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

[SED-ML-discuss] KiSAO: algorithm parameter survey

[Anna Z. <zhu...@eb...>]

Dear KiSAO/SED-ML users,

As many of you are aware, the current implementation of the Kinetic 
Simulation Algorithm Ontology (KiSAO http://www.biomodels.net/kisao) in 
OBO format is rather restrictive. For example, the multiple inheritance  
means that many algorithms occupy more than one position in the 
ontology, and often appear at different levels in the various component 
branches. An example of this would be the 'Bortz-Kalos-Liebowitz 
method', which possesses the characteristics 'discrete variables', 
'progression with adaptive time steps', 'non-spatial description' and 
'stochastic system behaviour', and hence appears in all four branches. 
This is in fact true of virtually all the methods in the ontology.

In our efforts to improve both the hierarchical arrangements of KiSAO 
terms, as well as make it more useful to the community from a reasoning 
standpoint, we are currently in the process of re-implementing KiSAO in 
OWL. This much richer language allows us to create a separate branch of 
algorithm characteristics ('progression with adaptive time steps', 
etc.), and subsequently link the algorithms to the characteristics using 
the 'hasProperty' relationship. This work is well under way.

In addition, we plan to incorporate, for each KiSAO method, information 
regarding the parameters that can be used in the simulation experiment 
settings. We would like to engage the community at this stage, and have 
created a survey to address the subject. It should take very little time 
to complete, as is it mostly composed of check boxes. It addresses the 
main points below:

* For the list of parameters we plan to include, are there any that you 
would like to suggest?
* Of the list of parameters on the survey page, do you think they are 
appropriately named, or are there more suitable names you have in mind?
* Do you know of any algorithms that you would like to see incorporated 
(associated references appreciated)?

The survey can be found here:

https://www.surveymonkey.com/s/kisao_parameters

The deadline for submitting responses to this survey is 31st May, 2011, 
after which we will notify you of the results.

Thank you for your continued co-operation and support,

Sincerely,

BioModels.net Team

[SED-ML-discuss] Nomination of candidates for editorship of SED-ML

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

Dear Colleagues,

On March 25th, the first specification of the Simulation Experiment
Description Markup Language was released. The authors of this document were
the de facto editors, either creators of the idea or developers of initial
software support. Now that a stable specification has been issued, and that
some software is available, it is time to structure the governance of the
project. This will strengthen the development process by increasing its
stability and legitimacy. We will therefore form an editorial board made of
individuals elected by the community. Those editors will be elected for a
term of two years. A standing elected editor will not be able to run for
election while still "in office".

By this e-mail, we are calling for nominations of possible candidates. The
nominations are anonymous. You may nominate anyone (including yourself)
that you believe is qualified and would act as a good SED-ML editor. You
may fill out this form more than once, for nominating multiple individuals.
The current SED-ML "editors" will gather the results and create a single
list of all unique candidates along with the rationales for their
nominations, then verify with each individual that they accept the
nomination, and finally
issue a call for voting.

Please, nominate your favorite editors before April 15th at:
https://www.surveymonkey.com/s/FLW78GD

Best regards,

Re: [SED-ML-discuss] Way forward

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

Hi Nicolas,

Firstly, congratulations to all the editors for getting L1V1 specified!

> Level 1: In future versions we only add to the existing language, without
> major restructuration. Examples are addition of simulation classes and
> enriching output description.
>
> Level 2: We allow ourselves to go a bit wild, and imagine more drastic
> changes, so as to encore iterative simulation tasks etc.
>
> This would allow development of solid implementations of Level 1, still
> improving and evolving, without stalling the expansion of the language.
>
> What do-you think?

I agree, this seems like a sensible way forward. It allows us all to
work on supporting a nice stable specification so that we can maintain
(achieve?) consistency across implementations and model encoding
languages, while at the same time pushing our various pet requirements
as Level 2 proposals.


Cheers,
David.

[SED-ML-discuss] Way forward

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

Hello,

L1 V1 is now out, and you are of course all busy implementing support. 
Don't forget to report any problem you find in the spec to the tracker:
http://sourceforge.net/tracker/?group_id=293618&atid=1345549

With the coming HARMONY, I think it would perhaps be useful to start 
discussing about a way forward. L1 V1 is great, but its purpose was mainly 
to provide a robust framework for future work. Indeed, the only simulation 
experiment we can encode at the moment is the single uniform timecourse. 
This covers the majority of simulations out there (at least among the ones 
used in papers describing models present in BioModels Db), but it is far to 
be sufficient.

The problem we face is to evolve slowly to allow painless implementation 
and maintenance, while providing structure to allow complex simulation 
experiments such as parameter scans and optimisation. In the past, most 
often project favoured one approach over the other, resulting either in 
languages not evolving fast enough for the needs, or being totally unstable 
and therefore not supported. In order to avoid this situation, I propose to 
have two concurrent lines of development:

Level 1: In future versions we only add to the existing language, without 
major restructuration. Examples are addition of simulation classes and 
enriching output description.

Level 2: We allow ourselves to go a bit wild, and imagine more drastic 
changes, so as to encore iterative simulation tasks etc.

This would allow development of solid implementations of Level 1, still 
improving and evolving, without stalling the expansion of the language.

What do-you think?

-- 
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] New jlibsedml release

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

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

[SED-ML-discuss] Final release of SED-ML Level 1 Version 1

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

Dear Colleagues,

We are pleased to announce the release of the final specification for the 
Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 
1. It is available now from:

http://sed-ml.org/

SED-ML is an XML-based format for encoding experiments involving the 
numerical simulations of quantitative models. SED-ML describes the 
selection and modifications of the models to be used in the experiment, the 
simulation procedures that will be applied, the simulation experiments 
themselves, and the post-processing and output of numerical results.

This first version of SED-ML covers non-nested simulation tasks, where the 
variables and parameters used to modify a model do not depend on prior 
simulations. Only one simulation approach is provided, that is uniform time 
course simulations. It is expected that SED-ML will become more 
comprehensive as software support grows.

We would like to thank all of the many members of the relevant communities 
who by their discussions and support made the development of SED-ML 
possible. The following people deserve special mention for their input 
towards the current specification.

# Mike Hucka
# Fedor Kolpakov
# Ion Moraru
# David Nickerson
# Sven Sahle
# Henning Schmidt
# Jacky Snoep

SED-ML is a community effort, involving software developers from different 
simulation tools and model representation formats. We do very much 
appreciate your contribution; please subscribe to sed-ml-discuss on 
SourceForge: https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

The SED-ML editors
Dagmar Waltemath, Frank Bergmann, Richard Adams, Nicolas Le Novère

[SED-ML-discuss] Algorithm parameters in KiSAO

[Anna Z. <zhu...@eb...>]

Dear SED-MLers,

I'm currently working on adding simulation algorithm parameters to KiSA 
Ontology <http://www.ebi.ac.uk/compneur-srv/kisao/> (ontology, which 
classifies simulation
algorithms, that can be referred to from a SED-ML description), such as 
those presented in simulation tools like COPASI <http://www.copasi.org> 
or Dizzy <http://magnet.systemsbiology.net/software/Dizzy/> (for 
example, 'Adams max order' for LSODA algorithm or 'epsilon' for 
tau-leaping method).

Any suggestions about which parameters are worth being added (or where 
should I look for them) are very welcome.

Thanks,

-- 
Anna Zhukova
Intern, Computational Systems Neurobiology Group,
European Bioinformatics Institute,
Wellcome Trust Genome Campus,
Hinxton, Cambridge
CB10 1SD, United Kingdom 

[SED-ML-discuss] New C++ SED-OM implementation developed (pre-release)

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

Hi all,

I've developed a new SED-OM implementation, on top of the CellML API 
infrastructure. It is currently pre-release, but will be released as 
part of the next CellML API.

The implementation is written in C++, but the API is specified in IDL, 
and the CellML API infrastructure means it can be accessed from C++, 
Python, Java, Javascript via XPCOM, or over CORBA (the latter two may 
not be well maintained; Python and Java accessibility is more reliable). 
The automatically generated wrappers handle reference counting, so no 
special effort is required to release objects.

Using Mercurial, the latest CellML API can be obtained by cloning 
http://cellml-api.hg.sourceforge.net/hg/cellml-api/cellml-api/

The SED-OM module is called SProS (SED-ML Processing Service); to enable 
it, pass --enable-spros to configure.

Full unit tests of the SED-OM have also been produced; it would 
theoretically be possible to use the CellML API language bridging 
infrastructure to use these test-suites to test an implementation in 
another language if it implemented the interface binding. SProS passes 
all the unit tests with no signs of any memory management problems / 
leaks according to valgrind.

Relevant files in the CellML API source tree:
   interfaces/SProS.idl - the SED-ML Processing Service interface
      definition in OMG IDL. Based closely on the SED-OM UML diagram.
   sources/SProS/SProSImpl.cpp - the internals of the C++ implementation.
   sources/SProS/SProSBootstrap.hpp - the external header file C++ users
     should include to bootstrap the service. After this, users of SProS
     should only access the service via the generated interface header
     (IfaceSProS.hxx).
   tests/SProSTest.cpp - the unit tests for the SED-OM.

Best wishes,
Andrew

[SED-ML-discuss] Announcing the 2011 CellML workshop

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

This is the first announcement for the 2011 CellML Workshop
(http://www.cellml.org/community/events/workshop/2011).  We plan to
hold a two day meeting at The University of Auckland from 11th-12th
April. If you are interested in attending this event please mark these
dates in your calendar. More details will be available in the near
future.


Cheers,
David.

[SED-ML-discuss] Request for Comments: IDL definition for SED-ML processing

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

Hi all,

I have created an IDL file describing an API for accessing SED-ML files. 
If there is sufficient interest, this could become a language and 
implementation neutral specification of a SED-ML API (obviously, each 
language developer would need to decide how to adapt the API to a 
particular language to make it as idiomatic as possible, but this could 
be in addition to the standard interfaces wherever possible).

No implementation of the API has been created yet; I expect that the 
implementing this could result in changes as implementation experience 
often shows where changes are required.

Note that this version refers to dom::Element and dom::NodeList, which 
is part of the W3C DOM API, and cellml_api::MathList, which is defined as:

   /**
    * A collection of math.
    */
   interface MathList : XPCOM::IObject
   {
     /**
      * The length of the collection.
      */
     readonly attribute unsigned long length;

     /**
      * Tests for the existance of an element in the set.
      * @param x The element to test for.
      * @return true if the element is present, or false otherwise.
      */
     boolean contains(in MathMLElement x);

     /**
      * Returns a CellMLElementIterator that can be used to iterate 
through the
      * elements. The iteration order is undefined.
      */
     MathMLElementIterator iterate();
   };

I could move MathList into another IDL file called something more 
language agnostic for the final version.

Best wishes,
Andrew

Re: [SED-ML-discuss] Domain names

[Mike H. <mh...@ca...>]

Very nice.  Impressive that there are any 5-letter domain names still available....

MH


On Wed, 19 Jan 2011 11:31:05 +0000, Nicolas Le novère wrote:
> Dear SED-MLers,
> 
> I purchased the following domains for 3 years:
> 
> sedml.org
> sedml.net
> sed-ml.org
> sed-ml.net
> 
> In the immediate future I will make them redirect to 
> http://biomodels.net/sed-ml/. But in the long term, an independent 
> sed[-]ml.org is probably better.
> 
> Cheers
> 
> -- 
> 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/
> 
> 
> ------------------------------------------------------------------------------
> Protect Your Site and Customers from Malware Attacks
> Learn about various malware tactics and how to avoid them. Understand 
> malware threats, the impact they can have on your business, and how you 
> can protect your company and customers by using code signing.
> http://p.sf.net/sfu/oracle-sfdevnl
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

[SED-ML-discuss] Domain names

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

Dear SED-MLers,

I purchased the following domains for 3 years:

sedml.org
sedml.net
sed-ml.org
sed-ml.net

In the immediate future I will make them redirect to 
http://biomodels.net/sed-ml/. But in the long term, an independent 
sed[-]ml.org is probably better.

Cheers

-- 
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] jlibsedml update

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

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

Re: [SED-ML-discuss] Standard API interface for SED-ML

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

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

Re: [SED-ML-discuss] Standard API interface for SED-ML

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

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

Re: [SED-ML-discuss] Standard API interface for SED-ML

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

Hello Andrew, 

> 
> I've had a look at libsedml and jlibsedml to see if they come with
interface
> definitions, and as far as I can tell, they don't, and there seems to be
> differences between the interfaces (for example, libsedml defines id and
> name attributes on SedMLBase, while jlibsedml has a corresponding abstract
> class called SEDBase which doesn't define name and id, and instead has a
> separate abstract class AbstractIdentifiableElement).
> 

These differences can be explained through the fact that jlibsedml at its
base has been generated out of Schema. However, these changes won't be vital
for developers. 

> Has there been any interest in defining a standard IDL or similar
language-
> neutral interface definition of an API for accessing SED-ML - and are
there
> any efforts to standardise these interfaces underway?
> 

Not that I am aware off. The current implementations have been developed to
suite the strengths of their maintainers. I'm open to add a compatibility
layer on top of libSedML if developers see a need for it. 

> I need to define an IDL to work with my framework anyway, so if there is
> sufficient interest and no one else has done it already, I'm happy to work
on
> making a 'standard' SED-ML IDL as a collaborative effort - from which
> implmentors can define how the IDL maps to their way of doing things in
> their language (or use an existing language binding).
> 

It might be interesting to see. At some level, I'm a bit skeptical as to how
much an API should be the same across programming languages. There are
different feature sets provided by different programming languages for
example language constructs like: Object / Collection Initializers, Language
Integrated Query in C#. Using these will make the task of using the library
much easier, even at the cost that the API would look different than it does
in other programming languages. 

Cheers
Frank

> Best wishes,
> Andrew
> 
>
----------------------------------------------------------------------------
--
> Protect Your Site and Customers from Malware Attacks Learn about various
> malware tactics and how to avoid them. Understand malware threats, the
> impact they can have on your business, and how you can protect your
> company and customers by using code signing.
> http://p.sf.net/sfu/oracle-sfdevnl
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

[SED-ML-discuss] Standard API interface for SED-ML

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

Hi all,

I'm looking at developing an API for accessing SED-ML, in C++, using the 
COM-like structure currently used for the CellML API, as a first step 
towards adding SED-ML support to the CellML API.

I've had a look at libsedml and jlibsedml to see if they come with 
interface definitions, and as far as I can tell, they don't, and there 
seems to be differences between the interfaces (for example, libsedml 
defines id and name attributes on SedMLBase, while jlibsedml has a 
corresponding abstract class called SEDBase which doesn't define name 
and id, and instead has a separate abstract class 
AbstractIdentifiableElement).

Has there been any interest in defining a standard IDL or similar 
language-neutral interface definition of an API for accessing SED-ML - 
and are there any efforts to standardise these interfaces underway?

I need to define an IDL to work with my framework anyway, so if there is 
sufficient interest and no one else has done it already, I'm happy to 
work on making a 'standard' SED-ML IDL as a collaborative effort - from 
which implmentors can define how the IDL maps to their way of doing 
things in their language (or use an existing language binding).

Best wishes,
Andrew

Re: [SED-ML-discuss] XPath explanations in the spec

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

Dear All,
  To bring this discussion to a conclusion, it seems like we have 3  
possible actions  resulting from these posts:

1) Leave everything unchanged, and explain in the spec that software  
tools consuming SEDML should  be able to match up XPath prefixes with  
model namespaces. We can then see if this turns out to be problematic  
in practice, and resolve if necessary  in future SED-ML versions.

2) Leave the schema unchanged, but state in the spec that ALL  
namespaces, including those in a model file that are referenced by  
XPath expressions in a SEDML file,  should be declared as  xmlns  
values in the top-level SedML element ( in the manner of XSLT).

3)  Edit the SEDML schema to include our own prefix/namespace mapping  
elements, in the way that, for example, Schematron has done.

It would be great if we could reach a concensus opinion to resolve this,

  Cheers
     Richard






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

Re: [SED-ML-discuss] XPath explanations in the spec

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

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

Re: [SED-ML-discuss] XPath explanations in the spec

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

Hi all,

I think Richard has already explained things as well as I could for most 
points, and given good examples, so I'll restrict myself to a couple of comments.

On 21/11/10 01:34, Frank T. Bergmann wrote:
>
> On Nov 20, 2010, at 4:50 PM, Richard Adams wrote:
>
> This could work, what I still don't understand is why this is necessary? 
> Once the model is resolved it is trivial to obtain the list of namespaces 
> it uses. Why do we need to state them like this again?

Partly, because it is standard XML practice to declare the namespaces you 
will use in the document in which they are used, using the xmlns:prefix 
approach.  Thus following this convention will make understanding of SED-ML 
easier.


>
>>
>> But both approaches allow software validation of prefix-URI mappings by 
>> software consuming or producing SEDML.
>>
>
> I would claim that we can still validate in the current version whether an 
> xpath expression is valid or not.

True, but you'd need to code up the algorithm explicitly, rather than relying 
on behaviour which will probably already exist in XML tools/libraries.

The design of SED-ML is already pretty restricted to tying a SED-ML document 
to a particular (collection of) static model document(s), so I don't think 
trying to allow for the model to have an arbitrary SBML version gains you 
anything.  So why not just specify it in the SED-ML?  Tools generating SED-ML 
can always look up the namespace from the model and put it in the SED-ML, 
after all.

Best wishes,
Jonathan

Re: [SED-ML-discuss] XPath explanations in the spec

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

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

Re: [SED-ML-discuss] XPath explanations in the spec

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

Hello again ... 


On Nov 20, 2010, at 4:50 PM, Richard Adams wrote:

> 
>  <sedML xmlns="http://www.biomodels.net/sed-ml" xmlns:sbml="http://www.sbml.org/sbml/level2" xmlns:math="http://www.w3.org/1998/Math/MathML">
> 

this won't work for me. I might want to refer to multiple SBML models for experiments. Some of which might be in different levels. 

> I.e., the XPath prefix-URI mappings are persisted using the the regular XML namespace declaration mechanism. (But we would never actually have SBML elements in a SEDML file, we're just using the mechanism, right?)
> 

we actually might have SBML elements in changeXML or newXML. 
> 
> But, Frank, is your concern that this is too strict: for example, the SBML model could be re-versioned ( with no structural changes that would cause the XPath to  break) and now the SEDML file could no longer be applied, as the  namespace URI for SBML in the SEDML file  would now disagree with the namespace URI in the SBML file? But perhaps this is not a problem, are we envisaging 1 SEDML file referring to a single base model or are we trying to get reuse of a SEDML file by being able to apply it to different versions ( in terms of model version ) of a model?

let us not restrict the use of SED-ML documents. I think it is a very common scenario to refer to multiple documents. It is not just re-versioning that is the issue here. 

> 
> Alternately, we could come up with our own elements in SEDML, perhaps by a 'target' element to hold this information:
> e.g., something like:
> <changeXML>
>    <target xpath="//sbml:reaction[@id='Reaction6']/sbml:kineticLaw/math:math/">
>       <listOfXPathPrefixMappings>
>          <xpath-mapping prefix="sbml">
>             <listOfNamespaces>
>                <namespace>http://www.sbml.org/sbml/level2 </namespace>
> 		<namespace>http://www.sbml.org/sbml/level3/core </namespace>
> 		<namespace>http://www.sbml.org/sbml/level2/version4 </namespace>
>             </listOfNamespaces>
> 
>          </xpath-mapping>
> 	<xpath-mapping prefix="math">
>             <listOfNamespaces>
>                <namespace>http://www.w3.org/1998/Math/MathML </namespace>
>             </listOfNamespaces>
>          </xpath-mapping">
>       </listOfXPathPrefixMappings>
>   </target>
>   <newXML>
>   </newXML>
> </changeXML>
> 
> which would allow multiple namespaces to be defined as  acceptable for a given prefix, at the expense of complexity.

This could work, what I still don't understand is why this is necessary? Once the model is resolved it is trivial to obtain the list of namespaces it uses. Why do we need to state them like this again? 

> 
> But both approaches allow software validation of prefix-URI mappings by software consuming or producing SEDML.
> 

I would claim that we can still validate in the current version whether an xpath expression is valid or not. 

Cheers
Frank


> 
> Cheers
> Richard
> 
> 
> 
> 
> 
> 
> On 20 Nov 2010, at 19:11, Frank T. Bergmann wrote:
> 
>> Hello Jonathan, 
>> 
>>> 
>>> Surely the prefix -> namespace URI binding should be contained within the SED-ML file?  That's what happens in XSLT after all.  So somewhere in the SED-ML document (e.g. on the root element) you'd use xmlns:prefix="url" to declare all the prefixes you are going to use in XPath expressions later in the document.
>>> 
>> 
>> Of course! But what this discussion was about is about the prefixes / uri's defined in model files that are referred to from the SED-ML document. This would be used when referring (via xpath) for example to a particular species of an included sbml model. (Or to stick with Richards example a specific MIRIAM annotation of a species in an included model.) 
>> 
>> Or maybe I misunderstand ... can you give a snippet how it would look? I have a feel it would restrict the SED-ML document. So that I could no longer use it for both sbml l2v1 and l2v4. 
>> 
>> thanks
>> Frank
>> 
>> 
>> ------------------------------------------------------------------------------
>> Beautiful is writing same markup. Internet Explorer 9 supports
>> standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2 & L3.
>> Spend less time writing and  rewriting code and more time creating great
>> experiences on the web. Be a part of the beta today
>> http://p.sf.net/sfu/msIE9-sfdev2dev
>> _______________________________________________
>> SED-ML-discuss mailing list
>> SED...@li...
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>> 
> 
> Dr Richard Adams
> Software Development Team Leader,
> Centre For Systems Biology Edinburgh
> University of Edinburgh 
> Tel: 0131 651 9019
> email : ric...@ed...
> Web: http://csbe.bio.ed.ac.uk/adams.php
> 
> 
> 
> 
> 
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
> ------------------------------------------------------------------------------
> Beautiful is writing same markup. Internet Explorer 9 supports
> standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2 & L3.
> Spend less time writing and  rewriting code and more time creating great
> experiences on the web. Be a part of the beta today
> http://p.sf.net/sfu/msIE9-sfdev2dev_______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

Re: [SED-ML-discuss] XPath explanations in the spec

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

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

Re: [SED-ML-discuss] XPath explanations in the spec

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

>> Surely the prefix -> namespace URI binding should be contained within the
>> SED-ML file?  That's what happens in XSLT after all.  So somewhere in the
>> SED-ML document (e.g. on the root element) you'd use xmlns:prefix="url" to
>> declare all the prefixes you are going to use in XPath expressions later in
>> the document.
> 
> yep - I agree with Jonathan. and XSLT is a good example to follow...
> 

I still wonder what it would look like ... I mean we are stuck to XPath, right? in XSLT one could write queries like: 

<xsl:choose>
	<xsl:when test="name()">xmlns:<xsl:value-of select="name()" /> </xsl:when>
	<xsl:otherwise>xmlns</xsl:otherwise>
<.xsl:choose>

but again that would be similar to simply defer it to what namespaces are referenced in the model. 

Frank

Re: [SED-ML-discuss] XPath explanations in the spec

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

Hello Jonathan, 

> 
> Surely the prefix -> namespace URI binding should be contained within the SED-ML file?  That's what happens in XSLT after all.  So somewhere in the SED-ML document (e.g. on the root element) you'd use xmlns:prefix="url" to declare all the prefixes you are going to use in XPath expressions later in the document.
> 

Of course! But what this discussion was about is about the prefixes / uri's defined in model files that are referred to from the SED-ML document. This would be used when referring (via xpath) for example to a particular species of an included sbml model. (Or to stick with Richards example a specific MIRIAM annotation of a species in an included model.) 

Or maybe I misunderstand ... can you give a snippet how it would look? I have a feel it would restrict the SED-ML document. So that I could no longer use it for both sbml l2v1 and l2v4. 

thanks
Frank