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

Re: [SED-ML-discuss] Nested Proposal v2

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

> One of my biggest concern with the current structure of the proposal is 
> that it disrupts the distinction simulation/model/task.
> 
> I think that what should probably be nested is the task. I don't think this 
> would change your proposal much. We could still have uber-simulations 
> called by tasks, such as parameter optimisation (with an associated method 
> of sampling associated with a kisao term). More difficult would be to keep 
> the model changes in the model definitions and calling them from the task.
> 
> 

I would be fine with making it a subclass of Task, i see no immediate concerns. One question though, would we always reference exactly one original Task ? Or will we ever get into the situation where we would want to calculate solutions for more than one task? 

Frank

Re: [SED-ML-discuss] Nested Proposal v2

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

Hi Frank,

Thank-you very much for this.

On 19/01/12 07:17, Frank T. Bergmann wrote:

> As many of you know early in 2010 I proposed a simple nested simulation
> experiment for SED-ML. Of course that was well before the SED-ML spec was
> released. Since then I listened to your feedback and made adjustments. With
> the start of the new year it is time to get the Nested Simulation Proposal
> for SED-ML ready for wide-spread adoption. I believe nested simulations are
> vital for SED-ML so that we can cover a much larger variety of simulation
> experiments.

I could not agree more. Repeated simulations are at the core of parameter 
estimations, dose-responses, bifurcation analyses, population simulations 
etc. The vast majority of "interesting" simulation experiments are using them.

> I've taken these past weeks to fully flesh out all the details and the
> document is now available from Nature Proceedings:
>
> http://precedings.nature.com/documents/4257/version/2

One of my biggest concern with the current structure of the proposal is 
that it disrupts the distinction simulation/model/task.

I think that what should probably be nested is the task. I don't think this 
would change your proposal much. We could still have uber-simulations 
called by tasks, such as parameter optimisation (with an associated method 
of sampling associated with a kisao term). More difficult would be to keep 
the model changes in the model definitions and calling them from the task.


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

Re: [SED-ML-discuss] Nested Proposal v2

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

On 19/01/12 20:17, Frank T. Bergmann wrote:
> Hello,
>
> As many of you know early in 2010 I proposed a simple nested simulation
> experiment for SED-ML. Of course that was well before the SED-ML spec was
> released. Since then I listened to your feedback and made adjustments. With
> the start of the new year it is time to get the Nested Simulation Proposal
> for SED-ML ready for wide-spread adoption. I believe nested simulations are
> vital for SED-ML so that we can cover a much larger variety of simulation
> experiments.

Hi Frank and others,

I think that if a proposal like this was included in SED-ML, it would 
fundamentally change what SED-ML is, and make SED-ML into something 
which has no distinct utility over and beyond a general purpose 
programming language.

I see the place of a SED-ML document as a *description* of a simulation 
experiment, rather than merely a procedure for replicating a simulation 
experiment.

 From a description of a simulation experiment, it is possible to 
replicate the experiment, but it is also possible to do other types of 
analysis - for example, inferring the intent of the simulation 
experiment and perhaps performing automated reasoning from the result.

The nested simulations approach is getting dangerously close to simply 
describing the procedure for performing simulation experiments, rather 
than describing a simulation experiment.

Someone wanting to code a procedure, without necessarily describing 
higher level semantic information about the procedure, would be better 
off using an existing general purpose imperative programming language - 
they don't need SED-ML for that. Languages like C and Python have a 
large number of existing implementations which have already been 
thoroughly tested, build on lessons learnt from previous languages to 
give a huge amount of cumulate language design legacy, and have more 
expressive power than the nested simulations proposal. If all SED-ML is 
going to be is a general purpose way to reproduce simulation 
experiments, there is no point reinventing the wheel and competing with 
existing imperative languages.

However, SED-ML is far more useful if it is targeted at describing 
simulation experiments. This means that it does need to incorporate 
facilities for a large number of different types of simulation 
experiments. This is a significant amount of work, but it is the 
meaningful approach consistent with the current SED-ML. It means we need 
to have very streamlined processes for adding new types of simulation 
experiments to the language, and to make the language more extensible.

Best wishes,
Andrew

>
> I've taken these past weeks to fully flesh out all the details and the
> document is now available from Nature Proceedings:
>
> http://precedings.nature.com/documents/4257/version/2
>
> Unlike the last version this time there is a full description of each
> element along with examples. If you only have a couple of seconds, have a
> look at my blog where you see the examples:
>
> http://frank-fbergmann.blogspot.com/2012/01/sed-ml-nested-simulation-proposa
> l-v2.html
>
> Or try the SED-ML Web Tools, that I updated to be able to simulate the
> nested experiment:
>
> http://sysbioapps.dyndns.org/SED-ML_Web_Tools/
>
> I look forward to your feedback!
>
>
> Best
> Frank
>
>
> ------------------------------------------------------------------------------
> Keep Your Developer Skills Current with LearnDevNow!
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> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

[SED-ML-discuss] Nested Proposal v2

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

Hello, 

As many of you know early in 2010 I proposed a simple nested simulation
experiment for SED-ML. Of course that was well before the SED-ML spec was
released. Since then I listened to your feedback and made adjustments. With
the start of the new year it is time to get the Nested Simulation Proposal
for SED-ML ready for wide-spread adoption. I believe nested simulations are
vital for SED-ML so that we can cover a much larger variety of simulation
experiments.  

I've taken these past weeks to fully flesh out all the details and the
document is now available from Nature Proceedings: 

http://precedings.nature.com/documents/4257/version/2

Unlike the last version this time there is a full description of each
element along with examples. If you only have a couple of seconds, have a
look at my blog where you see the examples: 

http://frank-fbergmann.blogspot.com/2012/01/sed-ml-nested-simulation-proposa
l-v2.html

Or try the SED-ML Web Tools, that I updated to be able to simulate the
nested experiment: 

http://sysbioapps.dyndns.org/SED-ML_Web_Tools/

I look forward to your feedback!


Best
Frank

[SED-ML-discuss] Registration for the 2012 CellML Workshop is now open

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

Hi all,

Registration for the 2012 CellML Workshop is now open. Please see
http://www.cellml.org/community/events/workshop/2012 for information
on how to register. Registration for the workshop is free and remote
attendance at the workshop will be possible.


Cheers,
David.

[SED-ML-discuss] Guidelines for SED-ML proposals

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

Dear colleagues,

the SED-ML editors have specified guidelines for feature requests and proposals to extend the current SED-ML format. We would like to encourage all of you to help us moving on with the development by submitting requests and proposals via the sourceforge trackers.

A feature request is considered a "wish" for a feature that should be covered by SED-ML in the future. Submitting a feature request does not require to develop a solution to it. So don't hesitate to share your vision with us! Feature requests can be made via the sourceforge tracker on http://sourceforge.net/tracker/?group_id=293618&atid=1240598

A proposal for an extension to SED-ML, on the contrary, comes with a detailed description of the extension, and a list of new elements. Both should be backed up by sample SED-ML files where the new elements should be placed as annotations for the time of extension development. Proposals can be submitted via the sourceforge tracker on http://sourceforge.net/tracker/?group_id=293618&atid=2532228
Proposals will be voted on by the community. Accepted proposals will be integrated with the SED-ML spec for the next release if the requirements are met (detailed description, prototype implementations and examples).


You will find a more detailed description of the submission procedure on our homepage on http://sed-ml.org<http://sed-ml.org/> ("Guidelines for feature requests and proposals").


Thanks for your contributions,
Dagmar (on behalf of the editors)

[SED-ML-discuss] [Combine-announce] Results of the COMBINE 2012 date survey

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

Dear potential COMBINE attendees,

We recently ran a survey to identify the best dates to hold COMBINE 2012.  Based on the votes received, the following is the winning combination:

   Wednesday August 15 (all day) to Sunday Aug. 19 (morning half-day), 2012

As the attached table shows, this combination of dates was voted both (a) good/best by the most people and (b) "impossible" by the fewest people.

We thank all of the people who took the time to fill out the date survey, and we hope to see everyone in Toronto, Canada, at COMBINE 2012 and ICSB 2012!

Best regards,
Mike, Gary, Nicolas

Re: [SED-ML-discuss] Namespaces in NewXML

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

Hi all,

I think Andrew's option 1 is actually the best approach.  The 
unfortunate consequence of the approach outlined by Richard below is 
that it will lead to different behaviour from the same SED-ML files in 
different implementations, depending on whether they handle XML 
namespaces properly or not.

Personally, it doesn't seem to me a big issue to require the correct 
namespace. A SED-ML file is already tightly tied to a particular 
XML-encoded model by virtue of using XPath to locate model variables, 
and this will need to use the correct namespace (if a SED-ML 
implementation is compliant with XML rules) so there's no added burden.

Best wishes,
Jonathan

On 27/11/2011 23:03, Richard Adams wrote:
> On 27 Nov 2011, at 18:48, Andrew Miller wrote:
>
> I like Andrew's  suggestion - that we point out the consequences of
> not using a namespace for children of NewXML, but we don't mandate it
> - namely that it won't play nicely with standard XML processing tools
> which will presume the subelements of new XML are in SED-ML namespace.
> But, by not mandating it, it's still possible to insert new XML with
> no namespace into different versions of a language, where that
> language uses different namespaces for different versions.
>
> Considering the addition-of-a-new-parameter example :
>    <newXML>
>         <parameter id="a" value="2.4"/>
>    </newXML>
> Although the 'parameter' element is intended to be SBML, 'parameter'
> elements also exist in SED-ML, so XPath expressions like //
> sed:parameter would match the 'SBML' parameter as well. This would
> mean that any XPath expressions used to navigate/query SED-ML would
> frequently  need a 'not(ancestor::newXML') filter, which would be
> annoying for implementers to have to remember.
>
> Unless we can come up with a perfect solution that satisfies both XML
> rigour and the flexibility to insert the new XML into different
> versions of the same language that have different namespaces, perhaps
> we should summarise both sides of the argument in the next revision?
>
>
> Cheers
> Richard
>
>
>
>> We could have some text to explain that this rule means that a
>> non-namespaced child of a non-namespaced NewXML element will be in the
> I think newXML is always in SED-ML namespace, so it would be immediate
> child elements which should state a namespace.
>
>
>> SED-ML namespace, and so will be wrong in most modelling languages
>> that
>> use namespaces - however, this statement would simply be explaining
>> the
>> natural consequence of a clear definition of how XML is inserted,
>> rather
>> than defining a new rule. In the future, we could look at separating
>> out
>> the formal normative rules into one document, and such explanations
>> into
>> another 'tutorial' document, but at present, the one specification
>> serves both purposes.
>>
>> Best wishes,
>> Andrew
>>
>>
>> ------------------------------------------------------------------------------
>> All the data continuously generated in your IT infrastructure
>> contains a definitive record of customers, application performance,
>> security threats, fraudulent activity, and more. Splunk takes this
>> data and makes sense of it. IT sense. And common sense.
>> http://p.sf.net/sfu/splunk-novd2d
>> _______________________________________________
>> 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
>
>
>
>
>
>

Re: [SED-ML-discuss] Standard error codes for SED-ML

[Lucian S. <lp...@sp...>]

* Andrew Miller <ak....@au...> [2011-11-27 19:04] writes:
> On 25/11/11 23:51, Richard Adams wrote:
> > Thanks Mike, that was really helpful.
> >
> > Even if all the stipulations in the specification could be encoded in
> > one schema or another, that doesn't necessarily translate into a good
> > experience for the end user - I suppose Schematron diagnostic messages
> > are user-readable, but XML schema error messages are not very end-user
> > friendly. The explicit listing of validation rules in SBML ( and
> > especially the textual description and references back to the spec  )
> > are incredibly useful when helping non-SBML fluent modellers who are
> > stuck with an error in their SBML,  and greatly facilitate its
> 
> Surely the most important thing is therefore that we simply number the 
> rules in our specification well, so that it is possible for validators 
> to refer to a particular section of the specification that is violated 
> by any particular piece of invalid SED-ML.
> 
> I support numbering the parts of the specification clearly and with 
> detailed granularity.
> 
> However, I think that explicitly tabulating a list of error codes is 
> something that is best done externally to SED-ML itself, so that there 
> can be multiple such lists tailored to particular groups of users or the 
> needs of specific tools. I don't think there would be anything wrong 
> with embedding such lists in software packages - the tool developer can 
> make the error messages make sense in the context of the particular tool 
> being developed; better yet, interface specifications like XPSEDAPI 
> could provide a programmatic interface for receiving error messages, 
> libraries could implement this, and end user tools could provide a 
> translation from the error messages on the programmatic interface to 
> some kind of presentation of the error to the end user.

Would it make sense to set things up so that the messages could be 
translated to other languages by particular implementations?  This would 
require teh 'personalized' bits to be saved separately from the main 
message, but it could be valuable...

-Lucian

Re: [SED-ML-discuss] Namespaces in NewXML

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

On 27 Nov 2011, at 18:48, Andrew Miller wrote:

I like Andrew's  suggestion - that we point out the consequences of  
not using a namespace for children of NewXML, but we don't mandate it  
- namely that it won't play nicely with standard XML processing tools  
which will presume the subelements of new XML are in SED-ML namespace.  
But, by not mandating it, it's still possible to insert new XML with  
no namespace into different versions of a language, where that  
language uses different namespaces for different versions.

Considering the addition-of-a-new-parameter example :
  <newXML>
       <parameter id="a" value="2.4"/>
  </newXML>
Although the 'parameter' element is intended to be SBML, 'parameter'  
elements also exist in SED-ML, so XPath expressions like // 
sed:parameter would match the 'SBML' parameter as well. This would  
mean that any XPath expressions used to navigate/query SED-ML would  
frequently  need a 'not(ancestor::newXML') filter, which would be  
annoying for implementers to have to remember.

Unless we can come up with a perfect solution that satisfies both XML  
rigour and the flexibility to insert the new XML into different  
versions of the same language that have different namespaces, perhaps  
we should summarise both sides of the argument in the next revision?


Cheers
Richard



>
> We could have some text to explain that this rule means that a

> non-namespaced child of a non-namespaced NewXML element will be in the

I think newXML is always in SED-ML namespace, so it would be immediate  
child elements which should state a namespace.


> SED-ML namespace, and so will be wrong in most modelling languages  
> that
> use namespaces - however, this statement would simply be explaining  
> the
> natural consequence of a clear definition of how XML is inserted,  
> rather
> than defining a new rule. In the future, we could look at separating  
> out
> the formal normative rules into one document, and such explanations  
> into
> another 'tutorial' document, but at present, the one specification
> serves both purposes.
>
> Best wishes,
> Andrew
>
>
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure
> contains a definitive record of customers, application performance,
> security threats, fraudulent activity, and more. Splunk takes this
> data and makes sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-novd2d
> _______________________________________________
> 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.

Re: [SED-ML-discuss] Standard error codes for SED-ML

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

On Mon, 28 Nov 2011 07:59:42 +1300, Andrew Miller wrote:
> Surely the most important thing is therefore that we simply number the 
> rules in our specification well, so that it is possible for validators 
> to refer to a particular section of the specification that is violated 
> by any particular piece of invalid SED-ML.

That's certainly an alternative.  In SBML, we pulled out the rules separately because we thought it make things more readable and manageable, but one could indeed integrate them into the main text instead.

Best regards,
MH

Re: [SED-ML-discuss] Standard error codes for SED-ML

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

On 25/11/11 23:51, Richard Adams wrote:
> Thanks Mike, that was really helpful.
>
> Even if all the stipulations in the specification could be encoded in
> one schema or another, that doesn't necessarily translate into a good
> experience for the end user - I suppose Schematron diagnostic messages
> are user-readable, but XML schema error messages are not very end-user
> friendly. The explicit listing of validation rules in SBML ( and
> especially the textual description and references back to the spec  )
> are incredibly useful when helping non-SBML fluent modellers who are
> stuck with an error in their SBML,  and greatly facilitate its

Surely the most important thing is therefore that we simply number the 
rules in our specification well, so that it is possible for validators 
to refer to a particular section of the specification that is violated 
by any particular piece of invalid SED-ML.

I support numbering the parts of the specification clearly and with 
detailed granularity.

However, I think that explicitly tabulating a list of error codes is 
something that is best done externally to SED-ML itself, so that there 
can be multiple such lists tailored to particular groups of users or the 
needs of specific tools. I don't think there would be anything wrong 
with embedding such lists in software packages - the tool developer can 
make the error messages make sense in the context of the particular tool 
being developed; better yet, interface specifications like XPSEDAPI 
could provide a programmatic interface for receiving error messages, 
libraries could implement this, and end user tools could provide a 
translation from the error messages on the programmatic interface to 
some kind of presentation of the error to the end user.

Best wishes,
Andrew

> resolution. So there does seem to be a place for these rules  outside
> of a software implementation, as you say. Ultimately we need to serve
> end user modellers who are at best ambivalent towards data standards,
> and to encourage their adoption we need to let them know as
> straightforwardly as possible when there is a problem, and, wherever
> possible,  how to fix it.  I'm not sure that burying them in a
> technical software specification is the right approach to this.
>
>
> Richard
>
>
> 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
>
>
>
>
>
>

Re: [SED-ML-discuss] Namespaces in NewXML

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

On 26/11/11 07:26, Frank T. Bergmann wrote:
>> Also, as it stands , the XML is in the SED-ML namespace, which is
> incorrect -
>> isn't the situation more akin to that of annotations, where any content is
> OK
>> so long as it's in its own namespace?
>>
> That is a restriction we make in the spec, not something that would be
> enforced by the schema as it stands.
I think the restriction you refer to is this one: "NewXML must hold a 
valid piece of XML which after insertion into the original model must 
lead to a valid model file, according to the model language 
specification (as given by the language attribute)".

To determine if a model complies with that rule, you need to take into 
account both the original model and the model language specification; I 
therefore don't think it is something the schema will ever be able to 
enforce (and especially not a generic SED-ML schema that shouldn't know 
anything about particular model language specifications).

> In any case I don't mind adding the namespaces there. But as I said I don't
> see it as providing any real benefit, it is not going to add more safety or
> make it *more likely* that the raw XML manipulation succeeds, in fact it
> makes it less likely in cases like the one described above.

I agree with the proposed change because I think the specification, as 
it reads now, is unclear:
"NewXML must hold a valid piece of XML which after insertion into the 
original model must lead to a valid model file, according to the model 
language specification".

It is unclear because it doesn't define what it means to 'hold a valid 
piece of XML'. For example, each of the following could be meaningful 
under a particular interpretation of that text:

1 - The 'valid piece of XML' refers to an XML Element Information Item 
(as defined here http://www.w3.org/TR/xml-infoset/), and should be 
inserted as an XML Element Information Item into the new document. As a 
consequence, the namespacing rules are applied in the SED-ML document, 
and elements are inserted with the corresponding namespace into the 
target document, even if the prefix used is not defined in the target 
document. This is the most natural approach to implement when using the 
DOM, and is the interpretation taken by the SProS and SRuS packages 
currently included with the CellML API.

<NewXML target="cellml:variable[@name=myvariable]">
<!-- cellml prefix is defined in SED-ML document, but not necessarily in 
target model document -->
<cellml:variable name='myvariable' initial_value='5' units='metre' 
public_interface='out' />
</NewXML>

2 - The SED-ML document is used as a container for raw XML, which is 
inserted into the target document as a string of text before it is 
parsed. XML is technically the serialisation format, so this could be 
the result that someone would come to if they tried to strictly construe 
the 'valid piece of XML' text without any other context or looking at 
the examples. Because it is inserted into an XML document as a string, 
any namespaces are in the context of the target document:
<NewXML target="cellml:variable[@name=myvariable]">
<![CDATA[
<variable name='myvariable' initial_value='5' units='metre' 
public_interface='out' />
]]>
</NewXML>

3 - Similar to 2, except a custom XML parser is used to extricate the 
contents of the NewXML element, and interpret them in the context of the 
target XML document. This is a custom XML rule and would mean that the 
SED-ML document might not comply with the Namespaces In XML 
specification, and it is difficult to implement using commodity XML 
parsers through the DOM API, so I would advise against taking this 
interpretation:
<NewXML target="cellml:variable[@name=myvariable]">
<!-- cellml prefix is defined in  target model document, but not 
necessarily in SED-ML document -->
<cellml:variable name='myvariable' initial_value='5' units='metre' 
public_interface='out' />
</NewXML>

I think we should rewrite the text to make it clear that we mean option 
1 above.

We could have some text to explain that this rule means that a 
non-namespaced child of a non-namespaced NewXML element will be in the 
SED-ML namespace, and so will be wrong in most modelling languages that 
use namespaces - however, this statement would simply be explaining the 
natural consequence of a clear definition of how XML is inserted, rather 
than defining a new rule. In the future, we could look at separating out 
the formal normative rules into one document, and such explanations into 
another 'tutorial' document, but at present, the one specification 
serves both purposes.

Best wishes,
Andrew

Re: [SED-ML-discuss] Standard error codes for SED-ML

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

On Fri, 25 Nov 2011 10:51:27 +0000, Richard Adams wrote:
> I'm not sure that burying them in a  
> technical software specification is the right approach to this.

I agree about that.  

If someone comes up with a general solution to this problem, I'd be interested in finding out more.  

Best regards,
MH

Re: [SED-ML-discuss] Namespaces in NewXML

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

> But that's just lucky, if the ' parameter' elements haven't changed
> between level 2 and level 3. Presumably the idea behind encoding levels
into
> the SBML namespace is to indicate infrequent but substantial changes
within
> the schema - so it's not a general solution that is guaranteed to work.
One
> solution might be to have 'list of namespaces'  element which would be the
> namespaces that the newxml is valid for, which by default would just be
the
> namespace of the model to which the change should be applied.
> 

Correct, this is pure luck :) ... This was precisely my point before, all
the changes that happen through raw XML manipulation is mostly luck if we
can make it work. There are no guarantees that you will get a valid document
at the end (just imagine the target xpath being just slightly different and
suddenly things would no longer work out). No lust of namespaces will work
:) What would work is to have more refined constructs, but those would
likely have to be more language specific. 

> Also, as it stands , the XML is in the SED-ML namespace, which is
incorrect -
> isn't the situation more akin to that of annotations, where any content is
OK
> so long as it's in its own namespace?
> 

That is a restriction we make in the spec, not something that would be
enforced by the schema as it stands. 

In any case I don't mind adding the namespaces there. But as I said I don't
see it as providing any real benefit, it is not going to add more safety or
make it *more likely* that the raw XML manipulation succeeds, in fact it
makes it less likely in cases like the one described above. 

Frank

> Cheers
> 
> Richard
> 
> 
> 
> 
> 
> >
> > So what happens if we now tag the XML with its own namespace?
> >
> > - it looks nicer and we are sure that the parameters really are not in
> > the SED-ML namespace (but we knew that, right?)
> >
> > However, when *blindly* applying this change now to an SBML L3 model,
> > this results in an invalid model.
> 
> 
> 
> >
> > I'm on the fence on this one. While it looks nicer it also ties the
> > change closer to a specific model. We don't gain any validation
> > capabilities at this point (as the schema says anything goes). So the
> > best you can hope for is for a tool to exit sooner and refusing the
> > modification of the source model.
> >
> > Frank
> >
> >> -----Original Message-----
> >> From: Nicolas Le Novère [mailto:le...@eb...]
> >> Sent: Friday, November 25, 2011 9:27 AM
> >> To: sed...@li...
> >> Subject: Re: [SED-ML-discuss] Namespaces in NewXML
> >>
> >> I think you are right.
> >>
> >> On 25/11/11 17:25, Richard Adams wrote:
> >>> Hello All,
> >>>   I'm doing some work with adding /changing model XML via the Change
> >>> elements - I think we really need to state somewhere   that the
> >>> added
> >>> XML should be in its own namespace. As it stands,  arbritary XML
> >>> contained in a NewXML element is included in  the SED-ML namespace.
> >>>
> >>> E.g., currently ( for an SBML model, for example )
> >>> 	<listOfChanges>
> >>> 				<addXML
> >> target="/sbml:sbml/sbml:model/sbml:listOfParameters">
> >>> 					<newXML>
> >>> 						<parameter
> >> metaid="metaid_0000010" id="newParam1" value="0.7" />
> >>> 						<parameter
> >> metaid="metaid_0000011" id="newParam2" value="0.7" />
> >>> 					</newXML>
> >>> 				</addXML>
> >>> 			</listOfChanges>
> >>>
> >>> is  currently valid, but I think  it should be:
> >>>
> >>> 	<listOfChanges>
> >>> 				<addXML
> >> target="/sbml:sbml/sbml:model/sbml:listOfParameters">
> >>> 					<newXML>
> >>> 						<parameter
> >> xmlns="http://www.sbml.org/sbml/level2"
> >>> metaid="metaid_0000010" id="newParam1" value="0.7" />
> >>> 						<parameter
> >> xmlns="http://www.sbml.org/sbml/level2"
> >>> metaid="metaid_0000011" id="newParam2" value="0.7" />
> >>> 					</newXML>
> >>> 				</addXML>
> >>> 			</listOfChanges>
> >>>
> >>> Or, declare in the toplevel of the sedML, for example.
> >>> <sedML xmlns:sbml="http://www.sbml.org/sbml/level2" ...> ...
> >>> <listOfChanges>
> >>> 				<addXML
> >> target="/sbml:sbml/sbml:model/sbml:listOfParameters">
> >>> 					<newXML>
> >>> 						<sbml:parameter
> >> metaid="metaid_0000010" id="newParam1"
> >>> value="0.7" />
> >>> 						<sbml:parameter
> >> metaid="metaid_0000011" id="newParam2"
> >>> value="0.7" />
> >>> 					</newXML>
> >>> 				</addXML>
> >>> 			</listOfChanges>
> >>>
> >>>
> >>> Cheers
> >>> Richard
> >>>
> >>>
> >>>
> >>> 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
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>
> >>
> >> --
> >> Nicolas LE NOVERE, Computational Systems Neurobiology, EMBL-EBI,
> >> WTGC,
> >> Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521 Fax:468,
> >> le...@eb..., Skype:n.lenovere, twitter:@lenovere
> >> http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/
> >>
> >> Fight against prostate cancer (and support my moustache):
> >> Donate at http://mobro.co/lenov
> >>
> >>
> >>
> >
----------------------------------------------------------------------------
> > --
> >> All the data continuously generated in your IT infrastructure
> >> contains a definitive record of customers, application performance,
> >> security threats, fraudulent activity, and more. Splunk takes this
> >> data and makes sense of it. IT sense. And common sense.
> >> http://p.sf.net/sfu/splunk-novd2d
> >> _______________________________________________
> >> SED-ML-discuss mailing list
> >> SED...@li...
> >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
> >
> >
> >
----------------------------------------------------------------------------
--
> > All the data continuously generated in your IT infrastructure
> > contains a definitive record of customers, application performance,
> > security threats, fraudulent activity, and more. Splunk takes this
> > data and makes sense of it. IT sense. And common sense.
> > http://p.sf.net/sfu/splunk-novd2d
> > _______________________________________________
> > 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.
> 
> 
>
----------------------------------------------------------------------------
--
> All the data continuously generated in your IT infrastructure
> contains a definitive record of customers, application performance,
> security threats, fraudulent activity, and more. Splunk takes this
> data and makes sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-novd2d
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

Re: [SED-ML-discuss] Namespaces in NewXML

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

On 25 Nov 2011, at 17:46, Frank T. Bergmann wrote:

> The changes of the model using raw XML transformation is always  
> dangerous.
>
> As far as implementation of the feature goes, it is not needed to  
> change the
> current description:
>
> - which says take whatever is below newXML and add it to the xml  
> node of the
> target
>
> For validation we even say anything goes below newXML.
>
> This is how I implemented it currently and it would work fine. You  
> can add
> parameters without namespace just fine to any SBML L2 or L3 model!

But that's just lucky, if the ' parameter' elements haven't changed   
between level 2 and level 3. Presumably the idea behind encoding  
levels into the SBML namespace is to indicate infrequent but  
substantial changes within the schema - so it's not a general solution  
that is guaranteed to work. One solution might be to have 'list of  
namespaces'  element which would be the namespaces that the newxml is  
valid for, which by default would just be the namespace of the
model to which the change should be applied.

Also, as it stands , the XML is in the SED-ML namespace, which is  
incorrect - isn't the situation more akin to that of annotations,  
where any content is OK so long as it's in its own namespace?

Cheers

Richard





>
> So what happens if we now tag the XML with its own namespace?
>
> - it looks nicer and we are sure that the parameters really are not  
> in the
> SED-ML namespace (but we knew that, right?)
>
> However, when *blindly* applying this change now to an SBML L3  
> model, this
> results in an invalid model.



>
> I'm on the fence on this one. While it looks nicer it also ties the  
> change
> closer to a specific model. We don't gain any validation  
> capabilities at
> this point (as the schema says anything goes). So the best you can  
> hope for
> is for a tool to exit sooner and refusing the modification of the  
> source
> model.
>
> Frank
>
>> -----Original Message-----
>> From: Nicolas Le Novère [mailto:le...@eb...]
>> Sent: Friday, November 25, 2011 9:27 AM
>> To: sed...@li...
>> Subject: Re: [SED-ML-discuss] Namespaces in NewXML
>>
>> I think you are right.
>>
>> On 25/11/11 17:25, Richard Adams wrote:
>>> Hello All,
>>>   I'm doing some work with adding /changing model XML via the Change
>>> elements - I think we really need to state somewhere   that the  
>>> added
>>> XML should be in its own namespace. As it stands,  arbritary XML
>>> contained in a NewXML element is included in  the SED-ML namespace.
>>>
>>> E.g., currently ( for an SBML model, for example )
>>> 	<listOfChanges>
>>> 				<addXML
>> target="/sbml:sbml/sbml:model/sbml:listOfParameters">
>>> 					<newXML>
>>> 						<parameter
>> metaid="metaid_0000010" id="newParam1" value="0.7" />
>>> 						<parameter
>> metaid="metaid_0000011" id="newParam2" value="0.7" />
>>> 					</newXML>
>>> 				</addXML>
>>> 			</listOfChanges>
>>>
>>> is  currently valid, but I think  it should be:
>>>
>>> 	<listOfChanges>
>>> 				<addXML
>> target="/sbml:sbml/sbml:model/sbml:listOfParameters">
>>> 					<newXML>
>>> 						<parameter
>> xmlns="http://www.sbml.org/sbml/level2"
>>> metaid="metaid_0000010" id="newParam1" value="0.7" />
>>> 						<parameter
>> xmlns="http://www.sbml.org/sbml/level2"
>>> metaid="metaid_0000011" id="newParam2" value="0.7" />
>>> 					</newXML>
>>> 				</addXML>
>>> 			</listOfChanges>
>>>
>>> Or, declare in the toplevel of the sedML, for example.
>>> <sedML xmlns:sbml="http://www.sbml.org/sbml/level2" ...> ...
>>> <listOfChanges>
>>> 				<addXML
>> target="/sbml:sbml/sbml:model/sbml:listOfParameters">
>>> 					<newXML>
>>> 						<sbml:parameter
>> metaid="metaid_0000010" id="newParam1"
>>> value="0.7" />
>>> 						<sbml:parameter
>> metaid="metaid_0000011" id="newParam2"
>>> value="0.7" />
>>> 					</newXML>
>>> 				</addXML>
>>> 			</listOfChanges>
>>>
>>>
>>> Cheers
>>> Richard
>>>
>>>
>>>
>>> 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
>>>
>>>
>>>
>>>
>>>
>>>
>>
>>
>> --
>> Nicolas LE NOVERE, Computational Systems Neurobiology, EMBL-EBI,
>> WTGC,
>> Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521 Fax:468,
>> le...@eb..., Skype:n.lenovere, twitter:@lenovere
>> http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/
>>
>> Fight against prostate cancer (and support my moustache):
>> Donate at http://mobro.co/lenov
>>
>>
>>
> ----------------------------------------------------------------------------
> --
>> All the data continuously generated in your IT infrastructure
>> contains a definitive record of customers, application performance,
>> security threats, fraudulent activity, and more. Splunk takes this
>> data and makes sense of it. IT sense. And common sense.
>> http://p.sf.net/sfu/splunk-novd2d
>> _______________________________________________
>> SED-ML-discuss mailing list
>> SED...@li...
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
>
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure
> contains a definitive record of customers, application performance,
> security threats, fraudulent activity, and more. Splunk takes this
> data and makes sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-novd2d
> _______________________________________________
> 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.

Re: [SED-ML-discuss] Namespaces in NewXML

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

The changes of the model using raw XML transformation is always dangerous. 

As far as implementation of the feature goes, it is not needed to change the
current description: 

- which says take whatever is below newXML and add it to the xml node of the
target

For validation we even say anything goes below newXML. 

This is how I implemented it currently and it would work fine. You can add
parameters without namespace just fine to any SBML L2 or L3 model!

So what happens if we now tag the XML with its own namespace? 

- it looks nicer and we are sure that the parameters really are not in the
SED-ML namespace (but we knew that, right?)

However, when *blindly* applying this change now to an SBML L3 model, this
results in an invalid model. 

I'm on the fence on this one. While it looks nicer it also ties the change
closer to a specific model. We don't gain any validation capabilities at
this point (as the schema says anything goes). So the best you can hope for
is for a tool to exit sooner and refusing the modification of the source
model. 

Frank

> -----Original Message-----
> From: Nicolas Le Novère [mailto:le...@eb...]
> Sent: Friday, November 25, 2011 9:27 AM
> To: sed...@li...
> Subject: Re: [SED-ML-discuss] Namespaces in NewXML
> 
> I think you are right.
> 
> On 25/11/11 17:25, Richard Adams wrote:
> > Hello All,
> >    I'm doing some work with adding /changing model XML via the Change
> > elements - I think we really need to state somewhere   that the added
> > XML should be in its own namespace. As it stands,  arbritary XML
> > contained in a NewXML element is included in  the SED-ML namespace.
> >
> > E.g., currently ( for an SBML model, for example )
> > 	<listOfChanges>
> > 				<addXML
> target="/sbml:sbml/sbml:model/sbml:listOfParameters">
> > 					<newXML>
> > 						<parameter
> metaid="metaid_0000010" id="newParam1" value="0.7" />
> > 						<parameter
> metaid="metaid_0000011" id="newParam2" value="0.7" />
> > 					</newXML>
> > 				</addXML>
> > 			</listOfChanges>
> >
> > is  currently valid, but I think  it should be:
> >
> > 	<listOfChanges>
> > 				<addXML
> target="/sbml:sbml/sbml:model/sbml:listOfParameters">
> > 					<newXML>
> > 						<parameter
> xmlns="http://www.sbml.org/sbml/level2"
> > metaid="metaid_0000010" id="newParam1" value="0.7" />
> > 						<parameter
> xmlns="http://www.sbml.org/sbml/level2"
> > metaid="metaid_0000011" id="newParam2" value="0.7" />
> > 					</newXML>
> > 				</addXML>
> > 			</listOfChanges>
> >
> > Or, declare in the toplevel of the sedML, for example.
> > <sedML xmlns:sbml="http://www.sbml.org/sbml/level2" ...> ...
> > <listOfChanges>
> > 				<addXML
> target="/sbml:sbml/sbml:model/sbml:listOfParameters">
> > 					<newXML>
> > 						<sbml:parameter
> metaid="metaid_0000010" id="newParam1"
> > value="0.7" />
> > 						<sbml:parameter
> metaid="metaid_0000011" id="newParam2"
> > value="0.7" />
> > 					</newXML>
> > 				</addXML>
> > 			</listOfChanges>
> >
> >
> > Cheers
> > Richard
> >
> >
> >
> > 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
> >
> >
> >
> >
> >
> >
> 
> 
> --
> Nicolas LE NOVERE, Computational Systems Neurobiology, EMBL-EBI,
> WTGC,
> Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521 Fax:468,
> le...@eb..., Skype:n.lenovere, twitter:@lenovere
> http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/
> 
> Fight against prostate cancer (and support my moustache):
> Donate at http://mobro.co/lenov
> 
> 
>
----------------------------------------------------------------------------
--
> All the data continuously generated in your IT infrastructure
> contains a definitive record of customers, application performance,
> security threats, fraudulent activity, and more. Splunk takes this
> data and makes sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-novd2d
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

Re: [SED-ML-discuss] Namespaces in NewXML

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

I think you are right.

On 25/11/11 17:25, Richard Adams wrote:
> Hello All,
>    I'm doing some work with adding /changing model XML via the Change
> elements - I think we really need to state somewhere   that the added
> XML should be in its own namespace. As it stands,  arbritary XML
> contained in a NewXML element is included in  the SED-ML namespace.
>
> E.g., currently ( for an SBML model, for example )
> 	<listOfChanges>
> 				<addXML target="/sbml:sbml/sbml:model/sbml:listOfParameters">
> 					<newXML>
> 						<parameter metaid="metaid_0000010" id="newParam1" value="0.7" />
> 						<parameter metaid="metaid_0000011" id="newParam2" value="0.7" />
> 					</newXML>
> 				</addXML>
> 			</listOfChanges>
>
> is  currently valid, but I think  it should be:
>
> 	<listOfChanges>
> 				<addXML target="/sbml:sbml/sbml:model/sbml:listOfParameters">
> 					<newXML>
> 						<parameter xmlns="http://www.sbml.org/sbml/level2"
> metaid="metaid_0000010" id="newParam1" value="0.7" />
> 						<parameter xmlns="http://www.sbml.org/sbml/level2"
> metaid="metaid_0000011" id="newParam2" value="0.7" />
> 					</newXML>
> 				</addXML>
> 			</listOfChanges>
>
> Or, declare in the toplevel of the sedML, for example.
> <sedML xmlns:sbml="http://www.sbml.org/sbml/level2" ...>
> ...
> <listOfChanges>
> 				<addXML target="/sbml:sbml/sbml:model/sbml:listOfParameters">
> 					<newXML>
> 						<sbml:parameter metaid="metaid_0000010" id="newParam1"
> value="0.7" />
> 						<sbml:parameter  metaid="metaid_0000011" id="newParam2"
> value="0.7" />
> 					</newXML>
> 				</addXML>
> 			</listOfChanges>
>
>
> Cheers
> Richard
>
>
>
> 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
>
>
>
>
>
>


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

Fight against prostate cancer (and support my moustache):
Donate at http://mobro.co/lenov

[SED-ML-discuss] Namespaces in NewXML

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

Hello All,
  I'm doing some work with adding /changing model XML via the Change  
elements - I think we really need to state somewhere   that the added  
XML should be in its own namespace. As it stands,  arbritary XML  
contained in a NewXML element is included in  the SED-ML namespace.

E.g., currently ( for an SBML model, for example )
	<listOfChanges>
				<addXML target="/sbml:sbml/sbml:model/sbml:listOfParameters">
					<newXML>
						<parameter metaid="metaid_0000010" id="newParam1" value="0.7" />
						<parameter metaid="metaid_0000011" id="newParam2" value="0.7" />
					</newXML>
				</addXML>
			</listOfChanges>

is  currently valid, but I think  it should be:

	<listOfChanges>
				<addXML target="/sbml:sbml/sbml:model/sbml:listOfParameters">
					<newXML>
						<parameter xmlns="http://www.sbml.org/sbml/level2"  
metaid="metaid_0000010" id="newParam1" value="0.7" />
						<parameter xmlns="http://www.sbml.org/sbml/level2"  
metaid="metaid_0000011" id="newParam2" value="0.7" />
					</newXML>
				</addXML>
			</listOfChanges>

Or, declare in the toplevel of the sedML, for example.
<sedML xmlns:sbml="http://www.sbml.org/sbml/level2" ... >
...
<listOfChanges>
				<addXML target="/sbml:sbml/sbml:model/sbml:listOfParameters">
					<newXML>
						<sbml:parameter metaid="metaid_0000010" id="newParam1"  
value="0.7" />
						<sbml:parameter  metaid="metaid_0000011" id="newParam2"  
value="0.7" />
					</newXML>
				</addXML>
			</listOfChanges>


Cheers
Richard



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.

Re: [SED-ML-discuss] Standard error codes for SED-ML

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

Thanks Mike, that was really helpful.

Even if all the stipulations in the specification could be encoded in  
one schema or another, that doesn't necessarily translate into a good  
experience for the end user - I suppose Schematron diagnostic messages  
are user-readable, but XML schema error messages are not very end-user  
friendly. The explicit listing of validation rules in SBML ( and  
especially the textual description and references back to the spec  )  
are incredibly useful when helping non-SBML fluent modellers who are  
stuck with an error in their SBML,  and greatly facilitate its  
resolution. So there does seem to be a place for these rules  outside  
of a software implementation, as you say. Ultimately we need to serve  
end user modellers who are at best ambivalent towards data standards,  
and to encourage their adoption we need to let them know as  
straightforwardly as possible when there is a problem, and, wherever  
possible,  how to fix it.  I'm not sure that burying them in a  
technical software specification is the right approach to this.


Richard


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.

[SED-ML-discuss] SED-ML to HTML stylesheet

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

Dear All,

  Just to say that I've created a basic SED-ML->HTML stylesheet, in  
case it's of any interest to people who still use XSLT. Details and  
features are documented  in the stylesheet itself.

  It's  available here :
   http://jlibsedml.svn.sourceforge.net/viewvc/jlibsedml/trunk/sedml2html.xsl?revision=345&view=markup

  and is used at http://www.sbsi.ed.ac.uk/html/sedml/index.html to  
produce views of SED-ML files.

  Any comments /suggestions / complaints gratefully received,

Best wishes
  Richard





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.

[SED-ML-discuss] [Combine-announce] Survey regarding COMBINE 2012

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

Dear Colleagues,

The third COMBINE forum, COMBINE2012, is planned to be a satellite of the 
13th ICSB that will take place in Toronton on August 19-23.

In order to choose the best possible dates, we would like to have your 
opinion. Please help us by filling the very short survey at:

http://www.surveymonkey.com/s/combine-2012-date-survey

The COMBINE coordinators
Gary Bader
Michael Hucka
Nicolas Le Novère

_______________________________________________
Combine-announce mailing list
Com...@eb...
http://listserver.ebi.ac.uk/mailman/listinfo/combine-announce

Re: [SED-ML-discuss] Question about model IDs

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

Dear Richard,

I agree that we should move this discussion at the COMBINE level. It is 
clear that such an archive need to include all the model descriptions and 
representations, simulation descriptions, but also required datasets 
necessary. It is not a project that necessarily belong to a particular 
language. Would-you like to initiate the discussion there?

As soon as we have a semblance of agreement at least about the idea, we'll 
create a page on the website, with links to the discussions and documents.

Best regards

On 19/11/11 22:36, Richard Adams wrote:
> Hello All,
> Some of us have been contributing to a document over the last few weesk
> describing some potential use-cases for 'SED-ML archives' or perhaps
> "Combine-Archives" would now be a more appropriate term, based on the
> discussion started in this thread.
>
> This link gives edit access to the document,
> https://docs.google.com/document/d/1fz04BbPvoGJ6OeXv4_JZRMO3QAYoJkZFqxc58snWBeg/edit
>
> A possible concensus so far might be that source URIs shouldn't include
> links to SCM repositories, and and that the actual structure of an archive
> should be as loosely specified as possible, with documents referring to
> each other using relative URIs.
>
> Nicolas, would now be a good time to move this to Combine Discuss list? As
> you say an archive format need not include SED-ML at all - it could be, for
> example an SBML file, diagram and experimental data to produce a heat-map,
> with no simulation involved at all ( We could extend the potential
> use-cases to include non-simulation based examples ).
>
> Cheers
> Richard
>
> On 7 Oct 2011, at 09:53, Richard Adams wrote:
>
>> Clearly we need to establish a set of use cases for SED-ML consumers,
>> since there are at least 3 usage scenarios.
>>
>> 1) Model consumers, who wish to run simulations straight off with as
>> little manual intervention as possible ( I suppose this is the core
>> scenario that SED-ML addresses )
>> 2) Model developers, for whom version tracking is important (e.g.,
>> David's post )
>> 3) Archivists and curators, who will perhaps be generating the SED-ML for
>> users in 1)
>>
>> Herbert was asking about SED-ML use cases, we don't really have this
>> information on the SED-ML website but probably should do so, it would
>> help clarify its purpose to newcomers.
>>
>> David, is there any reason why SED-ML files can't use SVN or mercurial
>> URLs to access the resources? In this case an archive file isn't really
>> needed - just exchange a SED-ML file, which could itself be under version
>> control within a project.
>>
>> Best wishes,
>>
>> Richard
>>
>>
>>
>>
>> On 6 Oct 2011, at 22:28, David Nickerson wrote:
>>
>>> The idea of an archive file works well when you have a single
>>> transferable set of data that gets shipped from user to user with no
>>> need to track or merge changes from different users (i.e., one
>>> developer many users). DOCX archives work because Word provides very
>>> sophisticated edit tracking and merging functionality - is this
>>> functionality something that SED-ML tools want to develop and support?
>>>
>>> An alternative, that we have been using successfully in the Physiome
>>> Model Repository, is the idea of using mercurial repositories as a
>>> "workspace" in which you contain all data related to a piece of work.
>>> This piece of work could be anything from a complete model with
>>> simulation descriptions and outputs, experimental data used to fit the
>>> model, etc. to a single sub-component of a generic model constituent
>>> designed as part of a component library. While we use mercurial, any
>>> versioning system could be used instead. The advantage of this
>>> approach is that the user is able to embed repositories within
>>> repositories (subrepos in mercurial, submodules in git, externals in
>>> svn) and manage the versioning of embedded repositories such that the
>>> user can choose whether to track latest changes or fix on a specific
>>> version that is know to be "correct".
>>>
>>> We find that this allows modellers to easily[1] ship their work
>>> between each other while maintaining a decent provenance record of the
>>> developments. While it is not always going to be optimal to include
>>> all types of data in a single type of repository, mercurial at least
>>> (and probably the other systems), allows embedding different types of
>>> repository within a repository. We're starting now to think about how
>>> this would work when you start wanting to include datasets that are
>>> huge (e.g., large image collections used to fit patient specific
>>> cardiac models, or the simulation results of several million cell
>>> models in a stomach). But at least in terms of the work currently
>>> being done with CellML models, mercurial repositories are proving
>>> sufficient.
>>>
>>> When a user simply wants to grab a particular piece of work from the
>>> repository for their own use, the website (and soon webservices)
>>> provide a way to download a static archive containing the contents of
>>> the workspace. Again, we're still trying to work out what to do in the
>>> case where an workspace links to datasets that can easily be multiple
>>> gigabytes in size. And we are certainly open to any help on this
>>> issue.
>>>
>>> Cheers,
>>> David.
>>>
>>> [1] There is currently a lack of tool support for this, so users
>>> pretty much have to manage their mercurial workspaces using mercurial
>>> directly. This is not always ideal and is also something we are
>>> thinking about and working on to some degree for certain applications.
>>>
>>> On Fri, Oct 7, 2011 at 9:41 AM, Richard Adams <ric...@ed...
>>> <mailto:ric...@ed...>> wrote:
>>>>
>>>> For those unfamiliar with the concept of the SEDX archive format: It's a
>>>> zipped archive of a SED-ML file and >=1 model file. Would an equally simple
>>>> solution be acceptable to incorporate other data files as well?
>>>> For example, a zip with subfolders
>>>> models/
>>>> simulations/
>>>> data/
>>>> diagrams/
>>>> results/
>>>> Each resource could refer to other resources via relative URIs. E.g.,
>>>> in the
>>>> scenario above, a SedML file would refer to ../models/model.xml. Of course,
>>>> within an archive, external public resources can still be referred to if
>>>> need be - for example, if a dataset is very large.
>>>> In this approach all the folders are 'source' folders (i.e., inputs to
>>>> computational tasks) except for results/, which could be used to
>>>> contain the
>>>> results of an experiment if need be.
>>>> In SBSI we have the concept of a 'project' for modelling resources, with a
>>>> defined folder structure largely similar to that proposed above, to enable
>>>> tooling to reliably link and detect resource files, and allow export of
>>>> zipped archives for exchange between collaborators. I'm not especially
>>>> advocating its exact usage but just to say it's worked well for us.
>>>> Best wishes
>>>> Richard
>>>> On 6 Oct 2011, at 17:05, Nicolas Le Novère wrote:
>>>>
>>>> It seems to me that the need of an archive is pervasive in all the M&S
>>>> efforts. We want the models and the simulation descriptions together, but
>>>> also the simulation results or the data-sets used to complement or fit the
>>>> models, and of course the SBGN-ML files.
>>>>
>>>> And we are going in the same direction in DDMoRe, where the need is clearer
>>>> since the mathematics only represent part of the "model".
>>>>
>>>> After all the it is just like ODF or DOCX.
>>>>
>>>> I therefore propose to move that discussion to combine-discuss.
>>>>
>>>> On 06/10/11 16:43, Herbert Sauro wrote:
>>>>
>>>> Thank you Richard, that is exactly what I wanted to know, will read
>>>> appendix
>>>> D. The zip file idea has been floated around for a while (since 2004 I
>>>> think by Cliff Shaffer in particular) but in the past there was never
>>>> anything to zip with the sbml model until the advent of sedml.
>>>>
>>>> Herbert
>>>>
>>>> Sent from my iPad, hence excuse my typos.
>>>>
>>>> ------------------------------------------------------------------------------
>>>>
>>>> All the data continuously generated in your IT infrastructure contains a
>>>>
>>>> definitive record of customers, application performance, security
>>>>
>>>> threats, fraudulent activity and more. Splunk takes this data and makes
>>>>
>>>> sense of it. Business sense. IT sense. Common sense.
>>>>
>>>> http://p.sf.net/sfu/splunk-d2dcopy1
>>>>
>>>> _______________________________________________
>>>>
>>>> SED-ML-discuss mailing list
>>>>
>>>> SED...@li...
>>>> <mailto:SED...@li...>
>>>>
>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>>>
>>>>
>>>> --
>>>> 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/
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> All the data continuously generated in your IT infrastructure contains a
>>>> definitive record of customers, application performance, security
>>>> threats, fraudulent activity and more. Splunk takes this data and makes
>>>> sense of it. Business sense. IT sense. Common sense.
>>>> http://p.sf.net/sfu/splunk-d2dcopy1
>>>> _______________________________________________
>>>> SED-ML-discuss mailing list
>>>> SED...@li...
>>>> <mailto: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... <mailto: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.
>>>>
>>>> ------------------------------------------------------------------------------
>>>> All the data continuously generated in your IT infrastructure contains a
>>>> definitive record of customers, application performance, security
>>>> threats, fraudulent activity and more. Splunk takes this data and makes
>>>> sense of it. Business sense. IT sense. Common sense.
>>>> http://p.sf.net/sfu/splunk-d2dcopy1
>>>> _______________________________________________
>>>> SED-ML-discuss mailing list
>>>> SED...@li...
>>>> <mailto:SED...@li...>
>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>>>
>>>>
>>>
>>> ------------------------------------------------------------------------------
>>> All the data continuously generated in your IT infrastructure contains a
>>> definitive record of customers, application performance, security
>>> threats, fraudulent activity and more. Splunk takes this data and makes
>>> sense of it. Business sense. IT sense. Common sense.
>>> http://p.sf.net/sfu/splunk-d2dcopy1
>>> _______________________________________________
>>> SED-ML-discuss mailing list
>>> SED...@li...
>>> <mailto: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... <mailto: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.
>> ------------------------------------------------------------------------------
>> All of the data generated in your IT infrastructure is seriously valuable.
>> Why? It contains a definitive record of application performance, security
>> threats, fraudulent activity, and more. Splunk takes this data and makes
>> sense of it. IT sense. And common sense.
>> http://p.sf.net/sfu/splunk-d2dcopy2_______________________________________________
>> 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... <mailto: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.
>
>
>
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure
> contains a definitive record of customers, application performance,
> security threats, fraudulent activity, and more. Splunk takes this
> data and makes sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-novd2d
>
>
>
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss


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

Fight against prostate cancer (and support my moustache):
Donate at http://mobro.co/lenov

Re: [SED-ML-discuss] Question about model IDs

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

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

[SED-ML-discuss] [Combine-announce] HARMONY 2012

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

Dear Colleagues,

We have the pleasure to announce that the 2nd joint COMBINE hackathons,
HARMONY 2012, will take place in Maastricht on May 21 to 25 2012. More
information will be posted on the following page as we go along.

http://co.mbine.org/events/HARMONY_2012

Looking forward to see you all there,

Nicolas LE NOVERE
On the behalf of the COMBINE coordinators and HARMONY 2012 organizers
_______________________________________________
Combine-announce mailing list
Com...@eb...
http://listserver.ebi.ac.uk/mailman/listinfo/combine-announce