->name, " from ", > $service->authority, " is of type ", $service->type, "\n"; > print "It consumes: \n"; > $inputs = $service->input; > foreach $in ( @{$inputs} ) { > eval {print "\t", $in->objectType, "\n"; }; > print "\t\tin namespace(s)\n"; > eval { > my $namespaces = $in->namespaces; > foreach $ns ( @{$namespaces} ) { > print "\t\t\t\t$ns\n"; > } > }; > } > > print "It generates "; > $outputs = $service->output; > foreach $out ( @{$outputs} ) { > # Check for isCollection, each element of the collection should have > an objectType > if ($out->isCollection) { > print "a collection of outputs:\n"; > foreach my $simple (@{$out->Simples}) { > print "\t", $simple->objectType, "\n"; > print "\t\tin namespace(s)\n"; > foreach $ns ( @{$simple->namespaces} ) { print "\t\t\t\t$ns\n"; } > } > } > else { > print "a single output:\n"; > print "\t", $out->objectType, "\n"; > print "\t\tin namespace(s)\n"; > foreach $ns ( @{$out->namespaces} ) { print "\t\t\t\t$ns\n"; } > } > } > print "\n", '-'x80, "\n"; > } > > print "Services by authority:\n"; > #while (my ($k, $v) = each $Count{authority}) { > for my $s (sort {lc $a cmp lc $b} keys %{$Count{authority}}) { > print "$Count{authority}{$s} $s\n"; > } > > > 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 > > _______________________________________________ > moby-l mailing list > moby-l at biomoby.org > http://biomoby.org/mailman/listinfo/moby-l -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From gss at ncgr.org Tue Nov 16 12:39:01 2004 From: gss at ncgr.org (Gary Schiltz) Date: Tue, 16 Nov 2004 10:39:01 -0700 Subject: [MOBY-l] MOBY Meeting: LAST CALL In-Reply-To: <419531B1.20208@ncgr.org> References: <4191470F.9010001@ncgr.org> <419531B1.20208@ncgr.org> Message-ID: <419A3B35.4020400@ncgr.org> This is a final reminder that the MOBY autumn 2004 meeting is next Saturday and Sunday, November 20 & 21 at NCGR in Santa Fe, New Mexico (four days from now) - see www.semanticmoby.org/meeting for details, www.semanticmoby.org/meeting/registration-form.html to register. If you plan to attend, please register as soon as possible. The list of people I have recorded as registering are the following; please let me know if you are planning to attend and your name is not on the list: Andrew Farmer (NCGR) Bill Beavis (NCGR) Damian Gessler (NCGR) Dirk Haase (MIPS) Fernando Rojas (CIAT) Gary Schiltz (NCGR) Guy Davenport (CIMMYT) Manuel Ruiz (CIRAD) Mark Wilkinson (UBC) Martin Senger (EBI) Milko Skofic (IPGRI) Rex Nelson (USDA-ARS CICGR) Richard Bruskiewich (IRRI) Thomas Hazekamp (IPGRI) ---- Gary Schiltz Principal Software Engineer National Center for Genome Resources Santa Fe, New Mexico USA From gss at ncgr.org Tue Nov 16 17:37:36 2004 From: gss at ncgr.org (Gary Schiltz) Date: Tue, 16 Nov 2004 15:37:36 -0700 Subject: [MOBY-l] [Fwd: an application for MOBY developers to consider] Message-ID: <419A8130.6010103@ncgr.org> Bill Beavis of NCGR asked that I pass this along to the list. Since I seem to remember the Listsrv software sometimes not liking attachments, I have put the attachments from Bill's email at www.semanticmoby.org/meeting/vpn instead of leaving them attached. The white paper Bill refers to is the file An_app_for_MOBY.pdf // Gary -------- Original Message -------- Subject: an application for MOBY developers to consider Date: Tue, 16 Nov 2004 14:55:23 -0700 From: Bill Beavis Greetings from Santa Fe, As many of you are aware, we'd like to visit about an application for the BioMOBY projects during our meeting this weekend. Because many of us work with Plant Information Resources we'd like to discuss the potential of using BioMOBY for development of a Virtual Plant Network (we may have to name it something else so that the acronym is not confused with another VPN). After visiting with the cognizant program officers, Stinger Guala and Manfred Zorn, I believe that we would have a reasonably good chance of obtaining support from the NSF-BDI for such a proposal. In order to stimulate discussion of the idea, please find attached a white paper utlining the concept and specific aims that might be included in such a proposal. Note that yellow highlights indicate areas that need clarification. Also, please find attached a couple of references that are germane to the discussion. For those of you who have been interested in utilizing MOBY for the CGIAR - Grand Challenge Program, there is a mechanism to obtain supplemental funding in this proposal for development of international collaborations. Thus, for those of you from non-US institutions, participation in this proposal could bring in some funding to support your efforts to utilize MOBY. For those of you who are not able to attend the MOBY meeting, you can join the discussion, which will begin at 1:00 pm MST, through a teleconference. Instructions for joining us: Date : Saturday, Nov. 20, 2004 Time : 1 pm Mountain Standard Time Discussion : Integrating Semantic MOBY and MOBY Services in a real world, distributed application: The Virtual Plant Network. Instructions to join: 1 - Dial the toll-free On-Demand Plus Number: 1-888-387-8686 (For international users, dial the international dial-out plus the country code (1) followed by 303-928-3281) 2 - Enter the Room number: 4139056, and press # 3 - You will be placed directly into the meeting if the moderator has already joined. If the moderator hasn't joined, you will be placed on hold for up to 10 minutes. Best regards, Bill Beavis From rebecca.ernst at gsf.de Wed Nov 17 05:10:20 2004 From: rebecca.ernst at gsf.de (Rebecca Ernst) Date: Wed, 17 Nov 2004 11:10:20 +0100 Subject: [MOBY-l] python services Message-ID: <419B238C.5020100@gsf.de> Hi Yan! within the PlaNet consortium there are currently two people that would like to use the Python API. Obviously it is not perfectly clear how a python service should be implemented. (does it work with a cgi and a dispatch like in perl?) Are there any examples available? E.g. a simple 'hello world' service which can be used to establish the system? Thanks a lot for your help! Rebecca -- Rebecca Ernst MIPS, Inst. for Bioinformatics GSF Research Center for Environment and Health Ingolstaedter Landstr. 1 85764 Neuherberg fon: +49 89 3187 3583 email: Rebecca.Ernst at gsf.de From lstein at cshl.edu Wed Nov 17 15:55:42 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Wed, 17 Nov 2004 15:55:42 -0500 Subject: [MOBY-l] MOBY Meeting: Reminder & Details In-Reply-To: <4191470F.9010001@ncgr.org> References: <4191470F.9010001@ncgr.org> Message-ID: <200411171555.42826.lstein@cshl.edu> You'll provide me with a dial-in number, right? Lincoln On Tuesday 09 November 2004 05:39 pm, Gary Schiltz wrote: > This is a reminder that the MOBY autumn 2004 meeting is approaching > quickly (11 days from now) - see www.semanticmoby.org/meeting for > details, www.semanticmoby.org/meeting/registration-form.html to > register: > > Date : November 20-21 (Saturday & Sunday) > Location : Santa Fe, New Mexico USA > Venue : National Center for Genome Resources (www.ncgr.org) > Fee : $50 USD/person (covers lunch and transportation > between hotels and NCGR) > > The tentative agenda is as follows; please post any suggestions to > the moby-l or moby-dev lists: > > Saturday, November 20, 2004: > 8:30 am Bagels and coffee > 9:00 am Semantic MOBY (Damian Gessler) > 10:00 am Taverna (Martin Senger) > 10:45 am Break > 11:00 am MOBY Services (Mark Wilkinson) > 12:00 pm Lunch provided > 1:00 pm: Virtual Plant Network (Bill Beavis, discussion > leader) 2:00 pm: Conceptual ways to merge S-MOBY, MOBY-S, and > MyGrid in a real-world application (joined by Phil Lord via telecon > [Manchester is seven hours ahead of Santa Fe]) 6:00pm Dinner > > Sunday, November 21, 2004 > 9:00 am Bagels and coffee > 9:30 am Technical challenges to merging S-MOBY, MOBY-S, > and MyGrid > 11:30 am Next steps > > > > > > _______________________________________________ > moby-l mailing list > moby-l at biomoby.org > http://biomoby.org/mailman/listinfo/moby-l -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 NOTE: Please copy Sandra Michelsen on all emails regarding scheduling and other time-critical topics. From markw at illuminae.com Sat Nov 20 12:26:42 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Sat, 20 Nov 2004 09:26:42 -0800 Subject: [MOBY-l] Santa Fe developers Meeting Blog Message-ID: <419F7E52.6070806@illuminae.com> Link on the biomoby.org homepage. Updated every few minutes. Cheers all! M From markw at illuminae.com Sat Nov 20 12:51:23 2004 From: markw at illuminae.com (Mark Wilkinson) Date: Sat, 20 Nov 2004 09:51:23 -0800 Subject: [MOBY-l] we were just hacked...?? Message-ID: <419F841B.5090003@illuminae.com> In the past 10 minutes, it appears that someone hacked the biomoby.org website. It seems so far that only the index.html file was affected... I will try to get it back up ASAP. In the meantime, interested people can find the blog of the ongoing developers meeting at: http://biomoby.org/twiki/bin//view/Moby/MobyDevelopersMeetingSantaFe M From michael at acutrans.net Mon Nov 29 12:40:40 2004 From: michael at acutrans.net (Michael Jensen) Date: Mon, 29 Nov 2004 11:40:40 -0600 Subject: [MOBY-l] we were just hacked...?? In-Reply-To: <419F841B.5090003@illuminae.com> References: <419F841B.5090003@illuminae.com> Message-ID: Where's the meeting blog? Didn't see a link on biomoby.org and the URL below gives me a 403 error. -Michael Jensen michael at inblosam.com On Nov 20, 2004, at 11:51 AM, Mark Wilkinson wrote: > In the past 10 minutes, it appears that someone hacked the biomoby.org > website. It seems so far that only the index.html file was > affected... > > I will try to get it back up ASAP. > > In the meantime, interested people can find the blog of the ongoing > developers meeting at: > http://biomoby.org/twiki/bin//view/Moby/MobyDevelopersMeetingSantaFe > > M > > > _______________________________________________ > moby-l mailing list > moby-l at biomoby.org > http://biomoby.org/mailman/listinfo/moby-l >