sed-ml-discuss — Migrating to google groups: https://groups.google.com/d/forum/sed-ml-discuss

[SED-ML-discuss] [Combine-announce] COMBINE mailing lists

[Nicolas Le N. <le...@eb...>]

Dear Colleagues,

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-- 
Nicolas LE NOVERE, Computational Systems Neurobiology, EMBL-EBI, WTGC,
Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521 Fax:468,
Skype:n.lenovere, AIM:nlenovere, twitter:@lenovere
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[SED-ML-discuss] Overlap between SED-ML and SBML

[Richard A. <ric...@ed...>]

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

Re: [SED-ML-discuss] Configuring algorithm-specific parameters

[Richard A. <ric...@ed...>]

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

Re: [SED-ML-discuss] Configuring algorithm-specific parameters

[Dagmar W. <dag...@un...>]

Hello,

I agree with Richard that an optional <algorithmParameter> specification seems to make good sense as it allows us to be more specific in defining the algorithm we're using in a simulation. (And I would also like to see the underscore eliminated from the element name :-))

Dagmar



________________________________
From: Richard Adams [ric...@ed...]
Sent: 05 September 2011 11:17
To: sed...@li...
Subject: [SED-ML-discuss] Configuring algorithm-specific parameters

Hello all,
 The new release of the Kisao ontology contains some information about algorithm-specific  configuration parameters (e.g., error control parameters).
Currently in SED-ML only general settings ( start time, end time, number of Intervals )  can be defined, and an algorithm type.
 I'd like to open a discussion that we extend the 'Algorithm' element to include these specific configuration parameters.
 For example the XML might look something like this:
   <algorithm kisaoID="KISAO_0000071">
      <algorithm_parameter kisaoID="KISAO_0000211" value="0.000001"/>
  </algorithm>

would set the absolute tolerance  for an LSODA algorithm. The 'value' attribute could be a string, since the actual data type of the parameter value
 can be resolved  from the Kisao ontology description for that parameter.  Cardinality would be 0*, i.e., algorithm_parameter elements
 would be optional.

Regards,

Richard


Software Development Team Leader,
Centre For Systems Biology Edinburgh
University of Edinburgh
Tel: 0131 651 9019
email : ric...@ed...<mailto:ric...@ed...>
Web: http://csbe.bio.ed.ac.uk/adams.php

Re: [SED-ML-discuss] Configuring algorithm-specific parameters

[Nicolas Le N. <le...@eb...>]

On 13/09/11 04:36, David Nickerson wrote:

> That seems like a sensible approach, and if I remember the discussions
> correctly its also why algorithm was moved to be an element instead of
> an attribute. I should probably look myself, but does anyone know off
> the top of their head whether KiSAO defines default values for all the
> parameters for all the algorithms?

Default values are not provided at the moment (and this is not on the 
agenda). We provide types, such as "double" or "integer".


-- 
Nicolas LE NOVERE, Computational Systems Neurobiology, EMBL-EBI, WTGC,
Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521 Fax:468,
Skype:n.lenovere, AIM:nlenovere, twitter:@lenovere
http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/

Re: [SED-ML-discuss] Configuring algorithm-specific parameters

[Jonathan C. <jon...@cs...>]

On 13/09/2011 04:36, David Nickerson wrote:
> On Mon, Sep 5, 2011 at 9:17 PM, Richard Adams<ric...@ed...>  wrote:
>> Hello all,
>>   The new release of the Kisao ontology contains some information about
>> algorithm-specific  configuration parameters (e.g., error control
>> parameters).
>> Currently in SED-ML only general settings ( start time, end time, number of
>> Intervals )  can be defined, and an algorithm type.
>>   I'd like to open a discussion that we extend the 'Algorithm' element to
>> include these specific configuration parameters.
>>   For example the XML might look something like this:
>>     <algorithm kisaoID="KISAO_0000071">
>>        <algorithm_parameter kisaoID="KISAO_0000211" value="0.000001"/>
>>    </algorithm>
>> would set the absolute tolerance  for an LSODA algorithm. The 'value'
>> attribute could be a string, since the actual data type of the parameter
>> value
>>   can be resolved  from the Kisao ontology description for that parameter.
>>   Cardinality would be 0*, i.e., algorithm_parameter elements
>>   would be optional.
> That seems like a sensible approach, and if I remember the discussions
> correctly its also why algorithm was moved to be an element instead of
> an attribute. I should probably look myself, but does anyone know off
> the top of their head whether KiSAO defines default values for all the
> parameters for all the algorithms?

I can't see any defaults from a quick browse, and I'd guess they 
wouldn't be included (different implementations of the same algorithm 
are likely to use different defaults), but I'm not that familiar with KiSAO.

I also like the approach, although I think the element name 
"algorithmParameter" would be more consistent with the rest of SED-ML.

Best wishes,
Jonathan

Re: [SED-ML-discuss] Configuring algorithm-specific parameters

[David N. <dav...@gm...>]

On Mon, Sep 5, 2011 at 9:17 PM, Richard Adams <ric...@ed...> wrote:
> Hello all,
>  The new release of the Kisao ontology contains some information about
> algorithm-specific  configuration parameters (e.g., error control
> parameters).
> Currently in SED-ML only general settings ( start time, end time, number of
> Intervals )  can be defined, and an algorithm type.
>  I'd like to open a discussion that we extend the 'Algorithm' element to
> include these specific configuration parameters.
>  For example the XML might look something like this:
>    <algorithm kisaoID="KISAO_0000071">
>       <algorithm_parameter kisaoID="KISAO_0000211" value="0.000001"/>
>   </algorithm>
> would set the absolute tolerance  for an LSODA algorithm. The 'value'
> attribute could be a string, since the actual data type of the parameter
> value
>  can be resolved  from the Kisao ontology description for that parameter.
>  Cardinality would be 0*, i.e., algorithm_parameter elements
>  would be optional.

That seems like a sensible approach, and if I remember the discussions
correctly its also why algorithm was moved to be an element instead of
an attribute. I should probably look myself, but does anyone know off
the top of their head whether KiSAO defines default values for all the
parameters for all the algorithms?


Cheers,
David.

[SED-ML-discuss] Notes from SED-ML sessions at Combine

[Richard A. <ric...@ed...>]

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

Re: [SED-ML-discuss] Sampling sensitivity analyses in SED-ML when uncertainty described in the model

[Andrew M. <ak....@au...>]

On 05/09/11 19:14, Frank T. Bergmann wrote:
>>
>> However, I think this raises an issue of whether it is important that we
>> are performing a sampling sensitivity analysis rather than some other
>> kind of simulation experiment involving repetition.
>>
>> If it is only important to describe how to produce the same results in a
>> more compressed form than enumerating the results, then there is no need
>> for SED-ML - we might as well just describe how to reproduce results in
>> an existing imperative language.
>
> I'm afraid I have to disagree. The overarching goal is to be able to reproduce the results,
> independent of the tool, of the programming language and of the environments they were
 > originally defined in.

Hi Frank,

There is a distinction between explaining how to reproduce the results 
(an explanation which can be used for a number of different things - 
more than just reproducing results), and providing a procedure which 
produces the same results without explaining the procedure.

If we did simply want to produce the results, using an existing 
programming language would be a far better approach. It wouldn't make 
much sense to invent a new programming language in the name of 
'programming language independence', but that is what the result will be 
if we try to describe simulations out of imperative primitives.

> At the same time it has to be implementable, we will be getting
> nowhere if we don't find primitives to connect together to describe more complicated experiments.
> Otherwise it is unimplementable and without tool support the whole standard becomes an exercise.

There are a finite set of common simulation experiment types - I think 
we should aim to enumerate them rather than require them to be described 
by SED-ML document authors.

Not all software tools need to support all simulation types, but tools 
can use the simulation description in multiple different ways - 
reproducing the experiment, explaining it, allowing it to be edited and 
changed graphically.

Best wishes,
Andrew

>
> However, you should be able to preserve that what you did was a sampling analysis. But that is
> something better left to ontologies (perhaps KISAO can be used for that), or a MIRIAM annotation block.
>
> All the best
> Frank
> ------------------------------------------------------------------------------
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[SED-ML-discuss] Configuring algorithm-specific parameters

[Richard A. <ric...@ed...>]

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

Re: [SED-ML-discuss] Sampling sensitivity analyses in SED-ML when uncertainty described in the model

[Frank T. B. <fbe...@ca...>]

> 
> However, I think this raises an issue of whether it is important that we 
> are performing a sampling sensitivity analysis rather than some other 
> kind of simulation experiment involving repetition.
> 
> If it is only important to describe how to produce the same results in a 
> more compressed form than enumerating the results, then there is no need 
> for SED-ML - we might as well just describe how to reproduce results in 
> an existing imperative language.

I'm afraid I have to disagree. The overarching goal is to be able to reproduce the results, independent of the tool, of the programming language and of the environments they were originally defined in. At the same time it has to be implementable, we will be getting nowhere if we don't find primitives to connect together to describe more complicated experiments. Otherwise it is unimplementable and without tool support the whole standard becomes an exercise. 

However, you should be able to preserve that what you did was a sampling analysis. But that is something better left to ontologies (perhaps KISAO can be used for that), or a MIRIAM annotation block. 

All the best
Frank

Re: [SED-ML-discuss] [sbml-discuss] Identifiers.org, the resolvable MIRIAM URIs

[Neil S. <nei...@ma...>]

Hi Nicolas, hi Camille,

I really welcome this and hope that the introduction of this will lower the bar for those who wish (or currently don't wish) to annotate their models.

Just wondered what the roadmap is / would be for implementing web services? Web services down to the third level (i.e. for the specific GO term) would be fantastic. What are the current plans?

Cheers / Prost,

Neil. 

On 31 Aug 2011, at 13:11, Nicolas Le Novère <le...@eb...> wrote:

> Dear Colleagues,
> 
> As you know, since 2005 we have developed a system of shared identifiers, 
> the MIRIAM URNs, that allow people to annotate data-sets with unambiguous, 
> perennial and common identifiers, that could be resolved to different 
> sources of information. One of the issues people encountered was the lack 
> of direct dereferencing. Over the summer 2011, we developed 
> Identifiers.org, the dereferencable version of the MIRIAM URIs. Also based 
> on MIRIAM Registry, it combines the advantage of MIRIAM URNs (everyone uses 
> the same URI to describe the same data-set, multiple targets of 
> resolutions, maintenance of IDs by the data providers but the full URIs 
> centrally provided, no cost etc.) and the advantages of PURLs (persistent 
> URLs).
> 
> You can already play with it. Try:
> 
> * http://identifiers.org/
> 
> (Info on the whole project)
> 
> * http://identifiers.org/obo.go/
> 
> (the entry for GO in MIRIAM registry, used by identifiers.org)
> 
> * http://identifiers.org/obo.go/GO:0006915
> 
> The URI for this GO term. This is what you should store in your database 
> instead of just GO:0006915, and this is what should be distributed with 
> your dataset. That will provide your users with links to the GO term in all 
> the resources referenced in the registry.
> 
> * http://identifiers.org/obo.go/GO:0006915?resource=MIR:00100012
> 
> This configuration of the URI allow you to restrict the resolution of the 
> GO term to QuickGO. MIR:00100012 is the identifier of QuickGO in MIRIAM 
> registry. The corresponding URI is:
> http://identifiers.org/miriam.resource/MIR:00100012
> 
> Finally, we are developing something that will be called 
> "MyIdentifiers.org". This will allow a project, for instance "demo", to 
> setup a whole range of choice in one go. Instead of specifying the resource 
> to use at the level of each separate identifier, you generate the URIs as:
> 
> http://identifiers.org/pubmed/16333295?project=demo
> 
> IMPORTANT: The URN form of MIRIAM URIs will remain valid! MIRIAM Registry 
> will still resolve them and all your code remains correct. We nevertheless 
> encourage you to use the new URIs in new developments. In order to 
> back-propagate the change, We will provide services to convert from the URN 
> form to the URL one.
> 
> Best regards,
> 
> Camille Laibe
> Nicolas Le Novere
> ____________________________________________________________
> To manage your sbml-discuss list subscription, visit 
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> 
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> 
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> contact sbm...@ca...

Re: [SED-ML-discuss] Sampling sensitivity analyses in SED-ML when uncertainty described in the model

[Andrew M. <ak....@au...>]

On 13/07/11 22:24, Jonathan Cooper wrote:
> Hi Andrew,
>
> I don't see why nested simulations couldn't be used for this.  You don't need
> to set a variable within a nested simulation - it could just repeat the same
> inner simulation 'numberOfSamples' times, surely?  Assuming that the random
> seed wasn't reset each time, this should work.

Hi all,

As the nested simulations specification is worded now, I don't think you 
can omit the 'SetVariables' part from Frank's nested simulation 
experiment proposal - it says that the experiment will always refer to a 
SetValue object, and that requirement wouldn't be met under your proposal.

It would be possible to modify the nested simulation proposal to include 
support this case; this would mean that the SED-ML file would produce 
the same output.

However, I think this raises an issue of whether it is important that we 
are performing a sampling sensitivity analysis rather than some other 
kind of simulation experiment involving repetition.

If it is only important to describe how to produce the same results in a 
more compressed form than enumerating the results, then there is no need 
for SED-ML - we might as well just describe how to reproduce results in 
an existing imperative language.

If we want to encode some structural information about what type of 
experiment is being carried out in a declarative way, so that 
information is useful for more than just running the simulation, then I 
think that marking out a sampling sensitivity analysis experiment as 
such is more useful than continuously rebuilding one out of more 
fundamental constructs in every experiment description.

Best wishes,
Andrew

>
> Best wishes,
> Jonathan
>
> On 12/07/11 01:21, Andrew Miller wrote:
>> Hi all,
>>
>> I've recently created and implemented proposal for representing
>> parameter uncertainty in CellML models (so the posterior probability
>> distribution for the parameter is part of the model); this immediately
>> creates the possibility of performing sampling sensitivity analyses on
>> the model to determine distributions of other parameters given the
>> uncertainty in the model.
>>
>> Has anyone considered how to describe this type of simulation experiment
>> in SED-ML? It is simpler than a parameter scan - essentially just an
>> instruction to sample from the distributions already described in the
>> model multiple times. Frank Bergemann's nested experiments proposal is
>> also not directly useful in this case, because we don't want to
>> explicitly set the values of variables, but instead, let them be sampled
>> from the distribution in the model.
>>
>> I think one possible approach would be to inherit from UniformTimeCourse
>> with a new simulation type, SamplingSensitivityAnalysis, with all the
>> attributes and operations from UniformTimeCourse, along with
>> 'numberOfSamples'.
>>
>> Best wishes,
>> Andrew
>>
>> ------------------------------------------------------------------------------
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>> sense of it. IT sense. And common sense.
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>> _______________________________________________
>> SED-ML-discuss mailing list
>> SED...@li...
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
> ------------------------------------------------------------------------------
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Re: [SED-ML-discuss] demonstration of a web based SED-ML repository

[Nicolas Le N. <le...@eb...>]

They all should be here ;-)
--  from BlackBerry - Nicolas LE NOVERE,  EMBL-EBI, Mob:+447833147074, Tel:+441223494521, Skype:n.lenovere, http://www.ebi.ac.uk/~lenov/

-----Original Message-----
From: Dagmar Waltemath <dag...@un...>
Date: Sat, 3 Sep 2011 16:29:16 
To: M.A...@cw...<M.A...@cw...>; sed...@li...<sed...@li...>
Reply-To: sed...@li...
Subject: Re: [SED-ML-discuss] demonstration of a web based SED-ML repository

------------------------------------------------------------------------------
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download Logger. Secure your free ArcSight Logger TODAY!
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Re: [SED-ML-discuss] demonstration of a web based SED-ML repository

[Dagmar W. <dag...@un...>]

Dear all,

(and sorry to spam those who are on sed-ml-discuss but not at the COMBINE)

the SED-ML break-out session will start at 9am tomorrow morning.
So far we have on the "schedule" to look at Michaels implementation, explore ways of extracting reasonable information from SED-ML files with Robert Hoehndorf, look at a couple of suggestions for extension of SED-ML as made today by Jonathan Cooper (slides available at http://co.mbine.org/events/COMBINE_2011/agenda?q=system/files/2011-09-03-combine-cooper-functional-curation.pdf) and also look at Frank Bergmanns nested simulation proposal (available from http://precedings.nature.com/documents/4257/version/1).

Please, join us tomorrow if you should be interested in any of these topics, but also if you have further points to discuss :-)
You can as well sign up for the break out on https://docs.google.com/spreadsheet/ccc?key=0ApbKgxVhXxVydGJxazZjRTgxdnE4R0hULVlfajdHNVE&hl=en_US#gid=0
if you would like to be notified in case of updates.

Dagmar


________________________________
From: Michael Guravage [M.A...@cw...]
Sent: 03 September 2011 17:51
To: sed...@li...
Subject: [SED-ML-discuss] demonstration of a web based SED-ML repository

Hello all,

During tomorrow's SED-ML breakout session, if there is interest,  I would be glad to demonstrate our web based SED-ML repository. In brief, we have instantiated the SED-ML object model as a set of custom content types for a content management system called PLONE. The contents types faithfully represent the SED-ML object model, and can export a simulation-experiment description in SED-ML compliant XML. What is new is that we have extended the schema slightly to accommodate source code models. We also take advantage of the meta data and workflow facilities in PLONE to facilitate searching and realize a curation workflow.

Till tomorrow then.

With kind regards,

Michael Guravage

--

Michael A. Guravage
Centrum Wiskunde & Informatica (CWI)
Science Park 123, 1098 XG Amsterdam, The Netherlands
Mailing address: P.O. Box 94079, 1090 GB Amsterdam
CWI Office Room M245
Mic...@cw...<mailto:Mic...@cw...>
http://www.cwi.nl/~guravage
Phone +31 20 592 4028
Fax +31 20 592 4199

Re: [SED-ML-discuss] demonstration of a web based SED-ML repository

[Richard A. <ric...@ed...>]

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

Re: [SED-ML-discuss] demonstration of a web based SED-ML repository

[Richard A. <ric...@ed...>]

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

[SED-ML-discuss] demonstration of a web based SED-ML repository

[Michael G. <M.A...@cw...>]

Hello all,

During tomorrow's SED-ML breakout session, if there is interest,  I would be
glad to demonstrate our web based SED-ML repository. In brief, we have
instantiated the SED-ML object model as a set of custom content types for a
content management system called PLONE. The contents types faithfully
represent the SED-ML object model, and can export a simulation-experiment
description in SED-ML compliant XML. What is new is that we have extended
the schema slightly to accommodate source code models. We also take
advantage of the meta data and workflow facilities in PLONE to facilitate
searching and realize a curation workflow.

Till tomorrow then.

With kind regards,

Michael Guravage

-- 

Michael A. Guravage
Centrum Wiskunde & Informatica (CWI)
Science Park 123, 1098 XG Amsterdam, The Netherlands
Mailing address: P.O. Box 94079, 1090 GB Amsterdam
CWI Office Room M245
Mic...@cw...
http://www.cwi.nl/~guravage
Phone +31 20 592 4028
Fax +31 20 592 4199

Re: [SED-ML-discuss] Specifying the type of output

[Jonathan C. <jon...@cs...>]

Hi all,

On 02/09/2011 20:04, David Nickerson wrote:
> This issue in general is probably something we can discuss in 
> tomorrow's session at COMBINE if there is time.

I'd certainly be interested in doing so - quite a few of the points you 
raise David touch on topics I'll mention in my talk tomorrow!

Best wishes,
Jonathan

Re: [SED-ML-discuss] Specifying the type of output

[David N. <dav...@gm...>]

> At the moment, the data stream output by implementing a SED-ML description
> is defined by the model variable targeted. It is not explicitly stated in
> the SED-ML file. Would-it be useful to constraint the type of output for
> instance as concentration or amount? This could use a SED-ML attribute, or
> terms from an external vocabulary such as SBO.

I'm not completely sure I understand what you are after here, so I'll
just work though it out loud, so to speak...

SED-ML links to a specific target in the model (xpath) and then,
possibly with some post-processing described in MathML, this is one
data stream output by implementing the experiment. Correct? And the
type is essentially the units of the data in the stream?

If I've got it wrong here, you should probably stop reading now.

At least for CellML models, the type of the output stream would be
completely defined if we could specify units on any parameters used in
the post-processing. I think we have discussed this briefly before,
but units in SED-ML are pretty much essential in my view. With the
addition of units, and assuming the target in the encoded model format
has its type well defined, then the type of the output is completely
specified. Although as you mention below, the SED-ML would need to
understand the model encoding format to be able to determine its
type....

> Of course the simulator(s) must know what the raw output is, and know how
> to transform it, which means a knowledge of the internal structure of the
> model encoding format. But this is required to run the simulation
> experiment anyway.

Typically, SED-ML tools simply hand over running the simulation to a
model encoding language specific tool - and I think this is the right
way to be handling things. As long as you have a simulation tool that
will take in the encoded model, numerical method, etc., a SED-ML tool
only needs to operate at the XML level without needing to understand
the model encoding format at all. To completely determine the type of
the output(s) you would also need to define in the SED-ML the type of
the target in the encoded model - either through the SED-ML units or
referring to the units definition in the encoded model. If you define
the units in SED-ML you'd then have to ask the simulation tool to
ensure that the target is converted to those units on output. This has
the advantage that the SED-ML doesn't need to understand the model
encoding format, but relies on SED-ML having a units system compatible
with all possible model encoding formats and the simulation tool being
able to perform the conversion (or to know that no conversion is
necessary). Some common conversions, concentration to amount for
example, require the use of additional parameters which may or may not
be present in the model being simulated and therefore the simulation
tool may not always be able to convert targets to the appropriate
type.

Which starts to suggest that the type of the target in the encoded
model is irrelevant, and it is up to the SED-ML author to declare the
target's type correctly in the SED-ML document. Or another way to look
at it, is that the author of the experiment needs to ensure they are
using a model that is compatible with what they want to do with it.
You can then define any post-processing required to convert types in
the experiment description and where possible link parameters used in
the conversion formulas back to the encoded model.

This then leads to making standard templates available for reuse which
define the mathematics of these common transformations as well as the
ports (?) for connecting the required parameters. This is something we
have been thinking about as part of best practices for modular
modelling, in terms of providing these kinds of templates (in CellML)
for use as intermediate models when combing multiple models together
that are based on different formalism's. Something to consider as part
of extending the capabilities of post-processing in SED-ML.

This issue in general is probably something we can discuss in
tomorrow's session at COMBINE if there is time.

Cheers,
David.

[SED-ML-discuss] Specifying the type of output

[Nicolas Le N. <le...@eb...>]

Hello,

At the moment, the data stream output by implementing a SED-ML description 
is defined by the model variable targeted. It is not explicitly stated in 
the SED-ML file. Would-it be useful to constraint the type of output for 
instance as concentration or amount? This could use a SED-ML attribute, or 
terms from an external vocabulary such as SBO.

Of course the simulator(s) must know what the raw output is, and know how 
to transform it, which means a knowledge of the internal structure of the 
model encoding format. But this is required to run the simulation 
experiment anyway.

-- 
Nicolas LE NOVERE, Computational Systems Neurobiology, EMBL-EBI, WTGC,
Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521 Fax:468,
Skype:n.lenovere, AIM:nlenovere, twitter:@lenovere
http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/

[SED-ML-discuss] Identifiers.org, the resolvable MIRIAM URIs

[Nicolas Le N. <le...@eb...>]

Dear Colleagues,

As you know, since 2005 we have developed a system of shared identifiers, 
the MIRIAM URNs, that allow people to annotate data-sets with unambiguous, 
perennial and common identifiers, that could be resolved to different 
sources of information. One of the issues people encountered was the lack 
of direct dereferencing. Over the summer 2011, we developed 
Identifiers.org, the dereferencable version of the MIRIAM URIs. Also based 
on MIRIAM Registry, it combines the advantage of MIRIAM URNs (everyone uses 
the same URI to describe the same data-set, multiple targets of 
resolutions, maintenance of IDs by the data providers but the full URIs 
centrally provided, no cost etc.) and the advantages of PURLs (persistent 
URLs).

You can already play with it. Try:

* http://identifiers.org/

(Info on the whole project)

* http://identifiers.org/obo.go/

(the entry for GO in MIRIAM registry, used by identifiers.org)

* http://identifiers.org/obo.go/GO:0006915

The URI for this GO term. This is what you should store in your database 
instead of just GO:0006915, and this is what should be distributed with 
your dataset. That will provide your users with links to the GO term in all 
the resources referenced in the registry.

* http://identifiers.org/obo.go/GO:0006915?resource=MIR:00100012

This configuration of the URI allow you to restrict the resolution of the 
GO term to QuickGO. MIR:00100012 is the identifier of QuickGO in MIRIAM 
registry. The corresponding URI is:
http://identifiers.org/miriam.resource/MIR:00100012

Finally, we are developing something that will be called 
"MyIdentifiers.org". This will allow a project, for instance "demo", to 
setup a whole range of choice in one go. Instead of specifying the resource 
to use at the level of each separate identifier, you generate the URIs as:

http://identifiers.org/pubmed/16333295?project=demo

IMPORTANT: The URN form of MIRIAM URIs will remain valid! MIRIAM Registry 
will still resolve them and all your code remains correct. We nevertheless 
encourage you to use the new URIs in new developments. In order to 
back-propagate the change, We will provide services to convert from the URN 
form to the URL one.

Best regards,

Camille Laibe
Nicolas Le Novere

[SED-ML-discuss] SED-ML /simulation session at Combine

[Richard A. <ric...@ed...>]

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

Re: [SED-ML-discuss] A SED-ML visualizer/editor tool

[Richard A. <ric...@ed...>]

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

[SED-ML-discuss] Workshop on Interoperability in Scientific Computing - Deadline extended

[Dagmar W. <dag...@un...>]

IEEE e-Science 2011 Workshop on Interoperability in Scientific Computing
========================================================================
5th December 2011, Stockholm, Sweden.
http://www.cs.ox.ac.uk/david.johnson/wisc11/
**EXTENDED DEADLINE**
**FULL PAPERS DUE: MONDAY 25th JULY 2011**


The seventh IEEE e-Science conference, sponsored by the IEEE Computer Society's Technical Committee for Scalable Computing (TCSC), will be held in Stockholm, Sweden from 5th - 8th December 2011. The Workshop on Interoperability in Scientific Computing will be held on the morning of Monday 5th of December, and is co-located with the main conference.

Approaches to modelling take many forms. The mathematical, computational and encapsulated components of models can be diverse in terms of complexity and scale, as well as in published implementation (mathematics, source code, and executable files). Many of these systems are attempting to solve real-world problems in isolation. However the long-term scientific interest is in allowing greater access to models and their data, and to enable simulations to be combined in order to address ever more complex issues. Markup languages, metadata specifications, and ontologies for different scientific domains have emerged as pathways to greater interoperability. Domain specific modelling languages allow for a declarative development process to be achieved. Metadata specifications enable coupling while ontologies allow cross platform integration of data.

The goal of this workshop is to bring together researchers from across scientific disciplines whose computational models require interoperability. This may arise through interactions between different domains, systems being modelled, connecting model repositories, or coupling models themselves, for instance in multi-scale or hybrid simulations. The outcomes of this workshop will be to better understand the nature of multidisciplinary computational modelling and data handling. Moreover we hope to identify common abstractions and cross-cutting themes in future interoperability research applied to the broader domain of scientific computing.

FINAL CALL FOR PAPERS

We invite submissions for high-quality papers (up to 8 pages in length) within the context of scientific computing in any of the traditional sciences (physics, chemistry, biology), engineering, or scientific/mathematical modelling applied to the social sciences and humanities. Papers should address progress, results or positions in one or more of the following areas:

* Use of metadata standards for annotating scientific models and data
* Curating and publishing digital models and data to online repositories
* Meta-modelling and markup languages for model description
* Theoretical frameworks for combining disparate models, multi-scale models
* Using standardised data formats in computational models
* Domain-specific ontologies for the sciences

It is expected that the proceedings of the e-Science 2011 workshops will be published by the IEEE Computer Society Press, USA, and will be made available online through the IEEE Digital Library.

SUBMISSION PROCESS

Authors are invited to submit papers with unpublished, original work of not more than 8 pages of double column text using single spaced 10 point size on 8.5 x 11 inch pages, as per IEEE 8.5 x 11 manuscript guidelines.

Templates are available from here:
http://www.ieee.org/web/publications/pubservices/confpub/AuthorTools/conferenceTemplates.html.

Authors should submit a PDF or PostScript (level 2) file that will print on a PostScript printer. Papers conforming to the above guidelines should be submitted through the EasyChair submission system here: 
https://www.easychair.org/account/signin.cgi?conf=wisc11

Note, papers should NOT be submitted to the main e-Science 2011 paper submission system, as they will not be directed to the workshop organisers.

It is requested that at least one author of each accepted paper attend the conference and workshop.

IMPORTANT DATES
**EXTENDED DEADLINE**
**FULL PAPERS DUE: MONDAY 25th JULY 2011**
Notification of acceptance: 18th August 2011
Camera-ready: 16th September 2011
Workshop date: 5th December 2011

CHAIRS/ORGANISERS

David Johnson, Steve McKeever, (University of Oxford, UK)

PROGRAMME COMMITTEE

David Nickerson (University of Auckland, New Zealand)
Herbert Sauro (University of Washington, USA)
Steve Harris (University of Oxford, UK)
Jonathan Cooper (University of Oxford, UK)
Rutger Vos (University of Reading, UK)
Dagmar Waltemath (University of Rostock, Germany)
Daniele Gianni (European Space Agency)
Mike Stout (University of Nottingham, UK)