From gordonp at ucalgary.ca Fri Apr 1 09:38:14 2005
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Fri Apr 1 09:32:14 2005
Subject: [MOBY-l] secondary articles
In-Reply-To: <424C9F08.8030507@sfu.ca>
References: <424C9F08.8030507@sfu.ca>
Message-ID: <424D5CD6.30803@ucalgary.ca>
Yup. Secondary data is generally things like word-length parameters for
running BLAST. These would often be set by the client at run-time. You
are limited to Integer, Float, String, and DateTime. You would never
lookup a service because it takes an int that modifies its behaviour, so
(AFAIK) although it's part of the service description, it's not part of
the method signature...
>
> I believe the secondary articles are not part of the DataType
> registration phenomenon, but rather the service registration. So you
> can say I am a service that accepts DNASequence object with secondary
> data bla bla bla.
From beatrice at arabidopsis.info Mon Apr 4 12:11:58 2005
From: beatrice at arabidopsis.info (Beatrice Schildknecht)
Date: Mon Apr 4 12:04:13 2005
Subject: [moby] [MOBY-l] service deregistration
In-Reply-To: <1103042264.32326.34.camel@mobycentral.icapture.ubc.ca>
References: <41BEABF1.4050902@gsf.de>
<1103042264.32326.34.camel@mobycentral.icapture.ubc.ca>
Message-ID: <4251674E.7090202@arabidopsis.info>
Has this problem been identified? The thread disappears after a while....
I would like to deregister my services as the url where they are located
changed a while back.
But can't! :-(
> "it is illegal to deregister a service that has a signatureURL. Such
> services must be deregistered by deleting the RDF at the location
> identified by the signatureURL"
I removed the RDF file several months ago.
Beatrice
Mark Wilkinson wrote:
>Doh! DOH!
>
>You're right.
>
>The MOBY Central code is currently broken. Eddie is going to
>troubleshoot, and hopefully we'll have it up by the end of the day. In
>the meantime, MOBY Central is running on an older codebase, so almost
>everything is functioning properly. I'll restart the server again when
>the problem is identified.
>
>Sorry!
>
>M
>
>
>
>On Tue, 2004-12-14 at 01:01, Rebecca Ernst wrote:
>
>
>>Hi Mark!
>>
>>the server restart didn't solve the problem. I still can only deregister
>>services which are registered without RDF.
>>
>>Rebecca
>>
>>
--
Nottingham Arabidopsis Stock Centre
School of Biosciences
Plant Science Division
University of Nottingham
Sutton Bonington Campus
Loughborough
LE12 5RD
Tel: +44 115 951 3091
Catalogue: http://arabidopsis.info
Affymetrix: http://affy.arabidopsis.info
Genomics: http://atensembl.arabidopsis.info/
This message has been checked for viruses but the contents of an attachment
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From mwilkinson at mrl.ubc.ca Mon Apr 4 12:37:11 2005
From: mwilkinson at mrl.ubc.ca (Mark Wilkinson)
Date: Mon Apr 4 12:30:01 2005
Subject: [moby] [MOBY-l] service deregistration
In-Reply-To: <4251674E.7090202@arabidopsis.info>
References: <41BEABF1.4050902@gsf.de>
<1103042264.32326.34.camel@mobycentral.icapture.ubc.ca>
<4251674E.7090202@arabidopsis.info>
Message-ID: <1112632631.28422.78.camel@mobycentral.icapture.ubc.ca>
You can deregister them now. We are just doing the final tests on the
new RDF agent and will be asking people to retrieve their new RDF
signature within the next few days. In the meantime, I have purged the
database of all signatureURL's so you will be able to deregister your
service as usual.
M
On Mon, 2005-04-04 at 09:11, Beatrice Schildknecht wrote:
> Has this problem been identified? The thread disappears after a while....
> I would like to deregister my services as the url where they are located
> changed a while back.
> But can't! :-(
>
> > "it is illegal to deregister a service that has a signatureURL. Such
> > services must be deregistered by deleting the RDF at the location
> > identified by the signatureURL"
>
> I removed the RDF file several months ago.
>
> Beatrice
>
>
>
> Mark Wilkinson wrote:
>
> >Doh! DOH!
> >
> >You're right.
> >
> >The MOBY Central code is currently broken. Eddie is going to
> >troubleshoot, and hopefully we'll have it up by the end of the day. In
> >the meantime, MOBY Central is running on an older codebase, so almost
> >everything is functioning properly. I'll restart the server again when
> >the problem is identified.
> >
> >Sorry!
> >
> >M
> >
> >
> >
> >On Tue, 2004-12-14 at 01:01, Rebecca Ernst wrote:
> >
> >
> >>Hi Mark!
> >>
> >>the server restart didn't solve the problem. I still can only deregister
> >>services which are registered without RDF.
> >>
> >>Rebecca
> >>
> >>
--
Mark Wilkinson
Assistant Professor (Bioinformatics)
Dept. Medical Genetics, UBC, Canada
From letondal at pasteur.fr Sat Apr 9 11:28:59 2005
From: letondal at pasteur.fr (Catherine Letondal)
Date: Sat Apr 9 11:18:13 2005
Subject: [MOBY-l] CFP NETTAB 2005: Network Tools and Applications in Biology
/ Workflows
Message-ID: <31125a35c2a87cb4d6b9b0f4d6c6d6ef@pasteur.fr>
Hi,
{Please pass the word! ... and apologize for cross-posting}
NETTAB 2005: Network Tools and Applications in Biology
Workflows management: new abilities for the biological information
overflow
5-7 October, 2005, Second University of Naples
Naples, Italy
Web page : http://www.nettab.org/2005
Call for Papers: http://www.nettab.org/2005/call.html
--
Catherine Letondal -- Institut Pasteur
www.pasteur.fr/~letondal
From bmg at sfu.ca Fri Apr 15 00:36:50 2005
From: bmg at sfu.ca (Benjamin Good)
Date: Fri Apr 15 00:30:24 2005
Subject: [MOBY-l] MobyDataSetInstance vs MobyDataSimpleinstance
Message-ID: <6800eaa575bb0c8f33a18c8d87b0dec3@sfu.ca>
There is no .setXmlMode in MobyDataSetInstance . I think this will
cause problems requesting services from Central ..??
Has anyone built a collection in a java and used it to query for
services successfully?
I built a collection of Objects as below and didn't find any matching
services? This should match anything that accepts a collection as
input because of the inheritance from object right??
//specify a dataype for use in the input to the template
service
MobyDataType type = new MobyDataType("Object");
//make a jMoby object to act as the input to the template (and later
the actual call)
MobyDataSimpleInstance input1 = new MobyDataSimpleInstance
("");
input1.setDataType (type);
input1.addNamespace (new MobyNamespace ("NCBI_gi"));
input1.setId("111076");
MobyDataSimpleInstance input2 = new MobyDataSimpleInstance
("");
input2.setDataType (type);
input2.addNamespace (new MobyNamespace ("NCBI_gi"));
input2.setId("111077");
MobyDataSimpleInstance[] inputset = new
MobyDataSimpleInstance[2];
inputset[0] = input1;
inputset[1] = input2;
MobyDataSetInstance input = new
MobyDataSetInstance("",inputset);
//specify that the xml generated for this object by the getXML method
//is suitable for communicating with moby central --- doesn't exist!
// input.setXmlMode(MobyDataSimpleInstance.CENTRAL_XML_MODE);
//add the moby object as input to the template service
templateService.addInput(input);
//Find services that match this template service
MobyService[] validServices =
worker.findService(templateService);
-> finds none
-> why?
thanks!
-Ben
http://bioinfo.icapture.ubc.ca/bgood
From gordonp at ucalgary.ca Fri Apr 15 10:21:36 2005
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Fri Apr 15 10:16:10 2005
Subject: [MOBY-l] MobyDataSetInstance vs MobyDataSimpleinstance
In-Reply-To: <6800eaa575bb0c8f33a18c8d87b0dec3@sfu.ca>
References: <6800eaa575bb0c8f33a18c8d87b0dec3@sfu.ca>
Message-ID: <425FCDF0.4090903@ucalgary.ca>
Benjamin Good wrote:
> There is no .setXmlMode in MobyDataSetInstance . I think this will
> cause problems requesting services from Central ..??
You're right, there probably should be! I'll fix that right now...
From mwilkinson at mrl.ubc.ca Fri Apr 15 13:03:57 2005
From: mwilkinson at mrl.ubc.ca (Mark Wilkinson)
Date: Fri Apr 15 12:57:51 2005
Subject: [moby] [MOBY-l] MobyDataSetInstance vs MobyDataSimpleinstance
In-Reply-To: <6800eaa575bb0c8f33a18c8d87b0dec3@sfu.ca>
References: <6800eaa575bb0c8f33a18c8d87b0dec3@sfu.ca>
Message-ID: <1113584637.11343.31.camel@mobycentral.icapture.ubc.ca>
Nope. Searches for Collections of Objects will only find things that
consume Collections of Objects. Searches for Collections of
DNASequences will find things that consume Collections of Objects
(complex search finding simple interface); however the reverse (simple
search finding complex interface) will not happen.
M
On Thu, 2005-04-14 at 21:36, Benjamin Good wrote:
> There is no .setXmlMode in MobyDataSetInstance . I think this will
> cause problems requesting services from Central ..??
>
> Has anyone built a collection in a java and used it to query for
> services successfully?
>
> I built a collection of Objects as below and didn't find any matching
> services? This should match anything that accepts a collection as
> input because of the inheritance from object right??
>
> //specify a dataype for use in the input to the template
> service
> MobyDataType type = new MobyDataType("Object");
> //make a jMoby object to act as the input to the template (and later
> the actual call)
> MobyDataSimpleInstance input1 = new MobyDataSimpleInstance
> ("");
> input1.setDataType (type);
> input1.addNamespace (new MobyNamespace ("NCBI_gi"));
> input1.setId("111076");
>
> MobyDataSimpleInstance input2 = new MobyDataSimpleInstance
> ("");
> input2.setDataType (type);
> input2.addNamespace (new MobyNamespace ("NCBI_gi"));
> input2.setId("111077");
>
> MobyDataSimpleInstance[] inputset = new
> MobyDataSimpleInstance[2];
> inputset[0] = input1;
> inputset[1] = input2;
> MobyDataSetInstance input = new
> MobyDataSetInstance("",inputset);
>
> //specify that the xml generated for this object by the getXML method
> //is suitable for communicating with moby central --- doesn't exist!
> // input.setXmlMode(MobyDataSimpleInstance.CENTRAL_XML_MODE);
> //add the moby object as input to the template service
> templateService.addInput(input);
>
> //Find services that match this template service
> MobyService[] validServices =
> worker.findService(templateService);
>
> -> finds none
> -> why?
>
> thanks!
> -Ben
>
>
> http://bioinfo.icapture.ubc.ca/bgood
>
> _______________________________________________
> 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 gordonp at ucalgary.ca Fri Apr 15 14:24:29 2005
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Fri Apr 15 14:22:59 2005
Subject: [moby] [MOBY-l] MobyDataSetInstance vs MobyDataSimpleinstance
In-Reply-To: <1113584637.11343.31.camel@mobycentral.icapture.ubc.ca>
References: <6800eaa575bb0c8f33a18c8d87b0dec3@sfu.ca>
<1113584637.11343.31.camel@mobycentral.icapture.ubc.ca>
Message-ID: <426006DD.9050200@ucalgary.ca>
Right. This follows the PAHFBL (Prevent All Hell From Breaking Loose)
principle. :-)
>Nope. Searches for Collections of Objects will only find things that
>consume Collections of Objects. Searches for Collections of
>DNASequences will find things that consume Collections of Objects
>(complex search finding simple interface); however the reverse (simple
>search finding complex interface) will not happen.
>
>
From gordonp at ucalgary.ca Fri Apr 15 17:22:38 2005
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Fri Apr 15 17:20:11 2005
Subject: [MOBY-l] MobyDataSetInstance vs MobyDataSimpleinstance
In-Reply-To: <6800eaa575bb0c8f33a18c8d87b0dec3@sfu.ca>
References: <6800eaa575bb0c8f33a18c8d87b0dec3@sfu.ca>
Message-ID: <4260309E.7060603@ucalgary.ca>
Hi Ben,
You should now be able to query with a Collection. I've bumped
setXmlMode(), getXmlMode() and the static variables SERVICE_XML_MODE and
CENTRAL_XML_MODE to the MobyDataInstance interface. Any references to
these static variables will need to be updated in your code.
You can run your code as before, but the simplified code for your
example is now:
... // setup templateService and worker
MobyDataSimpleInstance input1 = new MobyDataSimpleInstance ("NCBI_gi",
"111076");
MobyDataSimpleInstance input2 = new MobyDataSimpleInstance ("NCBI_gi",
"111077");
MobyDataSetInstance input = new MobyDataSetInstance("");
input.add(input1);
input.add(input2);
templateService.addInput(input);
MobyService[] validServices = worker.findService(templateService);
Also note that I've made MobyDataSetInstance implement
java.util.Collection, so you can conveniently call all of your favorite
Collection methods on it now such as removeAll(), size(), iterator(),
equals(), etc.
The CENTRAL_XML_MODE output for this call would be:
Object
NCBI_gi
I hope this is correct! :-)
From senger at ebi.ac.uk Tue Apr 19 05:32:21 2005
From: senger at ebi.ac.uk (Martin Senger)
Date: Tue Apr 19 05:28:15 2005
Subject: [MOBY-l] MobyDataSetInstance vs MobyDataSimpleinstance
In-Reply-To: <6800eaa575bb0c8f33a18c8d87b0dec3@sfu.ca>
Message-ID:
Ben,
I gues that Paul already answered your questions about this - but still
I wonder what have you been trying to do... It seems to me that you were
creating a service template to send it to the registry in order to find
matching services. Correct? I wonder why you needed MobyDataSetInstance at
all for that? The MobyDataSetInstance is Paul's extension to
MobyPrimaryDataSimple - but the class MobyPrimaryDataSimple already has
everything (I hope) to create a template for communicating with the
registry.
This probably reflects one of the bad things in jMoby - we have a lot
of similarly named classes that (perhaps) overlap each other. I hope we
will have chance to discuss it in the jMoby BoF in Vancouver. Paul, are
you coming there?
Regards,
Martin
On Thu, 14 Apr 2005, Benjamin Good wrote:
> There is no .setXmlMode in MobyDataSetInstance . I think this will
> cause problems requesting services from Central ..??
>
> Has anyone built a collection in a java and used it to query for
> services successfully?
>
> I built a collection of Objects as below and didn't find any matching
> services? This should match anything that accepts a collection as
> input because of the inheritance from object right??
>
> //specify a dataype for use in the input to the template
> service
> MobyDataType type = new MobyDataType("Object");
> //make a jMoby object to act as the input to the template (and later
> the actual call)
> MobyDataSimpleInstance input1 = new MobyDataSimpleInstance
> ("");
> input1.setDataType (type);
> input1.addNamespace (new MobyNamespace ("NCBI_gi"));
> input1.setId("111076");
>
> MobyDataSimpleInstance input2 = new MobyDataSimpleInstance
> ("");
> input2.setDataType (type);
> input2.addNamespace (new MobyNamespace ("NCBI_gi"));
> input2.setId("111077");
>
> MobyDataSimpleInstance[] inputset = new
> MobyDataSimpleInstance[2];
> inputset[0] = input1;
> inputset[1] = input2;
> MobyDataSetInstance input = new
> MobyDataSetInstance("",inputset);
>
> //specify that the xml generated for this object by the getXML method
> //is suitable for communicating with moby central --- doesn't exist!
> // input.setXmlMode(MobyDataSimpleInstance.CENTRAL_XML_MODE);
> //add the moby object as input to the template service
> templateService.addInput(input);
>
> //Find services that match this template service
> MobyService[] validServices =
> worker.findService(templateService);
>
> -> finds none
> -> why?
>
> thanks!
> -Ben
>
>
> http://bioinfo.icapture.ubc.ca/bgood
>
> _______________________________________________
> moby-l mailing list
> moby-l@biomoby.org
> http://biomoby.org/mailman/listinfo/moby-l
>
--
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 bmg at sfu.ca Tue Apr 19 07:58:47 2005
From: bmg at sfu.ca (Benjamin Good)
Date: Tue Apr 19 07:55:18 2005
Subject: [MOBY-l] MobyDataSetInstance vs MobyDataSimpleinstance
In-Reply-To:
References:
Message-ID: <7ad0aee71d280d9b4a0e4ead22f30b2b@sfu.ca>
How would you indicate that you want services that consume a collection
with MobyPrimaryDataSimple?
-Ben
On Apr 19, 2005, at 5:32 AM, Martin Senger wrote:
> Ben,
> I gues that Paul already answered your questions about this - but
> still
> I wonder what have you been trying to do... It seems to me that you
> were
> creating a service template to send it to the registry in order to find
> matching services. Correct? I wonder why you needed
> MobyDataSetInstance at
> all for that? The MobyDataSetInstance is Paul's extension to
> MobyPrimaryDataSimple - but the class MobyPrimaryDataSimple already has
> everything (I hope) to create a template for communicating with the
> registry.
> This probably reflects one of the bad things in jMoby - we have a
> lot
> of similarly named classes that (perhaps) overlap each other. I hope we
> will have chance to discuss it in the jMoby BoF in Vancouver. Paul, are
> you coming there?
>
> Regards,
> Martin
>
> On Thu, 14 Apr 2005, Benjamin Good wrote:
>
>> There is no .setXmlMode in MobyDataSetInstance . I think this will
>> cause problems requesting services from Central ..??
>>
>> Has anyone built a collection in a java and used it to query for
>> services successfully?
>>
>> I built a collection of Objects as below and didn't find any matching
>> services? This should match anything that accepts a collection as
>> input because of the inheritance from object right??
>>
>> //specify a dataype for use in the input to the template
>> service
>> MobyDataType type = new MobyDataType("Object");
>> //make a jMoby object to act as the input to the template (and later
>> the actual call)
>> MobyDataSimpleInstance input1 = new MobyDataSimpleInstance
>> ("");
>> input1.setDataType (type);
>> input1.addNamespace (new MobyNamespace ("NCBI_gi"));
>> input1.setId("111076");
>>
>> MobyDataSimpleInstance input2 = new MobyDataSimpleInstance
>> ("");
>> input2.setDataType (type);
>> input2.addNamespace (new MobyNamespace ("NCBI_gi"));
>> input2.setId("111077");
>>
>> MobyDataSimpleInstance[] inputset = new
>> MobyDataSimpleInstance[2];
>> inputset[0] = input1;
>> inputset[1] = input2;
>> MobyDataSetInstance input = new
>> MobyDataSetInstance("",inputset);
>>
>> //specify that the xml generated for this object by the getXML method
>> //is suitable for communicating with moby central --- doesn't exist!
>> //
>> input.setXmlMode(MobyDataSimpleInstance.CENTRAL_XML_MODE);
>> //add the moby object as input to the template service
>> templateService.addInput(input);
>>
>> //Find services that match this template service
>> MobyService[] validServices =
>> worker.findService(templateService);
>>
>> -> finds none
>> -> why?
>>
>> thanks!
>> -Ben
>>
>>
>> http://bioinfo.icapture.ubc.ca/bgood
>>
>> _______________________________________________
>> moby-l mailing list
>> moby-l@biomoby.org
>> http://biomoby.org/mailman/listinfo/moby-l
>>
>
> --
> 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
>
>
http://bioinfo.icapture.ubc.ca/bgood
From senger at ebi.ac.uk Tue Apr 19 08:47:51 2005
From: senger at ebi.ac.uk (Martin Senger)
Date: Tue Apr 19 08:48:17 2005
Subject: [MOBY-l] MobyDataSetInstance vs MobyDataSimpleinstance
In-Reply-To:
Message-ID:
> I suppose MobyPrimaryDataSet is the answer to my question.
>
Yes, That was my guess, too :-)
> The main difference between Instance and Primary - for communicating
> with Moby Central
>
Well, the Instance should never really be used for communicating with
Central in the first place. Either Primary is good enough, or we can fix
it. But not by just adding new class doing similar thing.
> is the presence of different serializations for talking with Central
> versus executing a service
>
Yes, Instance should be used in time of executing a service. Or calling
a service, I am not sure now (I nbever wrote any BioMoby service myself,
yet :-)).
But I may still be a bit confused. So my question is still here: Could
you or could you not to use MobyPrimaryDataSet to create a service
template and use it for finding matching services in a registry?
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 ucalgary.ca Tue Apr 19 10:16:40 2005
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Tue Apr 19 10:12:08 2005
Subject: [MOBY-l] MobyDataSetInstance vs MobyDataSimpleinstance
In-Reply-To:
References:
Message-ID: <426512C8.7050503@ucalgary.ca>
Yup, I'll be there. We've definitely got critical mass on the Java side
for a good BoF!
I think that the advantage of using MobyDataSetInstance instead of
MobyPrimaryDataSet (I assume MobyPrimaryDataSimple was a typo in the
original e-mail) is that you get a two-for-one. Why build a
MobyPrimaryDataSet to find a service (including creating all of the
MobyPrimaryDataSimple that go in it), then use some other classes to
generate the XML to run the service? The MobyDataInstance implementers
allow you to do both by instantiating one object, or even better, if you
got data back from a service, you don't need to instantiate any objects
yourself at all...
All of the extension classes I've made inherit methods from the parent
class when possible,
but all of the toXML() methods are overriden because they must be able
to generate
service request formatted XML, not just service template XML (hence
MobyDataInstance.setXmlMode()).
You are right though, I should move the modified MOBY Central parts of
MobyDataSetInstance.toXML() up to MobyPrimaryDataSet and call the
super's method explicitly when the requested XML mode is appropriate.
Doing that now...
Martin Senger wrote:
>Ben,
> I gues that Paul already answered your questions about this - but still
>I wonder what have you been trying to do... It seems to me that you were
>creating a service template to send it to the registry in order to find
>matching services. Correct? I wonder why you needed MobyDataSetInstance at
>all for that? The MobyDataSetInstance is Paul's extension to
>MobyPrimaryDataSimple - but the class MobyPrimaryDataSimple already has
>everything (I hope) to create a template for communicating with the
>registry.
> This probably reflects one of the bad things in jMoby - we have a lot
>of similarly named classes that (perhaps) overlap each other. I hope we
>will have chance to discuss it in the jMoby BoF in Vancouver. Paul, are
>you coming there?
>
> Regards,
> Martin
>
>On Thu, 14 Apr 2005, Benjamin Good wrote:
>
>
>
>>There is no .setXmlMode in MobyDataSetInstance . I think this will
>>cause problems requesting services from Central ..??
>>
>>Has anyone built a collection in a java and used it to query for
>>services successfully?
>>
>>I built a collection of Objects as below and didn't find any matching
>>services? This should match anything that accepts a collection as
>>input because of the inheritance from object right??
>>
>> //specify a dataype for use in the input to the template
>>service
>> MobyDataType type = new MobyDataType("Object");
>>//make a jMoby object to act as the input to the template (and later
>>the actual call)
>> MobyDataSimpleInstance input1 = new MobyDataSimpleInstance
>>("");
>> input1.setDataType (type);
>> input1.addNamespace (new MobyNamespace ("NCBI_gi"));
>> input1.setId("111076");
>>
>> MobyDataSimpleInstance input2 = new MobyDataSimpleInstance
>>("");
>> input2.setDataType (type);
>> input2.addNamespace (new MobyNamespace ("NCBI_gi"));
>> input2.setId("111077");
>>
>> MobyDataSimpleInstance[] inputset = new
>>MobyDataSimpleInstance[2];
>> inputset[0] = input1;
>> inputset[1] = input2;
>> MobyDataSetInstance input = new
>>MobyDataSetInstance("",inputset);
>>
>>//specify that the xml generated for this object by the getXML method
>>//is suitable for communicating with moby central --- doesn't exist!
>> // input.setXmlMode(MobyDataSimpleInstance.CENTRAL_XML_MODE);
>>//add the moby object as input to the template service
>> templateService.addInput(input);
>>
>>//Find services that match this template service
>> MobyService[] validServices =
>>worker.findService(templateService);
>>
>>-> finds none
>>-> why?
>>
>>thanks!
>>-Ben
>>
>>
>>http://bioinfo.icapture.ubc.ca/bgood
>>
>>_______________________________________________
>>moby-l mailing list
>>moby-l@biomoby.org
>>http://biomoby.org/mailman/listinfo/moby-l
>>
>>
>>
>
>
>
From bmg at sfu.ca Tue Apr 19 08:32:51 2005
From: bmg at sfu.ca (Benjamin Good)
Date: Tue Apr 19 10:25:14 2005
Subject: [MOBY-l] MobyDataSetInstance vs MobyDataSimpleinstance
In-Reply-To:
References:
Message-ID:
I suppose MobyPrimaryDataSet is the answer to my question. The main
difference between Instance and Primary - for communicating with Moby
Central is the presence of different serializations for talking with
Central versus executing a service - coming from this method.
public String toXML(){
if(xmlMode == SERVICE_XML_MODE)
return "" + dataValue + "";
else{
MobyNamespace[] ns = getNamespaces();
String result = "\n" +
getDataType().getName() + "\n";
for(int i = 0; ns != null && i < ns.length; i++){
result += "" + ns[i].getName() + "\n";
}
result += "";
return result;
}
}
Can this be avoided? It adds another step and another complication to
client development that seems like it could be handled higher up the
API ????
-Ben
On Apr 19, 2005, at 5:32 AM, Martin Senger wrote:
> Ben,
> I gues that Paul already answered your questions about this - but
> still
> I wonder what have you been trying to do... It seems to me that you
> were
> creating a service template to send it to the registry in order to find
> matching services. Correct? I wonder why you needed
> MobyDataSetInstance at
> all for that? The MobyDataSetInstance is Paul's extension to
> MobyPrimaryDataSimple - but the class MobyPrimaryDataSimple already has
> everything (I hope) to create a template for communicating with the
> registry.
> This probably reflects one of the bad things in jMoby - we have a
> lot
> of similarly named classes that (perhaps) overlap each other. I hope we
> will have chance to discuss it in the jMoby BoF in Vancouver. Paul, are
> you coming there?
>
> Regards,
> Martin
>
> On Thu, 14 Apr 2005, Benjamin Good wrote:
>
>> There is no .setXmlMode in MobyDataSetInstance . I think this will
>> cause problems requesting services from Central ..??
>>
>> Has anyone built a collection in a java and used it to query for
>> services successfully?
>>
>> I built a collection of Objects as below and didn't find any matching
>> services? This should match anything that accepts a collection as
>> input because of the inheritance from object right??
>>
>> //specify a dataype for use in the input to the template
>> service
>> MobyDataType type = new MobyDataType("Object");
>> //make a jMoby object to act as the input to the template (and later
>> the actual call)
>> MobyDataSimpleInstance input1 = new MobyDataSimpleInstance
>> ("");
>> input1.setDataType (type);
>> input1.addNamespace (new MobyNamespace ("NCBI_gi"));
>> input1.setId("111076");
>>
>> MobyDataSimpleInstance input2 = new MobyDataSimpleInstance
>> ("");
>> input2.setDataType (type);
>> input2.addNamespace (new MobyNamespace ("NCBI_gi"));
>> input2.setId("111077");
>>
>> MobyDataSimpleInstance[] inputset = new
>> MobyDataSimpleInstance[2];
>> inputset[0] = input1;
>> inputset[1] = input2;
>> MobyDataSetInstance input = new
>> MobyDataSetInstance("",inputset);
>>
>> //specify that the xml generated for this object by the getXML method
>> //is suitable for communicating with moby central --- doesn't exist!
>> //
>> input.setXmlMode(MobyDataSimpleInstance.CENTRAL_XML_MODE);
>> //add the moby object as input to the template service
>> templateService.addInput(input);
>>
>> //Find services that match this template service
>> MobyService[] validServices =
>> worker.findService(templateService);
>>
>> -> finds none
>> -> why?
>>
>> thanks!
>> -Ben
>>
>>
>> http://bioinfo.icapture.ubc.ca/bgood
>>
>> _______________________________________________
>> moby-l mailing list
>> moby-l@biomoby.org
>> http://biomoby.org/mailman/listinfo/moby-l
>>
>
> --
> 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
>
>
http://bioinfo.icapture.ubc.ca/bgood
From gordonp at ucalgary.ca Tue Apr 19 10:59:59 2005
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Tue Apr 19 10:53:18 2005
Subject: [MOBY-l] MobyDataSetInstance vs MobyDataSimpleinstance
In-Reply-To:
References:
Message-ID: <42651CEF.5060103@ucalgary.ca>
Ha! Just as I received this e-mail, I was commiting a change to this
very code, which calls super.toXML() in CENTRAL_XML_MODE. The fact that
toXML() can generate both XMLs is a bit of a retrofit into the
nomenclature that existed before I started adding classes. I was going
to do the same for MobyDataSetInstance, but
it is not clear to me (no javadocs) from the MobyPrimaryDataSet class if
setElements() should be given just a list of the datatypes the
set will hold, or if it is expecting instances. The latter would be
wierd, because the class does not encode data instances (and toXML()
as implemented would provide a very, very long service template XML if
you had 1000 DNASequences, for example). If the method
should be registering data types contained in the set, perhaps it should
be renamed...
Benjamin Good wrote:
> I suppose MobyPrimaryDataSet is the answer to my question. The main
> difference between Instance and Primary - for communicating with Moby
> Central is the presence of different serializations for talking with
> Central versus executing a service - coming from this method.
>
> public String toXML(){
> if(xmlMode == SERVICE_XML_MODE)
> return " (getName() != null ? "\" xmlns:moby=\""+
> MobyPrefixResolver.MOBY_XML_NAMESPACE+"\"
> moby:articleName=\"" + getName() : "")+
> "\">" + dataValue + "";
> else{
> MobyNamespace[] ns = getNamespaces();
> String result = " xmlns=\""+MobyPrefixResolver.MOBY_XML_NAMESPACE+"\">\n" +
> getDataType().getName() + "\n";
> for(int i = 0; ns != null && i < ns.length; i++){
> result += "" + ns[i].getName() + "\n";
> }
> result += "";
> return result;
> }
> }
>
> Can this be avoided? It adds another step and another complication to
> client development that seems like it could be handled higher up the
> API ????
>
> -Ben
>
> On Apr 19, 2005, at 5:32 AM, Martin Senger wrote:
>
>> Ben,
>> I gues that Paul already answered your questions about this - but
>> still
>> I wonder what have you been trying to do... It seems to me that you were
>> creating a service template to send it to the registry in order to find
>> matching services. Correct? I wonder why you needed
>> MobyDataSetInstance at
>> all for that? The MobyDataSetInstance is Paul's extension to
>> MobyPrimaryDataSimple - but the class MobyPrimaryDataSimple already has
>> everything (I hope) to create a template for communicating with the
>> registry.
>> This probably reflects one of the bad things in jMoby - we have a lot
>> of similarly named classes that (perhaps) overlap each other. I hope we
>> will have chance to discuss it in the jMoby BoF in Vancouver. Paul, are
>> you coming there?
>>
>> Regards,
>> Martin
>>
>> On Thu, 14 Apr 2005, Benjamin Good wrote:
>>
>>> There is no .setXmlMode in MobyDataSetInstance . I think this will
>>> cause problems requesting services from Central ..??
>>>
>>> Has anyone built a collection in a java and used it to query for
>>> services successfully?
>>>
>>> I built a collection of Objects as below and didn't find any matching
>>> services? This should match anything that accepts a collection as
>>> input because of the inheritance from object right??
>>>
>>> //specify a dataype for use in the input to the template
>>> service
>>> MobyDataType type = new MobyDataType("Object");
>>> //make a jMoby object to act as the input to the template (and later
>>> the actual call)
>>> MobyDataSimpleInstance input1 = new MobyDataSimpleInstance
>>> ("");
>>> input1.setDataType (type);
>>> input1.addNamespace (new MobyNamespace ("NCBI_gi"));
>>> input1.setId("111076");
>>>
>>> MobyDataSimpleInstance input2 = new MobyDataSimpleInstance
>>> ("");
>>> input2.setDataType (type);
>>> input2.addNamespace (new MobyNamespace ("NCBI_gi"));
>>> input2.setId("111077");
>>>
>>> MobyDataSimpleInstance[] inputset = new
>>> MobyDataSimpleInstance[2];
>>> inputset[0] = input1;
>>> inputset[1] = input2;
>>> MobyDataSetInstance input = new
>>> MobyDataSetInstance("",inputset);
>>>
>>> //specify that the xml generated for this object by the getXML method
>>> //is suitable for communicating with moby central --- doesn't exist!
>>> //
>>> input.setXmlMode(MobyDataSimpleInstance.CENTRAL_XML_MODE);
>>> //add the moby object as input to the template service
>>> templateService.addInput(input);
>>>
>>> //Find services that match this template service
>>> MobyService[] validServices =
>>> worker.findService(templateService);
>>>
>>> -> finds none
>>> -> why?
>>>
>>> thanks!
>>> -Ben
>>>
>>>
>>> http://bioinfo.icapture.ubc.ca/bgood
>>>
>>> _______________________________________________
>>> moby-l mailing list
>>> moby-l@biomoby.org
>>> http://biomoby.org/mailman/listinfo/moby-l
>>>
>>
>> --
>> 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
>>
>>
> http://bioinfo.icapture.ubc.ca/bgood
>
> _______________________________________________
> moby-l mailing list
> moby-l@biomoby.org
> http://biomoby.org/mailman/listinfo/moby-l
>
From gordonp at ucalgary.ca Tue Apr 19 11:19:38 2005
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Tue Apr 19 11:13:33 2005
Subject: [MOBY-l] MobyDataSetInstance vs MobyDataSimpleinstance
In-Reply-To:
References:
Message-ID: <4265218A.1020505@ucalgary.ca>
> Yes, Instance should be used in time of executing a service. Or calling
>a service, I am not sure now (I nbever wrote any BioMoby service myself,
>yet :-)).
>
>
Aha :-)
> But I may still be a bit confused. So my question is still here: Could
>you or could you not to use MobyPrimaryDataSet to create a service
>template and use it for finding matching services in a registry?
>
>
MobyDataSimpleInstance now calls super.toXML() when appropriate, but
for now, MobyDataSetInstance reimplements the central-mode toXML()
because it is unclear how
MobyDataSetInstance.setElements() should be used. Us people
implementing services run into these snags ;-)
Personally, I'd be much more comfortable with a
MobyPrimaryDataSet.setElementTypes()/addElementType() structure, since
it doesn't make much sense to pass in an actual number of items (as an
array encodes) unless you've got MobyDataInstances. In this case, I
could update the MobyPrimaryDataSet datatypes list in a reasonably
efficient way within MobyDataSetInstance.setElements(), and call
super.toXML() when appropriate.
From senger at ebi.ac.uk Tue Apr 19 11:31:09 2005
From: senger at ebi.ac.uk (Martin Senger)
Date: Tue Apr 19 11:28:19 2005
Subject: [MOBY-l] MobyDataSetInstance vs MobyDataSimpleinstance
In-Reply-To: <4265218A.1020505@ucalgary.ca>
Message-ID:
It seems that I need to look into all these classes to re-undersatand what
I put there, and to start understand what Paul had in mind. I will do it
probably this evening and let you know. I will also move this topic to
moby-dev where it belongs more I guess.
Paul, just to help me, your classes (those with 'Instance') are used both
on a client side, and on the service provider side, or just on one of
them? And, do I understand correctly that they are here to hold the
real data?
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 suzi at fruitfly.org Wed Apr 20 18:54:18 2005
From: suzi at fruitfly.org (Suzanna Lewis)
Date: Wed Apr 20 18:47:44 2005
Subject: [MOBY-l] Hackathon 2005
Message-ID: <67b6042c95fe1754aab32cc1307579b9@fruitfly.org>
(sorry for multiple postings, but please do forward to
anyone else who you think might be interested)
------------------------------------------------------------------------
-----------
Dear everyone,
It has been a long time and we Bioinformatics devotees are overdue for
another total-immersion coding-fest (the last hackathon was held in
Singapore February 2003, more than two years ago). Apple has offered
to host us this year, and as an added bonus include free admission to
the World-Wide Developers Conference in San Francisco the prior week.
They are also looking for some people to present interesting new
developments at the WWDC, so if you have something noteworthy please
let us know. Apple is not attaching any strings, so our work need not
address Apple-specific software or hardware areas. Apple will provide
space and hardware (and access to their engineers if we'd like).
Week 1 (June 6-10) would be spent at the WWDC. Week 2 (June 12-16)
would be in Cupertino, at Apple's headquarters. We're free to focus
on what interests us, our tentative plans include:
1. Bio-ontologies software
2. High-performance computing (e.g. large scale computations,
optimization)
3. Image analysis
4. Documentation
5. Anything else that may interest you
Our plan is to organize this much as the Aspen Center for Physics
computational biology workshops were organized (for those old enough to
remember): A couple of presentations to start the day; collaboration
and coding afterwards; time for a bit of fun (does anyone else
cycle?), and discussions in the late afternoons and evenings.
Would everyone who is interested in attending please send us a short
description of what you would like to do, and perhaps other people who
you would like to work with. There is somewhat limited space, so we
will try to prioritize groups that have a clear focus and a need to
interact. We now this is very short notice, but we hope that there
will be enough interest to make it possible.
We are looking into additional funding support, to pay for travel
expenses, but this is still to be decided.
Looking forward to hearing from everyone.
George, Cyrus, Steve, and Suzanna (the Bay Area locals)
From mwilkinson at mrl.ubc.ca Fri Apr 22 12:26:47 2005
From: mwilkinson at mrl.ubc.ca (Mark Wilkinson)
Date: Fri Apr 22 12:19:12 2005
Subject: [MOBY-l] Hot off the presses..
Message-ID: <1114187207.5335.17.camel@mobycentral.icapture.ubc.ca>
Wilkinson M, Schoof H, Ernst R, Haase D (2005). BioMOBY successfully
integrates disributed heterogenous bioinformatics web services. The
PlaNet exemplar case. Plant Physol 138, p1-13
--
Mark Wilkinson
Assistant Professor (Bioinformatics)
Dept. Medical Genetics, UBC, Canada
From p.lord at cs.man.ac.uk Mon Apr 25 09:01:19 2005
From: p.lord at cs.man.ac.uk (Phillip Lord)
Date: Mon Apr 25 09:50:33 2005
Subject: [MOBY-l] The Eighth Annual Bio-Ontologies Meeting Call for
Submissions: Deadline FRIDAY 29th APRIL
Message-ID:
This will be the final call for submissions as the deadline is
Friday. Please not that this year we are also hoping to have a demo
session of tools for bio-ontologies, so please submit abstracts.
Submissions or questions to bio-ont-sig@cs.man.ac.uk
Please note that this year bio-ontologies is in the beautiful city of
Detroit. Ask yourself, can you afford to miss this opportunity?
Phil
The Eighth Annual Bio-Ontologies Meeting Call for Submissions
=============================================================
Key Information
===============
Organisers: Robert Stevens(1), Phillip Lord(1),
Robin McEntire(2), and James.A.Butler(2)
(1) School of Computer Science, University of Manchester
(2) GlaxoSmithKline
Website: http://bio-ontologies.man.ac.uk
Location: Detroit, Michigan
Submission Deadline: 29th April
Main Conference: http://www.iscb.org/ismb2005
General Information
===================
The Bio-Ontologies workshop has been a satellite meeting to the annual
ISMB conference since 1998, and is now operated as a Special Interest
Group at the ISMB Conference. Bio-Ontologies is well established as
one of the key meetings for dissemination of latest information and
research on ontologies in the life sciences and has drawn the key
researchers in the field.
Ontologies provide a mechanism for organising, sharing and reconciling
data. Within recent years there has been a great deal of interest in
the use of ontologies within bioinformatics, particularly in providing
computationally accessible annotation, or standard data models for
complex data for microarray or pathway information.
Meetings such as last years workshop and SOFG have made it clear that
there are many important uses of ontologies and a clear realisation of
the importance of implementing mechanisms for integrating source
ontologies rather than duplicating effort or causing confusion by
extending a given ontology to include everything.
However, with the increase in scope and use of ontologies within
bioinformatics, issues of scalability, expressivity and best practices
for modelling are becoming more important. We are particularly
interested, therefore, in work involving multiple source ontologies,
and which cut across the different levels of granularity implicit
within biological systems.
BioOntologies is an informal workshop. Submissions will be reviewed by
the programme committee. A number of talks will be invited for ***full
publication*** as papers in Comparative and Functional Genomics
(see http://www3.interscience.wiley.com/cgi-bin/jissue/109860809 for
last years papers)
Submissions
===========
Submission
We invite submissions to this years Bio-Ontologies. Suitable topics
include but are not restricted to:
* Biological Applications of Ontologies.
* Reports on Newly Developed or Existing Bio-Ontologies.
* Tools for Developing Ontologies.
* Use of Semantic Web technologies in BioInformatics
* The implications of Bio-Ontologies or the Semantic Web for the drug discovery process
* Current Research In Ontology Languages and its implication for Bio-Ontologies
This year, for the first time, we would like to have a number of short
software or ontology demonstrations, showing new or existing tools for
building or using ontologies, or describing the design of
ontologies. Submissions for these demonstrations are particularly encouraged.
Submission Instructions
=======================
Submissions are limited to 2 pages. Please submit using word using the
templates available at
http://bio-ontologies.man.ac.uk/submissions.html.
Alternatively, submissions may be as a text file.
Submissions should be emailed to bio-ont-sig@cs.man.ac.uk. We will
acknowledge within a day or two.
Bio-Ontologies is an informal meeting. Abstracts are reviewed by the
programme committee. All accepted abstracts will be published by the
organisers on their web site and in the main programme booklet. By
submitting your paper, you consent to this publication.
Authors of abstracts accepted for full publication as long (8 page)
papers in Comparative and Functional Genomics will be notified
following the meeting, for publication around October. Full
details will be given later.
Authors will be informed of acceptance within a few days of the
submission deadline.
From markw at illuminae.com Wed Apr 27 22:23:45 2005
From: markw at illuminae.com (Mark Wilkinson)
Date: Wed Apr 27 22:18:42 2005
Subject: [MOBY-l] Central back up and stable :-)
Message-ID: <42704931.7090603@illuminae.com>
Hi all,
There is a DNS change filtering itself through the world. MOBY Central
is now running on a Linux machine and appears to be completely stable.
It is configured almost identically to the old machine so you don't need
to change anything on your end. If you have registered new services in
the past 3-4 days they will not be registered in the new database as it
was installed from a dump four days ago.
Sorry for all the problems - it took a while to identify a machine that
we could use as a replacement. If you notice any instability in the new
machine please let me know. I've been watching the error logs for the
past few days, and haven't seen anything at all, but... yeah...
M
From robert.stevens at cs.man.ac.uk Thu Apr 28 11:53:37 2005
From: robert.stevens at cs.man.ac.uk (Robert Stevens)
Date: Thu Apr 28 11:47:21 2005
Subject: [MOBY-l] Re: CFP: Semantic Webs for the Life Sciences -- PSB06
In-Reply-To: <6.1.2.0.2.20050427205204.01ebb650@mailhost.cs.man.ac.uk>
References: <6.1.2.0.2.20050427205204.01ebb650@mailhost.cs.man.ac.uk>
Message-ID: <6.1.2.0.2.20050428165326.01ea7b30@mailhost.cs.man.ac.uk>
At 20:54 27/04/2005, Robert Stevens wrote:
>
>
>Michael,
>
>I'm not sure if you're on any of my bio-ontology lists, so I'vce sent you
>a personal CFP.....
>
>Robert.
>
>I can't remember if yo're on any of my lists. So, read on. I'm away until
>next thrusday, so will not answer much email.
>
>Robert
>_______________________________________________________________________
>
> This message is posted to several lists.
> We apologize if you receive multiple copies.
> Please forward it to everyone who might be interested.
>_______________________________________________________________________
>
>
> Call for Papers and Posters
>
> Semantic Webs for Life Sciences
>
> at the Pacific Symposium on Biocomputing 2006
> http://psb.stanford.edu/
> January 3-7, 2006
> Grand Wailea Resort, Wailea, Maui, Hawaii
>
>_______________________________________________________________________
>
>Biology is evolving from a science of organisms and molecules to one
>that increasingly relies on processing data. These data range from raw
>sequences represented in a reasonably computational form, to the vast
>body of annotation of these data that are less amenable to computational
>processing. The shift from hypothesis-driven experiments to data-driven
>experiments relies on having computational access to all these data and
>the tools that manipulate those data.
>
>The Semantic Web is a vision that moves the Web from a form that is only
>really usable by humans, to one where the data and services are open to
>autonomous computational agents. This vision relies on the semantics of
>both the content and services on the Web being accessible to computers.
>Semantic markup through ontologies developed in OWl or RDF are meant to
>provide this semantic markup -- OWL is, after all, the web Ontology
>Language. As the recent biomedical ontology sessions at PSB have
>revealed, there is much activity within bioinformatics in the field of
>semantic markup of data. The discipline is well poised to build
>Semantic Webs for Life Sciences that will afford bioinformatics
>applications deeper computational access to the knowledge element of
>bioinformatics resources.
>
>This session on Semantic Webs for Life Sciences would therefore welcome
>papers that discuss:
>
> * The creation and use of Semantic Web applications
> * Reasoning about the biomedical domain based on Semantic Web
> technologies to make scientific insights
> * Intelligent agent technologies and associated ontologies
> * Use of Semantic Web technologies to bridge between heterogeneous
> information resources (e.g., to connect genotype to gene
> expression and ultimately to clinical medicine, drug discoveries,
> etc.)
> * Use of Semantic Web technologies to make biomedical applications
> interoperable
> * The use of OWL, RDF, etc. to describe and use knowledge in the
> biomedical arena
> * Advances in Semantic Web related technologies as applied to
> bioinformatics and biomedical problems
> * Other research associated with Semantic Webs for Life Sciences
>
>_______________________________________________________________________
>
>
> Session co-chairs
>
> * Robert Stevens (Contact Person)
> University of Manchester, UK
> robert.stevens@manchester.ac.uk
>
> * Olivier Bodenreider
> National Library of Medicine
> olivier@nlm.nih.gov
>
> * Yves A. Lussier
> Columbia University, NY, USA
> yves.lussier@dbmi.columbia.edu
>
>_______________________________________________________________________
>
>
> Submission information
>
>
> Papers and Posters
>
>The core of the conference consists of rigorously peer-reviewed
>full-length papers reporting on original work. Accepted papers will be
>published in a hard-bound archival proceedings, and the best of these
>will be presented orally to the entire conference. Researchers wishing
>to present their research without official publication are encouraged to
>submit a one page abstract by November 1, 2005 to present their work in
>the poster sessions.
>
>
> Important dates
>
> * Paper submissions due: July 18, 2005
> * Notification of paper acceptance: September 6, 2005
> * Final paper deadline: September 23, 2005
> * Abstract deadline: November 1, 2005
> * Meeting: January 3-7, 2006
>
>
> Paper format
>
>All papers must be submitted to russ.altman@stanford.edu in electronic
>format. The file formats we accept are: postscript (*.ps), Adobe Acrobat
>(*.pdf) and Microsoft Word documents (*.doc). Attached files should be
>named with the last name of the first author (e.g. altman.ps, altman.pdf,
>or altman.doc).
>Hardcopy submissions or unprocessed TEX or LATEX files will be rejected
>without review.
>
>Each paper must be accompanied by a cover letter. The *cover letter must
>state* the following:
>
> * The email address of the corresponding author
> * The specific PSB session that should review the paper or abstract
> * The submitted paper contains original, unpublished results, and
> is not currently under consideration elsewhere.
> * All co-authors concur with the contents of the paper.
>
>
>Submitted papers are limited to twelve (12) pages in our publication
>format. Please format your paper according to instructions found at
>http://psb.stanford.edu/psb-online/psb-submit/. If figures can not be
>easily resized and placed precisely in the text, then it should be clear
>that with appropriate modifications, the total manuscript length would
>be within the page limit.
>
>Color pictures can be printed at the expense of the authors. The fee is
>$500 per page of color pictures, payable at the time of camera ready
>submission.
>
>Contact Russ Altman (russ.altman@stanford.edu) for additional information
>about paper submission requirements.
From david.baux at cirad.fr Fri Apr 29 09:04:35 2005
From: david.baux at cirad.fr (David Baux)
Date: Fri Apr 29 08:54:55 2005
Subject: [MOBY-l] how can I modify an object
Message-ID: <427230E3.8070508@cirad.fr>
hello,
I'm just beginning with Biomoby.
I'd like to modify an existing object (created by manuel ruiz from
cirad) and I don't know how to manage it.
Is it possible to modify an object directly?
Or can I deregister the object and then reregister it?
thanks for your answer.
ps: I posted that question on the moby-s FAQs but got no answer.
From mlangill at sfu.ca Fri Apr 29 13:32:06 2005
From: mlangill at sfu.ca (Morgan Langille)
Date: Fri Apr 29 13:26:28 2005
Subject: [MOBY-l] how can I modify an object
In-Reply-To: <427230E3.8070508@cirad.fr>
References: <427230E3.8070508@cirad.fr>
Message-ID: <1114795926.4207.395.camel@moosehead.mrl.ubc.ca>
Hello,
Unless you are the owner of an existing object you should not be
modifying it at all. If you need to add more things to an existing
object then you should create a new moby object that inherits the
existing object (ISA relationship) and add your own things with HAS and
HASA relationships. If you need to remove things from an existing object
then you should inherit from the next higher moby object that does not
have the thing in it (i.e. make a new moby object with a different
name). Hope this helps!
Morgan
On Fri, 2005-04-29 at 06:04, David Baux wrote:
> hello,
> I'm just beginning with Biomoby.
> I'd like to modify an existing object (created by manuel ruiz from
> cirad) and I don't know how to manage it.
> Is it possible to modify an object directly?
> Or can I deregister the object and then reregister it?
> thanks for your answer.
> ps: I posted that question on the moby-s FAQs but got no answer.
>
>
> _______________________________________________
> moby-l mailing list
> moby-l@biomoby.org
> http://biomoby.org/mailman/listinfo/moby-l
>
From gordonp at ucalgary.ca Fri Apr 1 09:38:14 2005
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Fri, 01 Apr 2005 07:38:14 -0700
Subject: [MOBY-l] secondary articles
In-Reply-To: <424C9F08.8030507@sfu.ca>
References: <424C9F08.8030507@sfu.ca>
Message-ID: <424D5CD6.30803@ucalgary.ca>
Yup. Secondary data is generally things like word-length parameters for
running BLAST. These would often be set by the client at run-time. You
are limited to Integer, Float, String, and DateTime. You would never
lookup a service because it takes an int that modifies its behaviour, so
(AFAIK) although it's part of the service description, it's not part of
the method signature...
>
> I believe the secondary articles are not part of the DataType
> registration phenomenon, but rather the service registration. So you
> can say I am a service that accepts DNASequence object with secondary
> data bla bla bla.
From beatrice at arabidopsis.info Mon Apr 4 12:11:58 2005
From: beatrice at arabidopsis.info (Beatrice Schildknecht)
Date: Mon, 04 Apr 2005 17:11:58 +0100
Subject: [moby] [MOBY-l] service deregistration
In-Reply-To: <1103042264.32326.34.camel@mobycentral.icapture.ubc.ca>
References: <41BEABF1.4050902@gsf.de>
<1103042264.32326.34.camel@mobycentral.icapture.ubc.ca>
Message-ID: <4251674E.7090202@arabidopsis.info>
Has this problem been identified? The thread disappears after a while....
I would like to deregister my services as the url where they are located
changed a while back.
But can't! :-(
> "it is illegal to deregister a service that has a signatureURL. Such
> services must be deregistered by deleting the RDF at the location
> identified by the signatureURL"
I removed the RDF file several months ago.
Beatrice
Mark Wilkinson wrote:
>Doh! DOH!
>
>You're right.
>
>The MOBY Central code is currently broken. Eddie is going to
>troubleshoot, and hopefully we'll have it up by the end of the day. In
>the meantime, MOBY Central is running on an older codebase, so almost
>everything is functioning properly. I'll restart the server again when
>the problem is identified.
>
>Sorry!
>
>M
>
>
>
>On Tue, 2004-12-14 at 01:01, Rebecca Ernst wrote:
>
>
>>Hi Mark!
>>
>>the server restart didn't solve the problem. I still can only deregister
>>services which are registered without RDF.
>>
>>Rebecca
>>
>>
--
Nottingham Arabidopsis Stock Centre
School of Biosciences
Plant Science Division
University of Nottingham
Sutton Bonington Campus
Loughborough
LE12 5RD
Tel: +44 115 951 3091
Catalogue: http://arabidopsis.info
Affymetrix: http://affy.arabidopsis.info
Genomics: http://atensembl.arabidopsis.info/
This message has been checked for viruses but the contents of an attachment
may still contain software viruses, which could damage your computer system:
you are advised to perform your own checks. Email communications with the
University of Nottingham may be monitored as permitted by UK legislation.
From mwilkinson at mrl.ubc.ca Mon Apr 4 12:37:11 2005
From: mwilkinson at mrl.ubc.ca (Mark Wilkinson)
Date: Mon, 04 Apr 2005 09:37:11 -0700
Subject: [moby] [MOBY-l] service deregistration
In-Reply-To: <4251674E.7090202@arabidopsis.info>
References: <41BEABF1.4050902@gsf.de>
<1103042264.32326.34.camel@mobycentral.icapture.ubc.ca>
<4251674E.7090202@arabidopsis.info>
Message-ID: <1112632631.28422.78.camel@mobycentral.icapture.ubc.ca>
You can deregister them now. We are just doing the final tests on the
new RDF agent and will be asking people to retrieve their new RDF
signature within the next few days. In the meantime, I have purged the
database of all signatureURL's so you will be able to deregister your
service as usual.
M
On Mon, 2005-04-04 at 09:11, Beatrice Schildknecht wrote:
> Has this problem been identified? The thread disappears after a while....
> I would like to deregister my services as the url where they are located
> changed a while back.
> But can't! :-(
>
> > "it is illegal to deregister a service that has a signatureURL. Such
> > services must be deregistered by deleting the RDF at the location
> > identified by the signatureURL"
>
> I removed the RDF file several months ago.
>
> Beatrice
>
>
>
> Mark Wilkinson wrote:
>
> >Doh! DOH!
> >
> >You're right.
> >
> >The MOBY Central code is currently broken. Eddie is going to
> >troubleshoot, and hopefully we'll have it up by the end of the day. In
> >the meantime, MOBY Central is running on an older codebase, so almost
> >everything is functioning properly. I'll restart the server again when
> >the problem is identified.
> >
> >Sorry!
> >
> >M
> >
> >
> >
> >On Tue, 2004-12-14 at 01:01, Rebecca Ernst wrote:
> >
> >
> >>Hi Mark!
> >>
> >>the server restart didn't solve the problem. I still can only deregister
> >>services which are registered without RDF.
> >>
> >>Rebecca
> >>
> >>
--
Mark Wilkinson
Assistant Professor (Bioinformatics)
Dept. Medical Genetics, UBC, Canada
From letondal at pasteur.fr Sat Apr 9 11:28:59 2005
From: letondal at pasteur.fr (Catherine Letondal)
Date: Sat, 9 Apr 2005 17:28:59 +0200
Subject: [MOBY-l] CFP NETTAB 2005: Network Tools and Applications in Biology
/ Workflows
Message-ID: <31125a35c2a87cb4d6b9b0f4d6c6d6ef@pasteur.fr>
Hi,
{Please pass the word! ... and apologize for cross-posting}
NETTAB 2005: Network Tools and Applications in Biology
Workflows management: new abilities for the biological information
overflow
5-7 October, 2005, Second University of Naples
Naples, Italy
Web page : http://www.nettab.org/2005
Call for Papers: http://www.nettab.org/2005/call.html
--
Catherine Letondal -- Institut Pasteur
www.pasteur.fr/~letondal
From bmg at sfu.ca Fri Apr 15 00:36:50 2005
From: bmg at sfu.ca (Benjamin Good)
Date: Thu, 14 Apr 2005 21:36:50 -0700
Subject: [MOBY-l] MobyDataSetInstance vs MobyDataSimpleinstance
Message-ID: <6800eaa575bb0c8f33a18c8d87b0dec3@sfu.ca>
There is no .setXmlMode in MobyDataSetInstance . I think this will
cause problems requesting services from Central ..??
Has anyone built a collection in a java and used it to query for
services successfully?
I built a collection of Objects as below and didn't find any matching
services? This should match anything that accepts a collection as
input because of the inheritance from object right??
//specify a dataype for use in the input to the template
service
MobyDataType type = new MobyDataType("Object");
//make a jMoby object to act as the input to the template (and later
the actual call)
MobyDataSimpleInstance input1 = new MobyDataSimpleInstance
("");
input1.setDataType (type);
input1.addNamespace (new MobyNamespace ("NCBI_gi"));
input1.setId("111076");
MobyDataSimpleInstance input2 = new MobyDataSimpleInstance
("");
input2.setDataType (type);
input2.addNamespace (new MobyNamespace ("NCBI_gi"));
input2.setId("111077");
MobyDataSimpleInstance[] inputset = new
MobyDataSimpleInstance[2];
inputset[0] = input1;
inputset[1] = input2;
MobyDataSetInstance input = new
MobyDataSetInstance("",inputset);
//specify that the xml generated for this object by the getXML method
//is suitable for communicating with moby central --- doesn't exist!
// input.setXmlMode(MobyDataSimpleInstance.CENTRAL_XML_MODE);
//add the moby object as input to the template service
templateService.addInput(input);
//Find services that match this template service
MobyService[] validServices =
worker.findService(templateService);
-> finds none
-> why?
thanks!
-Ben
http://bioinfo.icapture.ubc.ca/bgood
From gordonp at ucalgary.ca Fri Apr 15 10:21:36 2005
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Fri, 15 Apr 2005 08:21:36 -0600
Subject: [MOBY-l] MobyDataSetInstance vs MobyDataSimpleinstance
In-Reply-To: <6800eaa575bb0c8f33a18c8d87b0dec3@sfu.ca>
References: <6800eaa575bb0c8f33a18c8d87b0dec3@sfu.ca>
Message-ID: <425FCDF0.4090903@ucalgary.ca>
Benjamin Good wrote:
> There is no .setXmlMode in MobyDataSetInstance . I think this will
> cause problems requesting services from Central ..??
You're right, there probably should be! I'll fix that right now...
From mwilkinson at mrl.ubc.ca Fri Apr 15 13:03:57 2005
From: mwilkinson at mrl.ubc.ca (Mark Wilkinson)
Date: Fri, 15 Apr 2005 10:03:57 -0700
Subject: [moby] [MOBY-l] MobyDataSetInstance vs MobyDataSimpleinstance
In-Reply-To: <6800eaa575bb0c8f33a18c8d87b0dec3@sfu.ca>
References: <6800eaa575bb0c8f33a18c8d87b0dec3@sfu.ca>
Message-ID: <1113584637.11343.31.camel@mobycentral.icapture.ubc.ca>
Nope. Searches for Collections of Objects will only find things that
consume Collections of Objects. Searches for Collections of
DNASequences will find things that consume Collections of Objects
(complex search finding simple interface); however the reverse (simple
search finding complex interface) will not happen.
M
On Thu, 2005-04-14 at 21:36, Benjamin Good wrote:
> There is no .setXmlMode in MobyDataSetInstance . I think this will
> cause problems requesting services from Central ..??
>
> Has anyone built a collection in a java and used it to query for
> services successfully?
>
> I built a collection of Objects as below and didn't find any matching
> services? This should match anything that accepts a collection as
> input because of the inheritance from object right??
>
> //specify a dataype for use in the input to the template
> service
> MobyDataType type = new MobyDataType("Object");
> //make a jMoby object to act as the input to the template (and later
> the actual call)
> MobyDataSimpleInstance input1 = new MobyDataSimpleInstance
> ("");
> input1.setDataType (type);
> input1.addNamespace (new MobyNamespace ("NCBI_gi"));
> input1.setId("111076");
>
> MobyDataSimpleInstance input2 = new MobyDataSimpleInstance
> ("");
> input2.setDataType (type);
> input2.addNamespace (new MobyNamespace ("NCBI_gi"));
> input2.setId("111077");
>
> MobyDataSimpleInstance[] inputset = new
> MobyDataSimpleInstance[2];
> inputset[0] = input1;
> inputset[1] = input2;
> MobyDataSetInstance input = new
> MobyDataSetInstance("",inputset);
>
> //specify that the xml generated for this object by the getXML method
> //is suitable for communicating with moby central --- doesn't exist!
> // input.setXmlMode(MobyDataSimpleInstance.CENTRAL_XML_MODE);
> //add the moby object as input to the template service
> templateService.addInput(input);
>
> //Find services that match this template service
> MobyService[] validServices =
> worker.findService(templateService);
>
> -> finds none
> -> why?
>
> thanks!
> -Ben
>
>
> http://bioinfo.icapture.ubc.ca/bgood
>
> _______________________________________________
> 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 gordonp at ucalgary.ca Fri Apr 15 14:24:29 2005
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Fri, 15 Apr 2005 12:24:29 -0600
Subject: [moby] [MOBY-l] MobyDataSetInstance vs MobyDataSimpleinstance
In-Reply-To: <1113584637.11343.31.camel@mobycentral.icapture.ubc.ca>
References: <6800eaa575bb0c8f33a18c8d87b0dec3@sfu.ca>
<1113584637.11343.31.camel@mobycentral.icapture.ubc.ca>
Message-ID: <426006DD.9050200@ucalgary.ca>
Right. This follows the PAHFBL (Prevent All Hell From Breaking Loose)
principle. :-)
>Nope. Searches for Collections of Objects will only find things that
>consume Collections of Objects. Searches for Collections of
>DNASequences will find things that consume Collections of Objects
>(complex search finding simple interface); however the reverse (simple
>search finding complex interface) will not happen.
>
>
From gordonp at ucalgary.ca Fri Apr 15 17:22:38 2005
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Fri, 15 Apr 2005 15:22:38 -0600
Subject: [MOBY-l] MobyDataSetInstance vs MobyDataSimpleinstance
In-Reply-To: <6800eaa575bb0c8f33a18c8d87b0dec3@sfu.ca>
References: <6800eaa575bb0c8f33a18c8d87b0dec3@sfu.ca>
Message-ID: <4260309E.7060603@ucalgary.ca>
Hi Ben,
You should now be able to query with a Collection. I've bumped
setXmlMode(), getXmlMode() and the static variables SERVICE_XML_MODE and
CENTRAL_XML_MODE to the MobyDataInstance interface. Any references to
these static variables will need to be updated in your code.
You can run your code as before, but the simplified code for your
example is now:
... // setup templateService and worker
MobyDataSimpleInstance input1 = new MobyDataSimpleInstance ("NCBI_gi",
"111076");
MobyDataSimpleInstance input2 = new MobyDataSimpleInstance ("NCBI_gi",
"111077");
MobyDataSetInstance input = new MobyDataSetInstance("");
input.add(input1);
input.add(input2);
templateService.addInput(input);
MobyService[] validServices = worker.findService(templateService);
Also note that I've made MobyDataSetInstance implement
java.util.Collection, so you can conveniently call all of your favorite
Collection methods on it now such as removeAll(), size(), iterator(),
equals(), etc.
The CENTRAL_XML_MODE output for this call would be:
Object
NCBI_gi
I hope this is correct! :-)
From senger at ebi.ac.uk Tue Apr 19 05:32:21 2005
From: senger at ebi.ac.uk (Martin Senger)
Date: Tue, 19 Apr 2005 10:32:21 +0100 (BST)
Subject: [MOBY-l] MobyDataSetInstance vs MobyDataSimpleinstance
In-Reply-To: <6800eaa575bb0c8f33a18c8d87b0dec3@sfu.ca>
Message-ID:
Ben,
I gues that Paul already answered your questions about this - but still
I wonder what have you been trying to do... It seems to me that you were
creating a service template to send it to the registry in order to find
matching services. Correct? I wonder why you needed MobyDataSetInstance at
all for that? The MobyDataSetInstance is Paul's extension to
MobyPrimaryDataSimple - but the class MobyPrimaryDataSimple already has
everything (I hope) to create a template for communicating with the
registry.
This probably reflects one of the bad things in jMoby - we have a lot
of similarly named classes that (perhaps) overlap each other. I hope we
will have chance to discuss it in the jMoby BoF in Vancouver. Paul, are
you coming there?
Regards,
Martin
On Thu, 14 Apr 2005, Benjamin Good wrote:
> There is no .setXmlMode in MobyDataSetInstance . I think this will
> cause problems requesting services from Central ..??
>
> Has anyone built a collection in a java and used it to query for
> services successfully?
>
> I built a collection of Objects as below and didn't find any matching
> services? This should match anything that accepts a collection as
> input because of the inheritance from object right??
>
> //specify a dataype for use in the input to the template
> service
> MobyDataType type = new MobyDataType("Object");
> //make a jMoby object to act as the input to the template (and later
> the actual call)
> MobyDataSimpleInstance input1 = new MobyDataSimpleInstance
> ("");
> input1.setDataType (type);
> input1.addNamespace (new MobyNamespace ("NCBI_gi"));
> input1.setId("111076");
>
> MobyDataSimpleInstance input2 = new MobyDataSimpleInstance
> ("");
> input2.setDataType (type);
> input2.addNamespace (new MobyNamespace ("NCBI_gi"));
> input2.setId("111077");
>
> MobyDataSimpleInstance[] inputset = new
> MobyDataSimpleInstance[2];
> inputset[0] = input1;
> inputset[1] = input2;
> MobyDataSetInstance input = new
> MobyDataSetInstance("",inputset);
>
> //specify that the xml generated for this object by the getXML method
> //is suitable for communicating with moby central --- doesn't exist!
> // input.setXmlMode(MobyDataSimpleInstance.CENTRAL_XML_MODE);
> //add the moby object as input to the template service
> templateService.addInput(input);
>
> //Find services that match this template service
> MobyService[] validServices =
> worker.findService(templateService);
>
> -> finds none
> -> why?
>
> thanks!
> -Ben
>
>
> http://bioinfo.icapture.ubc.ca/bgood
>
> _______________________________________________
> moby-l mailing list
> moby-l at biomoby.org
> http://biomoby.org/mailman/listinfo/moby-l
>
--
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 bmg at sfu.ca Tue Apr 19 07:58:47 2005
From: bmg at sfu.ca (Benjamin Good)
Date: Tue, 19 Apr 2005 07:58:47 -0400
Subject: [MOBY-l] MobyDataSetInstance vs MobyDataSimpleinstance
In-Reply-To:
References:
Message-ID: <7ad0aee71d280d9b4a0e4ead22f30b2b@sfu.ca>
How would you indicate that you want services that consume a collection
with MobyPrimaryDataSimple?
-Ben
On Apr 19, 2005, at 5:32 AM, Martin Senger wrote:
> Ben,
> I gues that Paul already answered your questions about this - but
> still
> I wonder what have you been trying to do... It seems to me that you
> were
> creating a service template to send it to the registry in order to find
> matching services. Correct? I wonder why you needed
> MobyDataSetInstance at
> all for that? The MobyDataSetInstance is Paul's extension to
> MobyPrimaryDataSimple - but the class MobyPrimaryDataSimple already has
> everything (I hope) to create a template for communicating with the
> registry.
> This probably reflects one of the bad things in jMoby - we have a
> lot
> of similarly named classes that (perhaps) overlap each other. I hope we
> will have chance to discuss it in the jMoby BoF in Vancouver. Paul, are
> you coming there?
>
> Regards,
> Martin
>
> On Thu, 14 Apr 2005, Benjamin Good wrote:
>
>> There is no .setXmlMode in MobyDataSetInstance . I think this will
>> cause problems requesting services from Central ..??
>>
>> Has anyone built a collection in a java and used it to query for
>> services successfully?
>>
>> I built a collection of Objects as below and didn't find any matching
>> services? This should match anything that accepts a collection as
>> input because of the inheritance from object right??
>>
>> //specify a dataype for use in the input to the template
>> service
>> MobyDataType type = new MobyDataType("Object");
>> //make a jMoby object to act as the input to the template (and later
>> the actual call)
>> MobyDataSimpleInstance input1 = new MobyDataSimpleInstance
>> ("");
>> input1.setDataType (type);
>> input1.addNamespace (new MobyNamespace ("NCBI_gi"));
>> input1.setId("111076");
>>
>> MobyDataSimpleInstance input2 = new MobyDataSimpleInstance
>> ("");
>> input2.setDataType (type);
>> input2.addNamespace (new MobyNamespace ("NCBI_gi"));
>> input2.setId("111077");
>>
>> MobyDataSimpleInstance[] inputset = new
>> MobyDataSimpleInstance[2];
>> inputset[0] = input1;
>> inputset[1] = input2;
>> MobyDataSetInstance input = new
>> MobyDataSetInstance("",inputset);
>>
>> //specify that the xml generated for this object by the getXML method
>> //is suitable for communicating with moby central --- doesn't exist!
>> //
>> input.setXmlMode(MobyDataSimpleInstance.CENTRAL_XML_MODE);
>> //add the moby object as input to the template service
>> templateService.addInput(input);
>>
>> //Find services that match this template service
>> MobyService[] validServices =
>> worker.findService(templateService);
>>
>> -> finds none
>> -> why?
>>
>> thanks!
>> -Ben
>>
>>
>> http://bioinfo.icapture.ubc.ca/bgood
>>
>> _______________________________________________
>> moby-l mailing list
>> moby-l at biomoby.org
>> http://biomoby.org/mailman/listinfo/moby-l
>>
>
> --
> 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
>
>
http://bioinfo.icapture.ubc.ca/bgood
From senger at ebi.ac.uk Tue Apr 19 08:47:51 2005
From: senger at ebi.ac.uk (Martin Senger)
Date: Tue, 19 Apr 2005 13:47:51 +0100 (BST)
Subject: [MOBY-l] MobyDataSetInstance vs MobyDataSimpleinstance
In-Reply-To:
Message-ID:
> I suppose MobyPrimaryDataSet is the answer to my question.
>
Yes, That was my guess, too :-)
> The main difference between Instance and Primary - for communicating
> with Moby Central
>
Well, the Instance should never really be used for communicating with
Central in the first place. Either Primary is good enough, or we can fix
it. But not by just adding new class doing similar thing.
> is the presence of different serializations for talking with Central
> versus executing a service
>
Yes, Instance should be used in time of executing a service. Or calling
a service, I am not sure now (I nbever wrote any BioMoby service myself,
yet :-)).
But I may still be a bit confused. So my question is still here: Could
you or could you not to use MobyPrimaryDataSet to create a service
template and use it for finding matching services in a registry?
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 ucalgary.ca Tue Apr 19 10:16:40 2005
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Tue, 19 Apr 2005 08:16:40 -0600
Subject: [MOBY-l] MobyDataSetInstance vs MobyDataSimpleinstance
In-Reply-To:
References:
Message-ID: <426512C8.7050503@ucalgary.ca>
Yup, I'll be there. We've definitely got critical mass on the Java side
for a good BoF!
I think that the advantage of using MobyDataSetInstance instead of
MobyPrimaryDataSet (I assume MobyPrimaryDataSimple was a typo in the
original e-mail) is that you get a two-for-one. Why build a
MobyPrimaryDataSet to find a service (including creating all of the
MobyPrimaryDataSimple that go in it), then use some other classes to
generate the XML to run the service? The MobyDataInstance implementers
allow you to do both by instantiating one object, or even better, if you
got data back from a service, you don't need to instantiate any objects
yourself at all...
All of the extension classes I've made inherit methods from the parent
class when possible,
but all of the toXML() methods are overriden because they must be able
to generate
service request formatted XML, not just service template XML (hence
MobyDataInstance.setXmlMode()).
You are right though, I should move the modified MOBY Central parts of
MobyDataSetInstance.toXML() up to MobyPrimaryDataSet and call the
super's method explicitly when the requested XML mode is appropriate.
Doing that now...
Martin Senger wrote:
>Ben,
> I gues that Paul already answered your questions about this - but still
>I wonder what have you been trying to do... It seems to me that you were
>creating a service template to send it to the registry in order to find
>matching services. Correct? I wonder why you needed MobyDataSetInstance at
>all for that? The MobyDataSetInstance is Paul's extension to
>MobyPrimaryDataSimple - but the class MobyPrimaryDataSimple already has
>everything (I hope) to create a template for communicating with the
>registry.
> This probably reflects one of the bad things in jMoby - we have a lot
>of similarly named classes that (perhaps) overlap each other. I hope we
>will have chance to discuss it in the jMoby BoF in Vancouver. Paul, are
>you coming there?
>
> Regards,
> Martin
>
>On Thu, 14 Apr 2005, Benjamin Good wrote:
>
>
>
>>There is no .setXmlMode in MobyDataSetInstance . I think this will
>>cause problems requesting services from Central ..??
>>
>>Has anyone built a collection in a java and used it to query for
>>services successfully?
>>
>>I built a collection of Objects as below and didn't find any matching
>>services? This should match anything that accepts a collection as
>>input because of the inheritance from object right??
>>
>> //specify a dataype for use in the input to the template
>>service
>> MobyDataType type = new MobyDataType("Object");
>>//make a jMoby object to act as the input to the template (and later
>>the actual call)
>> MobyDataSimpleInstance input1 = new MobyDataSimpleInstance
>>("");
>> input1.setDataType (type);
>> input1.addNamespace (new MobyNamespace ("NCBI_gi"));
>> input1.setId("111076");
>>
>> MobyDataSimpleInstance input2 = new MobyDataSimpleInstance
>>("");
>> input2.setDataType (type);
>> input2.addNamespace (new MobyNamespace ("NCBI_gi"));
>> input2.setId("111077");
>>
>> MobyDataSimpleInstance[] inputset = new
>>MobyDataSimpleInstance[2];
>> inputset[0] = input1;
>> inputset[1] = input2;
>> MobyDataSetInstance input = new
>>MobyDataSetInstance("",inputset);
>>
>>//specify that the xml generated for this object by the getXML method
>>//is suitable for communicating with moby central --- doesn't exist!
>> // input.setXmlMode(MobyDataSimpleInstance.CENTRAL_XML_MODE);
>>//add the moby object as input to the template service
>> templateService.addInput(input);
>>
>>//Find services that match this template service
>> MobyService[] validServices =
>>worker.findService(templateService);
>>
>>-> finds none
>>-> why?
>>
>>thanks!
>>-Ben
>>
>>
>>http://bioinfo.icapture.ubc.ca/bgood
>>
>>_______________________________________________
>>moby-l mailing list
>>moby-l at biomoby.org
>>http://biomoby.org/mailman/listinfo/moby-l
>>
>>
>>
>
>
>
From bmg at sfu.ca Tue Apr 19 08:32:51 2005
From: bmg at sfu.ca (Benjamin Good)
Date: Tue, 19 Apr 2005 08:32:51 -0400
Subject: [MOBY-l] MobyDataSetInstance vs MobyDataSimpleinstance
In-Reply-To:
References:
Message-ID:
I suppose MobyPrimaryDataSet is the answer to my question. The main
difference between Instance and Primary - for communicating with Moby
Central is the presence of different serializations for talking with
Central versus executing a service - coming from this method.
public String toXML(){
if(xmlMode == SERVICE_XML_MODE)
return "" + dataValue + "";
else{
MobyNamespace[] ns = getNamespaces();
String result = "\n" +
getDataType().getName() + "\n";
for(int i = 0; ns != null && i < ns.length; i++){
result += "" + ns[i].getName() + "\n";
}
result += "";
return result;
}
}
Can this be avoided? It adds another step and another complication to
client development that seems like it could be handled higher up the
API ????
-Ben
On Apr 19, 2005, at 5:32 AM, Martin Senger wrote:
> Ben,
> I gues that Paul already answered your questions about this - but
> still
> I wonder what have you been trying to do... It seems to me that you
> were
> creating a service template to send it to the registry in order to find
> matching services. Correct? I wonder why you needed
> MobyDataSetInstance at
> all for that? The MobyDataSetInstance is Paul's extension to
> MobyPrimaryDataSimple - but the class MobyPrimaryDataSimple already has
> everything (I hope) to create a template for communicating with the
> registry.
> This probably reflects one of the bad things in jMoby - we have a
> lot
> of similarly named classes that (perhaps) overlap each other. I hope we
> will have chance to discuss it in the jMoby BoF in Vancouver. Paul, are
> you coming there?
>
> Regards,
> Martin
>
> On Thu, 14 Apr 2005, Benjamin Good wrote:
>
>> There is no .setXmlMode in MobyDataSetInstance . I think this will
>> cause problems requesting services from Central ..??
>>
>> Has anyone built a collection in a java and used it to query for
>> services successfully?
>>
>> I built a collection of Objects as below and didn't find any matching
>> services? This should match anything that accepts a collection as
>> input because of the inheritance from object right??
>>
>> //specify a dataype for use in the input to the template
>> service
>> MobyDataType type = new MobyDataType("Object");
>> //make a jMoby object to act as the input to the template (and later
>> the actual call)
>> MobyDataSimpleInstance input1 = new MobyDataSimpleInstance
>> ("");
>> input1.setDataType (type);
>> input1.addNamespace (new MobyNamespace ("NCBI_gi"));
>> input1.setId("111076");
>>
>> MobyDataSimpleInstance input2 = new MobyDataSimpleInstance
>> ("");
>> input2.setDataType (type);
>> input2.addNamespace (new MobyNamespace ("NCBI_gi"));
>> input2.setId("111077");
>>
>> MobyDataSimpleInstance[] inputset = new
>> MobyDataSimpleInstance[2];
>> inputset[0] = input1;
>> inputset[1] = input2;
>> MobyDataSetInstance input = new
>> MobyDataSetInstance("",inputset);
>>
>> //specify that the xml generated for this object by the getXML method
>> //is suitable for communicating with moby central --- doesn't exist!
>> //
>> input.setXmlMode(MobyDataSimpleInstance.CENTRAL_XML_MODE);
>> //add the moby object as input to the template service
>> templateService.addInput(input);
>>
>> //Find services that match this template service
>> MobyService[] validServices =
>> worker.findService(templateService);
>>
>> -> finds none
>> -> why?
>>
>> thanks!
>> -Ben
>>
>>
>> http://bioinfo.icapture.ubc.ca/bgood
>>
>> _______________________________________________
>> moby-l mailing list
>> moby-l at biomoby.org
>> http://biomoby.org/mailman/listinfo/moby-l
>>
>
> --
> 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
>
>
http://bioinfo.icapture.ubc.ca/bgood
From gordonp at ucalgary.ca Tue Apr 19 10:59:59 2005
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Tue, 19 Apr 2005 08:59:59 -0600
Subject: [MOBY-l] MobyDataSetInstance vs MobyDataSimpleinstance
In-Reply-To:
References:
Message-ID: <42651CEF.5060103@ucalgary.ca>
Ha! Just as I received this e-mail, I was commiting a change to this
very code, which calls super.toXML() in CENTRAL_XML_MODE. The fact that
toXML() can generate both XMLs is a bit of a retrofit into the
nomenclature that existed before I started adding classes. I was going
to do the same for MobyDataSetInstance, but
it is not clear to me (no javadocs) from the MobyPrimaryDataSet class if
setElements() should be given just a list of the datatypes the
set will hold, or if it is expecting instances. The latter would be
wierd, because the class does not encode data instances (and toXML()
as implemented would provide a very, very long service template XML if
you had 1000 DNASequences, for example). If the method
should be registering data types contained in the set, perhaps it should
be renamed...
Benjamin Good wrote:
> I suppose MobyPrimaryDataSet is the answer to my question. The main
> difference between Instance and Primary - for communicating with Moby
> Central is the presence of different serializations for talking with
> Central versus executing a service - coming from this method.
>
> public String toXML(){
> if(xmlMode == SERVICE_XML_MODE)
> return " (getName() != null ? "\" xmlns:moby=\""+
> MobyPrefixResolver.MOBY_XML_NAMESPACE+"\"
> moby:articleName=\"" + getName() : "")+
> "\">" + dataValue + "";
> else{
> MobyNamespace[] ns = getNamespaces();
> String result = " xmlns=\""+MobyPrefixResolver.MOBY_XML_NAMESPACE+"\">\n" +
> getDataType().getName() + "\n";
> for(int i = 0; ns != null && i < ns.length; i++){
> result += "" + ns[i].getName() + "\n";
> }
> result += "";
> return result;
> }
> }
>
> Can this be avoided? It adds another step and another complication to
> client development that seems like it could be handled higher up the
> API ????
>
> -Ben
>
> On Apr 19, 2005, at 5:32 AM, Martin Senger wrote:
>
>> Ben,
>> I gues that Paul already answered your questions about this - but
>> still
>> I wonder what have you been trying to do... It seems to me that you were
>> creating a service template to send it to the registry in order to find
>> matching services. Correct? I wonder why you needed
>> MobyDataSetInstance at
>> all for that? The MobyDataSetInstance is Paul's extension to
>> MobyPrimaryDataSimple - but the class MobyPrimaryDataSimple already has
>> everything (I hope) to create a template for communicating with the
>> registry.
>> This probably reflects one of the bad things in jMoby - we have a lot
>> of similarly named classes that (perhaps) overlap each other. I hope we
>> will have chance to discuss it in the jMoby BoF in Vancouver. Paul, are
>> you coming there?
>>
>> Regards,
>> Martin
>>
>> On Thu, 14 Apr 2005, Benjamin Good wrote:
>>
>>> There is no .setXmlMode in MobyDataSetInstance . I think this will
>>> cause problems requesting services from Central ..??
>>>
>>> Has anyone built a collection in a java and used it to query for
>>> services successfully?
>>>
>>> I built a collection of Objects as below and didn't find any matching
>>> services? This should match anything that accepts a collection as
>>> input because of the inheritance from object right??
>>>
>>> //specify a dataype for use in the input to the template
>>> service
>>> MobyDataType type = new MobyDataType("Object");
>>> //make a jMoby object to act as the input to the template (and later
>>> the actual call)
>>> MobyDataSimpleInstance input1 = new MobyDataSimpleInstance
>>> ("");
>>> input1.setDataType (type);
>>> input1.addNamespace (new MobyNamespace ("NCBI_gi"));
>>> input1.setId("111076");
>>>
>>> MobyDataSimpleInstance input2 = new MobyDataSimpleInstance
>>> ("");
>>> input2.setDataType (type);
>>> input2.addNamespace (new MobyNamespace ("NCBI_gi"));
>>> input2.setId("111077");
>>>
>>> MobyDataSimpleInstance[] inputset = new
>>> MobyDataSimpleInstance[2];
>>> inputset[0] = input1;
>>> inputset[1] = input2;
>>> MobyDataSetInstance input = new
>>> MobyDataSetInstance("",inputset);
>>>
>>> //specify that the xml generated for this object by the getXML method
>>> //is suitable for communicating with moby central --- doesn't exist!
>>> //
>>> input.setXmlMode(MobyDataSimpleInstance.CENTRAL_XML_MODE);
>>> //add the moby object as input to the template service
>>> templateService.addInput(input);
>>>
>>> //Find services that match this template service
>>> MobyService[] validServices =
>>> worker.findService(templateService);
>>>
>>> -> finds none
>>> -> why?
>>>
>>> thanks!
>>> -Ben
>>>
>>>
>>> http://bioinfo.icapture.ubc.ca/bgood
>>>
>>> _______________________________________________
>>> moby-l mailing list
>>> moby-l at biomoby.org
>>> http://biomoby.org/mailman/listinfo/moby-l
>>>
>>
>> --
>> 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
>>
>>
> http://bioinfo.icapture.ubc.ca/bgood
>
> _______________________________________________
> moby-l mailing list
> moby-l at biomoby.org
> http://biomoby.org/mailman/listinfo/moby-l
>
From gordonp at ucalgary.ca Tue Apr 19 11:19:38 2005
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Tue, 19 Apr 2005 09:19:38 -0600
Subject: [MOBY-l] MobyDataSetInstance vs MobyDataSimpleinstance
In-Reply-To:
References:
Message-ID: <4265218A.1020505@ucalgary.ca>
> Yes, Instance should be used in time of executing a service. Or calling
>a service, I am not sure now (I nbever wrote any BioMoby service myself,
>yet :-)).
>
>
Aha :-)
> But I may still be a bit confused. So my question is still here: Could
>you or could you not to use MobyPrimaryDataSet to create a service
>template and use it for finding matching services in a registry?
>
>
MobyDataSimpleInstance now calls super.toXML() when appropriate, but
for now, MobyDataSetInstance reimplements the central-mode toXML()
because it is unclear how
MobyDataSetInstance.setElements() should be used. Us people
implementing services run into these snags ;-)
Personally, I'd be much more comfortable with a
MobyPrimaryDataSet.setElementTypes()/addElementType() structure, since
it doesn't make much sense to pass in an actual number of items (as an
array encodes) unless you've got MobyDataInstances. In this case, I
could update the MobyPrimaryDataSet datatypes list in a reasonably
efficient way within MobyDataSetInstance.setElements(), and call
super.toXML() when appropriate.
From senger at ebi.ac.uk Tue Apr 19 11:31:09 2005
From: senger at ebi.ac.uk (Martin Senger)
Date: Tue, 19 Apr 2005 16:31:09 +0100 (BST)
Subject: [MOBY-l] MobyDataSetInstance vs MobyDataSimpleinstance
In-Reply-To: <4265218A.1020505@ucalgary.ca>
Message-ID:
It seems that I need to look into all these classes to re-undersatand what
I put there, and to start understand what Paul had in mind. I will do it
probably this evening and let you know. I will also move this topic to
moby-dev where it belongs more I guess.
Paul, just to help me, your classes (those with 'Instance') are used both
on a client side, and on the service provider side, or just on one of
them? And, do I understand correctly that they are here to hold the
real data?
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 suzi at fruitfly.org Wed Apr 20 18:54:18 2005
From: suzi at fruitfly.org (Suzanna Lewis)
Date: Wed, 20 Apr 2005 15:54:18 -0700
Subject: [MOBY-l] Hackathon 2005
Message-ID: <67b6042c95fe1754aab32cc1307579b9@fruitfly.org>
(sorry for multiple postings, but please do forward to
anyone else who you think might be interested)
------------------------------------------------------------------------
-----------
Dear everyone,
It has been a long time and we Bioinformatics devotees are overdue for
another total-immersion coding-fest (the last hackathon was held in
Singapore February 2003, more than two years ago). Apple has offered
to host us this year, and as an added bonus include free admission to
the World-Wide Developers Conference in San Francisco the prior week.
They are also looking for some people to present interesting new
developments at the WWDC, so if you have something noteworthy please
let us know. Apple is not attaching any strings, so our work need not
address Apple-specific software or hardware areas. Apple will provide
space and hardware (and access to their engineers if we'd like).
Week 1 (June 6-10) would be spent at the WWDC. Week 2 (June 12-16)
would be in Cupertino, at Apple's headquarters. We're free to focus
on what interests us, our tentative plans include:
1. Bio-ontologies software
2. High-performance computing (e.g. large scale computations,
optimization)
3. Image analysis
4. Documentation
5. Anything else that may interest you
Our plan is to organize this much as the Aspen Center for Physics
computational biology workshops were organized (for those old enough to
remember): A couple of presentations to start the day; collaboration
and coding afterwards; time for a bit of fun (does anyone else
cycle?), and discussions in the late afternoons and evenings.
Would everyone who is interested in attending please send us a short
description of what you would like to do, and perhaps other people who
you would like to work with. There is somewhat limited space, so we
will try to prioritize groups that have a clear focus and a need to
interact. We now this is very short notice, but we hope that there
will be enough interest to make it possible.
We are looking into additional funding support, to pay for travel
expenses, but this is still to be decided.
Looking forward to hearing from everyone.
George, Cyrus, Steve, and Suzanna (the Bay Area locals)
From mwilkinson at mrl.ubc.ca Fri Apr 22 12:26:47 2005
From: mwilkinson at mrl.ubc.ca (Mark Wilkinson)
Date: Fri, 22 Apr 2005 09:26:47 -0700
Subject: [MOBY-l] Hot off the presses..
Message-ID: <1114187207.5335.17.camel@mobycentral.icapture.ubc.ca>
Wilkinson M, Schoof H, Ernst R, Haase D (2005). BioMOBY successfully
integrates disributed heterogenous bioinformatics web services. The
PlaNet exemplar case. Plant Physol 138, p1-13
--
Mark Wilkinson
Assistant Professor (Bioinformatics)
Dept. Medical Genetics, UBC, Canada
From p.lord at cs.man.ac.uk Mon Apr 25 09:01:19 2005
From: p.lord at cs.man.ac.uk (Phillip Lord)
Date: 25 Apr 2005 14:01:19 +0100
Subject: [MOBY-l] The Eighth Annual Bio-Ontologies Meeting Call for
Submissions: Deadline FRIDAY 29th APRIL
Message-ID:
This will be the final call for submissions as the deadline is
Friday. Please not that this year we are also hoping to have a demo
session of tools for bio-ontologies, so please submit abstracts.
Submissions or questions to bio-ont-sig at cs.man.ac.uk
Please note that this year bio-ontologies is in the beautiful city of
Detroit. Ask yourself, can you afford to miss this opportunity?
Phil
The Eighth Annual Bio-Ontologies Meeting Call for Submissions
=============================================================
Key Information
===============
Organisers: Robert Stevens(1), Phillip Lord(1),
Robin McEntire(2), and James.A.Butler(2)
(1) School of Computer Science, University of Manchester
(2) GlaxoSmithKline
Website: http://bio-ontologies.man.ac.uk
Location: Detroit, Michigan
Submission Deadline: 29th April
Main Conference: http://www.iscb.org/ismb2005
General Information
===================
The Bio-Ontologies workshop has been a satellite meeting to the annual
ISMB conference since 1998, and is now operated as a Special Interest
Group at the ISMB Conference. Bio-Ontologies is well established as
one of the key meetings for dissemination of latest information and
research on ontologies in the life sciences and has drawn the key
researchers in the field.
Ontologies provide a mechanism for organising, sharing and reconciling
data. Within recent years there has been a great deal of interest in
the use of ontologies within bioinformatics, particularly in providing
computationally accessible annotation, or standard data models for
complex data for microarray or pathway information.
Meetings such as last years workshop and SOFG have made it clear that
there are many important uses of ontologies and a clear realisation of
the importance of implementing mechanisms for integrating source
ontologies rather than duplicating effort or causing confusion by
extending a given ontology to include everything.
However, with the increase in scope and use of ontologies within
bioinformatics, issues of scalability, expressivity and best practices
for modelling are becoming more important. We are particularly
interested, therefore, in work involving multiple source ontologies,
and which cut across the different levels of granularity implicit
within biological systems.
BioOntologies is an informal workshop. Submissions will be reviewed by
the programme committee. A number of talks will be invited for ***full
publication*** as papers in Comparative and Functional Genomics
(see http://www3.interscience.wiley.com/cgi-bin/jissue/109860809 for
last years papers)
Submissions
===========
Submission
We invite submissions to this years Bio-Ontologies. Suitable topics
include but are not restricted to:
* Biological Applications of Ontologies.
* Reports on Newly Developed or Existing Bio-Ontologies.
* Tools for Developing Ontologies.
* Use of Semantic Web technologies in BioInformatics
* The implications of Bio-Ontologies or the Semantic Web for the drug discovery process
* Current Research In Ontology Languages and its implication for Bio-Ontologies
This year, for the first time, we would like to have a number of short
software or ontology demonstrations, showing new or existing tools for
building or using ontologies, or describing the design of
ontologies. Submissions for these demonstrations are particularly encouraged.
Submission Instructions
=======================
Submissions are limited to 2 pages. Please submit using word using the
templates available at
http://bio-ontologies.man.ac.uk/submissions.html.
Alternatively, submissions may be as a text file.
Submissions should be emailed to bio-ont-sig at cs.man.ac.uk. We will
acknowledge within a day or two.
Bio-Ontologies is an informal meeting. Abstracts are reviewed by the
programme committee. All accepted abstracts will be published by the
organisers on their web site and in the main programme booklet. By
submitting your paper, you consent to this publication.
Authors of abstracts accepted for full publication as long (8 page)
papers in Comparative and Functional Genomics will be notified
following the meeting, for publication around October. Full
details will be given later.
Authors will be informed of acceptance within a few days of the
submission deadline.
From markw at illuminae.com Wed Apr 27 22:23:45 2005
From: markw at illuminae.com (Mark Wilkinson)
Date: Wed, 27 Apr 2005 19:23:45 -0700
Subject: [MOBY-l] Central back up and stable :-)
Message-ID: <42704931.7090603@illuminae.com>
Hi all,
There is a DNS change filtering itself through the world. MOBY Central
is now running on a Linux machine and appears to be completely stable.
It is configured almost identically to the old machine so you don't need
to change anything on your end. If you have registered new services in
the past 3-4 days they will not be registered in the new database as it
was installed from a dump four days ago.
Sorry for all the problems - it took a while to identify a machine that
we could use as a replacement. If you notice any instability in the new
machine please let me know. I've been watching the error logs for the
past few days, and haven't seen anything at all, but... yeah...
M
From robert.stevens at cs.man.ac.uk Thu Apr 28 11:53:37 2005
From: robert.stevens at cs.man.ac.uk (Robert Stevens)
Date: Thu, 28 Apr 2005 16:53:37 +0100
Subject: [MOBY-l] Re: CFP: Semantic Webs for the Life Sciences -- PSB06
In-Reply-To: <6.1.2.0.2.20050427205204.01ebb650@mailhost.cs.man.ac.uk>
References: <6.1.2.0.2.20050427205204.01ebb650@mailhost.cs.man.ac.uk>
Message-ID: <6.1.2.0.2.20050428165326.01ea7b30@mailhost.cs.man.ac.uk>
At 20:54 27/04/2005, Robert Stevens wrote:
>
>
>Michael,
>
>I'm not sure if you're on any of my bio-ontology lists, so I'vce sent you
>a personal CFP.....
>
>Robert.
>
>I can't remember if yo're on any of my lists. So, read on. I'm away until
>next thrusday, so will not answer much email.
>
>Robert
>_______________________________________________________________________
>
> This message is posted to several lists.
> We apologize if you receive multiple copies.
> Please forward it to everyone who might be interested.
>_______________________________________________________________________
>
>
> Call for Papers and Posters
>
> Semantic Webs for Life Sciences
>
> at the Pacific Symposium on Biocomputing 2006
> http://psb.stanford.edu/
> January 3-7, 2006
> Grand Wailea Resort, Wailea, Maui, Hawaii
>
>_______________________________________________________________________
>
>Biology is evolving from a science of organisms and molecules to one
>that increasingly relies on processing data. These data range from raw
>sequences represented in a reasonably computational form, to the vast
>body of annotation of these data that are less amenable to computational
>processing. The shift from hypothesis-driven experiments to data-driven
>experiments relies on having computational access to all these data and
>the tools that manipulate those data.
>
>The Semantic Web is a vision that moves the Web from a form that is only
>really usable by humans, to one where the data and services are open to
>autonomous computational agents. This vision relies on the semantics of
>both the content and services on the Web being accessible to computers.
>Semantic markup through ontologies developed in OWl or RDF are meant to
>provide this semantic markup -- OWL is, after all, the web Ontology
>Language. As the recent biomedical ontology sessions at PSB have
>revealed, there is much activity within bioinformatics in the field of
>semantic markup of data. The discipline is well poised to build
>Semantic Webs for Life Sciences that will afford bioinformatics
>applications deeper computational access to the knowledge element of
>bioinformatics resources.
>
>This session on Semantic Webs for Life Sciences would therefore welcome
>papers that discuss:
>
> * The creation and use of Semantic Web applications
> * Reasoning about the biomedical domain based on Semantic Web
> technologies to make scientific insights
> * Intelligent agent technologies and associated ontologies
> * Use of Semantic Web technologies to bridge between heterogeneous
> information resources (e.g., to connect genotype to gene
> expression and ultimately to clinical medicine, drug discoveries,
> etc.)
> * Use of Semantic Web technologies to make biomedical applications
> interoperable
> * The use of OWL, RDF, etc. to describe and use knowledge in the
> biomedical arena
> * Advances in Semantic Web related technologies as applied to
> bioinformatics and biomedical problems
> * Other research associated with Semantic Webs for Life Sciences
>
>_______________________________________________________________________
>
>
> Session co-chairs
>
> * Robert Stevens (Contact Person)
> University of Manchester, UK
> robert.stevens at manchester.ac.uk
>
> * Olivier Bodenreider
> National Library of Medicine
> olivier at nlm.nih.gov
>
> * Yves A. Lussier
> Columbia University, NY, USA
> yves.lussier at dbmi.columbia.edu
>
>_______________________________________________________________________
>
>
> Submission information
>
>
> Papers and Posters
>
>The core of the conference consists of rigorously peer-reviewed
>full-length papers reporting on original work. Accepted papers will be
>published in a hard-bound archival proceedings, and the best of these
>will be presented orally to the entire conference. Researchers wishing
>to present their research without official publication are encouraged to
>submit a one page abstract by November 1, 2005 to present their work in
>the poster sessions.
>
>
> Important dates
>
> * Paper submissions due: July 18, 2005
> * Notification of paper acceptance: September 6, 2005
> * Final paper deadline: September 23, 2005
> * Abstract deadline: November 1, 2005
> * Meeting: January 3-7, 2006
>
>
> Paper format
>
>All papers must be submitted to russ.altman at stanford.edu in electronic
>format. The file formats we accept are: postscript (*.ps), Adobe Acrobat
>(*.pdf) and Microsoft Word documents (*.doc). Attached files should be
>named with the last name of the first author (e.g. altman.ps, altman.pdf,
>or altman.doc).
>Hardcopy submissions or unprocessed TEX or LATEX files will be rejected
>without review.
>
>Each paper must be accompanied by a cover letter. The *cover letter must
>state* the following:
>
> * The email address of the corresponding author
> * The specific PSB session that should review the paper or abstract
> * The submitted paper contains original, unpublished results, and
> is not currently under consideration elsewhere.
> * All co-authors concur with the contents of the paper.
>
>
>Submitted papers are limited to twelve (12) pages in our publication
>format. Please format your paper according to instructions found at
>http://psb.stanford.edu/psb-online/psb-submit/. If figures can not be
>easily resized and placed precisely in the text, then it should be clear
>that with appropriate modifications, the total manuscript length would
>be within the page limit.
>
>Color pictures can be printed at the expense of the authors. The fee is
>$500 per page of color pictures, payable at the time of camera ready
>submission.
>
>Contact Russ Altman (russ.altman at stanford.edu) for additional information
>about paper submission requirements.
From david.baux at cirad.fr Fri Apr 29 09:04:35 2005
From: david.baux at cirad.fr (David Baux)
Date: Fri, 29 Apr 2005 15:04:35 +0200
Subject: [MOBY-l] how can I modify an object
Message-ID: <427230E3.8070508@cirad.fr>
hello,
I'm just beginning with Biomoby.
I'd like to modify an existing object (created by manuel ruiz from
cirad) and I don't know how to manage it.
Is it possible to modify an object directly?
Or can I deregister the object and then reregister it?
thanks for your answer.
ps: I posted that question on the moby-s FAQs but got no answer.
From mlangill at sfu.ca Fri Apr 29 13:32:06 2005
From: mlangill at sfu.ca (Morgan Langille)
Date: Fri, 29 Apr 2005 10:32:06 -0700
Subject: [MOBY-l] how can I modify an object
In-Reply-To: <427230E3.8070508@cirad.fr>
References: <427230E3.8070508@cirad.fr>
Message-ID: <1114795926.4207.395.camel@moosehead.mrl.ubc.ca>
Hello,
Unless you are the owner of an existing object you should not be
modifying it at all. If you need to add more things to an existing
object then you should create a new moby object that inherits the
existing object (ISA relationship) and add your own things with HAS and
HASA relationships. If you need to remove things from an existing object
then you should inherit from the next higher moby object that does not
have the thing in it (i.e. make a new moby object with a different
name). Hope this helps!
Morgan
On Fri, 2005-04-29 at 06:04, David Baux wrote:
> hello,
> I'm just beginning with Biomoby.
> I'd like to modify an existing object (created by manuel ruiz from
> cirad) and I don't know how to manage it.
> Is it possible to modify an object directly?
> Or can I deregister the object and then reregister it?
> thanks for your answer.
> ps: I posted that question on the moby-s FAQs but got no answer.
>
>
> _______________________________________________
> moby-l mailing list
> moby-l at biomoby.org
> http://biomoby.org/mailman/listinfo/moby-l
>