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

Re: [Miase-discuss] new namespace

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

> Frank, good catch. The dataGenerator time is still not right though.  
> You write:
>
> ...

>
> But the XPath "time" does not mean anything, even with the math  
> pointing to
> the SBML special variable time. The problem is that 1) "time" is not  
> the
> string representing the simulation time and 2) there are no links  
> between
> the math and the variable. I am still unsure if this is a problem of
> SED-ML, SBML, XPath etc. In CellML, the time is a regular variable,  
> so it
> is easier. For SBML, would the following be better?

	All true. In fact in my prototype i treat xpath (or target as it has  
now been renamed to) 'time' as keyword, until this is resolved. I take  
it to mean that it is the time as produced by a given task. I do think  
that some reserved symbols would do fine ...

>
>
> <dataGenerator id="time"
>                name="Time">
>   <listOfVariables>
>     <variable id="time"
>               taskReference="task1"
>               XPath="http://www.sbml.org/sbml/symbols/time" />
>   </listOfVariables>
>   <listOfParameters />
>   <math xmlns="http://www.w3.org/1998/Math/MathML">
>     <ci>time</ci>
>   </math>
> </dataGenerator>
>
>

again this XPath query would not refer to anything, in fact it would  
be just another way of saying "time".

As to your question whether this is a problem of SBML, CellML, XPath  
or our description format, i think we should make this problem our  
own. After all theoretically, each task could reference a model in a  
different language. Or even worse what happens later on when we have  
steady-state  experiments?what would 'time' mean then? It is up to us  
to define what should happen and how to represent it.

On my end this problem is again a bit superficial, if a task can be  
executed, then at the time of execution the meaning of 'time' is  
clear. The only question is how to capture it :)

Frank

> -- 
> Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome- 
> Trust
> Genome Campus, Hinxton CB101SD UK, Mob:+447833147074, Tel: 
> +441223494521
> Fax:468, Skype:n.lenovere, AIM:nlenovere, MSN:nle...@ho...
> http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/
>
>
>
> ------------------------------------------------------------------------------
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Re: [Miase-discuss] sed-ml library?

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

> 
> Now, MIRIAM imposes that a model's annotation carry "The time and date
> of
> creation, and the date and time of last modification" (rule 4, box 4 of
> the
> paper). In SBML we have elements to encode that. One possibility would
> be
> to implement tests in SED-ML. The model processing could only be
> performed
> if the source model passed the tests. Those tests could be anything.
> But
> the timestamps could be subjected to one. "if date is less than X, then
> proceed, otherwise stop and send a message".
> 
> Which brings me to another point: Should-we need a message throwing
> system,
> or is-it a tool problem?

I guess the question is what you would like to have happen. When you try and
run a description file, would you feel happy about such messages? Would you
know what to do? Personally I like to circumvent the whole issue, and I'll
keep the model with the description. Then I can guarantee, that the model
that was run by the simulator is the one references by the description file.


We should first resolve more pressing matters such as: 

- where does the 'time' come from
- which transformations are allowed in DataGenerator-mathML
- how do we reference measurement data, and in what format should it be so
that it is accessible for use in datagenerators
- other minor issues:
	- other tasks but uniformTimeCourse

Cheers
Frank

> 
> --
> Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome-Trust
> Genome Campus, Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521
> Fax:468, Skype:n.lenovere, AIM:nlenovere, MSN:nle...@ho...
> http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/
> 
> 
> 
> -----------------------------------------------------------------------
> -------
> This SF.net email is sponsored by:
> SourcForge Community
> SourceForge wants to tell your story.
> http://p.sf.net/sfu/sf-spreadtheword
> _______________________________________________
> Miase-discuss mailing list
> Mia...@li...
> https://lists.sourceforge.net/lists/listinfo/miase-discuss

Re: [Miase-discuss] new namespace

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

Frank Bergmann wrote:
> By the way the example on the *official* site still has problems: 
> 
> - the mathml elements in the datagenerators won't work like that
> - referring to "time" is problematic, you should refer to the time of one of
> the tasks ... otherwise it's not clear which one to take (even though in
> this case they are identical)
> - (optionally we really could go with XPath 1.0)
> 
> All those changes have been made to the attached miaseFile. 

Frank, good catch. The dataGenerator time is still not right though. You write:

<dataGenerator id="time" name="Time">
   <listOfVariables>
     <variable id="time" taskReference="task1" XPath="time" />
   </listOfVariables>
   <listOfParameters />
   <math xmlns="http://www.w3.org/1998/Math/MathML">
   <!-- THERE IS TROUBLE HERE, refering to the time symbol this way is bad 
for a lot of reasons. -->
     <csymbol encoding="text" 
definitionURL="http://www.sbml.org/sbml/symbols/time">time</csymbol>
   </math>
</dataGenerator>

But the XPath "time" does not mean anything, even with the math pointing to 
the SBML special variable time. The problem is that 1) "time" is not the 
string representing the simulation time and 2) there are no links between 
the math and the variable. I am still unsure if this is a problem of 
SED-ML, SBML, XPath etc. In CellML, the time is a regular variable, so it 
is easier. For SBML, would the following be better?

<dataGenerator id="time"
                name="Time">
   <listOfVariables>
     <variable id="time"
               taskReference="task1"
               XPath="http://www.sbml.org/sbml/symbols/time" />
   </listOfVariables>
   <listOfParameters />
   <math xmlns="http://www.w3.org/1998/Math/MathML">
     <ci>time</ci>
   </math>
</dataGenerator>


-- 
Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome-Trust
Genome Campus, Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521
Fax:468, Skype:n.lenovere, AIM:nlenovere, MSN:nle...@ho...
http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/

Re: [Miase-discuss] sed-ml library?

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

Frank Bergmann wrote:

>> The fact that we are not allowing SBML models to be embedded in the
>> SED-ML files does not change a thing. The actual problem with referring
>> to external sources which might address different versions of (even
>> curated) models remains. Imho we cannot get around having either a
>> "version" attribute in the <model> element or making sure the model
>> resources we allow for reference have unambigious URIs for each version
>> of the models ;-)
> 
> I honestly think this is making live much more difficult. If I read a
> description file which tells me the models is at: 
> 
> http://modelrepository.net/interestingModel.xml
> 
> I know exactly what to do and how to get it. Even if your give me a
> biomodels urn. That is all well. Now if you start and say, "oh but take
> version X" ... then I cannot automatically resolve it anymore. I don't know
> how to go to the source repository and request a different version. And I
> don't see how you can unambiguously describe how models and versions are to
> be kept on all repositories. But again, this is a non-issue. At the time of
> writing, the software tool knows exactly which model was run, so the tool
> can make sure the description is correct. 

That would be solved if a unique identifier scheme was adopted. In 2006, I 
succeeded to have almost everyone around a table to talk about model 
repository interoperability. And the first thing we agreed upon was to 
develop a single identifier scheme and set-up a resolver. It did not happen 
because I so hopelessly disorganised. But everyone agree in principle.

Now, MIRIAM imposes that a model's annotation carry "The time and date of 
creation, and the date and time of last modification" (rule 4, box 4 of the 
paper). In SBML we have elements to encode that. One possibility would be 
to implement tests in SED-ML. The model processing could only be performed 
if the source model passed the tests. Those tests could be anything. But 
the timestamps could be subjected to one. "if date is less than X, then 
proceed, otherwise stop and send a message".

Which brings me to another point: Should-we need a message throwing system, 
or is-it a tool problem?

-- 
Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome-Trust
Genome Campus, Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521
Fax:468, Skype:n.lenovere, AIM:nlenovere, MSN:nle...@ho...
http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/

Re: [Miase-discuss] new namespace

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

By the way the example on the *official* site still has problems: 

- the mathml elements in the datagenerators won't work like that
- referring to "time" is problematic, you should refer to the time of one of
the tasks ... otherwise it's not clear which one to take (even though in
this case they are identical)
- (optionally we really could go with XPath 1.0)

All those changes have been made to the attached miaseFile. 

Cheers
Frank

> -----Original Message-----
> From: Dagmar Köhn [mailto:da...@eb...]
> Sent: Friday, January 23, 2009 6:18 AM
> To: mia...@li...
> Subject: [Miase-discuss] new namespace
> 
> Hej all,
> 
> please note that the new and official namespace for the sed-ml schema
> is
> www.biomodels.net/sed-ml
> 
> The XSD Schema on sourceforge is already updated.
> 
> Best,
> Dagmar
> 
> -----------------------------------------------------------------------
> -------
> This SF.net email is sponsored by:
> SourcForge Community
> SourceForge wants to tell your story.
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> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/miase-discuss

Re: [Miase-discuss] sed-ml library?

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

Hello again :) 

> 
> In my opinion it should not and so far it does not have one ... But
> people might have a different opinion? Does anyone see a need to have
> an
> id for the curves?

As described in my previous mail we might not have right now, but that does
not mean we should preclude people from doing it. 

> 
> Hmm, I would keep the ids where they are as there are (up to now) quite
> a few elements without id... unless another identifiableSedBase class
> would make life far easier for you!?
> 

Definitely, I can't see any harm done with having an id (maybe even a name)
in the base class. 

> 
> The fact that we are not allowing SBML models to be embedded in the
> SED-ML files does not change a thing. The actual problem with referring
> to external sources which might address different versions of (even
> curated) models remains. Imho we cannot get around having either a
> "version" attribute in the <model> element or making sure the model
> resources we allow for reference have unambigious URIs for each version
> of the models ;-)

I honestly think this is making live much more difficult. If I read a
description file which tells me the models is at: 

http://modelrepository.net/interestingModel.xml

I know exactly what to do and how to get it. Even if your give me a
biomodels urn. That is all well. Now if you start and say, "oh but take
version X" ... then I cannot automatically resolve it anymore. I don't know
how to go to the source repository and request a different version. And I
don't see how you can unambiguously describe how models and versions are to
be kept on all repositories. But again, this is a non-issue. At the time of
writing, the software tool knows exactly which model was run, so the tool
can make sure the description is correct. 



Frank

Re: [Miase-discuss] sed-ml library?

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

Hello All, 

> >
> > Well, what for example about the <curve> element which might have an
> > annotation "The following curve shows the osciallation of bla bla
> bla",
> > but does not have an id!?
> 
>   Do you mean that a curve should have an ID or shouldn't? If an id is
> going to be problematic to fit into an inheritsnce hierarcy, then
> probably it should juet be included where needed, but if there is an
> argument for all elements having an ID then it would make sense to
> have id in a common base class, like in sbml.
> 
>   One solution would be to add another base class with an 'id'
> attribute which extends SedBase ,so you have
> 
>                           SedBase
>                         /         \
>        IdentifiableSedBase         \
>           /             \            \
>        Simulation,   Output           Curve
> 
> 

IMHO: I'd have id in the base class. There might be lots of reasons why one
would like to uniquely identify *all* elements in the description. We don't
have to have it mandatory but we should not altogether prohibit it. What
about in half a year we  see the need to access curve elements, to change
one of the attributes. 


>   I'll try and expland. I was thinking of a case of a non-curated
> model. For a ccurated model it is in a sense fixed, can be referred
> to, changes can be relative to it because it, or at least that version
> of the model is immutable. MAybe I don't understand the model creation
> process very well, but if you have different sedml files with embedded
> sbml files, each referring to a  different version of a particular
> model, then it is confusing to the user to have lots of slightly
> different model files in their system. But maybe htis isn't actually a
> problem, as it is up to a tool developer to provide support to the
> user, and I suppose from a library developlment point of view, so long
> as the combined sedml/sbml file is internally consistent, then that's
> the important thing.
> 

I still think, in order to keep the miase documents consistent, we should
not depend on users to manually sync models and description. That should be
a tool issue. However, I'm a bit worried by what you mean with 'immutable'.
Right now there is nothing that says that a model has to be immutable. A
model comes from a 'source' attribute, and after that a set of changes is
applied to it. For the software it should not be relevant where the model is
coming from. The only difference of having a remote file reference is
greater latency times, and possibly timeouts while accessing the file, other
than that it will and SHOULD behave exactly as if it came from a local
directory. 


> 
> 
> Just one more issue, how big do you think these files are likely to
> get, realistically, over the next few years? I'm thinking that as most
> models are relatively small then the sed-ml files will be easily held
> in memory for the forseeable future?
> 

Again, I'm against embedding the model (and later measurement data) directly
into the description file. Which then of course limits the file size
drastically. But even model + description data should fit into memory
easily. I'm not so sure if it comes to measurement data, but of course that
has not been decided upon. 

> Cheers
> 
> Richard
> 
> 
> 
> --
> Dr Richard Adams
> Senior Software Developer,
> Computational Systems Biology Group,
> University of Edinburgh
> Tel: 0131 650 8281/8285
> email : ric...@ed...
> 
> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
> 
> 
> 
> -----------------------------------------------------------------------
> -------
> This SF.net email is sponsored by:
> SourcForge Community
> SourceForge wants to tell your story.
> http://p.sf.net/sfu/sf-spreadtheword
> _______________________________________________
> Miase-discuss mailing list
> Mia...@li...
> https://lists.sourceforge.net/lists/listinfo/miase-discuss

Re: [Miase-discuss] sed-ml library?

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

Richard Adams wrote:
>>>       2. Most if not all top-level elements have an 'id' attribute,
>>> would it make sense to put the 'id' field in SEDBase?
>>>
>>>       
>> Well, what for example about the <curve> element which might have an
>> annotation "The following curve shows the osciallation of bla bla bla",
>> but does not have an id!?
>>     
>
>   Do you mean that a curve should have an ID or shouldn't? 

In my opinion it should not and so far it does not have one ... But 
people might have a different opinion? Does anyone see a need to have an 
id for the curves?

> If an id is  
> going to be problematic to fit into an inheritsnce hierarcy, then  
> probably it should juet be included where needed, but if there is an  
> argument for all elements having an ID then it would make sense to  
> have id in a common base class, like in sbml.
>
>   One solution would be to add another base class with an 'id'  
> attribute which extends SedBase ,so you have
>
>                           SedBase
>                         /         \
>        IdentifiableSedBase         \
>           /             \            \
>        Simulation,   Output           Curve
>
>
>   Or, if a complex inheritance hierarchy is preferred to be avoided,  
> then an 'Annotation' class  could be defined which is composed into  
> the top level elements, and a base class just has an ID.
>   

Hmm, I would keep the ids where they are as there are (up to now) quite 
a few elements without id... unless another identifiableSedBase class 
would make life far easier for you!?

>>>          3) Could a model file be optionally  embedded in a sedml file?
>>>
>>>       
>> For the moment, no. And  I would really like to avoid that. But if
>> people want to do that they could wrap some additional XML element
>> around a model and a sed-ml file... :-)
>>
>>     
>>>    This gets round the need to keep sedml independent of sbml, also a
>>> single file gets round the file coordination issue,  but it raises new
>>> problems of keeping in synch possibly multiple copies of a model. But
>>> for non-curated models that must be an issue anyway?
>>>
>>>       
>   I'll try and expland. I was thinking of a case of a non-curated  
> model. For a ccurated model it is in a sense fixed, can be referred  
> to, changes can be relative to it because it, or at least that version  
> of the model is immutable. MAybe I don't understand the model creation  
> process very well, but if you have different sedml files with embedded  
> sbml files, each referring to a  different version of a particular  
> model, then it is confusing to the user to have lots of slightly  
> different model files in their system. 

The fact that we are not allowing SBML models to be embedded in the 
SED-ML files does not change a thing. The actual problem with referring 
to external sources which might address different versions of (even 
curated) models remains. Imho we cannot get around having either a 
"version" attribute in the <model> element or making sure the model 
resources we allow for reference have unambigious URIs for each version 
of the models ;-)

(Of course, users can always use their personal/internal model base, but 
for those who use official ones, it should be guaranteed that 
everybody's really talking about the same model.)

> Re Frank's comments about a C/C++ library and ported versions being  
> the ideal, I can't disagree with that based on the success of libsbml,  
> but  I do think there is room for a native Java implementation as well  
> -   the Java bioinformatics community is quite large and just looking  
> at the sbml interopperability forum there are a lot of questions about  
> linking in the Java bindings. Just being able to drop a jar into your  
> classpath would be quite handy for a lot of Java apps especially as  
> often incorporating libsbml causes portability problems for what were  
> previously  completley Xplatform apps.
>   

Agree.

> Just one more issue, how big do you think these files are likely to  
> get, realistically, over the next few years? I'm thinking that as most  
> models are relatively small then the sed-ml files will be easily held  
> in memory for the forseeable future?
>   

Can't imagine size will be a problem... but there are other things 
around today that have not been foreseen a couple of years ago ;-)

Cheers,
Dagmar

[Miase-discuss] sed-ml library?

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

>
> ------------------------------
>
> Message: 6
> Date: Fri, 23 Jan 2009 17:35:11 +0100
> From: Dagmar K?hn <da...@eb...>
> Subject: Re: [Miase-discuss] sed-ml library?
> To: mia...@li...
> Message-ID: <497...@eb...>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hej,
> regarding some of the issues:
>
>>    A Schema issues:
>>    --------------
>>       1.  According to the spec SEDBase is a superclass of all the main
>> classes, yest in the schema only SedML class inherits from it. This
>> means that notes and annotation cannot be added to other elements,
>> e.g., uniform time course, dataset, datagenerator etc.,
>>
>
> In the XML Schema it is missing indeed. I will add them, probably the
> easiest way is by adding the <xs:extension base="SEDBase"> tag to (all)
> complex type definitions.
>
>>       2. Most if not all top-level elements have an 'id' attribute,
>> would it make sense to put the 'id' field in SEDBase?
>>
>
> Well, what for example about the <curve> element which might have an
> annotation "The following curve shows the osciallation of bla bla bla",
> but does not have an id!?

  Do you mean that a curve should have an ID or shouldn't? If an id is  
going to be problematic to fit into an inheritsnce hierarcy, then  
probably it should juet be included where needed, but if there is an  
argument for all elements having an ID then it would make sense to  
have id in a common base class, like in sbml.

  One solution would be to add another base class with an 'id'  
attribute which extends SedBase ,so you have

                          SedBase
                        /         \
       IdentifiableSedBase         \
          /             \            \
       Simulation,   Output           Curve


  Or, if a complex inheritance hierarchy is preferred to be avoided,  
then an 'Annotation' class  could be defined which is composed into  
the top level elements, and a base class just has an ID.

>
>>    B)    Coordination with model
>>    ----------
>>      PRevious posts have raised this issue, is there any progress on
>> this? There is a lot of validation that can be done just with the
>> sedml file, but if we want to check that a parameter or variable name
>> exists, or the xpath is correct,
>>    then we need access to the model. It seems to me that there are
>> different scenarios:
>>

>
>>
>>          2) A model is not yet in the public domain, but for example
>> the client wants to share  simulation info with a collaborator. In
>> this case probably the model and  the sedml file would have to sent
>> together in a zip file to preserve
>>    relative file paths, but this leaves quite an onus on the user or
>> tool to keep the two files coordinated.
>>
>
> Hmm. This is indeed not really satisfying. Probably something to  think
> about.
>
>>          3) Could a model file be optionally  embedded in a sedml file?
>>
>
> For the moment, no. And  I would really like to avoid that. But if
> people want to do that they could wrap some additional XML element
> around a model and a sed-ml file... :-)
>
>>    This gets round the need to keep sedml independent of sbml, also a
>> single file gets round the file coordination issue,  but it raises new
>> problems of keeping in synch possibly multiple copies of a model. But
>> for non-curated models that must be an issue anyway?
>>
  I'll try and expland. I was thinking of a case of a non-curated  
model. For a ccurated model it is in a sense fixed, can be referred  
to, changes can be relative to it because it, or at least that version  
of the model is immutable. MAybe I don't understand the model creation  
process very well, but if you have different sedml files with embedded  
sbml files, each referring to a  different version of a particular  
model, then it is confusing to the user to have lots of slightly  
different model files in their system. But maybe htis isn't actually a  
problem, as it is up to a tool developer to provide support to the  
user, and I suppose from a library developlment point of view, so long  
as the combined sedml/sbml file is internally consistent, then that's  
the important thing.


>> C Validation requirements
>> --------------------------
>>
>>    VAlidation against the schema offers one level of validation, but
>> there are many more assertions to validate, here are
>> some below, would be good to have a list of these somewhere to
>> construct a test-suite.
>> Validation tasks below with an asterisk are ones needing access to   
>> the model:
>>
>
> As you said in an earlier email, I think the syntax checker is
> sufficient for the moment and the following validation criteria might be
> for the future!? However, this list could go to the feature request on SF.

OK I'll transfer it across. Some basic checkers( eg for uniform time  
course st and end time checking) are implemented just now, but need to  
work out how get the line numbers back post parsing.


Re Frank's comments about a C/C++ library and ported versions being  
the ideal, I can't disagree with that based on the success of libsbml,  
but  I do think there is room for a native Java implementation as well  
-   the Java bioinformatics community is quite large and just looking  
at the sbml interopperability forum there are a lot of questions about  
linking in the Java bindings. Just being able to drop a jar into your  
classpath would be quite handy for a lot of Java apps especially as  
often incorporating libsbml causes portability problems for what were  
previously  completley Xplatform apps.

I think what I'll try to do next is set up some more automated testing  
system so that as new example sedml afiles are added to svn they can  
be validated easily. Also need to think about design of aPI, code  
generation is great for getting started but the api is rather ungainly  
at present.


Just one more issue, how big do you think these files are likely to  
get, realistically, over the next few years? I'm thinking that as most  
models are relatively small then the sed-ml files will be easily held  
in memory for the forseeable future?

Cheers

Richard



-- 
Dr Richard Adams
Senior Software Developer,
Computational Systems Biology Group,
University of Edinburgh
Tel: 0131 650 8281/8285
email : ric...@ed...

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

Re: [Miase-discuss] sed-ml library?

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

On Jan 23, 2009, at 12:48 AM, Nicolas Le Novere wrote:

> Frank Bergmann wrote:
>
>>>        3) Could a model file be optionally  embedded in a sedml  
>>> file?
>>>  This gets round the need to keep sedml independent of sbml, also a
>>> single file gets round the file coordination issue,  but it raises  
>>> new
>>> problems of keeping in synch possibly multiple copies of a model.  
>>> But
>>> for non-curated models that must be an issue anyway?
>>>
>>
>> personally I don't like this option too much. If an embedding  
>> solution
>> is wanted, I prefer it to work the other way around, have MIASE  
>> embedded
>> in i.e. SBML. That is the solution  that was favored by some people  
>> in
>> the discussions as well.
>
> Yes, but that would preclude the use of SED-ML for using two  
> different external models. At the moment, we only use two models for  
> comparing them. But nothing precludes the post-processing of the  
> simulation results of one model using variables coming for another  
> model. Same thing for the changeMath definition. We will be able to  
> modify a model prior to a task by using values coming from another  
> model.
>

right ... but before we start embedding the model in the experiment  
description, let us keep them separate then. We still have option 1  
and 2, which is good enough for interoperability.

Frank

Re: [Miase-discuss] sed-ml library?

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

Hej,
regarding some of the issues:

>    A Schema issues:
>    --------------
>       1.  According to the spec SEDBase is a superclass of all the main
> classes, yest in the schema only SedML class inherits from it. This
> means that notes and annotation cannot be added to other elements,
> e.g., uniform time course, dataset, datagenerator etc.,
>   

In the XML Schema it is missing indeed. I will add them, probably the 
easiest way is by adding the <xs:extension base="SEDBase"> tag to (all) 
complex type definitions.

>       2. Most if not all top-level elements have an 'id' attribute,
> would it make sense to put the 'id' field in SEDBase?
>   

Well, what for example about the <curve> element which might have an 
annotation "The following curve shows the osciallation of bla bla bla", 
but does not have an id!?

>       3. If more than one simulation can be in the listOfSimulations,
> then I think
>         UniformTimeCourse needs a 'max=unbounded' attribute in its declaration,
>         else ListOfSimulations only contains a single element.
>   

It is in the schema (in the declaration of the listOfSimulations) - so I 
supposed that is what you fixed already!?

>    B)    Coordination with model
>    ----------
>      PRevious posts have raised this issue, is there any progress on
> this? There is a lot of validation that can be done just with the
> sedml file, but if we want to check that a parameter or variable name
> exists, or the xpath is correct,
>    then we need access to the model. It seems to me that there are
> different scenarios:
>
>         1) A model is referenced to a validated public repository e.g.,
> BioModels
>            In this case the library can download the model. This seems
> the  easiest solution, as revisions of Biomodels are versioned (btw,
> would a version attribute  for the model element be useful?) and so a
> tool can make decisions on whether the model is correct or not.
>   

Version attribute is under discussion. Probably even easier would be 
different URIs for different model versions!? Although we could of 
course not force that... so, maybe an optional version attribute then.

>
>          2) A model is not yet in the public domain, but for example
> the client wants to share  simulation info with a collaborator. In
> this case probably the model and  the sedml file would have to sent
> together in a zip file to preserve
>    relative file paths, but this leaves quite an onus on the user or
> tool to keep the two files coordinated.
>   

Hmm. This is indeed not really satisfying. Probably something to  think 
about.

>          3) Could a model file be optionally  embedded in a sedml file?
>   

For the moment, no. And  I would really like to avoid that. But if 
people want to do that they could wrap some additional XML element 
around a model and a sed-ml file... :-)

>    This gets round the need to keep sedml independent of sbml, also a
> single file gets round the file coordination issue,  but it raises new
> problems of keeping in synch possibly multiple copies of a model. But
> for non-curated models that must be an issue anyway?
>   

Not sure I understand what you argument for here - could you elaborate 
on that again, please?
> C Validation requirements
> --------------------------
>
>    VAlidation against the schema offers one level of validation, but  
> there are many more assertions to validate, here are
> some below, would be good to have a list of these somewhere to
> construct a test-suite.
> Validation tasks below with an asterisk are ones needing access to the model:
>   

As you said in an earlier email, I think the syntax checker is 
sufficient for the moment and the following validation criteria might be 
for the future!? However, this list could go to the feature request on SF.

Dagmar

>
>    List of simulations (schema needs to be altered to hold 'max=unbounded'?)
>      Unique simulation ids
> 1) Uniform time course -
>      outputstart time < output end time
>      outputst time >= initial time
>      algorithm = valid Kisao id
>
> 2) List of Models
>        how to check existence of model? *
>        source = accessible url ( e.g., BioModelsDB)* or reference to
> previously defined model
>        No duplicate model IDs
>        List of changes -> Check parameter name exists *
>
> 3) List of tasks
>
>         One task must be baseline?
>
>         model reference must refer to defined model id
>         simulation reference must refer to defined simulation id
>         No duplicate task IDs
>
> 4) list of data generators
>       unique ids
>       variable ID exists in model, target path exists in model
>       task ref refers to valid task reference
>
> 5) List of outputs
>         Plot ID is unique
>         x and y data references refer to defined dataGenerator ID
>         If listOfOuputs present, at least one of plot2d. plot3d, or
> report is present.
>
> Richard
>
> Dr Richard Adams
> Senior Software Developer,
> Computational Systems Biology Group,
> University of Edinburgh
> Tel: 0131 650 8281/8285
> email : ric...@ed...
>
>
>   

[Miase-discuss] new namespace

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

Hej all,

please note that the new and official namespace for the sed-ml schema is
www.biomodels.net/sed-ml

The XSD Schema on sourceforge is already updated.

Best,
Dagmar

Re: [Miase-discuss] sed-ml library?

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

Frank Bergmann wrote:

> The next thing would be to broaden the scope to maybe include  
> something else but uniform time courses.

Yes. May-I suggest to start the work on parameter-scans? Dose-response and sensitivity analysis are by far the most common tasks we have to reproduce when curating models.

-- 
Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome-Trust 
Genome Campus, Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521
Fax:468, Skype:n.lenovere, AIM:nlenovere, MSN:nle...@ho...
http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/

Re: [Miase-discuss] sed-ml library?

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

Frank Bergmann wrote:

>>         3) Could a model file be optionally  embedded in a sedml file?
>>   This gets round the need to keep sedml independent of sbml, also a
>> single file gets round the file coordination issue,  but it raises new
>> problems of keeping in synch possibly multiple copies of a model. But
>> for non-curated models that must be an issue anyway?
>>
> 
> personally I don't like this option too much. If an embedding solution 
> is wanted, I prefer it to work the other way around, have MIASE embedded 
> in i.e. SBML. That is the solution  that was favored by some people in 
> the discussions as well. 

Yes, but that would preclude the use of SED-ML for using two different external models. At the moment, we only use two models for comparing them. But nothing precludes the post-processing of the simulation results of one model using variables coming for another model. Same thing for the changeMath definition. We will be able to modify a model prior to a task by using values coming from another model.  

But more importantly, with SED-ML one can define a simulation experiment using both SBML and CellML models (or VCML etc.) Several groups are working on integrating different formalisms. The approach is generally to import the different model to have an internal integrated view. SED-ML would offer an alternative in some case, where the integration could be done at run-time. We have actually a real-case in the group (although not using CellML and SBML). On PhD here is running hybrid simulations of neurons, with electrical and biochemical representations. The models are defined separately, because using completely different formalisms. The integration is done at run-time, with some variables of a simulation affected by the variables of the other one.

-- 
Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome-Trust 
Genome Campus, Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521
Fax:468, Skype:n.lenovere, AIM:nlenovere, MSN:nle...@ho...
http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/

Re: [Miase-discuss] sed-ml library?

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

  fbergman> but but ... who was talking about XPath 2.0
  fbergman> ... really Xpath 1.0 is not all bad, it is
  fbergman> available on (almost) all (windows) machines and
  fbergman> just works.

... and apparently fatally flawed for this application, if
it can't deal with default namespaces ...

I didn't check: are there no xpath 2.0 implementations?
That would be a bit of a show-stopper, I agree.

MH

Re: [Miase-discuss] sed-ml library?

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

>
> Hmm.  I may be barking up the wrong tree, but in XPath 2.0,
> it appears to me (reading very quickly) that default
> namespaces are in fact supported.  See section "2 Basics"
> here: http://www.w3.org/TR/xpath20/.  Near the end, it says:

but but ... who was talking about XPath 2.0 ... really Xpath 1.0 is  
not all bad, it is available on (almost) all (windows) machines and  
just works.

Frank 

Re: [Miase-discuss] sed-ml library?

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

  fbergman> The biggest issue I had in my implementation was
  fbergman> with XPath and the problem that SBML models have
  fbergman> a default namespace, which is not supported by
  fbergman> XPath.

Hmm.  I may be barking up the wrong tree, but in XPath 2.0,
it appears to me (reading very quickly) that default
namespaces are in fact supported.  See section "2 Basics"
here: http://www.w3.org/TR/xpath20/.  Near the end, it says:

   Element nodes have a property called in-scope
   namespaces. [Definition: The in-scope namespaces property
   of an element node is a set of namespace bindings, each
   of which associates a namespace prefix with a URI, thus
   defining the set of namespace prefixes that are available
   for interpreting QNames within the scope of the
   element. For a given element, one namespace binding may
   have an empty prefix; the URI of this namespace binding
   is the default namespace within the scope of the element.]
   
MH

Re: [Miase-discuss] sed-ml library?

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

Hello Richard,

>
>   The project is at
>
>     http://miase.svn.sourceforge.net/viewvc/miase/sed-ml/jlibsedml/
>
>   Any input on API design etc very welcome!

I'd be hoping for library in the style of libSBML, i.e. a C/C++ based  
library with wrappers for other languages. Though I do realize that  
generation from the schema won't quite work for that.

>
>   Dagmar suggested further implementation issues to be discussed on
> the sourceforge miase bugzilla.
>
>   Just working with this now there seem to be quite a lot of issues  
> to address
> in order to achieve an implementation. Here are some,
>
>   A Schema issues:
>   --------------

I ended up not using the Schema as such but rather the schema +  
example + the notes from our discussions. But your points are valid  
and should be adopted.

The biggest issue I had in my implementation was with XPath and the  
problem that SBML models have a default namespace, which is not  
supported by XPath.

http://shrinkster.com/13w7


>
>
>   B)    Coordination with model
>   ----------
>     PRevious posts have raised this issue, is there any progress on
> this? There is a lot of validation that can be done just with the
> sedml file, but if we want to check that a parameter or variable name
> exists, or the xpath is correct,
>   then we need access to the model. It seems to me that there are
> different scenarios:
>
>        1) A model is referenced to a validated public repository e.g.,
> BioModels
>           In this case the library can download the model. This seems
> the  easiest solution, as revisions of Biomodels are versioned (btw,
> would a version attribute  for the model element be useful?) and so a
> tool can make decisions on whether the model is correct or not.
>

While 1) is possible personally, I prefer a more local solution :),  
IMHO we don't need a version attribute, the model that is pointed to  
is the one the software should read, not another version.

>
>         2) A model is not yet in the public domain, but for example
> the client wants to share  simulation info with a collaborator. In
> this case probably the model and  the sedml file would have to sent
> together in a zip file to preserve
>   relative file paths, but this leaves quite an onus on the user or
> tool to keep the two files coordinated.
>

as pointed out in my previous mail, I don't think there will be any  
hassle whatsoever with this solution. as soon as we think of it not as  
a zip file, but as a miase-file that only software handles that will  
be resolved.

>         3) Could a model file be optionally  embedded in a sedml file?
>   This gets round the need to keep sedml independent of sbml, also a
> single file gets round the file coordination issue,  but it raises new
> problems of keeping in synch possibly multiple copies of a model. But
> for non-curated models that must be an issue anyway?
>

personally I don't like this option too much. If an embedding solution  
is wanted, I prefer it to work the other way around, have MIASE  
embedded in i.e. SBML. That is the solution  that was favored by some  
people in the discussions as well.

> C Validation requirements
> --------------------------

the offered validations certainly make sense. The only thing i like to  
add, is that i like my id's to be unique in general.

Cheers
Frank

Re: [Miase-discuss] sed-ml library?

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

Hello Mike & all,

On Jan 22, 2009, at 6:33 PM, Michael Hucka wrote:

> Hi Richard,
>
> It's exciting to see work restarting on miase and sed-ml.  I
> was just thinking that working on this (or whatever is not
> resolved by that time) would be an excellent topic for the
> April super-workshop in Auckland.  Will you (and others on
> this list) be attending that meeting?  If not, can I
> convince you to go? :-)

I'll be there ...

>
>
> What would be ideal to make this a productive MIASE meeting
> is to identify 1-2 concrete goal(s).  Perhaps we can
> collectively discuss what those objectives should be?
>

I was sort of hoping for it to be like one of the early SBML  
hackathon. It would be great if the groups could bring their MIASE  
prototypes and we could share some files and compare results.

The next thing would be to broaden the scope to maybe include  
something else but uniform time courses. The combination of MIASE  
description and dynamic model / data needs to be clarified. As i  
proposed last year an archive format would be ideal to keep all data  
together, a registered MIME extension would help all of us. Again  
think of it not so much as a zip file, that users of our software  
would have to keep in sync with the description, but rather as a miase  
file, that only software handles. suddenly there is no hassle for the  
users anymore. Even software has no problems, as at the moment of  
writing the file, it is precisely clear for which model to save what  
data and experiment description.

cheers
Frank


> MH
>
> -- 
> Mike Hucka,  mh...@ca...,  http://sbml.org
>
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by:
> SourcForge Community
> SourceForge wants to tell your story.
> http://p.sf.net/sfu/sf-spreadtheword
> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/miase-discuss

Re: [Miase-discuss] sed-ml library?

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

Hi Richard,

It's exciting to see work restarting on miase and sed-ml.  I
was just thinking that working on this (or whatever is not
resolved by that time) would be an excellent topic for the
April super-workshop in Auckland.  Will you (and others on
this list) be attending that meeting?  If not, can I
convince you to go? :-)

What would be ideal to make this a productive MIASE meeting
is to identify 1-2 concrete goal(s).  Perhaps we can
collectively discuss what those objectives should be?

MH

-- 
Mike Hucka,  mh...@ca...,  http://sbml.org

Re: [Miase-discuss] sed-ml library?

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

Hi all,
   Thanks to Dagmar's suggestions I've set up a Java project on
sourceforge for writing a library to support the specs. This uses JaxB
to parse the schema file and autogenerate classes, plan to add an API
on top of that. In order to get JaxB to work, there are a few small
changes needed in the schema, for example making some local element
declarations global, I don't think the semantics are changed.

   The project is at

     http://miase.svn.sourceforge.net/viewvc/miase/sed-ml/jlibsedml/

   Any input on API design etc very welcome!
   Dagmar suggested further implementation issues to be discussed on
the sourceforge miase bugzilla.

   Just working with this now there seem to be quite a lot of issues to address
in order to achieve an implementation. Here are some,

   A Schema issues:
   --------------
      1.  According to the spec SEDBase is a superclass of all the main
classes, yest in the schema only SedML class inherits from it. This
means that notes and annotation cannot be added to other elements,
e.g., uniform time course, dataset, datagenerator etc.,

      2. Most if not all top-level elements have an 'id' attribute,
would it make sense to put the 'id' field in SEDBase?

      3. If more than one simulation can be in the listOfSimulations,
then I think
        UniformTimeCourse needs a 'max=unbounded' attribute in its declaration,
        else ListOfSimulations only contains a single element.

   B)    Coordination with model
   ----------
     PRevious posts have raised this issue, is there any progress on
this? There is a lot of validation that can be done just with the
sedml file, but if we want to check that a parameter or variable name
exists, or the xpath is correct,
   then we need access to the model. It seems to me that there are
different scenarios:

        1) A model is referenced to a validated public repository e.g.,
BioModels
           In this case the library can download the model. This seems
the  easiest solution, as revisions of Biomodels are versioned (btw,
would a version attribute  for the model element be useful?) and so a
tool can make decisions on whether the model is correct or not.


         2) A model is not yet in the public domain, but for example
the client wants to share  simulation info with a collaborator. In
this case probably the model and  the sedml file would have to sent
together in a zip file to preserve
   relative file paths, but this leaves quite an onus on the user or
tool to keep the two files coordinated.

         3) Could a model file be optionally  embedded in a sedml file?
   This gets round the need to keep sedml independent of sbml, also a
single file gets round the file coordination issue,  but it raises new
problems of keeping in synch possibly multiple copies of a model. But
for non-curated models that must be an issue anyway?

C Validation requirements
--------------------------

   VAlidation against the schema offers one level of validation, but  
there are many more assertions to validate, here are
some below, would be good to have a list of these somewhere to
construct a test-suite.
Validation tasks below with an asterisk are ones needing access to the model:


   List of simulations (schema needs to be altered to hold 'max=unbounded'?)
     Unique simulation ids
1) Uniform time course -
     outputstart time < output end time
     outputst time >= initial time
     algorithm = valid Kisao id

2) List of Models
       how to check existence of model? *
       source = accessible url ( e.g., BioModelsDB)* or reference to
previously defined model
       No duplicate model IDs
       List of changes -> Check parameter name exists *

3) List of tasks

        One task must be baseline?

        model reference must refer to defined model id
        simulation reference must refer to defined simulation id
        No duplicate task IDs

4) list of data generators
      unique ids
      variable ID exists in model, target path exists in model
      task ref refers to valid task reference

5) List of outputs
        Plot ID is unique
        x and y data references refer to defined dataGenerator ID
        If listOfOuputs present, at least one of plot2d. plot3d, or
report is present.

Richard

Dr Richard Adams
Senior Software Developer,
Computational Systems Biology Group,
University of Edinburgh
Tel: 0131 650 8281/8285
email : ric...@ed...


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

[Miase-discuss] CFP: (HiBi 2009) International Workshop on High Performance Computational Systems Biology

[mazza <ma...@co...>]

Please find attached the Call For Papers for:


****************************************************************************
International Workshop on High Performance Computational Systems Biology
                               (HiBi 2009)
                    Trento, Italy, October 14-16, 2009
                       http://www.cosbi.eu/hibi09/
****************************************************************************


The HiBi (High performance computational systems Biology) workshop
establishes a forum to link researchers in the areas of parallel computing
and computational systems biology.
One of the main limitations in managing models of biological systems comes
from the fundamental difference between the high parallelism evident in
biochemical reactions and the sequential environments employed for the
analysis of these reactions. Such limitations affect all varieties of
continuous, deterministic, discrete and stochastic models; undermining the
applicability of simulation techniques and analysis of biological models.
The goal of HiBi is therefore to bring together researchers in the fields
of high performance computing and computational systems biology. Experts
from around the world will present their current work, discuss profound
challenges, new ideas, results, applications and their experience relating
to key aspects of high performance computing in biology.


IMPORTANT DEADLINES:

paper submission deadline (abstract only) April 24, 2009
paper submission deadline                 May 1, 2009
acceptance notification                   June 23, 2009
revised papers due                        July 15, 2009
early registration deadline               July 31, 2009


Best regards,
HiBi organizing committee


********************************************************************************
We apologize if you received multiple copies of this Call for Papers.
Please feel free to distribute it to those who might be interested.
********************************************************************************

--------------------------------------------------------------------------------

                International Workshop on
      High Performance Computational Systems Biology
                       (HiBi 2009)
                   October 14-16, 2009
                      Trento, Italy
---------------------------------------------------------------------------------



1st Call for Papers (http://www.cosbi.eu/hibi09/cfp.pdf)


*****************

The HiBi (High performance computational systems Biology) workshop
establishes a forum to link researchers in the areas of parallel computing
and computational systems biology.

One of the main limitations in managing models of biological systems comes
from the fundamental difference between the high parallelism evident in
biochemical reactions and the sequential environments employed for the
analysis of these reactions. Such limitations affect all varieties of
continuous, deterministic, discrete and stochastic models; undermining the
applicability of simulation techniques and analysis of biological models.

The goal of HiBi is therefore to bring together researchers in the fields
of high performance computing and computational systems biology. Experts
from around the world will present their current work, discuss profound
challenges, new ideas, results, applications and their experience relating
to key aspects of high performance computing in biology.


Topics of interest include high performance algorithms, systems,
architecture, and tools for the following: (but are not limited to the
following list)

   - Parallel and distributed Stochastic simulation
   - Biological and Numerical parallel computing
   - Parallel and distributed architectures
   - Emerging processing architectures (Cell processors, GPUs, mixed
CPU-FPGA)
   - Parallel Model Checking techniques
   - Parallel parameters estimation
   - Parallel algorithms for biological analysis
   - Application of concurrency theory to biology
   - Parallel visualization algorithms
   - Web-services and internet computing for e-Science
   - Tools and applications


SUBMISSION INFORMATION:

HiBi welcomes submissions for:

   - *full research papers* describing recent advances at the border
between parallel computing and systems biology;
   - *short tool papers* describing implemented parallel techniques and
tools for systems biology.


PROCEEDINGS:

All submitted papers will be reviewed by the Program Committee. The review
process will include a rebuttal phase whereby authors will be given the
possibility to send their comments on the received review. Full papers as
well as short (tool) papers will be published in the proceedings of the
workshop. Detailed information about papers format and publisher will be
available soon. A selection of best (full) papers will also be published on
a dedicated special issue of the Briefings in Bioinformatics journal.
Submission of papers to HiBi09 will be through the EasyChair conference
system.



PROGRAM COMMITTEE MEMBERS:

   - Tommaso Mazza (CoSBi, Italy) - chair
   - Mateo Valero (Technical University of Catalonia, Spain) - co-chair
   - Yutaka Akiyama (Tokyo Institute of Technology, Japan)
   - Paolo Ballarini (CoSBi, Italy)
   - Gianfranco Balbo (University of Torino, Italy)
   - Lubos Brim (Masaryk University, Czech Republic)
   - Kevin Burrage (University of Oxford, UK)
   - Hidde De Jong (INRIA Rhône-Alpes, France)
   - François Fages (INRIA Paris-Rocquencourt, France)
   - Fabrizio Gagliardi (Microsoft Research Cambridge, United Kingdom)
   - Martin Leucker (Technische Universität München, Germany)
   - Gethin Norman (Oxford University Computing Laboratory, United Kingdom)
   - Dave Parker (Oxford University Computing Laboratory, United Kingdom)
   - Davide Prandi (CoSBi, Italy)
   - Assaf Schuster (Israel Institute of Technology, Israel)
   - Koichi Takahashi (RIKEN, Japan)
   - David Torrents Arenales (Barcelona Supercomputing Center, Spain)
   - Adelinde Uhrmacher (University of Rostock, Germany)


Information related to HiBi 2009 is available at the official HiBi 2009 Web
site: http://www.cosbi.eu/hibi09/

Re: [Miase-discuss] sed-ml library?

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

Hello Richard,

welcome on miase-discuss and sorry for the late reply. It is nice to 
hear that people in Edinburgh are interested in SED-ML!
Concerning your questions about a libsedml: we met last year during the 
SBML Hackathon and started developing *some* ideas for the SED-ML 
import/export for simulation tools. On the tool developers side, Frank 
Bergman (roadrunner), Ion Moraru (VCell), Henning Schmidt (SBToolbox) 
and Sven Sahle (COPASI) worked with us on the format and started some 
test implementation work during the meeting, but I haven't got any 
recent update how far they got and/or if they are still working on it.

I would be very glad if you could help with a libsedml for Java, maybe 
the others could join you to support other languages as well (as I think 
I remember Frank does not use Java...).
Did you think about using JAXB http://jaxb-builder.sourceforge.net/ to 
convert SED-ML into Java classes? In that case, the current XML Schema 
for SED-ML can be found on sourceforge 
http://miase.svn.sourceforge.net/viewvc/miase/sed-ml/documents/schema/ . 
Please note that it is still a draft - however, you're more than welcome 
to work with it, please report any bugs you might find :-)
Otherwise, the UML diagrams can be found on the projects' homepage 
http://www.ebi.ac.uk/compneur-srv/sed-ml/index.html

I'd suggest you become a member of the MIASE project on sourceforge and 
start your own sub-project for the library work. You might even want to 
use another mailing-list for implementation issues and bug reporting? 
Just let me know what you need and I'll help if I can.

By the way, we are having our next MIASE meeting in April during the 
combined CellML meeting, if you'd be interested to join: 
http://www.cellml.org/workshop/workshop2009/

Best regards,
Dagmar Koehn

Richard Adams wrote:
> Hello,
>   My name is Richard Adams and I just wanted to introduce myself to  
> the list. I work as a software developer for the Goryanin and Millar  
> labs in Edinburgh, where there's a fair amount of interest in SED-ML  
> amongst modellers and developers here for  exchanging simulation expt  
> information, as we currently don't have any structured way of doing  
> this, even internally. I was wondering if there were any plans to  
> produce a 'libsedml' along the lines of libsbml? Just looking through  
> this list it's not very clear to me what the current status is - would  
> there be any point in us  attempting  an initial Java implementation  
> based on the UML specs,  if there will be a reference implementation  
> in the near future? Or, if there is already an effort underway to  
> develop such a library, is it something we could perhaps contribute  
> to, if that could help? As we're effectively starting from scratch,  
> and would have to develop our own internal exchange format anyway,  
> we'd be keen to help out, if we can.
>
> Thanks,
>
>
> Richard Adams
>
>   

[Miase-discuss] sed-ml library?

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

Hello,
  My name is Richard Adams and I just wanted to introduce myself to  
the list. I work as a software developer for the Goryanin and Millar  
labs in Edinburgh, where there's a fair amount of interest in SED-ML  
amongst modellers and developers here for  exchanging simulation expt  
information, as we currently don't have any structured way of doing  
this, even internally. I was wondering if there were any plans to  
produce a 'libsedml' along the lines of libsbml? Just looking through  
this list it's not very clear to me what the current status is - would  
there be any point in us  attempting  an initial Java implementation  
based on the UML specs,  if there will be a reference implementation  
in the near future? Or, if there is already an effort underway to  
develop such a library, is it something we could perhaps contribute  
to, if that could help? As we're effectively starting from scratch,  
and would have to develop our own internal exchange format anyway,  
we'd be keen to help out, if we can.

Thanks,


Richard Adams

-- 
Dr Richard Adams
Senior Software Developer,
Computational Systems Biology Group,
University of Edinburgh
Tel: 0131 650 8281
email : ric...@ed...

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

[Miase-discuss] ISML & relevance to SED-ML

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

Greetings,

I'm at a symposium and was introduced to another effort that
defines its own ML, a project called insilicoIDE.  They
developed this for the Physiome project and it's heavily
influenced by CellML 1.0, and they want to translate to
SBML, MML, blah, blah, blah.  What struck me, however, is
that their format includes information about the algorithm
and solver library used for a simulation.  I haven't looked
too closely at what they do, but I wanted to send this along
in case this might provide some additional ideas for
MIASE/SED-ML development regarding what kinds of information
other people find necessary to include in a representation
of simulation experiments.

With the authors' permission, the insilico ML 1.0
specification doc and a related paper (accepted but not
published yet) is available here:

  http://drop.io/ars2cut

See in particular start at about p.24.

Just consider this additional data points, nothing huge.

MH