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

Re: [SED-ML-discuss] A SED-ML Test suite?

[Lucian S. <luc...@gm...>]

At first, I thought you were talking about including SED-ML at all, which
was amusing, but you actually mean the 'SED-ML Script' language, which is
sort of 'the XML with the <>'s filed off', right?  Sure, if that would be
helpful, I'm happy to include them, especially if there's a translator out
there that could make it automatic.  As noted, the phraSED is only there in
the text descriptions, anyway.

-Lucian
On Dec 3, 2015 12:15 AM, "Frank Bergmann" <fbe...@ca...> wrote:

> Indeed I would love to see some SED-ML Scripts there, especially since we
> know that there might be concepts not yet in phraSED.
>
> Cheers
> Frank
>
> > On Dec 3, 2015, at 1:31 AM, David Nickerson <dav...@gm...>
> wrote:
> >
> > Thanks Lucian - that is a great start. Now we just need to fill that
> > contributions folder up :)
> >
> > I think it is fine to include Antimony or phraSED-ML in the
> > description (or any other domain specific simple text format people
> > use).
> >
> >
> > Cheers,
> > David.
> >
> > On Thu, Dec 3, 2015 at 1:15 PM, Lucian Smith <luc...@gm...>
> wrote:
> >> I agree that we can model the suite after the SBML test suite, but it
> should
> >> both be its own thing, and have CellML models in it, too. In fact, I
> think
> >> that each directory/test should basically be modeling-language
> agnostic--the
> >> point is to test SED-ML, not the modeling.
> >>
> >> I put together a bare-bones repository with a single test in it on
> github so
> >> we can have an actual thing to talk about:
> >>
> >> https://github.com/luciansmith/sedml-test-suite/
> >>
> >> If anyone wants access to it, I'll gladly add them to the
> 'collaborators'
> >> list, which I think should work?  Github and I don't get along all that
> well
> >> ;-)
> >>
> >> I modeled everything off of the SBML test suite, with some changes:  I
> now
> >> have an 'info' file instead of the '.m' file in the SBML test suite,
> which
> >> was an artifact of how the tests used to be created.  There's no longer
> a
> >> 'settings' file, since everything there in the SBML test suite is here
> >> covered by SED-ML itself.
> >>
> >> All suggestions welcome!
> >>
> >> -Lucian
> >>
> >>
> >> On Dec 2, 2015 12:54 AM, "Alan Garny" <ala...@in...> wrote:
> >>>
> >>> +1 regarding David’s suggestion of a GitHub repository for a SED-ML
> test
> >>> suite and a test suite that is not SBML centric. And, as much as
> possible, I
> >>> would be happy to contribute to it when it comes to CellML.
> >>>
> >>>
> >>>
> >>> Alan
> >>>
> >>> On 02/12/2015, 03:07, "David Nickerson" <dav...@gm...>
> wrote:
> >>>
> >>>>> To make this effective, I think it would be nice to integrate with
> the
> >>>>> SBML Test Suite, since comparing simulation results is again what
> you will
> >>>>> need to do.  You already have some SED-ML files there, so it would
> mostly be
> >>>>> adding some more sophisticated ones.
> >>>>>
> >>>>
> >>>> I think that since we need to cater to a broader community than SBML,
> >>>> the SED-ML test suite should be independent from the SBML test suite,
> >>>> but it would be fine to be using the same framework if that can be
> >>>> easily adapted and used in such a manner. I have an inking that
> >>>> discussing this in the past with SBML developers that this might not
> >>>> be such a straightforward task...
> >>>>
> >>>>>> It seems like it would be really helpful to have a
> >>>>>> collectively-agreed-on test suite that put SED-ML through its
> paces, to make
> >>>>>> sure everyone agreed that the same file meant the same thing to
> everyone.
> >>>>>> At least, I assume that this doesn't already exist and I missed it?
> >>>>>>
> >>>>
> >>>> No, nothing like that exists in a general sense. I know a few tools
> >>>> that probably have their own internal tests, but nothing commonly used
> >>>> by more than one tool.
> >>>>
> >>>>>> Assuming it doesn't, two questions:  if I started putting such a
> thing
> >>>>>> together, would making it have the same format as the SBML Test
> Suite work
> >>>>>> for everyone--directory-demarked sets of files with input files,
> expected
> >>>>>> output files, and a setup file that listed with 'tags' what
> different
> >>>>>> aspects of SED-ML were being tested in each?  Is that overkill, not
> enough,
> >>>>>> just right?
> >>>>
> >>>> I think that makes sense, and if you, Lucian, are willing and able to
> >>>> set something like that up then it would be a great resource for the
> >>>> community. As long as it is something that is easy to maintain and add
> >>>> to over time, then I'd imagine once the initial hurdle of setting it
> >>>> up is achieved, then we should be able to keep improving it with
> >>>> future releases of the specification.
> >>>>
> >>>>>> Secondly, if you have files you're using that you'd be willing to
> send
> >>>>>> in/deposit/point me to somewhere, that'd be great!
> >>>>
> >>>> Something like a github repo where we could submit pull requests to
> >>>> bring in more tests or corrections to existing tests would seem to be
> >>>> a good way to get the community contributing tests. Would provide a
> >>>> good forum to discuss the "correctness" of specific tests as well :)
> >>>>
> >>>>
> >>>> Cheers,
> >>>> David.
> >>>>
> >>>
> >>>>>
> ------------------------------------------------------------------------------
> >>>> Go from Idea to Many App Stores Faster with Intel(R) XDK
> >>>> Give your users amazing mobile app experiences with Intel(R) XDK.
> >>>> Use one codebase in this all-in-one HTML5 development environment.
> >>>> Design, debug & build mobile apps & 2D/3D high-impact games for
> multiple
> >>>> OSs.
> >>>> http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140
> >>>> _______________________________________________
> >>>> SED-ML-discuss mailing list
> >>>> SED...@li...
> >>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
> >>>
> >>>
> >>>
> >>>
> ------------------------------------------------------------------------------
> >>> Go from Idea to Many App Stores Faster with Intel(R) XDK
> >>> Give your users amazing mobile app experiences with Intel(R) XDK.
> >>> Use one codebase in this all-in-one HTML5 development environment.
> >>> Design, debug & build mobile apps & 2D/3D high-impact games for
> multiple
> >>> OSs.
> >>> http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140
> >>> _______________________________________________
> >>> SED-ML-discuss mailing list
> >>> SED...@li...
> >>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
> >>
> >>
> >>
> ------------------------------------------------------------------------------
> >> Go from Idea to Many App Stores Faster with Intel(R) XDK
> >> Give your users amazing mobile app experiences with Intel(R) XDK.
> >> Use one codebase in this all-in-one HTML5 development environment.
> >> Design, debug & build mobile apps & 2D/3D high-impact games for multiple
> >> OSs.
> >> http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140
> >> _______________________________________________
> >> SED-ML-discuss mailing list
> >> SED...@li...
> >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
> >>
> >
> >
> >
> > --
> >
> >
> > David Nickerson
> > about.me/david.nickerson
> >
> >
> ------------------------------------------------------------------------------
> > Go from Idea to Many App Stores Faster with Intel(R) XDK
> > Give your users amazing mobile app experiences with Intel(R) XDK.
> > Use one codebase in this all-in-one HTML5 development environment.
> > Design, debug & build mobile apps & 2D/3D high-impact games for multiple
> OSs.
> > http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140
> > _______________________________________________
> > SED-ML-discuss mailing list
> > SED...@li...
> > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
>
>
> ------------------------------------------------------------------------------
> Go from Idea to Many App Stores Faster with Intel(R) XDK
> Give your users amazing mobile app experiences with Intel(R) XDK.
> Use one codebase in this all-in-one HTML5 development environment.
> Design, debug & build mobile apps & 2D/3D high-impact games for multiple
> OSs.
> http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>

Re: [SED-ML-discuss] A SED-ML Test suite?

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

Indeed I would love to see some SED-ML Scripts there, especially since we know that there might be concepts not yet in phraSED. 

Cheers
Frank

> On Dec 3, 2015, at 1:31 AM, David Nickerson <dav...@gm...> wrote:
> 
> Thanks Lucian - that is a great start. Now we just need to fill that
> contributions folder up :)
> 
> I think it is fine to include Antimony or phraSED-ML in the
> description (or any other domain specific simple text format people
> use).
> 
> 
> Cheers,
> David.
> 
> On Thu, Dec 3, 2015 at 1:15 PM, Lucian Smith <luc...@gm...> wrote:
>> I agree that we can model the suite after the SBML test suite, but it should
>> both be its own thing, and have CellML models in it, too. In fact, I think
>> that each directory/test should basically be modeling-language agnostic--the
>> point is to test SED-ML, not the modeling.
>> 
>> I put together a bare-bones repository with a single test in it on github so
>> we can have an actual thing to talk about:
>> 
>> https://github.com/luciansmith/sedml-test-suite/
>> 
>> If anyone wants access to it, I'll gladly add them to the 'collaborators'
>> list, which I think should work?  Github and I don't get along all that well
>> ;-)
>> 
>> I modeled everything off of the SBML test suite, with some changes:  I now
>> have an 'info' file instead of the '.m' file in the SBML test suite, which
>> was an artifact of how the tests used to be created.  There's no longer a
>> 'settings' file, since everything there in the SBML test suite is here
>> covered by SED-ML itself.
>> 
>> All suggestions welcome!
>> 
>> -Lucian
>> 
>> 
>> On Dec 2, 2015 12:54 AM, "Alan Garny" <ala...@in...> wrote:
>>> 
>>> +1 regarding David’s suggestion of a GitHub repository for a SED-ML test
>>> suite and a test suite that is not SBML centric. And, as much as possible, I
>>> would be happy to contribute to it when it comes to CellML.
>>> 
>>> 
>>> 
>>> Alan
>>> 
>>> On 02/12/2015, 03:07, "David Nickerson" <dav...@gm...> wrote:
>>> 
>>>>> To make this effective, I think it would be nice to integrate with the
>>>>> SBML Test Suite, since comparing simulation results is again what you will
>>>>> need to do.  You already have some SED-ML files there, so it would mostly be
>>>>> adding some more sophisticated ones.
>>>>> 
>>>> 
>>>> I think that since we need to cater to a broader community than SBML,
>>>> the SED-ML test suite should be independent from the SBML test suite,
>>>> but it would be fine to be using the same framework if that can be
>>>> easily adapted and used in such a manner. I have an inking that
>>>> discussing this in the past with SBML developers that this might not
>>>> be such a straightforward task...
>>>> 
>>>>>> It seems like it would be really helpful to have a
>>>>>> collectively-agreed-on test suite that put SED-ML through its paces, to make
>>>>>> sure everyone agreed that the same file meant the same thing to everyone.
>>>>>> At least, I assume that this doesn't already exist and I missed it?
>>>>>> 
>>>> 
>>>> No, nothing like that exists in a general sense. I know a few tools
>>>> that probably have their own internal tests, but nothing commonly used
>>>> by more than one tool.
>>>> 
>>>>>> Assuming it doesn't, two questions:  if I started putting such a thing
>>>>>> together, would making it have the same format as the SBML Test Suite work
>>>>>> for everyone--directory-demarked sets of files with input files, expected
>>>>>> output files, and a setup file that listed with 'tags' what different
>>>>>> aspects of SED-ML were being tested in each?  Is that overkill, not enough,
>>>>>> just right?
>>>> 
>>>> I think that makes sense, and if you, Lucian, are willing and able to
>>>> set something like that up then it would be a great resource for the
>>>> community. As long as it is something that is easy to maintain and add
>>>> to over time, then I'd imagine once the initial hurdle of setting it
>>>> up is achieved, then we should be able to keep improving it with
>>>> future releases of the specification.
>>>> 
>>>>>> Secondly, if you have files you're using that you'd be willing to send
>>>>>> in/deposit/point me to somewhere, that'd be great!
>>>> 
>>>> Something like a github repo where we could submit pull requests to
>>>> bring in more tests or corrections to existing tests would seem to be
>>>> a good way to get the community contributing tests. Would provide a
>>>> good forum to discuss the "correctness" of specific tests as well :)
>>>> 
>>>> 
>>>> Cheers,
>>>> David.
>>>> 
>>> 
>>>>> ------------------------------------------------------------------------------
>>>> Go from Idea to Many App Stores Faster with Intel(R) XDK
>>>> Give your users amazing mobile app experiences with Intel(R) XDK.
>>>> Use one codebase in this all-in-one HTML5 development environment.
>>>> Design, debug & build mobile apps & 2D/3D high-impact games for multiple
>>>> OSs.
>>>> http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140
>>>> _______________________________________________
>>>> SED-ML-discuss mailing list
>>>> SED...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>> 
>>> 
>>> 
>>> ------------------------------------------------------------------------------
>>> Go from Idea to Many App Stores Faster with Intel(R) XDK
>>> Give your users amazing mobile app experiences with Intel(R) XDK.
>>> Use one codebase in this all-in-one HTML5 development environment.
>>> Design, debug & build mobile apps & 2D/3D high-impact games for multiple
>>> OSs.
>>> http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140
>>> _______________________________________________
>>> SED-ML-discuss mailing list
>>> SED...@li...
>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>> 
>> 
>> ------------------------------------------------------------------------------
>> Go from Idea to Many App Stores Faster with Intel(R) XDK
>> Give your users amazing mobile app experiences with Intel(R) XDK.
>> Use one codebase in this all-in-one HTML5 development environment.
>> Design, debug & build mobile apps & 2D/3D high-impact games for multiple
>> OSs.
>> http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140
>> _______________________________________________
>> SED-ML-discuss mailing list
>> SED...@li...
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>> 
> 
> 
> 
> -- 
> 
> 
> David Nickerson
> about.me/david.nickerson
> 
> ------------------------------------------------------------------------------
> Go from Idea to Many App Stores Faster with Intel(R) XDK
> Give your users amazing mobile app experiences with Intel(R) XDK.
> Use one codebase in this all-in-one HTML5 development environment.
> Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs.
> http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

Re: [SED-ML-discuss] A SED-ML Test suite?

[Martin S. <ma...@bi...>]

Coincidentally, I created a github repository of SED-ML scripts about a
month ago: https://github.com/binfalse/SED-ML-Depository

This "depository" contains a SED-ML script for every model of the
curated branch of the Biomodels Database. (sorry don't have CellML, yet)
There are also COMBINE archives encoding for a simulation job (SBML
file plus SED-ML file) and the corresponding simulation results, as
obtained by running the simulation study in the SED-ML WebTools.

Not sure if that's going to help you, but feel free to use anything from
that repository. I'm also happy to add anyone as a collaborator! :)

Best wishes,
Martin

On 12/03/2015 01:31 AM, David Nickerson wrote:
> Thanks Lucian - that is a great start. Now we just need to fill that
> contributions folder up :)
> 
> I think it is fine to include Antimony or phraSED-ML in the
> description (or any other domain specific simple text format people
> use).
> 
> 
> Cheers,
> David.
> 
> On Thu, Dec 3, 2015 at 1:15 PM, Lucian Smith <luc...@gm...> wrote:
>> I agree that we can model the suite after the SBML test suite, but it should
>> both be its own thing, and have CellML models in it, too. In fact, I think
>> that each directory/test should basically be modeling-language agnostic--the
>> point is to test SED-ML, not the modeling.
>>
>> I put together a bare-bones repository with a single test in it on github so
>> we can have an actual thing to talk about:
>>
>> https://github.com/luciansmith/sedml-test-suite/
>>
>> If anyone wants access to it, I'll gladly add them to the 'collaborators'
>> list, which I think should work?  Github and I don't get along all that well
>> ;-)
>>
>> I modeled everything off of the SBML test suite, with some changes:  I now
>> have an 'info' file instead of the '.m' file in the SBML test suite, which
>> was an artifact of how the tests used to be created.  There's no longer a
>> 'settings' file, since everything there in the SBML test suite is here
>> covered by SED-ML itself.
>>
>> All suggestions welcome!
>>
>> -Lucian
>>
>>
>> On Dec 2, 2015 12:54 AM, "Alan Garny" <ala...@in...> wrote:
>>>
>>> +1 regarding David’s suggestion of a GitHub repository for a SED-ML test
>>> suite and a test suite that is not SBML centric. And, as much as possible, I
>>> would be happy to contribute to it when it comes to CellML.
>>>
>>>
>>>
>>> Alan
>>>
>>> On 02/12/2015, 03:07, "David Nickerson" <dav...@gm...> wrote:
>>>
>>>>> To make this effective, I think it would be nice to integrate with the
>>>>> SBML Test Suite, since comparing simulation results is again what you will
>>>>> need to do.  You already have some SED-ML files there, so it would mostly be
>>>>> adding some more sophisticated ones.
>>>>>
>>>>
>>>> I think that since we need to cater to a broader community than SBML,
>>>> the SED-ML test suite should be independent from the SBML test suite,
>>>> but it would be fine to be using the same framework if that can be
>>>> easily adapted and used in such a manner. I have an inking that
>>>> discussing this in the past with SBML developers that this might not
>>>> be such a straightforward task...
>>>>
>>>>>> It seems like it would be really helpful to have a
>>>>>> collectively-agreed-on test suite that put SED-ML through its paces, to make
>>>>>> sure everyone agreed that the same file meant the same thing to everyone.
>>>>>> At least, I assume that this doesn't already exist and I missed it?
>>>>>>
>>>>
>>>> No, nothing like that exists in a general sense. I know a few tools
>>>> that probably have their own internal tests, but nothing commonly used
>>>> by more than one tool.
>>>>
>>>>>> Assuming it doesn't, two questions:  if I started putting such a thing
>>>>>> together, would making it have the same format as the SBML Test Suite work
>>>>>> for everyone--directory-demarked sets of files with input files, expected
>>>>>> output files, and a setup file that listed with 'tags' what different
>>>>>> aspects of SED-ML were being tested in each?  Is that overkill, not enough,
>>>>>> just right?
>>>>
>>>> I think that makes sense, and if you, Lucian, are willing and able to
>>>> set something like that up then it would be a great resource for the
>>>> community. As long as it is something that is easy to maintain and add
>>>> to over time, then I'd imagine once the initial hurdle of setting it
>>>> up is achieved, then we should be able to keep improving it with
>>>> future releases of the specification.
>>>>
>>>>>> Secondly, if you have files you're using that you'd be willing to send
>>>>>> in/deposit/point me to somewhere, that'd be great!
>>>>
>>>> Something like a github repo where we could submit pull requests to
>>>> bring in more tests or corrections to existing tests would seem to be
>>>> a good way to get the community contributing tests. Would provide a
>>>> good forum to discuss the "correctness" of specific tests as well :)
>>>>
>>>>
>>>> Cheers,
>>>> David.
>>>>
>>>
>>>>> ------------------------------------------------------------------------------
>>>> Go from Idea to Many App Stores Faster with Intel(R) XDK
>>>> Give your users amazing mobile app experiences with Intel(R) XDK.
>>>> Use one codebase in this all-in-one HTML5 development environment.
>>>> Design, debug & build mobile apps & 2D/3D high-impact games for multiple
>>>> OSs.
>>>> http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140
>>>> _______________________________________________
>>>> SED-ML-discuss mailing list
>>>> SED...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Go from Idea to Many App Stores Faster with Intel(R) XDK
>>> Give your users amazing mobile app experiences with Intel(R) XDK.
>>> Use one codebase in this all-in-one HTML5 development environment.
>>> Design, debug & build mobile apps & 2D/3D high-impact games for multiple
>>> OSs.
>>> http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140
>>> _______________________________________________
>>> SED-ML-discuss mailing list
>>> SED...@li...
>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>
>>
>> ------------------------------------------------------------------------------
>> Go from Idea to Many App Stores Faster with Intel(R) XDK
>> Give your users amazing mobile app experiences with Intel(R) XDK.
>> Use one codebase in this all-in-one HTML5 development environment.
>> Design, debug & build mobile apps & 2D/3D high-impact games for multiple
>> OSs.
>> http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140
>> _______________________________________________
>> SED-ML-discuss mailing list
>> SED...@li...
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>
> 
> 
> 

Re: [SED-ML-discuss] A SED-ML Test suite?

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

Thanks Lucian - that is a great start. Now we just need to fill that
contributions folder up :)

I think it is fine to include Antimony or phraSED-ML in the
description (or any other domain specific simple text format people
use).


Cheers,
David.

On Thu, Dec 3, 2015 at 1:15 PM, Lucian Smith <luc...@gm...> wrote:
> I agree that we can model the suite after the SBML test suite, but it should
> both be its own thing, and have CellML models in it, too. In fact, I think
> that each directory/test should basically be modeling-language agnostic--the
> point is to test SED-ML, not the modeling.
>
> I put together a bare-bones repository with a single test in it on github so
> we can have an actual thing to talk about:
>
> https://github.com/luciansmith/sedml-test-suite/
>
> If anyone wants access to it, I'll gladly add them to the 'collaborators'
> list, which I think should work?  Github and I don't get along all that well
> ;-)
>
> I modeled everything off of the SBML test suite, with some changes:  I now
> have an 'info' file instead of the '.m' file in the SBML test suite, which
> was an artifact of how the tests used to be created.  There's no longer a
> 'settings' file, since everything there in the SBML test suite is here
> covered by SED-ML itself.
>
> All suggestions welcome!
>
> -Lucian
>
>
> On Dec 2, 2015 12:54 AM, "Alan Garny" <ala...@in...> wrote:
>>
>> +1 regarding David’s suggestion of a GitHub repository for a SED-ML test
>> suite and a test suite that is not SBML centric. And, as much as possible, I
>> would be happy to contribute to it when it comes to CellML.
>>
>>
>>
>> Alan
>>
>> On 02/12/2015, 03:07, "David Nickerson" <dav...@gm...> wrote:
>>
>> >> To make this effective, I think it would be nice to integrate with the
>> >> SBML Test Suite, since comparing simulation results is again what you will
>> >> need to do.  You already have some SED-ML files there, so it would mostly be
>> >> adding some more sophisticated ones.
>> >>
>> >
>> >I think that since we need to cater to a broader community than SBML,
>> >the SED-ML test suite should be independent from the SBML test suite,
>> >but it would be fine to be using the same framework if that can be
>> >easily adapted and used in such a manner. I have an inking that
>> >discussing this in the past with SBML developers that this might not
>> >be such a straightforward task...
>> >
>> >>> It seems like it would be really helpful to have a
>> >>> collectively-agreed-on test suite that put SED-ML through its paces, to make
>> >>> sure everyone agreed that the same file meant the same thing to everyone.
>> >>> At least, I assume that this doesn't already exist and I missed it?
>> >>>
>> >
>> >No, nothing like that exists in a general sense. I know a few tools
>> >that probably have their own internal tests, but nothing commonly used
>> >by more than one tool.
>> >
>> >>> Assuming it doesn't, two questions:  if I started putting such a thing
>> >>> together, would making it have the same format as the SBML Test Suite work
>> >>> for everyone--directory-demarked sets of files with input files, expected
>> >>> output files, and a setup file that listed with 'tags' what different
>> >>> aspects of SED-ML were being tested in each?  Is that overkill, not enough,
>> >>> just right?
>> >
>> >I think that makes sense, and if you, Lucian, are willing and able to
>> >set something like that up then it would be a great resource for the
>> >community. As long as it is something that is easy to maintain and add
>> >to over time, then I'd imagine once the initial hurdle of setting it
>> >up is achieved, then we should be able to keep improving it with
>> >future releases of the specification.
>> >
>> >>> Secondly, if you have files you're using that you'd be willing to send
>> >>> in/deposit/point me to somewhere, that'd be great!
>> >
>> >Something like a github repo where we could submit pull requests to
>> >bring in more tests or corrections to existing tests would seem to be
>> >a good way to get the community contributing tests. Would provide a
>> >good forum to discuss the "correctness" of specific tests as well :)
>> >
>> >
>> >Cheers,
>> >David.
>> >
>>
>> > >------------------------------------------------------------------------------
>> >Go from Idea to Many App Stores Faster with Intel(R) XDK
>> >Give your users amazing mobile app experiences with Intel(R) XDK.
>> >Use one codebase in this all-in-one HTML5 development environment.
>> >Design, debug & build mobile apps & 2D/3D high-impact games for multiple
>> > OSs.
>> >http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140
>> >_______________________________________________
>> >SED-ML-discuss mailing list
>> >SED...@li...
>> >https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Go from Idea to Many App Stores Faster with Intel(R) XDK
>> Give your users amazing mobile app experiences with Intel(R) XDK.
>> Use one codebase in this all-in-one HTML5 development environment.
>> Design, debug & build mobile apps & 2D/3D high-impact games for multiple
>> OSs.
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>> _______________________________________________
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>> SED...@li...
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
>
> ------------------------------------------------------------------------------
> Go from Idea to Many App Stores Faster with Intel(R) XDK
> Give your users amazing mobile app experiences with Intel(R) XDK.
> Use one codebase in this all-in-one HTML5 development environment.
> Design, debug & build mobile apps & 2D/3D high-impact games for multiple
> OSs.
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> _______________________________________________
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>



-- 


David Nickerson
about.me/david.nickerson

Re: [SED-ML-discuss] A SED-ML Test suite?

[Lucian S. <luc...@gm...>]

I agree that we can model the suite after the SBML test suite, but it
should both be its own thing, and have CellML models in it, too. In fact, I
think that each directory/test should basically be modeling-language
agnostic--the point is to test SED-ML, not the modeling.

I put together a bare-bones repository with a single test in it on github
so we can have an actual thing to talk about:

https://github.com/luciansmith/sedml-test-suite/

If anyone wants access to it, I'll gladly add them to the 'collaborators'
list, which I think should work?  Github and I don't get along all that
well ;-)

I modeled everything off of the SBML test suite, with some changes:  I now
have an 'info' file instead of the '.m' file in the SBML test suite, which
was an artifact of how the tests used to be created.  There's no longer a
'settings' file, since everything there in the SBML test suite is here
covered by SED-ML itself.

All suggestions welcome!

-Lucian


On Dec 2, 2015 12:54 AM, "Alan Garny" <ala...@in...> wrote:

> +1 regarding David’s suggestion of a GitHub repository for a SED-ML test
> suite and a test suite that is not SBML centric. And, as much as possible,
> I would be happy to contribute to it when it comes to CellML.
>
>
>
> Alan
>
> On 02/12/2015, 03:07, "David Nickerson" <dav...@gm...> wrote:
>
> >> To make this effective, I think it would be nice to integrate with the
> SBML Test Suite, since comparing simulation results is again what you will
> need to do.  You already have some SED-ML files there, so it would mostly
> be adding some more sophisticated ones.
> >>
> >
> >I think that since we need to cater to a broader community than SBML,
> >the SED-ML test suite should be independent from the SBML test suite,
> >but it would be fine to be using the same framework if that can be
> >easily adapted and used in such a manner. I have an inking that
> >discussing this in the past with SBML developers that this might not
> >be such a straightforward task...
> >
> >>> It seems like it would be really helpful to have a
> collectively-agreed-on test suite that put SED-ML through its paces, to
> make sure everyone agreed that the same file meant the same thing to
> everyone.  At least, I assume that this doesn't already exist and I missed
> it?
> >>>
> >
> >No, nothing like that exists in a general sense. I know a few tools
> >that probably have their own internal tests, but nothing commonly used
> >by more than one tool.
> >
> >>> Assuming it doesn't, two questions:  if I started putting such a thing
> together, would making it have the same format as the SBML Test Suite work
> for everyone--directory-demarked sets of files with input files, expected
> output files, and a setup file that listed with 'tags' what different
> aspects of SED-ML were being tested in each?  Is that overkill, not enough,
> just right?
> >
> >I think that makes sense, and if you, Lucian, are willing and able to
> >set something like that up then it would be a great resource for the
> >community. As long as it is something that is easy to maintain and add
> >to over time, then I'd imagine once the initial hurdle of setting it
> >up is achieved, then we should be able to keep improving it with
> >future releases of the specification.
> >
> >>> Secondly, if you have files you're using that you'd be willing to send
> in/deposit/point me to somewhere, that'd be great!
> >
> >Something like a github repo where we could submit pull requests to
> >bring in more tests or corrections to existing tests would seem to be
> >a good way to get the community contributing tests. Would provide a
> >good forum to discuss the "correctness" of specific tests as well :)
> >
> >
> >Cheers,
> >David.
> >
>
> >------------------------------------------------------------------------------
> >Go from Idea to Many App Stores Faster with Intel(R) XDK
> >Give your users amazing mobile app experiences with Intel(R) XDK.
> >Use one codebase in this all-in-one HTML5 development environment.
> >Design, debug & build mobile apps & 2D/3D high-impact games for multiple
> OSs.
> >http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140
> >_______________________________________________
> >SED-ML-discuss mailing list
> >SED...@li...
> >https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
>
>
> ------------------------------------------------------------------------------
> Go from Idea to Many App Stores Faster with Intel(R) XDK
> Give your users amazing mobile app experiences with Intel(R) XDK.
> Use one codebase in this all-in-one HTML5 development environment.
> Design, debug & build mobile apps & 2D/3D high-impact games for multiple
> OSs.
> http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>

Re: [SED-ML-discuss] A SED-ML Test suite?

[Chris J. M. <my...@ec...>]

I think using the SBML test suite infrastructure for both SBML and CellML examples should be possible.  Right now, the test suite includes examples for many versions of SBML, it would be cool if it also included CellML versions when applicable.  In fact, mixed examples where some submodels are SBML and other CellML would be very cool.

Chris

> On Dec 1, 2015, at 7:07 PM, David Nickerson <dav...@gm...> wrote:
> 
>> To make this effective, I think it would be nice to integrate with the SBML Test Suite, since comparing simulation results is again what you will need to do.  You already have some SED-ML files there, so it would mostly be adding some more sophisticated ones.
>> 
> 
> I think that since we need to cater to a broader community than SBML,
> the SED-ML test suite should be independent from the SBML test suite,
> but it would be fine to be using the same framework if that can be
> easily adapted and used in such a manner. I have an inking that
> discussing this in the past with SBML developers that this might not
> be such a straightforward task...
> 
>>> It seems like it would be really helpful to have a collectively-agreed-on test suite that put SED-ML through its paces, to make sure everyone agreed that the same file meant the same thing to everyone.  At least, I assume that this doesn't already exist and I missed it?
>>> 
> 
> No, nothing like that exists in a general sense. I know a few tools
> that probably have their own internal tests, but nothing commonly used
> by more than one tool.
> 
>>> Assuming it doesn't, two questions:  if I started putting such a thing together, would making it have the same format as the SBML Test Suite work for everyone--directory-demarked sets of files with input files, expected output files, and a setup file that listed with 'tags' what different aspects of SED-ML were being tested in each?  Is that overkill, not enough, just right?
> 
> I think that makes sense, and if you, Lucian, are willing and able to
> set something like that up then it would be a great resource for the
> community. As long as it is something that is easy to maintain and add
> to over time, then I'd imagine once the initial hurdle of setting it
> up is achieved, then we should be able to keep improving it with
> future releases of the specification.
> 
>>> Secondly, if you have files you're using that you'd be willing to send in/deposit/point me to somewhere, that'd be great!
> 
> Something like a github repo where we could submit pull requests to
> bring in more tests or corrections to existing tests would seem to be
> a good way to get the community contributing tests. Would provide a
> good forum to discuss the "correctness" of specific tests as well :)
> 
> 
> Cheers,
> David.
> 
> ------------------------------------------------------------------------------
> Go from Idea to Many App Stores Faster with Intel(R) XDK
> Give your users amazing mobile app experiences with Intel(R) XDK.
> Use one codebase in this all-in-one HTML5 development environment.
> Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs.
> http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

Re: [SED-ML-discuss] A SED-ML Test suite?

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

+1 from me as well.

Best wishes,
Jonathan

On 02/12/2015 08:53, Alan Garny wrote:
> +1 regarding David’s suggestion of a GitHub repository for a SED-ML test suite and a test suite that is not SBML centric. And, as much as possible, I would be happy to contribute to it when it comes to CellML.
>
>
>
> Alan
>
> On 02/12/2015, 03:07, "David Nickerson" <dav...@gm...> wrote:
>
>>> To make this effective, I think it would be nice to integrate with the SBML Test Suite, since comparing simulation results is again what you will need to do.  You already have some SED-ML files there, so it would mostly be adding some more sophisticated ones.
>>>
>> I think that since we need to cater to a broader community than SBML,
>> the SED-ML test suite should be independent from the SBML test suite,
>> but it would be fine to be using the same framework if that can be
>> easily adapted and used in such a manner. I have an inking that
>> discussing this in the past with SBML developers that this might not
>> be such a straightforward task...
>>
>>>> It seems like it would be really helpful to have a collectively-agreed-on test suite that put SED-ML through its paces, to make sure everyone agreed that the same file meant the same thing to everyone.  At least, I assume that this doesn't already exist and I missed it?
>>>>
>> No, nothing like that exists in a general sense. I know a few tools
>> that probably have their own internal tests, but nothing commonly used
>> by more than one tool.
>>
>>>> Assuming it doesn't, two questions:  if I started putting such a thing together, would making it have the same format as the SBML Test Suite work for everyone--directory-demarked sets of files with input files, expected output files, and a setup file that listed with 'tags' what different aspects of SED-ML were being tested in each?  Is that overkill, not enough, just right?
>> I think that makes sense, and if you, Lucian, are willing and able to
>> set something like that up then it would be a great resource for the
>> community. As long as it is something that is easy to maintain and add
>> to over time, then I'd imagine once the initial hurdle of setting it
>> up is achieved, then we should be able to keep improving it with
>> future releases of the specification.
>>
>>>> Secondly, if you have files you're using that you'd be willing to send in/deposit/point me to somewhere, that'd be great!
>> Something like a github repo where we could submit pull requests to
>> bring in more tests or corrections to existing tests would seem to be
>> a good way to get the community contributing tests. Would provide a
>> good forum to discuss the "correctness" of specific tests as well :)
>>
>>
>> Cheers,
>> David.
>>
>> ------------------------------------------------------------------------------
>> Go from Idea to Many App Stores Faster with Intel(R) XDK
>> Give your users amazing mobile app experiences with Intel(R) XDK.
>> Use one codebase in this all-in-one HTML5 development environment.
>> Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs.
>> http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140
>> _______________________________________________
>> SED-ML-discuss mailing list
>> SED...@li...
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
> ------------------------------------------------------------------------------
> Go from Idea to Many App Stores Faster with Intel(R) XDK
> Give your users amazing mobile app experiences with Intel(R) XDK.
> Use one codebase in this all-in-one HTML5 development environment.
> Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs.
> http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

Re: [SED-ML-discuss] A SED-ML Test suite?

[Alan G. <ala...@in...>]

+1 regarding David’s suggestion of a GitHub repository for a SED-ML test suite and a test suite that is not SBML centric. And, as much as possible, I would be happy to contribute to it when it comes to CellML.



Alan

On 02/12/2015, 03:07, "David Nickerson" <dav...@gm...> wrote:

>> To make this effective, I think it would be nice to integrate with the SBML Test Suite, since comparing simulation results is again what you will need to do.  You already have some SED-ML files there, so it would mostly be adding some more sophisticated ones.
>>
>
>I think that since we need to cater to a broader community than SBML,
>the SED-ML test suite should be independent from the SBML test suite,
>but it would be fine to be using the same framework if that can be
>easily adapted and used in such a manner. I have an inking that
>discussing this in the past with SBML developers that this might not
>be such a straightforward task...
>
>>> It seems like it would be really helpful to have a collectively-agreed-on test suite that put SED-ML through its paces, to make sure everyone agreed that the same file meant the same thing to everyone.  At least, I assume that this doesn't already exist and I missed it?
>>>
>
>No, nothing like that exists in a general sense. I know a few tools
>that probably have their own internal tests, but nothing commonly used
>by more than one tool.
>
>>> Assuming it doesn't, two questions:  if I started putting such a thing together, would making it have the same format as the SBML Test Suite work for everyone--directory-demarked sets of files with input files, expected output files, and a setup file that listed with 'tags' what different aspects of SED-ML were being tested in each?  Is that overkill, not enough, just right?
>
>I think that makes sense, and if you, Lucian, are willing and able to
>set something like that up then it would be a great resource for the
>community. As long as it is something that is easy to maintain and add
>to over time, then I'd imagine once the initial hurdle of setting it
>up is achieved, then we should be able to keep improving it with
>future releases of the specification.
>
>>> Secondly, if you have files you're using that you'd be willing to send in/deposit/point me to somewhere, that'd be great!
>
>Something like a github repo where we could submit pull requests to
>bring in more tests or corrections to existing tests would seem to be
>a good way to get the community contributing tests. Would provide a
>good forum to discuss the "correctness" of specific tests as well :)
>
>
>Cheers,
>David.
>
>------------------------------------------------------------------------------
>Go from Idea to Many App Stores Faster with Intel(R) XDK
>Give your users amazing mobile app experiences with Intel(R) XDK.
>Use one codebase in this all-in-one HTML5 development environment.
>Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs.
>http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140
>_______________________________________________
>SED-ML-discuss mailing list
>SED...@li...
>https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

Re: [SED-ML-discuss] A SED-ML Test suite?

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

> To make this effective, I think it would be nice to integrate with the SBML Test Suite, since comparing simulation results is again what you will need to do.  You already have some SED-ML files there, so it would mostly be adding some more sophisticated ones.
>

I think that since we need to cater to a broader community than SBML,
the SED-ML test suite should be independent from the SBML test suite,
but it would be fine to be using the same framework if that can be
easily adapted and used in such a manner. I have an inking that
discussing this in the past with SBML developers that this might not
be such a straightforward task...

>> It seems like it would be really helpful to have a collectively-agreed-on test suite that put SED-ML through its paces, to make sure everyone agreed that the same file meant the same thing to everyone.  At least, I assume that this doesn't already exist and I missed it?
>>

No, nothing like that exists in a general sense. I know a few tools
that probably have their own internal tests, but nothing commonly used
by more than one tool.

>> Assuming it doesn't, two questions:  if I started putting such a thing together, would making it have the same format as the SBML Test Suite work for everyone--directory-demarked sets of files with input files, expected output files, and a setup file that listed with 'tags' what different aspects of SED-ML were being tested in each?  Is that overkill, not enough, just right?

I think that makes sense, and if you, Lucian, are willing and able to
set something like that up then it would be a great resource for the
community. As long as it is something that is easy to maintain and add
to over time, then I'd imagine once the initial hurdle of setting it
up is achieved, then we should be able to keep improving it with
future releases of the specification.

>> Secondly, if you have files you're using that you'd be willing to send in/deposit/point me to somewhere, that'd be great!

Something like a github repo where we could submit pull requests to
bring in more tests or corrections to existing tests would seem to be
a good way to get the community contributing tests. Would provide a
good forum to discuss the "correctness" of specific tests as well :)


Cheers,
David.

Re: [SED-ML-discuss] A SED-ML Test suite?

[Chris J. M. <my...@ec...>]

To make this effective, I think it would be nice to integrate with the SBML Test Suite, since comparing simulation results is again what you will need to do.  You already have some SED-ML files there, so it would mostly be adding some more sophisticated ones.

Chris

> On Dec 1, 2015, at 5:50 PM, Lucian Smith <luc...@gm...> wrote:
> 
> So, as I'm getting my software ready for an official 1.0 release, I've been creating a lot of test files to make sure everything is interpreted correctly. However, they're all test files that I've created myself, so I'm not 100% sure that everyone else would interpret them the same way.  
> 
> It seems like it would be really helpful to have a collectively-agreed-on test suite that put SED-ML through its paces, to make sure everyone agreed that the same file meant the same thing to everyone.  At least, I assume that this doesn't already exist and I missed it?
> 
> Assuming it doesn't, two questions:  if I started putting such a thing together, would making it have the same format as the SBML Test Suite work for everyone--directory-demarked sets of files with input files, expected output files, and a setup file that listed with 'tags' what different aspects of SED-ML were being tested in each?  Is that overkill, not enough, just right?
> 
> Secondly, if you have files you're using that you'd be willing to send in/deposit/point me to somewhere, that'd be great!
> 
> -Lucian
> ------------------------------------------------------------------------------
> Go from Idea to Many App Stores Faster with Intel(R) XDK
> Give your users amazing mobile app experiences with Intel(R) XDK.
> Use one codebase in this all-in-one HTML5 development environment.
> Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs.
> http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140_______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

[SED-ML-discuss] A SED-ML Test suite?

[Lucian S. <luc...@gm...>]

So, as I'm getting my software ready for an official 1.0 release, I've been
creating a lot of test files to make sure everything is interpreted
correctly. However, they're all test files that I've created myself, so I'm
not 100% sure that everyone else would interpret them the same way.

It seems like it would be really helpful to have a collectively-agreed-on
test suite that put SED-ML through its paces, to make sure everyone agreed
that the same file meant the same thing to everyone.  At least, I assume
that this doesn't already exist and I missed it?

Assuming it doesn't, two questions:  if I started putting such a thing
together, would making it have the same format as the SBML Test Suite work
for everyone--directory-demarked sets of files with input files, expected
output files, and a setup file that listed with 'tags' what different
aspects of SED-ML were being tested in each?  Is that overkill, not enough,
just right?

Secondly, if you have files you're using that you'd be willing to send
in/deposit/point me to somewhere, that'd be great!

-Lucian

[SED-ML-discuss] Call for nominations for one SED-ML editor

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

Hi all,

This is a call for nominations for one SED-ML editor to replace
Jonathan Cooper, whose term ends on the 31st of December 2015. The
length of a SED-ML Editor's term is 3 years, starting from the 1st of
January 2016.

The current editors are Jonathan Cooper (to be replaced), Ion Moraru
(until 2016), Sven Sahle (until 2016), Brett Olivier (until 2017), and
David Nickerson (until 2017). The editor to be replaced is not
suitable to be nominated.

We would like to ask you to nominate suitable candidates. You may
nominate anyone (including yourself) who you think is qualified to act
as an editor. You can fill out this survey multiple times in order to
nominate multiple candidates.

The nomination form is at: http://goo.gl/forms/exTTMuaMS0

The call for nominations will close on December 14 2015.


Cheers,
David, on behalf of the SED-ML Editors.

Re: [SED-ML-discuss] Referencing nested data in repeated tasks

[Lucian S. <luc...@gm...>]

Just to recap our discussion at COMBINE about this:

It turns out that if you read the spec more carefully (which Ilya
fortunately did), you find that any one model for any one task is always
the same model throughout all the repeated subtasks:  if multiple tasks
reference it, it enters the second task from the state it arrived in from
the first task.

This means that as far as tasks go, the only reference you need is to the
model, with the 'modelRef' attribute.

For output, you might only want subsections of the data, and it will be
nice to have an additional constructs to 'slice' the data.  However, for
now, we agreed that the combination of a taskReference and a modelReference
would be sufficient:  you simply then get a record of all the changes that
the model went through during that task, and if there were subtasks
involved, all of the changes that took place during those subtasks are
likewise recorded.  If a model was uninvolved in one of the subtasks, no
data from it would be recorded during that stage of the simulation.

It would probably be helpful to come up with some more-complicated example
files and sample output; I'll see if I can manage to come up with some.

-Lucian

On Thu, Oct 15, 2015 at 12:13 PM, Lucian Smith <luc...@gm...>
wrote:

> Hi, everyone!  At COMBINE yesterday, we had a discussion about (among
> other things) the fact that 'taskReference' and 'modelReference' are
> sometimes not sufficient to uniquely identify a single model:  a repeated
> task may refer to multiple other tasks, which in turn may refer to multiple
> other tasks, which may refer to a variety of models, some of which may be
> the same model used in different simulations.  The example I used was (in
> my 'phraSED-ML' syntax):
>
> t1 = run sim1 on mod1
> t2 = run sim1 on mod2
> t3 = run sim2 on mod1
> t4 = repeat [t1, t2, t3] for t1.mod1.S1 in [1,3,6]
> t5 = repeat [t1, t2, t3] for t3.mod1.S1 in [3,6,10]
> t6 = repeat [t4, t5] for t4.t1.mod1.S1 in [0,1,10]
>
> Here, the last line cannot currently be expressed in SED-ML:  if you want
> to change the value of that particular instance of mod1, you really need to
> know both that it comes from task t1 from task t4.
>
> Similarly, when plotting data, the same issue is present.  We concluded
> that in that situation, we really need a way to get at particular results,
> and Frank suggested using a 'slicing' system similar to what is currently
> proposed for external data.
>
> However, this system seemed more difficult to implement in the 'repeated
> task' context, and we thought that especially since this was a made-up
> example designed to test the limits of SED-ML (I created it as a test case
> as I was implementing support for phraSED-ML), and because the restriction
> could be worked around by creating copies of models and using those
> instead, we could simply say in the spec something like "If multiple
> instantiated models match what is referenced by the combination of a
> 'taskReference' and 'modelReference', the assignment applies to all
> instances of that model."
>
> However, I realized last night that there is another problem:  if an
> ambiguous reference to a symbol is used to assign *to* another variable.
> In my above example:
>
> t6 = repeat [t4, t5] for t4.t1.mod1.S1 in [0,1,10], mod2.S3 = mod1.S1
>
> 'mod2.S3' is ambiguous, which is OK:  we just apply the assignment to all
> copies of mod2.S3.  But which version of mod1.S1 do we use?  If we say 'use
> any of them', we sacrifice reproducibility.  But what are our alternatives?
>
> I think we have two options:
>
> 1) Create a slicing system similar for repeated task variables, just like
> Frank proposed for plotting variables and for external data.
> 2) Declare that the above situation is invalid SED-ML.
>
> Either one is fine by me, as neither are ambiguous.  The second is
> obviously much easier to implement.  And again, if there were any use cases
> for this situation, you could resolve it by making multiple copies of the
> ambiguous models.
>
> I would also be OK with saying that instead of saying 'apply the
> assignment to all copies of the model' you just say 'it's illegal to do
> that', if we're going to declare this situation illegal, too.  But what do
> others think?
>
> -Lucian
>
>

[SED-ML-discuss] Referencing nested data in repeated tasks

[Lucian S. <luc...@gm...>]

Hi, everyone!  At COMBINE yesterday, we had a discussion about (among other
things) the fact that 'taskReference' and 'modelReference' are sometimes
not sufficient to uniquely identify a single model:  a repeated task may
refer to multiple other tasks, which in turn may refer to multiple other
tasks, which may refer to a variety of models, some of which may be the
same model used in different simulations.  The example I used was (in my
'phraSED-ML' syntax):

t1 = run sim1 on mod1
t2 = run sim1 on mod2
t3 = run sim2 on mod1
t4 = repeat [t1, t2, t3] for t1.mod1.S1 in [1,3,6]
t5 = repeat [t1, t2, t3] for t3.mod1.S1 in [3,6,10]
t6 = repeat [t4, t5] for t4.t1.mod1.S1 in [0,1,10]

Here, the last line cannot currently be expressed in SED-ML:  if you want
to change the value of that particular instance of mod1, you really need to
know both that it comes from task t1 from task t4.

Similarly, when plotting data, the same issue is present.  We concluded
that in that situation, we really need a way to get at particular results,
and Frank suggested using a 'slicing' system similar to what is currently
proposed for external data.

However, this system seemed more difficult to implement in the 'repeated
task' context, and we thought that especially since this was a made-up
example designed to test the limits of SED-ML (I created it as a test case
as I was implementing support for phraSED-ML), and because the restriction
could be worked around by creating copies of models and using those
instead, we could simply say in the spec something like "If multiple
instantiated models match what is referenced by the combination of a
'taskReference' and 'modelReference', the assignment applies to all
instances of that model."

However, I realized last night that there is another problem:  if an
ambiguous reference to a symbol is used to assign *to* another variable.
In my above example:

t6 = repeat [t4, t5] for t4.t1.mod1.S1 in [0,1,10], mod2.S3 = mod1.S1

'mod2.S3' is ambiguous, which is OK:  we just apply the assignment to all
copies of mod2.S3.  But which version of mod1.S1 do we use?  If we say 'use
any of them', we sacrifice reproducibility.  But what are our alternatives?

I think we have two options:

1) Create a slicing system similar for repeated task variables, just like
Frank proposed for plotting variables and for external data.
2) Declare that the above situation is invalid SED-ML.

Either one is fine by me, as neither are ambiguous.  The second is
obviously much easier to implement.  And again, if there were any use cases
for this situation, you could resolve it by making multiple copies of the
ambiguous models.

I would also be OK with saying that instead of saying 'apply the assignment
to all copies of the model' you just say 'it's illegal to do that', if
we're going to declare this situation illegal, too.  But what do others
think?

-Lucian

[SED-ML-discuss] SED-ML discussions at COMBINE 2015

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

Hi all,

I have just started a google doc to try and capture the SED-ML
discussion at COMBINE. You can access it here:
https://docs.google.com/document/d/1dgm6hGCK8MbxlrkXY-fdU1Y9UTph4G7WQ_Xjhq6HipU/edit?usp=sharing



Cheers,
David.

-- 


David Nickerson
about.me/david.nickerson

Re: [SED-ML-discuss] Using data with SED-ML at Combine

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

Hello Felix, 

the comments you sent have reached the SED-ML editors. As you know I’m not an editor, but would assume that they added the information to the spec, but they have not yet released an updated version. 

best
Frank

> On Sep 21, 2015, at 7:08 PM, Felix Winter <wi...@ka...> wrote:
> 
>>> 
>>> Basically, how stable is this draft?
>>> 
>> 
>> it is very stable, it resulted from discussions that happened two years ago,
>> and have not changed much since. primarily because other implementations were
>> missing … 
>> 
> 
> Frank, can you by any chance say what happened to the comments I did send last
> September to sed-ml-editors? I remember that I found a few typos and some
> ambiguity and it might be a good idea to create a public draft where these
> issues have been resolved. There were also some comments on the language design
> but I'm totally ok with these being ignored ;)
> 
> Felix
> 
> ------------------------------------------------------------------------------
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

Re: [SED-ML-discuss] Using data with SED-ML at Combine

[Lucian S. <luc...@gm...>]

I would think that investigation into the numerical issues would be well
served by having a robust SED-ML that could reliably exchange the formal
description of the problem in the first place.  Once the problem has been
clearly stated, different numerical approaches to achieving the answer
could be directly compared without worrying that different situations were
being compared erroneously.

It's sort of like SBML describing the model, and using it to compare a
stochastic vs. a deterministic simulation.  You know the only difference is
in how you ran it, and that other errors didn't creep into the description
of the model itself.

-Lucian

On Mon, Sep 21, 2015 at 9:22 AM, Herbert Sauro <hs...@gm...> wrote:

> I agree with Pedro, the big elephant in the room are the numerical issues
> with multiple-simulation scenarios which is not being addressed.
>
> Herbert
>
> On Fri, Sep 18, 2015 at 1:30 PM, Pedro Mendes <
> ped...@ma...> wrote:
>
>>
>>
>> On 09/18/2015 09:22 AM, Ally Hume wrote:
>> > It would be interesting to explore the options to be more declarative
>> > and simply specify an interpolation algorithm using an ontology
>> > rather than trying generate the piecewise function within the SED-ML
>> > document using xpath manipulation. But this could be a discussion for
>> > Combine.
>>
>> Actually when I had to do this I have used a general purpose function
>> fitter (Eureqa, which uses genetic programming) to obtain a non-linear
>> function that best fits the data (best in the sense of Akaike). Then
>> this continuous function is used in the model in place of the data. Of
>> course, this is a bit complicated but is a much better approach if the
>> rest of the model is continuous and is going to be integrated by an ODE
>> solver (which generally only work well with continuous functions).
>>
>> But I agree that we should develop a strategy in SED-ML to cope with
>> multiple-simulation scenarios. It is a problem that is much deeper than
>> simply coming up with a descriptive language (ML standard), as there are
>> serious numerical issues that I don't think have a proper solution at
>> this time (also with the current implementations like Karr et al).
>>
>> Pedro
>>
>> --
>> Pedro Mendes
>> Professor of Computational Systems Biology
>> School of Computer Science
>> Manchester Centre for Integrative Systems Biology
>> University of Manchester
>>
>> Manchester Institute of Biotechnology
>> 131 Princess Street
>> Manchester, M1 7DN, U.K.
>>
>>
>> ------------------------------------------------------------------------------
>> _______________________________________________
>> SED-ML-discuss mailing list
>> SED...@li...
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>
>
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
>

Re: [SED-ML-discuss] Using data with SED-ML at Combine

[Felix W. <wi...@ka...>]

> > 
> > Basically, how stable is this draft?
> > 
> 
> it is very stable, it resulted from discussions that happened two years ago,
> and have not changed much since. primarily because other implementations were
> missing … 
> 

Frank, can you by any chance say what happened to the comments I did send last
September to sed-ml-editors? I remember that I found a few typos and some
ambiguity and it might be a good idea to create a public draft where these
issues have been resolved. There were also some comments on the language design
but I'm totally ok with these being ignored ;)

Felix

Re: [SED-ML-discuss] Using data with SED-ML at Combine

[Felix W. <wi...@ka...>]

Hi everyone, 

just out of curiosity, can someone point us to a relevant publication regarding
the numerical issues? While I trust that your assessment of the situation is
correct this should not prevent SED-ML from allowing data to be included in
simple ways, such as different kinds of interpolation. I personally have good
experience with cubic splines which guarantee at least two times continuous
differentiability which should be enough "smoothness" for most uses.

Thanks,

Felix

> On September 21, 2015 at 6:22 PM Herbert Sauro <hs...@gm...> wrote:
> 
> 
> I agree with Pedro, the big elephant in the room are the numerical issues
> with multiple-simulation scenarios which is not being addressed.
> 
> Herbert
> 
> On Fri, Sep 18, 2015 at 1:30 PM, Pedro Mendes <ped...@ma...
> > wrote:
> 
> >
> >
> > On 09/18/2015 09:22 AM, Ally Hume wrote:
> > > It would be interesting to explore the options to be more declarative
> > > and simply specify an interpolation algorithm using an ontology
> > > rather than trying generate the piecewise function within the SED-ML
> > > document using xpath manipulation. But this could be a discussion for
> > > Combine.
> >
> > Actually when I had to do this I have used a general purpose function
> > fitter (Eureqa, which uses genetic programming) to obtain a non-linear
> > function that best fits the data (best in the sense of Akaike). Then
> > this continuous function is used in the model in place of the data. Of
> > course, this is a bit complicated but is a much better approach if the
> > rest of the model is continuous and is going to be integrated by an ODE
> > solver (which generally only work well with continuous functions).
> >
> > But I agree that we should develop a strategy in SED-ML to cope with
> > multiple-simulation scenarios. It is a problem that is much deeper than
> > simply coming up with a descriptive language (ML standard), as there are
> > serious numerical issues that I don't think have a proper solution at
> > this time (also with the current implementations like Karr et al).
> >
> > Pedro
> >
> > --
> > Pedro Mendes
> > Professor of Computational Systems Biology
> > School of Computer Science
> > Manchester Centre for Integrative Systems Biology
> > University of Manchester
> >
> > Manchester Institute of Biotechnology
> > 131 Princess Street
> > Manchester, M1 7DN, U.K.
> >
> >
> > ------------------------------------------------------------------------------
> > _______________________________________________
> > SED-ML-discuss mailing list
> > SED...@li...
> > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
> >
> ------------------------------------------------------------------------------
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
Felix Winter
Thomas-Müntzer-Platz 63
18057 Rostock, Germany

IM: fw...@ja...

Re: [SED-ML-discuss] Using data with SED-ML at Combine

[Herbert S. <hs...@gm...>]

I agree with Pedro, the big elephant in the room are the numerical issues
with multiple-simulation scenarios which is not being addressed.

Herbert

On Fri, Sep 18, 2015 at 1:30 PM, Pedro Mendes <ped...@ma...
> wrote:

>
>
> On 09/18/2015 09:22 AM, Ally Hume wrote:
> > It would be interesting to explore the options to be more declarative
> > and simply specify an interpolation algorithm using an ontology
> > rather than trying generate the piecewise function within the SED-ML
> > document using xpath manipulation. But this could be a discussion for
> > Combine.
>
> Actually when I had to do this I have used a general purpose function
> fitter (Eureqa, which uses genetic programming) to obtain a non-linear
> function that best fits the data (best in the sense of Akaike). Then
> this continuous function is used in the model in place of the data. Of
> course, this is a bit complicated but is a much better approach if the
> rest of the model is continuous and is going to be integrated by an ODE
> solver (which generally only work well with continuous functions).
>
> But I agree that we should develop a strategy in SED-ML to cope with
> multiple-simulation scenarios. It is a problem that is much deeper than
> simply coming up with a descriptive language (ML standard), as there are
> serious numerical issues that I don't think have a proper solution at
> this time (also with the current implementations like Karr et al).
>
> Pedro
>
> --
> Pedro Mendes
> Professor of Computational Systems Biology
> School of Computer Science
> Manchester Centre for Integrative Systems Biology
> University of Manchester
>
> Manchester Institute of Biotechnology
> 131 Princess Street
> Manchester, M1 7DN, U.K.
>
>
> ------------------------------------------------------------------------------
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>

Re: [SED-ML-discuss] Using data with SED-ML at Combine

[Pedro M. <ped...@ma...>]

On 09/18/2015 09:22 AM, Ally Hume wrote:
> It would be interesting to explore the options to be more declarative
> and simply specify an interpolation algorithm using an ontology
> rather than trying generate the piecewise function within the SED-ML
> document using xpath manipulation. But this could be a discussion for
> Combine.

Actually when I had to do this I have used a general purpose function 
fitter (Eureqa, which uses genetic programming) to obtain a non-linear 
function that best fits the data (best in the sense of Akaike). Then 
this continuous function is used in the model in place of the data. Of 
course, this is a bit complicated but is a much better approach if the 
rest of the model is continuous and is going to be integrated by an ODE 
solver (which generally only work well with continuous functions).

But I agree that we should develop a strategy in SED-ML to cope with 
multiple-simulation scenarios. It is a problem that is much deeper than 
simply coming up with a descriptive language (ML standard), as there are 
serious numerical issues that I don't think have a proper solution at 
this time (also with the current implementations like Karr et al).

Pedro

-- 
Pedro Mendes
Professor of Computational Systems Biology
School of Computer Science
Manchester Centre for Integrative Systems Biology
University of Manchester

Manchester Institute of Biotechnology
131 Princess Street
Manchester, M1 7DN, U.K.

Re: [SED-ML-discuss] Using data with SED-ML at Combine

[Ally H. <a....@ed...>]

I'll maybe give it a go and try to see how I can write up linear interpolation in xpath and use the computeChange functionality.  We'll see how it goes. I accept I may be trying to twist things to fit a use case different to what was in mind when the spec was designed.

It would be interesting to explore the options to be more declarative and simply specify an interpolation algorithm using an ontology rather than trying generate the piecewise function within the SED-ML document using xpath manipulation. But this could be a discussion for Combine.

Regards,

Ally


Ally Hume
Researcher, SynthSys, The University of Edinburgh
Software and Data Architect, EPCC, The University of Edinburgh



On 17 Sep 2015, at 20:15, Frank Bergmann <fbe...@ca...> wrote:

> Actually that is in the proposal, one of the primary differences in 1.3 is, that it is possible to refer to elements in the SED-ML document itself using the xpath expressions (i.e when model / taskreferences are not given). This allows the use of all sliced data  to be refered from data. In the example there is just a basic one that demonstrates how to define a data generator that references data, but the same would apply to computeChange, the range with math expressions and of course the setValue element. 
> 
> so this is already in there as far as I’m concerned. But I would be happy if people wanted to use the time to express examples as well during combine … 
> 
> cheers
> Frank
> 
> 
>> On Sep 17, 2015, at 6:17 PM, Nicolas Le Novere <n.l...@gm...> wrote:
>> 
>> Indeed. This would require two things:
>> 
>> 1- a way to call a DataSource from the parameter attribute of a change class.
>> 2- a way to change variable at runtime.
>> 
>> I thing 2) can be solved with a boolean attribute "runTime" on the class Change. If true, the changes are made during the simulation (synchronisation algorithms are a complete different can of worm). If false, the changes are only performed at initial time. To be honest, until we have that, no hybrid modelling is feasible with SED-ML, neither Karr et al, the dynamic FBA of Covert et al, or our biochemical-electrophysiological models.
>> 
>> 1) will be interesting ...
>> 
>> I believe what you want to do is part of a vast ensemble of models using matrices of values instead of computed values. They are used a lot in other fields, such as ecology, population dynamics etc. We are still catching up with formalism that differ significantly from the ODE+fixed initial conditions paradigm.
>> 
>> All that said, it is very likely that no-one could read back your model and simulation description, and run simulations out of the box. Because no software would understand what you would come up with to solve the problem. So I am almost tempted to say use placeholders for the evolving parameters, provide a NuML file with your values and put a text in the metadata file of the COMBINE archive describing how to generate the correct values at the correct time. Then, the users who really want to use your model just write a python script and create piecewise simulations (run, collect result, modify parameter value, run, append collected results etc.)
>> 
>> On 17/09/15 16:45, Ally Hume wrote:
>>> Hi everyone,
>>> 
>>> I've looked at the L1V3 spec and can't see how I would get time series data into a parameter of an SBML model.
>>> 
>>> The only way I know to represent that data in SBML is as a parameter with an associated piecewise assignment function that implements the interpolation.  I can't see how L1V3 supports the creation of this piecewise function from the data. I can't see how I would generate the XML for this piecewise function and specify that it must be inserted into the model.  So I assume I am talking about entirely new features here, or am I missing something?
>>> 
>>> Ally
>>> 
>>> 
>>> Ally Hume
>>> Researcher, SynthSys, The University of Edinburgh
>>> Software and Data Architect, EPCC, The University of Edinburgh
>>> 
>>> 
>>> 
>>> On 17 Sep 2015, at 09:16, Felix Winter <wi...@ka...> wrote:
>>> 
>>>> Hi everyone,
>>>> 
>>>> If I am not mistaken the current draft for SED-ML L1V3 does only cover part of
>>>> what Ally was proposing. While it provides a link to data (in the NuML format)
>>>> and a way of using it in the SED-ML file itself there is currently no way to
>>>> describe an interpolation algorithm (or any other pre-processing).
>>>> 
>>>> If the pre-processing is not described inside of SED-ML it is quite difficult to
>>>> describe anything slightly more complex than a linear interpolation. For a cubic
>>>> spline interpolation we would still need to pre-process the data and use an SBML
>>>> construct to describe the equation. While just listing (and adressing) the
>>>> individual points of data may be fine for tasks such as parameter value
>>>> estimation this might not suffice if the data is to be used as a continuous
>>>> input into the model.
>>>> 
>>>> I would therefore second the motion to use the COMBINE meeting to think beyond
>>>> the current draft and see whether there is a feasable way to describe the way
>>>> the data is used inside a model using SED-ML.
>>>> 
>>>> As one of the persons who do regularly not attend the COMBINE and the HARMONY
>>>> meetings but is still interested in SED-ML I would be really grateful if someone
>>>> can share any progress made with the mailing-list.
>>>> 
>>>> Thanks,
>>>> Felix
>>>> 
>>>>> On September 17, 2015 at 1:56 AM David Nickerson <dav...@gm...>
>>>>> wrote:
>>>>> 
>>>>> 
>>>>> Hi Ally, Herb, everyone,
>>>>> 
>>>>> We don't have a specific agendas set for any of the SED-ML breakout
>>>>> sessions at the COMBINE meeting and the current session titles reflect
>>>>> topics that we believe to be useful topics to at least kick off the
>>>>> sessions.
>>>>> 
>>>>> Just over a year ago, the SED-ML editors released a draft for the next
>>>>> version of SED-ML which is available here:
>>>>> http://co.mbine.org/specifications/sed-ml.level-1.version-3-draft-1.
>>>>> The main change in this specification is the addition of data to
>>>>> SED-ML and being able to use data to control the simulation
>>>>> experiment, model variables, etc. The additions to the specification
>>>>> represented the consensus achieved during much discussion over the
>>>>> preceding HARMONY and COMBINE meetings (and various google docs, etc).
>>>>> As far as I am aware, there is currently only one implementation that
>>>>> supports the L1V3 draft (Frank Bergmann's .NET framework) and while
>>>>> some of us hoped to get our own implementations up and running at the
>>>>> HARMONY meeting earlier this year, a second implementation has yet to
>>>>> appear. And thus the L1V3 draft is still a draft :)
>>>>> 
>>>>> For the COMBINE breakout on data with SED-ML, it would be good to
>>>>> discuss both the potential implementation of the L1V3 specification in
>>>>> code as well as producing some examples or use-cases (to also help
>>>>> address the issue of examples that Lucian has raised on this list
>>>>> recently). So yes - the topics you mentioned Ally would be ideal to
>>>>> discuss. The main background reading would be the L1V3 draft spec
>>>>> (http://co.mbine.org/specifications/sed-ml.level-1.version-3-draft-1)
>>>>> which would also lead you to the NuML specification:
>>>>> https://github.com/NuML/NuML/blob/master/numl-spec-l1v1.pdf. Since the
>>>>> use of data in SED-ML is dependent on NuML, we will also likely be
>>>>> discussing the state of NuML and where that project is heading.
>>>>> 
>>>>> 
>>>>> Cheers,
>>>>> David.
>>>>> 
>>>>> 
>>>>> 
>>>>> On Thu, Sep 17, 2015 at 4:39 AM, Herbert Sauro <hs...@gm...> wrote:
>>>>>> We'd be looking for the same things.
>>>>>> 
>>>>>> Herbert
>>>>>> 
>>>>>> On Wed, Sep 16, 2015 at 7:05 AM, Ally Hume <a....@ed...> wrote:
>>>>>>> 
>>>>>>> Hi,
>>>>>>> 
>>>>>>> I notice that there will be a session at Combine entitled "Using data with
>>>>>>> SED-ML". I was wondering if somebody could tell me a more detailed
>>>>>>> description of what may be discussed here? I've looked in the archives for
>>>>>>> recent posts to this list but nothing seems to cover this topic.
>>>>>>> 
>>>>>>> I've recently been looking at adding external time course data to SBML
>>>>>>> models. In our use case this is temperature data but it could obviously be
>>>>>>> many other measurements as well. I've written code to add external data to
>>>>>>> SBML models as a parameter with an associated assignment rule that defines
>>>>>>> the data using a piecewise function [1]. This works for our purposes but
>>>>>>> does not seem like the cleanest way to do things.
>>>>>>> 
>>>>>>> SED-ML looks like a place where this could be done a lot better.
>>>>>>> 
>>>>>>> Adopting similar strategies to those already used in SED-ML it would be
>>>>>>> nice to include:
>>>>>>> - references to datasets (similar to references to models)
>>>>>>> - link between entities in these datasets and parameters in a model
>>>>>>> - specification of an interpolation algorithm (ontology-based like
>>>>>>> simulation algorithms)
>>>>>>> 
>>>>>>> This would be a considerable improvement over my current approach of
>>>>>>> writing this into SBML where the interpolation algorithm and original
>>>>>>> dataset are effectively lost (although I could add annotations to document
>>>>>>> such details).
>>>>>>> 
>>>>>>> There could also be an argument made for some basic data pre-processing
>>>>>>> possibly similar to the post-processing of result data already in SED-ML.
>>>>>>> 
>>>>>>> I'm sure there will be alternative ideas but I just wondering if this is
>>>>>>> the type of thing that will be in the session.  I will be attending Combine
>>>>>>> but I don't want to wait for the session and discover it's actually on
>>>>>>> something totally different, or discover there is actually a lot of
>>>>>>> background documentation that I could have read in advance.
>>>>>>> 
>>>>>>> Thank you,
>>>>>>> 
>>>>>>> Ally
>>>>>>> 
>>>>>>> [1] https://github.com/allyhume/SBMLDataTools
>>>>>>> 
>>>>>>> 
>>>>>>> Ally Hume
>>>>>>> Researcher, SynthSys, The University of Edinburgh
>>>>>>> Software and Data Architect, EPCC, The University of Edinburgh
>>>>>>> 
>>>>>>> 
>>>>>>> --
>>>>>>> The University of Edinburgh is a charitable body, registered in
>>>>>>> Scotland, with registration number SC005336.
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> ------------------------------------------------------------------------------
>>>>>>> Monitor Your Dynamic Infrastructure at Any Scale With Datadog!
>>>>>>> Get real-time metrics from all of your servers, apps and tools
>>>>>>> in one place.
>>>>>>> SourceForge users - Click here to start your Free Trial of Datadog now!
>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=241902991&iu=/4140
>>>>>>> _______________________________________________
>>>>>>> SED-ML-discuss mailing list
>>>>>>> SED...@li...
>>>>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>>>>> 
>>>>>> 
>>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> --
>>>>> 
>>>>> 
>>>>> David Nickerson
>>>>> about.me/david.nickerson
>>>>> 
>>>> 
>>>>> _______________________________________________
>>>>> SED-ML-discuss mailing list
>>>>> SED...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>>> Felix Winter
>>>> Rostock, Germany
>>>> 
>>>> http://orcid.org/0000-0003-2987-6797
>>>> 
>>>> ------------------------------------------------------------------------------
>>>> Monitor Your Dynamic Infrastructure at Any Scale With Datadog!
>>>> Get real-time metrics from all of your servers, apps and tools
>>>> in one place.
>>>> SourceForge users - Click here to start your Free Trial of Datadog now!
>>>> http://pubads.g.doubleclick.net/gampad/clk?id=241902991&iu=/4140
>>>> _______________________________________________
>>>> SED-ML-discuss mailing list
>>>> SED...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>>> 
>>> 
>>> 
>> 
>> 
>> -- 
>> Nicolas LE NOVERE, Babraham Institute, Babraham Campus Cambridge, CB22 3AT
>> Tel: +441223496433, Mob:+447833147074, twitter:@lenovere, Skype:n.lenovere
>> n.l...@gm..., http://orcid.org/0000-0002-6309-7327
>> http://lenoverelab.org/, http://lenoverelab.org/perso/lenov/
>> 
>> ------------------------------------------------------------------------------
>> Monitor Your Dynamic Infrastructure at Any Scale With Datadog!
>> Get real-time metrics from all of your servers, apps and tools
>> in one place.
>> SourceForge users - Click here to start your Free Trial of Datadog now!
>> http://pubads.g.doubleclick.net/gampad/clk?id=241902991&iu=/4140
>> _______________________________________________
>> SED-ML-discuss mailing list
>> SED...@li...
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
> 
> 
> ------------------------------------------------------------------------------
> Monitor Your Dynamic Infrastructure at Any Scale With Datadog!
> Get real-time metrics from all of your servers, apps and tools
> in one place.
> SourceForge users - Click here to start your Free Trial of Datadog now!
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-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

Re: [SED-ML-discuss] Using data with SED-ML at Combine

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

Sounds like this is going to be a great session to end the meeting on :)

As Felix alluded to, the primary use-case driving the development of
data with SED-ML, to date, has been parameter estimation. Further
background reading is the ongoing google doc on this topic, which is
available here:
https://docs.google.com/document/d/1rrs0fYuKFr4fgL1b7eGwSnaLhRPW6NdXwAaJY0ZN_WY/edit?usp=sharing

It might also be useful to note that the aim of NuML is to describe
multidimensional data, there is no restriction that the data itself be
encoded in the XML file. Previous discussions we've had on this have
limited things to the use of CSV files in order to ease the
implementation burden, but there is no reason not to use HDF5 or other
compact binary formats to store the data. As Frank mentioned, in
previous discussions we have agreed on restricting SED-ML to link to
data in the NuML format which makes the implementation on the SED-ML
side nice and uniform. But this leaves a fair amount of work to be
done in libNuML to start supporting other data formats. This is also
something we can discuss at COMBINE.

Cheers,
David.


On Fri, Sep 18, 2015 at 7:15 AM, Frank Bergmann <fbe...@ca...> wrote:
> Actually that is in the proposal, one of the primary differences in 1.3 is, that it is possible to refer to elements in the SED-ML document itself using the xpath expressions (i.e when model / taskreferences are not given). This allows the use of all sliced data  to be refered from data. In the example there is just a basic one that demonstrates how to define a data generator that references data, but the same would apply to computeChange, the range with math expressions and of course the setValue element.
>
> so this is already in there as far as I’m concerned. But I would be happy if people wanted to use the time to express examples as well during combine …
>
> cheers
> Frank
>
>
>> On Sep 17, 2015, at 6:17 PM, Nicolas Le Novere <n.l...@gm...> wrote:
>>
>> Indeed. This would require two things:
>>
>> 1- a way to call a DataSource from the parameter attribute of a change class.
>> 2- a way to change variable at runtime.
>>
>> I thing 2) can be solved with a boolean attribute "runTime" on the class Change. If true, the changes are made during the simulation (synchronisation algorithms are a complete different can of worm). If false, the changes are only performed at initial time. To be honest, until we have that, no hybrid modelling is feasible with SED-ML, neither Karr et al, the dynamic FBA of Covert et al, or our biochemical-electrophysiological models.
>>
>> 1) will be interesting ...
>>
>> I believe what you want to do is part of a vast ensemble of models using matrices of values instead of computed values. They are used a lot in other fields, such as ecology, population dynamics etc. We are still catching up with formalism that differ significantly from the ODE+fixed initial conditions paradigm.
>>
>> All that said, it is very likely that no-one could read back your model and simulation description, and run simulations out of the box. Because no software would understand what you would come up with to solve the problem. So I am almost tempted to say use placeholders for the evolving parameters, provide a NuML file with your values and put a text in the metadata file of the COMBINE archive describing how to generate the correct values at the correct time. Then, the users who really want to use your model just write a python script and create piecewise simulations (run, collect result, modify parameter value, run, append collected results etc.)
>>
>> On 17/09/15 16:45, Ally Hume wrote:
>>> Hi everyone,
>>>
>>> I've looked at the L1V3 spec and can't see how I would get time series data into a parameter of an SBML model.
>>>
>>> The only way I know to represent that data in SBML is as a parameter with an associated piecewise assignment function that implements the interpolation.  I can't see how L1V3 supports the creation of this piecewise function from the data. I can't see how I would generate the XML for this piecewise function and specify that it must be inserted into the model.  So I assume I am talking about entirely new features here, or am I missing something?
>>>
>>> Ally
>>>
>>>
>>> Ally Hume
>>> Researcher, SynthSys, The University of Edinburgh
>>> Software and Data Architect, EPCC, The University of Edinburgh
>>>
>>>
>>>
>>> On 17 Sep 2015, at 09:16, Felix Winter <wi...@ka...> wrote:
>>>
>>>> Hi everyone,
>>>>
>>>> If I am not mistaken the current draft for SED-ML L1V3 does only cover part of
>>>> what Ally was proposing. While it provides a link to data (in the NuML format)
>>>> and a way of using it in the SED-ML file itself there is currently no way to
>>>> describe an interpolation algorithm (or any other pre-processing).
>>>>
>>>> If the pre-processing is not described inside of SED-ML it is quite difficult to
>>>> describe anything slightly more complex than a linear interpolation. For a cubic
>>>> spline interpolation we would still need to pre-process the data and use an SBML
>>>> construct to describe the equation. While just listing (and adressing) the
>>>> individual points of data may be fine for tasks such as parameter value
>>>> estimation this might not suffice if the data is to be used as a continuous
>>>> input into the model.
>>>>
>>>> I would therefore second the motion to use the COMBINE meeting to think beyond
>>>> the current draft and see whether there is a feasable way to describe the way
>>>> the data is used inside a model using SED-ML.
>>>>
>>>> As one of the persons who do regularly not attend the COMBINE and the HARMONY
>>>> meetings but is still interested in SED-ML I would be really grateful if someone
>>>> can share any progress made with the mailing-list.
>>>>
>>>> Thanks,
>>>> Felix
>>>>
>>>>> On September 17, 2015 at 1:56 AM David Nickerson <dav...@gm...>
>>>>> wrote:
>>>>>
>>>>>
>>>>> Hi Ally, Herb, everyone,
>>>>>
>>>>> We don't have a specific agendas set for any of the SED-ML breakout
>>>>> sessions at the COMBINE meeting and the current session titles reflect
>>>>> topics that we believe to be useful topics to at least kick off the
>>>>> sessions.
>>>>>
>>>>> Just over a year ago, the SED-ML editors released a draft for the next
>>>>> version of SED-ML which is available here:
>>>>> http://co.mbine.org/specifications/sed-ml.level-1.version-3-draft-1.
>>>>> The main change in this specification is the addition of data to
>>>>> SED-ML and being able to use data to control the simulation
>>>>> experiment, model variables, etc. The additions to the specification
>>>>> represented the consensus achieved during much discussion over the
>>>>> preceding HARMONY and COMBINE meetings (and various google docs, etc).
>>>>> As far as I am aware, there is currently only one implementation that
>>>>> supports the L1V3 draft (Frank Bergmann's .NET framework) and while
>>>>> some of us hoped to get our own implementations up and running at the
>>>>> HARMONY meeting earlier this year, a second implementation has yet to
>>>>> appear. And thus the L1V3 draft is still a draft :)
>>>>>
>>>>> For the COMBINE breakout on data with SED-ML, it would be good to
>>>>> discuss both the potential implementation of the L1V3 specification in
>>>>> code as well as producing some examples or use-cases (to also help
>>>>> address the issue of examples that Lucian has raised on this list
>>>>> recently). So yes - the topics you mentioned Ally would be ideal to
>>>>> discuss. The main background reading would be the L1V3 draft spec
>>>>> (http://co.mbine.org/specifications/sed-ml.level-1.version-3-draft-1)
>>>>> which would also lead you to the NuML specification:
>>>>> https://github.com/NuML/NuML/blob/master/numl-spec-l1v1.pdf. Since the
>>>>> use of data in SED-ML is dependent on NuML, we will also likely be
>>>>> discussing the state of NuML and where that project is heading.
>>>>>
>>>>>
>>>>> Cheers,
>>>>> David.
>>>>>
>>>>>
>>>>>
>>>>> On Thu, Sep 17, 2015 at 4:39 AM, Herbert Sauro <hs...@gm...> wrote:
>>>>>> We'd be looking for the same things.
>>>>>>
>>>>>> Herbert
>>>>>>
>>>>>> On Wed, Sep 16, 2015 at 7:05 AM, Ally Hume <a....@ed...> wrote:
>>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> I notice that there will be a session at Combine entitled "Using data with
>>>>>>> SED-ML". I was wondering if somebody could tell me a more detailed
>>>>>>> description of what may be discussed here? I've looked in the archives for
>>>>>>> recent posts to this list but nothing seems to cover this topic.
>>>>>>>
>>>>>>> I've recently been looking at adding external time course data to SBML
>>>>>>> models. In our use case this is temperature data but it could obviously be
>>>>>>> many other measurements as well. I've written code to add external data to
>>>>>>> SBML models as a parameter with an associated assignment rule that defines
>>>>>>> the data using a piecewise function [1]. This works for our purposes but
>>>>>>> does not seem like the cleanest way to do things.
>>>>>>>
>>>>>>> SED-ML looks like a place where this could be done a lot better.
>>>>>>>
>>>>>>> Adopting similar strategies to those already used in SED-ML it would be
>>>>>>> nice to include:
>>>>>>>  - references to datasets (similar to references to models)
>>>>>>>  - link between entities in these datasets and parameters in a model
>>>>>>>  - specification of an interpolation algorithm (ontology-based like
>>>>>>> simulation algorithms)
>>>>>>>
>>>>>>> This would be a considerable improvement over my current approach of
>>>>>>> writing this into SBML where the interpolation algorithm and original
>>>>>>> dataset are effectively lost (although I could add annotations to document
>>>>>>> such details).
>>>>>>>
>>>>>>> There could also be an argument made for some basic data pre-processing
>>>>>>> possibly similar to the post-processing of result data already in SED-ML.
>>>>>>>
>>>>>>> I'm sure there will be alternative ideas but I just wondering if this is
>>>>>>> the type of thing that will be in the session.  I will be attending Combine
>>>>>>> but I don't want to wait for the session and discover it's actually on
>>>>>>> something totally different, or discover there is actually a lot of
>>>>>>> background documentation that I could have read in advance.
>>>>>>>
>>>>>>> Thank you,
>>>>>>>
>>>>>>> Ally
>>>>>>>
>>>>>>> [1] https://github.com/allyhume/SBMLDataTools
>>>>>>>
>>>>>>>
>>>>>>> Ally Hume
>>>>>>> Researcher, SynthSys, The University of Edinburgh
>>>>>>> Software and Data Architect, EPCC, The University of Edinburgh
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> The University of Edinburgh is a charitable body, registered in
>>>>>>> Scotland, with registration number SC005336.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> ------------------------------------------------------------------------------
>>>>>>> Monitor Your Dynamic Infrastructure at Any Scale With Datadog!
>>>>>>> Get real-time metrics from all of your servers, apps and tools
>>>>>>> in one place.
>>>>>>> SourceForge users - Click here to start your Free Trial of Datadog now!
>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=241902991&iu=/4140
>>>>>>> _______________________________________________
>>>>>>> SED-ML-discuss mailing list
>>>>>>> SED...@li...
>>>>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>>
>>>>>
>>>>> David Nickerson
>>>>> about.me/david.nickerson
>>>>>
>>>>
>>>>> _______________________________________________
>>>>> SED-ML-discuss mailing list
>>>>> SED...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>>> Felix Winter
>>>> Rostock, Germany
>>>>
>>>> http://orcid.org/0000-0003-2987-6797
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Monitor Your Dynamic Infrastructure at Any Scale With Datadog!
>>>> Get real-time metrics from all of your servers, apps and tools
>>>> in one place.
>>>> SourceForge users - Click here to start your Free Trial of Datadog now!
>>>> http://pubads.g.doubleclick.net/gampad/clk?id=241902991&iu=/4140
>>>> _______________________________________________
>>>> SED-ML-discuss mailing list
>>>> SED...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>>>
>>>
>>>
>>
>>
>> --
>> Nicolas LE NOVERE, Babraham Institute, Babraham Campus Cambridge, CB22 3AT
>> Tel: +441223496433, Mob:+447833147074, twitter:@lenovere, Skype:n.lenovere
>> n.l...@gm..., http://orcid.org/0000-0002-6309-7327
>> http://lenoverelab.org/, http://lenoverelab.org/perso/lenov/
>>
>> ------------------------------------------------------------------------------
>> Monitor Your Dynamic Infrastructure at Any Scale With Datadog!
>> Get real-time metrics from all of your servers, apps and tools
>> in one place.
>> SourceForge users - Click here to start your Free Trial of Datadog now!
>> http://pubads.g.doubleclick.net/gampad/clk?id=241902991&iu=/4140
>> _______________________________________________
>> SED-ML-discuss mailing list
>> SED...@li...
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
>
> ------------------------------------------------------------------------------
> Monitor Your Dynamic Infrastructure at Any Scale With Datadog!
> Get real-time metrics from all of your servers, apps and tools
> in one place.
> SourceForge users - Click here to start your Free Trial of Datadog now!
> http://pubads.g.doubleclick.net/gampad/clk?id=241902991&iu=/4140
> _______________________________________________
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> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss



-- 


David Nickerson
about.me/david.nickerson

[SED-ML-discuss] libSEDML 0.3.1 released

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

Dear all, 

before starting with the bigger changes needed to implement the 1.3 draft, I have just released a bugfix version of libSEDML. This version should finally resolve all issues with C++ namespaces and incorrect namespace definitions. It also should no longer issue any warnings during compilation, and if you use newer versions of cmake and visual studio debugging into the library from other projects should be possible again. You will find the release as always on github under: 

https://github.com/fbergmann/libSEDML/releases/tag/v.0.3.1

A big thanks to all the people contributing to solving the issues, especially: David Nickerson, Antonio Trande, Alan Garny and Kyle Medley. 

All the best
Frank

Re: [SED-ML-discuss] Using data with SED-ML at Combine

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

Actually that is in the proposal, one of the primary differences in 1.3 is, that it is possible to refer to elements in the SED-ML document itself using the xpath expressions (i.e when model / taskreferences are not given). This allows the use of all sliced data  to be refered from data. In the example there is just a basic one that demonstrates how to define a data generator that references data, but the same would apply to computeChange, the range with math expressions and of course the setValue element. 

so this is already in there as far as I’m concerned. But I would be happy if people wanted to use the time to express examples as well during combine … 

cheers
Frank


> On Sep 17, 2015, at 6:17 PM, Nicolas Le Novere <n.l...@gm...> wrote:
> 
> Indeed. This would require two things:
> 
> 1- a way to call a DataSource from the parameter attribute of a change class.
> 2- a way to change variable at runtime.
> 
> I thing 2) can be solved with a boolean attribute "runTime" on the class Change. If true, the changes are made during the simulation (synchronisation algorithms are a complete different can of worm). If false, the changes are only performed at initial time. To be honest, until we have that, no hybrid modelling is feasible with SED-ML, neither Karr et al, the dynamic FBA of Covert et al, or our biochemical-electrophysiological models.
> 
> 1) will be interesting ...
> 
> I believe what you want to do is part of a vast ensemble of models using matrices of values instead of computed values. They are used a lot in other fields, such as ecology, population dynamics etc. We are still catching up with formalism that differ significantly from the ODE+fixed initial conditions paradigm.
> 
> All that said, it is very likely that no-one could read back your model and simulation description, and run simulations out of the box. Because no software would understand what you would come up with to solve the problem. So I am almost tempted to say use placeholders for the evolving parameters, provide a NuML file with your values and put a text in the metadata file of the COMBINE archive describing how to generate the correct values at the correct time. Then, the users who really want to use your model just write a python script and create piecewise simulations (run, collect result, modify parameter value, run, append collected results etc.)
> 
> On 17/09/15 16:45, Ally Hume wrote:
>> Hi everyone,
>> 
>> I've looked at the L1V3 spec and can't see how I would get time series data into a parameter of an SBML model.
>> 
>> The only way I know to represent that data in SBML is as a parameter with an associated piecewise assignment function that implements the interpolation.  I can't see how L1V3 supports the creation of this piecewise function from the data. I can't see how I would generate the XML for this piecewise function and specify that it must be inserted into the model.  So I assume I am talking about entirely new features here, or am I missing something?
>> 
>> Ally
>> 
>> 
>> Ally Hume
>> Researcher, SynthSys, The University of Edinburgh
>> Software and Data Architect, EPCC, The University of Edinburgh
>> 
>> 
>> 
>> On 17 Sep 2015, at 09:16, Felix Winter <wi...@ka...> wrote:
>> 
>>> Hi everyone,
>>> 
>>> If I am not mistaken the current draft for SED-ML L1V3 does only cover part of
>>> what Ally was proposing. While it provides a link to data (in the NuML format)
>>> and a way of using it in the SED-ML file itself there is currently no way to
>>> describe an interpolation algorithm (or any other pre-processing).
>>> 
>>> If the pre-processing is not described inside of SED-ML it is quite difficult to
>>> describe anything slightly more complex than a linear interpolation. For a cubic
>>> spline interpolation we would still need to pre-process the data and use an SBML
>>> construct to describe the equation. While just listing (and adressing) the
>>> individual points of data may be fine for tasks such as parameter value
>>> estimation this might not suffice if the data is to be used as a continuous
>>> input into the model.
>>> 
>>> I would therefore second the motion to use the COMBINE meeting to think beyond
>>> the current draft and see whether there is a feasable way to describe the way
>>> the data is used inside a model using SED-ML.
>>> 
>>> As one of the persons who do regularly not attend the COMBINE and the HARMONY
>>> meetings but is still interested in SED-ML I would be really grateful if someone
>>> can share any progress made with the mailing-list.
>>> 
>>> Thanks,
>>> Felix
>>> 
>>>> On September 17, 2015 at 1:56 AM David Nickerson <dav...@gm...>
>>>> wrote:
>>>> 
>>>> 
>>>> Hi Ally, Herb, everyone,
>>>> 
>>>> We don't have a specific agendas set for any of the SED-ML breakout
>>>> sessions at the COMBINE meeting and the current session titles reflect
>>>> topics that we believe to be useful topics to at least kick off the
>>>> sessions.
>>>> 
>>>> Just over a year ago, the SED-ML editors released a draft for the next
>>>> version of SED-ML which is available here:
>>>> http://co.mbine.org/specifications/sed-ml.level-1.version-3-draft-1.
>>>> The main change in this specification is the addition of data to
>>>> SED-ML and being able to use data to control the simulation
>>>> experiment, model variables, etc. The additions to the specification
>>>> represented the consensus achieved during much discussion over the
>>>> preceding HARMONY and COMBINE meetings (and various google docs, etc).
>>>> As far as I am aware, there is currently only one implementation that
>>>> supports the L1V3 draft (Frank Bergmann's .NET framework) and while
>>>> some of us hoped to get our own implementations up and running at the
>>>> HARMONY meeting earlier this year, a second implementation has yet to
>>>> appear. And thus the L1V3 draft is still a draft :)
>>>> 
>>>> For the COMBINE breakout on data with SED-ML, it would be good to
>>>> discuss both the potential implementation of the L1V3 specification in
>>>> code as well as producing some examples or use-cases (to also help
>>>> address the issue of examples that Lucian has raised on this list
>>>> recently). So yes - the topics you mentioned Ally would be ideal to
>>>> discuss. The main background reading would be the L1V3 draft spec
>>>> (http://co.mbine.org/specifications/sed-ml.level-1.version-3-draft-1)
>>>> which would also lead you to the NuML specification:
>>>> https://github.com/NuML/NuML/blob/master/numl-spec-l1v1.pdf. Since the
>>>> use of data in SED-ML is dependent on NuML, we will also likely be
>>>> discussing the state of NuML and where that project is heading.
>>>> 
>>>> 
>>>> Cheers,
>>>> David.
>>>> 
>>>> 
>>>> 
>>>> On Thu, Sep 17, 2015 at 4:39 AM, Herbert Sauro <hs...@gm...> wrote:
>>>>> We'd be looking for the same things.
>>>>> 
>>>>> Herbert
>>>>> 
>>>>> On Wed, Sep 16, 2015 at 7:05 AM, Ally Hume <a....@ed...> wrote:
>>>>>> 
>>>>>> Hi,
>>>>>> 
>>>>>> I notice that there will be a session at Combine entitled "Using data with
>>>>>> SED-ML". I was wondering if somebody could tell me a more detailed
>>>>>> description of what may be discussed here? I've looked in the archives for
>>>>>> recent posts to this list but nothing seems to cover this topic.
>>>>>> 
>>>>>> I've recently been looking at adding external time course data to SBML
>>>>>> models. In our use case this is temperature data but it could obviously be
>>>>>> many other measurements as well. I've written code to add external data to
>>>>>> SBML models as a parameter with an associated assignment rule that defines
>>>>>> the data using a piecewise function [1]. This works for our purposes but
>>>>>> does not seem like the cleanest way to do things.
>>>>>> 
>>>>>> SED-ML looks like a place where this could be done a lot better.
>>>>>> 
>>>>>> Adopting similar strategies to those already used in SED-ML it would be
>>>>>> nice to include:
>>>>>>  - references to datasets (similar to references to models)
>>>>>>  - link between entities in these datasets and parameters in a model
>>>>>>  - specification of an interpolation algorithm (ontology-based like
>>>>>> simulation algorithms)
>>>>>> 
>>>>>> This would be a considerable improvement over my current approach of
>>>>>> writing this into SBML where the interpolation algorithm and original
>>>>>> dataset are effectively lost (although I could add annotations to document
>>>>>> such details).
>>>>>> 
>>>>>> There could also be an argument made for some basic data pre-processing
>>>>>> possibly similar to the post-processing of result data already in SED-ML.
>>>>>> 
>>>>>> I'm sure there will be alternative ideas but I just wondering if this is
>>>>>> the type of thing that will be in the session.  I will be attending Combine
>>>>>> but I don't want to wait for the session and discover it's actually on
>>>>>> something totally different, or discover there is actually a lot of
>>>>>> background documentation that I could have read in advance.
>>>>>> 
>>>>>> Thank you,
>>>>>> 
>>>>>> Ally
>>>>>> 
>>>>>> [1] https://github.com/allyhume/SBMLDataTools
>>>>>> 
>>>>>> 
>>>>>> Ally Hume
>>>>>> Researcher, SynthSys, The University of Edinburgh
>>>>>> Software and Data Architect, EPCC, The University of Edinburgh
>>>>>> 
>>>>>> 
>>>>>> --
>>>>>> The University of Edinburgh is a charitable body, registered in
>>>>>> Scotland, with registration number SC005336.
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> ------------------------------------------------------------------------------
>>>>>> Monitor Your Dynamic Infrastructure at Any Scale With Datadog!
>>>>>> Get real-time metrics from all of your servers, apps and tools
>>>>>> in one place.
>>>>>> SourceForge users - Click here to start your Free Trial of Datadog now!
>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=241902991&iu=/4140
>>>>>> _______________________________________________
>>>>>> SED-ML-discuss mailing list
>>>>>> SED...@li...
>>>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>>>> 
>>>>> 
>>>>> 
>>>> 
>>>> 
>>>> 
>>>> --
>>>> 
>>>> 
>>>> David Nickerson
>>>> about.me/david.nickerson
>>>> 
>>> 
>>>> _______________________________________________
>>>> SED-ML-discuss mailing list
>>>> SED...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>> Felix Winter
>>> Rostock, Germany
>>> 
>>> http://orcid.org/0000-0003-2987-6797
>>> 
>>> ------------------------------------------------------------------------------
>>> Monitor Your Dynamic Infrastructure at Any Scale With Datadog!
>>> Get real-time metrics from all of your servers, apps and tools
>>> in one place.
>>> SourceForge users - Click here to start your Free Trial of Datadog now!
>>> http://pubads.g.doubleclick.net/gampad/clk?id=241902991&iu=/4140
>>> _______________________________________________
>>> SED-ML-discuss mailing list
>>> SED...@li...
>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>> 
>> 
>> 
> 
> 
> -- 
> Nicolas LE NOVERE, Babraham Institute, Babraham Campus Cambridge, CB22 3AT
> Tel: +441223496433, Mob:+447833147074, twitter:@lenovere, Skype:n.lenovere
> n.l...@gm..., http://orcid.org/0000-0002-6309-7327
> http://lenoverelab.org/, http://lenoverelab.org/perso/lenov/
> 
> ------------------------------------------------------------------------------
> Monitor Your Dynamic Infrastructure at Any Scale With Datadog!
> Get real-time metrics from all of your servers, apps and tools
> in one place.
> SourceForge users - Click here to start your Free Trial of Datadog now!
> http://pubads.g.doubleclick.net/gampad/clk?id=241902991&iu=/4140
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss