sed-ml-discuss

[Miase-discuss] listOfModels query

[Richard A. <ra...@st...>]

Hi,
  Just a query about the listOfModels element - is it assumed to be   
the case that, for a given sedml document, it will describe a single  
'reference' model version, which will be the first model in the list,  
and subsequent entries in the list will refer to that base model,  
applying changes (as is the case with the example 'oscillation to  
chaos' model)? Or, is it possible that a given sedml document could  
refer to >1 reference model?
  I'm asking from the point of view of how a self-contained .miase  
archive file might look. (By self contained, I mean that the  
application using it will be able to access all the information needed  
to run a simulation without having to query repositories -  with the  
help of a supporting library. ) In the first case above,  it would  
only ever contain a single model file, in the second case, it could  
contain multiple models.
Also, do we want to allow archives which contain all model variants as  
complete models, or are we going to stick with a 'reference' version  
of the model, and generate new, altered versions of the model by  
applying Xpath changes on the fly at runtime? I assume the latter, but  
I can't find anything in the current examples, or in the CMSB2008.pdf  
to distinguish between these possibilities.

  From the point of view of supporting library methods, I was thinking  
something along the lines of:

  MiaseArchive archive = libSedml.readArchive(String filepathToMiaseArchive);

  // A MiaseArchive enables access to a sedml document, and model file(s?)
  SedmlDocument document = archive.getSedMlDocument();
  // access Sedml DOM via
  document.getSedMlModel();

  //access model file ( or is it possible to have > 1 model file here??)
  // if the latter, need method to iterate over multiple model files.
   String referenceModelContents = archive.getModelAsString();

   //now, get XPath change from SedML model and apply it
   ListOfChanges changes =  
sedMl.getListOfModels.getModelById(modelID).getListOfChanges();
   String alteredModelContents =  
document.applyChanges(referenceModelContents,changes);

   // now use your model specific library to parse the altered model  
and run simulation.

  If we can clarify this I can put some examples into svn. I can send  
a class diagram if that would be more explanatory.

        Cheers
            Richard

-- 
Dr Richard Adams
Senior Software Developer,
Computational Systems Biology Group,
University of Edinburgh
Tel: 0131 650 8285
email : ric...@ed...

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

Re: [Miase-discuss] listOfModels query

[Frank B. <fbergman@u.washington.edu>]

Hello ... 

> Hi,
>   Just a query about the listOfModels element - is it assumed to be
> the case that, for a given sedml document, it will describe a single
> 'reference' model version, which will be the first model in the list,
> and subsequent entries in the list will refer to that base model,
> applying changes (as is the case with the example 'oscillation to
> chaos' model)? Or, is it possible that a given sedml document could
> refer to >1 reference model?

Definitely ... you can (and should be able to) refer to more than one model.


>   I'm asking from the point of view of how a self-contained .miase
> archive file might look. (By self contained, I mean that the
> application using it will be able to access all the information needed
> to run a simulation without having to query repositories -  with the
> help of a supporting library. ) In the first case above,  it would
> only ever contain a single model file, in the second case, it could
> contain multiple models.

In my implementation, the self-contained .miase file, still has the option
of referring to external sources. Thus There could be 0 or more models
contained in the archive. 

> Also, do we want to allow archives which contain all model variants as
> complete models, or are we going to stick with a 'reference' version
> of the model, and generate new, altered versions of the model by
> applying Xpath changes on the fly at runtime? I assume the latter, but
> I can't find anything in the current examples, or in the CMSB2008.pdf
> to distinguish between these possibilities.
> 

I hoped to keep the .miase file as simple as possible. It really just
provides the option of storing (locally) referenced files conveniently.
Apart from that there should not be more logic needed to interpret a .miase
file, as compared to the original experiment description. For that reason
I'd opt of making the changes on the fly, they won't be expensive to do.
While writing out you can opt to refer to the altered models if you so
desire, however with that you loose the information, that the second model
is actually the first model with a handful of changes ... 

>   From the point of view of supporting library methods, I was thinking
> something along the lines of:
> 
>   MiaseArchive archive = libSedml.readArchive(String
> filepathToMiaseArchive);
> 
>   // A MiaseArchive enables access to a sedml document, and model
> file(s?)
>   SedmlDocument document = archive.getSedMlDocument();
>   // access Sedml DOM via
>   document.getSedMlModel();
> 
>   //access model file ( or is it possible to have > 1 model file
> here??)

YES it is ... :) ... 

>   // if the latter, need method to iterate over multiple model files.
>    String referenceModelContents = archive.getModelAsString();
> 
>    //now, get XPath change from SedML model and apply it
>    ListOfChanges changes =
> sedMl.getListOfModels.getModelById(modelID).getListOfChanges();
>    String alteredModelContents =
> document.applyChanges(referenceModelContents,changes);
> 

Instead of 

	document.applyChanges(referenceModelContents,changes);

I'd prefer to just grab the changed model. That's what I did in my
implementation, for a user there is hardly a difference on the two model
types. Thy have the option of getting the model source from both, and in
that case the changed model, applies the changes automatically. 

Best
Frank

Re: [Miase-discuss] listOfModels query

[Dagmar K. <da...@eb...>]

Just to say that I agree with everything Frank wrote (hopefully I 
understood right what he meant ;-)).

Dagmar



Frank Bergmann wrote:
> Hello ... 
>
>   
>> Hi,
>>   Just a query about the listOfModels element - is it assumed to be
>> the case that, for a given sedml document, it will describe a single
>> 'reference' model version, which will be the first model in the list,
>> and subsequent entries in the list will refer to that base model,
>> applying changes (as is the case with the example 'oscillation to
>> chaos' model)? Or, is it possible that a given sedml document could
>> refer to >1 reference model?
>>     
>
> Definitely ... you can (and should be able to) refer to more than one model.
>
>
>   
>>   I'm asking from the point of view of how a self-contained .miase
>> archive file might look. (By self contained, I mean that the
>> application using it will be able to access all the information needed
>> to run a simulation without having to query repositories -  with the
>> help of a supporting library. ) In the first case above,  it would
>> only ever contain a single model file, in the second case, it could
>> contain multiple models.
>>     
>
> In my implementation, the self-contained .miase file, still has the option
> of referring to external sources. Thus There could be 0 or more models
> contained in the archive. 
>
>   
>> Also, do we want to allow archives which contain all model variants as
>> complete models, or are we going to stick with a 'reference' version
>> of the model, and generate new, altered versions of the model by
>> applying Xpath changes on the fly at runtime? I assume the latter, but
>> I can't find anything in the current examples, or in the CMSB2008.pdf
>> to distinguish between these possibilities.
>>
>>     
>
> I hoped to keep the .miase file as simple as possible. It really just
> provides the option of storing (locally) referenced files conveniently.
> Apart from that there should not be more logic needed to interpret a .miase
> file, as compared to the original experiment description. For that reason
> I'd opt of making the changes on the fly, they won't be expensive to do.
> While writing out you can opt to refer to the altered models if you so
> desire, however with that you loose the information, that the second model
> is actually the first model with a handful of changes ... 
>
>   
>>   From the point of view of supporting library methods, I was thinking
>> something along the lines of:
>>
>>   MiaseArchive archive = libSedml.readArchive(String
>> filepathToMiaseArchive);
>>
>>   // A MiaseArchive enables access to a sedml document, and model
>> file(s?)
>>   SedmlDocument document = archive.getSedMlDocument();
>>   // access Sedml DOM via
>>   document.getSedMlModel();
>>
>>   //access model file ( or is it possible to have > 1 model file
>> here??)
>>     
>
> YES it is ... :) ... 
>
>   
>>   // if the latter, need method to iterate over multiple model files.
>>    String referenceModelContents = archive.getModelAsString();
>>
>>    //now, get XPath change from SedML model and apply it
>>    ListOfChanges changes =
>> sedMl.getListOfModels.getModelById(modelID).getListOfChanges();
>>    String alteredModelContents =
>> document.applyChanges(referenceModelContents,changes);
>>
>>     
>
> Instead of 
>
> 	document.applyChanges(referenceModelContents,changes);
>
> I'd prefer to just grab the changed model. That's what I did in my
> implementation, for a user there is hardly a difference on the two model
> types. Thy have the option of getting the model source from both, and in
> that case the changed model, applies the changes automatically. 
>
> Best
> Frank
>
>
> ------------------------------------------------------------------------------
> Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are
> powering Web 2.0 with engaging, cross-platform capabilities. Quickly and
> easily build your RIAs with Flex Builder, the Eclipse(TM)based development
> software that enables intelligent coding and step-through debugging.
> Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com
> _______________________________________________
> Miase-discuss mailing list
> Mia...@li...
> https://lists.sourceforge.net/lists/listinfo/miase-discuss
>   

Re: [Miase-discuss] listOfModels query

[Richard A. <ra...@st...>]

Oh great,
  That all sounds fine then.
  I'll try to look at your example next week Dagmar.

  Frank, so you mean something like:

   String   sedMLDoc.getModel(String modelId);

    which would hide all the need for getting XPath terms, and return  
a String of the model? That would be more direct, for sure.

  Richard

> Just to say that I agree with everything Frank wrote (hopefully I
> understood right what he meant ;-)).
>
> Dagmar
>
>
>
> Frank Bergmann wrote:
>> Hello ...
>>
>>
>>> Hi,
>>>   Just a query about the listOfModels element - is it assumed to be
>>> the case that, for a given sedml document, it will describe a single
>>> 'reference' model version, which will be the first model in the list,
>>> and subsequent entries in the list will refer to that base model,
>>> applying changes (as is the case with the example 'oscillation to
>>> chaos' model)? Or, is it possible that a given sedml document could
>>> refer to >1 reference model?
>>>
>>
>> Definitely ... you can (and should be able to) refer to more than one model.
>>
>>
>>
>>>   I'm asking from the point of view of how a self-contained .miase
>>> archive file might look. (By self contained, I mean that the
>>> application using it will be able to access all the information needed
>>> to run a simulation without having to query repositories -  with the
>>> help of a supporting library. ) In the first case above,  it would
>>> only ever contain a single model file, in the second case, it could
>>> contain multiple models.
>>>
>>
>> In my implementation, the self-contained .miase file, still has the option
>> of referring to external sources. Thus There could be 0 or more models
>> contained in the archive.
>>
>>
>>> Also, do we want to allow archives which contain all model variants as
>>> complete models, or are we going to stick with a 'reference' version
>>> of the model, and generate new, altered versions of the model by
>>> applying Xpath changes on the fly at runtime? I assume the latter, but
>>> I can't find anything in the current examples, or in the CMSB2008.pdf
>>> to distinguish between these possibilities.
>>>
>>>
>>
>> I hoped to keep the .miase file as simple as possible. It really just
>> provides the option of storing (locally) referenced files conveniently.
>> Apart from that there should not be more logic needed to interpret a .miase
>> file, as compared to the original experiment description. For that reason
>> I'd opt of making the changes on the fly, they won't be expensive to do.
>> While writing out you can opt to refer to the altered models if you so
>> desire, however with that you loose the information, that the second model
>> is actually the first model with a handful of changes ...
>>
>>
>>>   From the point of view of supporting library methods, I was thinking
>>> something along the lines of:
>>>
>>>   MiaseArchive archive = libSedml.readArchive(String
>>> filepathToMiaseArchive);
>>>
>>>   // A MiaseArchive enables access to a sedml document, and model
>>> file(s?)
>>>   SedmlDocument document = archive.getSedMlDocument();
>>>   // access Sedml DOM via
>>>   document.getSedMlModel();
>>>
>>>   //access model file ( or is it possible to have > 1 model file
>>> here??)
>>>
>>
>> YES it is ... :) ...
>>
>>
>>>   // if the latter, need method to iterate over multiple model files.
>>>    String referenceModelContents = archive.getModelAsString();
>>>
>>>    //now, get XPath change from SedML model and apply it
>>>    ListOfChanges changes =
>>> sedMl.getListOfModels.getModelById(modelID).getListOfChanges();
>>>    String alteredModelContents =
>>> document.applyChanges(referenceModelContents,changes);
>>>
>>>
>>
>> Instead of
>>
>> 	document.applyChanges(referenceModelContents,changes);
>>
>> I'd prefer to just grab the changed model. That's what I did in my
>> implementation, for a user there is hardly a difference on the two model
>> types. Thy have the option of getting the model source from both, and in
>> that case the changed model, applies the changes automatically.
>>
>> Best
>> Frank
>>
>>
>> ------------------------------------------------------------------------------
>> Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are
>> powering Web 2.0 with engaging, cross-platform capabilities. Quickly and
>> easily build your RIAs with Flex Builder, the Eclipse(TM)based development
>> software that enables intelligent coding and step-through debugging.
>> Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com
>> _______________________________________________
>> Miase-discuss mailing list
>> Mia...@li...
>> https://lists.sourceforge.net/lists/listinfo/miase-discuss
>>
>
>
> ------------------------------------------------------------------------------
> Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are
> powering Web 2.0 with engaging, cross-platform capabilities. Quickly and
> easily build your RIAs with Flex Builder, the Eclipse(TM)based development
> software that enables intelligent coding and step-through debugging.
> Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com
> _______________________________________________
> Miase-discuss mailing list
> Mia...@li...
> https://lists.sourceforge.net/lists/listinfo/miase-discuss
>
>



-- 
Dr Richard Adams
Senior Software Developer,
Computational Systems Biology Group,
University of Edinburgh
Tel: 0131 650 8285
email : ric...@ed...

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

Re: [Miase-discuss] listOfModels query

[Frank B. <fbergman@u.washington.edu>]

> 
>   Frank, so you mean something like:
> 
>    String   sedMLDoc.getModel(String modelId);
> 

	Almost, while constructing models, you'd still want to deal with
properties of changed model. Something like: 

	changedModel = new Model(sourceModelReference);
	changedModel.AddChange(new ChangeAttribute(sbmlId, newValue));

	but then you'd have: 

	changedModel.ToSBML() / changedModel.ToCellML() /
changedModel.ToModelString()

	which return you the actual model string. 

>     which would hide all the need for getting XPath terms, and return
> a String of the model? That would be more direct, for sure.

	If I'm consuming a Miase description, I'd definitely not be
interested in the nitty-gritty of applying the Xpath queries, that's what
the library should do. 


Cheers
Frank

> 
>   Richard
> 
> > Just to say that I agree with everything Frank wrote (hopefully I
> > understood right what he meant ;-)).
> >
> > Dagmar
> >
> >
> >
> > Frank Bergmann wrote:
> >> Hello ...
> >>
> >>
> >>> Hi,
> >>>   Just a query about the listOfModels element - is it assumed to be
> >>> the case that, for a given sedml document, it will describe a
> single
> >>> 'reference' model version, which will be the first model in the
> list,
> >>> and subsequent entries in the list will refer to that base model,
> >>> applying changes (as is the case with the example 'oscillation to
> >>> chaos' model)? Or, is it possible that a given sedml document could
> >>> refer to >1 reference model?
> >>>
> >>
> >> Definitely ... you can (and should be able to) refer to more than
> one model.
> >>
> >>
> >>
> >>>   I'm asking from the point of view of how a self-contained .miase
> >>> archive file might look. (By self contained, I mean that the
> >>> application using it will be able to access all the information
> needed
> >>> to run a simulation without having to query repositories -  with
> the
> >>> help of a supporting library. ) In the first case above,  it would
> >>> only ever contain a single model file, in the second case, it could
> >>> contain multiple models.
> >>>
> >>
> >> In my implementation, the self-contained .miase file, still has the
> option
> >> of referring to external sources. Thus There could be 0 or more
> models
> >> contained in the archive.
> >>
> >>
> >>> Also, do we want to allow archives which contain all model variants
> as
> >>> complete models, or are we going to stick with a 'reference'
> version
> >>> of the model, and generate new, altered versions of the model by
> >>> applying Xpath changes on the fly at runtime? I assume the latter,
> but
> >>> I can't find anything in the current examples, or in the
> CMSB2008.pdf
> >>> to distinguish between these possibilities.
> >>>
> >>>
> >>
> >> I hoped to keep the .miase file as simple as possible. It really
> just
> >> provides the option of storing (locally) referenced files
> conveniently.
> >> Apart from that there should not be more logic needed to interpret a
> .miase
> >> file, as compared to the original experiment description. For that
> reason
> >> I'd opt of making the changes on the fly, they won't be expensive to
> do.
> >> While writing out you can opt to refer to the altered models if you
> so
> >> desire, however with that you loose the information, that the second
> model
> >> is actually the first model with a handful of changes ...
> >>
> >>
> >>>   From the point of view of supporting library methods, I was
> thinking
> >>> something along the lines of:
> >>>
> >>>   MiaseArchive archive = libSedml.readArchive(String
> >>> filepathToMiaseArchive);
> >>>
> >>>   // A MiaseArchive enables access to a sedml document, and model
> >>> file(s?)
> >>>   SedmlDocument document = archive.getSedMlDocument();
> >>>   // access Sedml DOM via
> >>>   document.getSedMlModel();
> >>>
> >>>   //access model file ( or is it possible to have > 1 model file
> >>> here??)
> >>>
> >>
> >> YES it is ... :) ...
> >>
> >>
> >>>   // if the latter, need method to iterate over multiple model
> files.
> >>>    String referenceModelContents = archive.getModelAsString();
> >>>
> >>>    //now, get XPath change from SedML model and apply it
> >>>    ListOfChanges changes =
> >>> sedMl.getListOfModels.getModelById(modelID).getListOfChanges();
> >>>    String alteredModelContents =
> >>> document.applyChanges(referenceModelContents,changes);
> >>>
> >>>
> >>
> >> Instead of
> >>
> >> 	document.applyChanges(referenceModelContents,changes);
> >>
> >> I'd prefer to just grab the changed model. That's what I did in my
> >> implementation, for a user there is hardly a difference on the two
> model
> >> types. Thy have the option of getting the model source from both,
> and in
> >> that case the changed model, applies the changes automatically.
> >>
> >> Best
> >> Frank
> >>
> >>
> >> --------------------------------------------------------------------
> ----------
> >> Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM)
> are
> >> powering Web 2.0 with engaging, cross-platform capabilities. Quickly
> and
> >> easily build your RIAs with Flex Builder, the Eclipse(TM)based
> development
> >> software that enables intelligent coding and step-through debugging.
> >> Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com
> >> _______________________________________________
> >> Miase-discuss mailing list
> >> Mia...@li...
> >> https://lists.sourceforge.net/lists/listinfo/miase-discuss
> >>
> >
> >
> > ---------------------------------------------------------------------
> ---------
> > Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM)
> are
> > powering Web 2.0 with engaging, cross-platform capabilities. Quickly
> and
> > easily build your RIAs with Flex Builder, the Eclipse(TM)based
> development
> > software that enables intelligent coding and step-through debugging.
> > Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com
> > _______________________________________________
> > Miase-discuss mailing list
> > Mia...@li...
> > https://lists.sourceforge.net/lists/listinfo/miase-discuss
> >
> >
> 
> 
> 
> --
> Dr Richard Adams
> Senior Software Developer,
> Computational Systems Biology Group,
> University of Edinburgh
> Tel: 0131 650 8285
> email : ric...@ed...
> 
> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
> 
> 
> 
> -----------------------------------------------------------------------
> -------
> Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are
> powering Web 2.0 with engaging, cross-platform capabilities. Quickly
> and
> easily build your RIAs with Flex Builder, the Eclipse(TM)based
> development
> software that enables intelligent coding and step-through debugging.
> Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com
> _______________________________________________
> Miase-discuss mailing list
> Mia...@li...
> https://lists.sourceforge.net/lists/listinfo/miase-discuss