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

Re: [SED-ML-discuss] SED-ML reports

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

Hej, 

so to say it again emphatically: I never wanted to store data in the SED-ML
file! 

All I wanted was to produce reports that can be exchanged with other groups!
For this there is not enough information there. If that is outside the scope
of SED-ML so be it. 

best
Frank


> -----Original Message-----
> From: Dagmar Waltemath [mailto:dag...@un...]
> Sent: Thursday, May 27, 2010 5:43 AM
> To: sed...@li...
> Subject: Re: [SED-ML-discuss] SED-ML reports
> 
> Hej Frank,
> 
> SED-ML by "reports" means "the construction of data tables".
> It is a set of dataGenerators that are mapped each to a column of a
> table. The dataGenerators contain the instructions for how to gain the
> data in the columns.
> 
> As such, there is no data in the reports, it really is the  "headings"
> of the columns, if you wish.
> 
> Storing the actual results of a simulation was a discussion point that
> was already raised by Henning in Okinawa. But until now it didn't make
> it in the spec - a thing that we could change for L1V2. In that case,
> we'd want something like a reference to an external "data database",
> and
> probably we'd want to specify the type of that data, i.e. the format it
> is stored in.
> 
> But that is imho not part of the report itself as it is defined right
> now in the spec.
> 
> Dagmar
> 
> 
> Frank T. Bergmann wrote:
> > Hello all,
> >
> > I've had a question today that was: What does SED-ML mean by
> 'reports' ??
> >
> > And honestly I was not quite sure how to answer it ... the current
> SED-ML
> > specification says:
> >
> > "The Report class defines an output type that returns the simulation
> result
> > in actual numbers.
> > The particular columns of the report table are defined by creating a
> DataSet
> > for each column."
> >
> > That might not be enough of a specification. What people probably
> expect is
> > to obtain results in form of CSV or SBRML, or is that a tool issue?
> > What do we expect tools to generate when we ask them for a report?
> >
> > As far as I interpret it ... we don't say anything about
> serialization of
> > the report ... thus the most likely interpretation is that the tool
> in some
> > form presents the table with the results to the user, who then
> chooses a
> > serialization format for the data in the table?
> >
> > Cheers
> > Frank
> >
> >
> > ---------------------------------------------------------------------
> ---------
> >
> > _______________________________________________
> > 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] SED-ML reports

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

Hej Frank,

SED-ML by "reports" means "the construction of data tables".
It is a set of dataGenerators that are mapped each to a column of a 
table. The dataGenerators contain the instructions for how to gain the 
data in the columns.

As such, there is no data in the reports, it really is the  "headings" 
of the columns, if you wish.

Storing the actual results of a simulation was a discussion point that 
was already raised by Henning in Okinawa. But until now it didn't make 
it in the spec - a thing that we could change for L1V2. In that case, 
we'd want something like a reference to an external "data database", and 
probably we'd want to specify the type of that data, i.e. the format it 
is stored in.

But that is imho not part of the report itself as it is defined right 
now in the spec.

Dagmar


Frank T. Bergmann wrote:
> Hello all, 
>
> I've had a question today that was: What does SED-ML mean by 'reports' ??
>
> And honestly I was not quite sure how to answer it ... the current SED-ML
> specification says: 
>
> "The Report class defines an output type that returns the simulation result
> in actual numbers.
> The particular columns of the report table are defined by creating a DataSet
> for each column."
>
> That might not be enough of a specification. What people probably expect is
> to obtain results in form of CSV or SBRML, or is that a tool issue?
> What do we expect tools to generate when we ask them for a report?
>
> As far as I interpret it ... we don't say anything about serialization of
> the report ... thus the most likely interpretation is that the tool in some
> form presents the table with the results to the user, who then chooses a
> serialization format for the data in the table?
>
> Cheers
> Frank
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>   

Re: [SED-ML-discuss] anySimulation class?

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

Hej Richard,

anySimulation was decided to be removed from SED-ML as it does not give 
us any benefit for the description of a simulation. Therefore, it's 
reference in the listofSimulations should be omitted.

I corrected the schema (revision 142).

Thanks for pointing out that mistake.
Please let me know any other inconsistencies you may find.
Dagmar


Richard Adams wrote:
> Hi Dagmar
>   I'm trying to merge Ion's and my Java libraries and so we need to  
> use a common schema. I'm using version 138 of the schema in  
> documents/schema/level1/version1 but the 'anySimulations' definition  
> has been removed since v135 yet is still referenced in the  
> 'listOfSimulations'.
>   Can you let us know which is correct? E.g., should the reference be  
> removed from 'ListOfSimulations' or the definition reinstated?
>   Cheers
>      Richard
>
>
>   

Re: [SED-ML-discuss] SED-ML reports

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

On 24/05/10 21:19, David Nickerson wrote:

> but why are reports any different to plots? we're not providing enough
> information to make two tools produce the same image from a plot
> description so why expect reports to be the same? personally, I
> currently use plot descriptions for generating reports - I simply say
> that my output format is CSV rather than PNG :)

I agree the naming is a bit confusing. A "plot" precise which variable to 
present in function of which variable. A report provides the recording of 
variables over time. I agree that for a 2D timecourse, they are equivalent. 
However, for complex returns, such as 3D etc. they may be quite different.

-- 
Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome-Trust
Genome Campus, Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521
Fax:468,Skype:n.lenovere,AIM:nlenovere,MSN:nle...@ho...(NOT email)
http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/, @lenovere

Re: [SED-ML-discuss] SED-ML reports

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

> I never advocated storing the results in XML. All I wanted is a bit more information, so that two tools creating reports would be able to produce the same reports, so that they could be compared later on. For this the minimum additional information needed seems to be the order of the columns.
>

but why are reports any different to plots? we're not providing enough
information to make two tools produce the same image from a plot
description so why expect reports to be the same? personally, I
currently use plot descriptions for generating reports - I simply say
that my output format is CSV rather than PNG :)

> (My tool currently writes out the report information in the order the DataGenerators appear in the XML file. However, I'm aware of one particular member of this group who will not like order at all, so making this a part of the spec seems wrong).
>

using document order would be bad!

> I suppose for the time being I would have to create a custom annotation that would store:
>
> - column order,
> - column precision,
> - desired output format
> and perhaps even desired output location

isn't this the same as line colour, axis tic marks, and image format?
In which case the custom annotations seem to be the way to go.


Cheers,
Andre.

Re: [SED-ML-discuss] Issues with ChangeXML

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

Hello Richard, 

I would love to see this in L1V1

best
Frank

On May 24, 2010, at 3:31 AM, Richard Adams wrote:

> 
> This seems much more precise - I prefer the idea of a nested element  
> as this gives
> more flexibility in adding in extra operations in the future without having to
> alter the 'changeXML' class, which can be a base class.
> 
> Are you planning to incorporate this into level1v1 spec? It's  
> certainly much clearer than the existing spec.
> 
> Cheers
>  Richard
> -- 
> Dr Richard Adams
> Software Development Team Leader,
> Centre For Systems Biology Edinburgh
> University of Edinburgh
> Tel: 0131 650 8285
> email : ric...@ed...
> 
> -- 
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
> 
> 
> 
> ------------------------------------------------------------------------------
> 
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

Re: [SED-ML-discuss] SED-ML reports

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

Hello Richard, 

I never advocated storing the results in XML. All I wanted is a bit more information, so that two tools creating reports would be able to produce the same reports, so that they could be compared later on. For this the minimum additional information needed seems to be the order of the columns. 

(My tool currently writes out the report information in the order the DataGenerators appear in the XML file. However, I'm aware of one particular member of this group who will not like order at all, so making this a part of the spec seems wrong). 

I suppose for the time being I would have to create a custom annotation that would store: 

- column order,
- column precision, 
- desired output format
and perhaps even desired output location

best
Frank

On May 24, 2010, at 3:22 AM, Richard Adams wrote:

> 
> Hi Frank
>   I think that to be consistent with 'Plots' which is the tool's job  
> to interpret, it should be up to the tool how results are presented in  
> a 'report' format. I don't think results should be included in the  
> XML, after all this is markup language for methodological information.
>  Cheers
>    Richard
> 
>> Hello all,
>> 
>> I've had a question today that was: What does SED-ML mean by 'reports' ??
>> 
>> And honestly I was not quite sure how to answer it ... the current SED-ML
>> specification says:
>> 
>> "The Report class defines an output type that returns the simulation result
>> in actual numbers.
>> The particular columns of the report table are defined by creating a DataSet
>> for each column."
>> 
>> That might not be enough of a specification. What people probably expect is
>> to obtain results in form of CSV or SBRML, or is that a tool issue?
>> What do we expect tools to generate when we ask them for a report?
>> 
>> As far as I interpret it ... we don't say anything about serialization of
>> the report ... thus the most likely interpretation is that the tool in some
>> form presents the table with the results to the user, who then chooses a
>> serialization format for the data in the table?
>> 
>> Cheers
>> Frank
>> 
>> 
>> ------------------------------------------------------------------------------
>> 
>> _______________________________________________
>> SED-ML-discuss mailing list
>> SED...@li...
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>> 
>> 
> 
> 
> 
> -- 
> Dr Richard Adams
> Software Development Team Leader,
> Centre For Systems Biology Edinburgh
> University of Edinburgh
> Tel: 0131 650 8285
> email : ric...@ed...
> 
> -- 
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
> 
> 
> 
> ------------------------------------------------------------------------------
> 
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

Re: [SED-ML-discuss] Issues with ChangeXML

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

This seems much more precise - I prefer the idea of a nested element  
as this gives
more flexibility in adding in extra operations in the future without having to
alter the 'changeXML' class, which can be a base class.

Are you planning to incorporate this into level1v1 spec? It's  
certainly much clearer than the existing spec.

Cheers
  Richard
-- 
Dr Richard Adams
Software Development Team Leader,
Centre For Systems Biology Edinburgh
University of Edinburgh
Tel: 0131 650 8285
email : ric...@ed...

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

Re: [SED-ML-discuss] SED-ML reports

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

Hi Frank
   I think that to be consistent with 'Plots' which is the tool's job  
to interpret, it should be up to the tool how results are presented in  
a 'report' format. I don't think results should be included in the  
XML, after all this is markup language for methodological information.
  Cheers
    Richard

> Hello all,
>
> I've had a question today that was: What does SED-ML mean by 'reports' ??
>
> And honestly I was not quite sure how to answer it ... the current SED-ML
> specification says:
>
> "The Report class defines an output type that returns the simulation result
> in actual numbers.
> The particular columns of the report table are defined by creating a DataSet
> for each column."
>
> That might not be enough of a specification. What people probably expect is
> to obtain results in form of CSV or SBRML, or is that a tool issue?
> What do we expect tools to generate when we ask them for a report?
>
> As far as I interpret it ... we don't say anything about serialization of
> the report ... thus the most likely interpretation is that the tool in some
> form presents the table with the results to the user, who then chooses a
> serialization format for the data in the table?
>
> Cheers
> Frank
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
>



-- 
Dr Richard Adams
Software Development Team Leader,
Centre For Systems Biology Edinburgh
University of Edinburgh
Tel: 0131 650 8285
email : ric...@ed...

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

[SED-ML-discuss] Issues with ChangeXML

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

Hello all, 

I know at the Hackathon we were briefly talking about ChangeXML, and that it
should be included in SEDML Level 1 Version 1. So I finally had a detailed
look at the construct and tried to map out what implications it would have.
Currently we have one construct: 

<changeXML target="<xpath expression to model variable>" newXML="<some
really long unvalidatable string here that might or might not be XML>" />

I assume this to be a typo. If I remember it correctly from our discussions
this really should look like this: 

<changeXML target="<xpath expression to model variable>">
<newXML>
	<some new xml here, validatable with target namespace and bells and
whistles>
</newXML>
</changeXML>

Ok ... this basically would work ... so the next important thing to ask, is
what would we like to do with this. Basically three things: 

- adding new elements (i.e.: a degradation reaction to an existing species)
- replacing an element by something else (i.e.: a lumped reaction by its
individual steps)
- deleting elements (i.e.: removing a reaction step)

Previously we discussed, that we could delete elements by replacing a target
with an empty newXML block. If we look at the draft specification we find an
example, that shows that we could add a parameter to a model, by replacing
one parameter with itself and another one: 

1 <model [..]>
2 <listOfChanges>
3 <changeXML target="/sbml:sbml/sbml:model/sbml:listOfParameters
4 /sbml:parameter[@id='V_mT ']"
5 newXML="<parameter metaid="metaid_0000010" id="V_mT" value="0.7">
6 <parameter metaid="metaid_0000050" id="V_mT_2" value="4.6">" />
7 </listOfChanges>
8 </model>

I would very much prefer to keep the individual operations separate, either
by introducing an additional attribute 'operation' on the changeXML element:


1 <model [..]>
2 <listOfChanges>
3 <changeXML target="/sbml:sbml/sbml:model/sbml:listOfParameters"
4  operation="add">
5 <newXML>
6       <parameter xmlns="<sbmlnshere>" metaid="metaid_0000050" id="V_mT_2"
value="4.6">
7 </newXML>
8 </listOfChanges>
9 </model>

The advantage here is that it is much easier to apply changes from one model
to another, without artificially having to replace existing elements by
itself + whatever one wants to add in the first place. 

Similarly: 

<changeXML
target="/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='V_mT
']"
  operation="delete"/>

would delete an element ... and so on ... alternatively if someone would
really be against the additional attribute, we could introduce differently
named elements like: 

<addXML target="<xpath>"><newXML> <stuff here/> </newXml> </addXML>
<removeXML target="xpath"/>

And changeXML would remain as is ... 


Let the floor be open for comments :) 

Cheers
Frank

Re: [SED-ML-discuss] The 'Surface' construct

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

Hi Lucian,

I believe this is maybe an avatar of the discussion about what are SED-ML 
"plots", and what we are specifying. We made a mistake using the name 
"plot", "surface", "line" etc. while we repeatedly agreed we were not 
describing the lookalike of the graphical output. The SED-ML output are of 
two types: The "report" presents unrelated numerical results. The "plot" 
(sic) presents variables in relation to each other (and yes Franck, the log 
is a kind of post-processing. But we want to keep it in the plot because 
then we can write the raw data in a report without having to write another 
data generator).

The "plot" does not say how to visually represent things. So there is no 
"stitching". We do not say that we want a soled surface, or lines, and 
which lines (do-they delimit tetragone or triangle?) I agree with David, 
what we export are points of the "line" (sic) or the "surface" (re-sic). I 
suspect each plotter has its algorithm to stitch anyway and there is little 
we can do to change it.

It is true that there is no concatenation at the moment. I guess we assumed 
it would work like gnuplot or alike. Same index of each data generator 
would be used.

We can open a task to revise the output for the future Level/Version, but I 
do not see the present situation as a release blocker.

On 15/05/10 08:47, Lucian Smith wrote:
> * David Nickerson<dav...@gm...>  [2010-05-15 08:04] writes:
>>> So, Frank and I were talking, and realized that there is a problem in the
>>> spec with the definition of the 'Surface' construct.  It cannot work as
>>> written, because while a surface can have a vector for x and a vector for
>>> y, it must have a matrix for z, and there is no current way to tell a data
>>> generator to generate a matrix.
>>
>> I must be missing something obvious, but why must you have a matrix
>> for z? is not each point on the surface uniquely defined by a (x,y,z)
>> triple and therefore all you need are three vectors?
>
> Each point can indeed be defined by an x,y,z triple, but a series of
> points is a line, not a surface.  I could see some sort of heuristic where
> you say 'just plot the points without connecting them in a line, then
> stitch the closest together', but you'd have to define 'closest' in such a
> way that you didn't get weird artifacts, and such that your surface could
> be oriented in multiple directions, and you'd still have to find a way to
> get a data generator that only ran time courses (in SEDML L1) to give you
> several time course z values stitched one after the next, a different data
> generator that gave you the time vector several times over, and a third
> data generator that gave you a bunch of 0s then a bunch of 1s then a bunch
> of 2s, etc.  I don't think these data generators currently exist, though I
> could be wrong.
>
>> in your example below, don't you just need to define a data generator
>> that concatenates each of the source transients into a set of three
>> vectors? perhaps that is the bit missing from the specification and
>> there is currently no way to describe such a concatenation...although
>> I'm not sure which is the better feature to add, the concatenation or
>> the list of curves for a surface.
>
> Yeah, I think this is a different way of formulating the problem (and
> could point to different solutions).
>
> -Lucian
>
>>
>>> If you wanted a bunch of stitched time courses that collectively formed a
>>> 'surface' you instead must define a surface as a collection of curves,
>>> perhaps something like:
>>>
>>> Surface:
>>>   ListofCurves:
>>>     Curve1:  x=0, y=datagenerator1, z=datagenerator2
>>>     Curve2:  x=1, y=datagenerator1, z=datagenerator3
>>>     [etc]
>>>
>>>
>>> (The 'x=0' is shorthand for 'a vector of all zeroes', since you are
>>> tracing out a curve in 3D space along one point in x (in this case).)
>>>
>>> -Lucian
>>>
>>> ------------------------------------------------------------------------------
>>>
>>> _______________________________________________
>>> 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
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss


-- 
Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome-Trust
Genome Campus, Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521
Fax:468,Skype:n.lenovere,AIM:nlenovere,MSN:nle...@ho...(NOT email)
http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/, @lenovere

Re: [SED-ML-discuss] The 'Surface' construct

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

* David Nickerson <dav...@gm...> [2010-05-15 08:04] writes:
> > So, Frank and I were talking, and realized that there is a problem in the
> > spec with the definition of the 'Surface' construct.  It cannot work as
> > written, because while a surface can have a vector for x and a vector for
> > y, it must have a matrix for z, and there is no current way to tell a data
> > generator to generate a matrix.
> 
> I must be missing something obvious, but why must you have a matrix
> for z? is not each point on the surface uniquely defined by a (x,y,z)
> triple and therefore all you need are three vectors?

Each point can indeed be defined by an x,y,z triple, but a series of 
points is a line, not a surface.  I could see some sort of heuristic where 
you say 'just plot the points without connecting them in a line, then 
stitch the closest together', but you'd have to define 'closest' in such a 
way that you didn't get weird artifacts, and such that your surface could 
be oriented in multiple directions, and you'd still have to find a way to 
get a data generator that only ran time courses (in SEDML L1) to give you 
several time course z values stitched one after the next, a different data 
generator that gave you the time vector several times over, and a third 
data generator that gave you a bunch of 0s then a bunch of 1s then a bunch 
of 2s, etc.  I don't think these data generators currently exist, though I 
could be wrong.

> in your example below, don't you just need to define a data generator
> that concatenates each of the source transients into a set of three
> vectors? perhaps that is the bit missing from the specification and
> there is currently no way to describe such a concatenation...although
> I'm not sure which is the better feature to add, the concatenation or
> the list of curves for a surface.

Yeah, I think this is a different way of formulating the problem (and 
could point to different solutions).

-Lucian

> 
> > If you wanted a bunch of stitched time courses that collectively formed a
> > 'surface' you instead must define a surface as a collection of curves,
> > perhaps something like:
> >
> > Surface:
> >  ListofCurves:
> >    Curve1:  x=0, y=datagenerator1, z=datagenerator2
> >    Curve2:  x=1, y=datagenerator1, z=datagenerator3
> >    [etc]
> >
> >
> > (The 'x=0' is shorthand for 'a vector of all zeroes', since you are
> > tracing out a curve in 3D space along one point in x (in this case).)
> >
> > -Lucian
> >
> > ------------------------------------------------------------------------------
> >
> > _______________________________________________
> > 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] The 'Surface' construct

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

> So, Frank and I were talking, and realized that there is a problem in the
> spec with the definition of the 'Surface' construct.  It cannot work as
> written, because while a surface can have a vector for x and a vector for
> y, it must have a matrix for z, and there is no current way to tell a data
> generator to generate a matrix.

I must be missing something obvious, but why must you have a matrix
for z? is not each point on the surface uniquely defined by a (x,y,z)
triple and therefore all you need are three vectors?

in your example below, don't you just need to define a data generator
that concatenates each of the source transients into a set of three
vectors? perhaps that is the bit missing from the specification and
there is currently no way to describe such a concatenation...although
I'm not sure which is the better feature to add, the concatenation or
the list of curves for a surface.

> If you wanted a bunch of stitched time courses that collectively formed a
> 'surface' you instead must define a surface as a collection of curves,
> perhaps something like:
>
> Surface:
>  ListofCurves:
>    Curve1:  x=0, y=datagenerator1, z=datagenerator2
>    Curve2:  x=1, y=datagenerator1, z=datagenerator3
>    [etc]
>
>
> (The 'x=0' is shorthand for 'a vector of all zeroes', since you are
> tracing out a curve in 3D space along one point in x (in this case).)
>
> -Lucian
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>

[SED-ML-discuss] The 'Surface' construct

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

So, Frank and I were talking, and realized that there is a problem in the 
spec with the definition of the 'Surface' construct.  It cannot work as 
written, because while a surface can have a vector for x and a vector for 
y, it must have a matrix for z, and there is no current way to tell a data 
generator to generate a matrix.

If you wanted a bunch of stitched time courses that collectively formed a 
'surface' you instead must define a surface as a collection of curves, 
perhaps something like:

Surface:
  ListofCurves:
    Curve1:  x=0, y=datagenerator1, z=datagenerator2
    Curve2:  x=1, y=datagenerator1, z=datagenerator3
    [etc]


(The 'x=0' is shorthand for 'a vector of all zeroes', since you are 
tracing out a curve in 3D space along one point in x (in this case).)

-Lucian

Re: [SED-ML-discuss] SED-ML reports

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

Hello Sven, 

Right ... that’s the way I implemented it ... my tools will open new windows
with a spreadsheet like display. Although what I really wanted was just a
file export. But since we cannot: 

- specify the output filename
- specify the output format
- specify the order of the columns
- specify the precision with which to output the information 

It seems a bit limited to me ... 

Best
Frank

> -----Original Message-----
> From: Sven Sahle [mailto:sve...@bi...]
> Sent: Wednesday, May 12, 2010 7:21 AM
> To: sed...@li...
> Subject: Re: [SED-ML-discuss] SED-ML reports
> 
> Hi Frank,
> 
> It is possible that "report" is a Copasi term that crept in during the
initial
> discussion in Okinawa. In Copasi "Report" means an output to a textfile. I
> guess what SED-ML means is that a report is a text file with a table of
> numbers arranged in columns (which would be a table report in copasi).
> Eventually it should be possible to define more complex output data
> structures, but for the first release I think it would be OK to say that a
report
> is a (2-dimensional) table of numbers, and leave the implementation to the
> software tools. It could be recommended that at least comma or tab
> separated text files should be supported but I could also imagine a tool
that
> displays the numbers in a spreadsheet- like way on the screen and writes
> excel files.
> 
> Sven
> 
> Am 11.05.2010 um 00:18 schrieb Frank T. Bergmann:
> 
> > Hello all,
> >
> > I've had a question today that was: What does SED-ML mean by 'reports'
> > ??
> >
> > And honestly I was not quite sure how to answer it ... the current
> > SED-ML specification says:
> >
> > "The Report class defines an output type that returns the simulation
> > result in actual numbers.
> > The particular columns of the report table are defined by creating a
> > DataSet for each column."
> >
> > That might not be enough of a specification. What people probably
> > expect is to obtain results in form of CSV or SBRML, or is that a tool
> > issue?
> > What do we expect tools to generate when we ask them for a report?
> >
> > As far as I interpret it ... we don't say anything about serialization
> > of the report ... thus the most likely interpretation is that the tool
> > in some form presents the table with the results to the user, who then
> > chooses a serialization format for the data in the table?
> >
> > Cheers
> > Frank
> >
> >
> >
----------------------------------------------------------------------------
--
> >
> > _______________________________________________
> > SED-ML-discuss mailing list
> > SED...@li...
> > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
> 
> Dr. Sven Sahle
> Abteilung Modellierung biologischer Prozesse
> Universität Heidelberg, BIOQUANT/Zoologie
> 
> 
> 
> 
>
----------------------------------------------------------------------------
--
> 
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

Re: [SED-ML-discuss] SED-ML reports

[Sven S. <sve...@bi...>]

Hi Frank,

It is possible that "report" is a Copasi term that crept in during the  
initial discussion in Okinawa. In Copasi "Report" means an output to a  
textfile. I guess what SED-ML means is that a report is a text file  
with a table of numbers arranged in columns (which would be a table  
report in copasi).
Eventually it should be possible to define more complex output data  
structures, but for the first release I think it would be OK to say  
that a report is a (2-dimensional) table of numbers, and leave the  
implementation to the software tools. It could be recommended that at  
least comma or tab separated text files should be supported but I  
could also imagine a tool that displays the numbers in a spreadsheet- 
like way on the screen and writes excel files.

Sven

Am 11.05.2010 um 00:18 schrieb Frank T. Bergmann:

> Hello all,
>
> I've had a question today that was: What does SED-ML mean by  
> 'reports' ??
>
> And honestly I was not quite sure how to answer it ... the current  
> SED-ML
> specification says:
>
> "The Report class defines an output type that returns the simulation  
> result
> in actual numbers.
> The particular columns of the report table are defined by creating a  
> DataSet
> for each column."
>
> That might not be enough of a specification. What people probably  
> expect is
> to obtain results in form of CSV or SBRML, or is that a tool issue?
> What do we expect tools to generate when we ask them for a report?
>
> As far as I interpret it ... we don't say anything about  
> serialization of
> the report ... thus the most likely interpretation is that the tool  
> in some
> form presents the table with the results to the user, who then  
> chooses a
> serialization format for the data in the table?
>
> Cheers
> Frank
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

Dr. Sven Sahle
Abteilung Modellierung biologischer Prozesse
Universität Heidelberg, BIOQUANT/Zoologie

[SED-ML-discuss] SED-ML reports

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

Hello all, 

I've had a question today that was: What does SED-ML mean by 'reports' ??

And honestly I was not quite sure how to answer it ... the current SED-ML
specification says: 

"The Report class defines an output type that returns the simulation result
in actual numbers.
The particular columns of the report table are defined by creating a DataSet
for each column."

That might not be enough of a specification. What people probably expect is
to obtain results in form of CSV or SBRML, or is that a tool issue?
What do we expect tools to generate when we ask them for a report?

As far as I interpret it ... we don't say anything about serialization of
the report ... thus the most likely interpretation is that the tool in some
form presents the table with the results to the user, who then chooses a
serialization format for the data in the table?

Cheers
Frank

[SED-ML-discuss] Meeting notes SED-ML break out at hackathon

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

Dear all,

please find attached the meeting notes taken during the SED-ML break out 
session of the biomodels.net/SBML hackathon.

We addressed mainly UML issues that hindered us from freezing the SED-ML 
L1V1 specification, and it seems we found quite a good consensus.

Please feel free to comment on any of the points made in the notes, 
especially if you were not able to attend.

Best,
Dagmar

Re: [SED-ML-discuss] Proposing a Nested Simulation Experiment

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

Dear all,

I'm still figuring out the details of my thoughts on SED-ML 
developments; we have a particular use-case we're working on. But given 
that I can't attend the SED-ML session next week, I thought it'd be 
worth sending some initial thoughts to contribute to the discussion.

Firstly, I really like the concept of Frank's nested simulation 
experiment. I think defining composable primitives is definitely the way 
to go to achieve an expressive yet implementable language.

I think it would definitely be worth allowing multiple setValue and 
range constructs within a nested simulation definition. It doesn't 
strike me as any more difficult to implement, and it would be useful for 
our work. I'd actually recommend requiring ranges to have an id for 
referencing within setValue anyway - the use of #current feels too much 
like magic to me.

As Andrew Miller has mentioned before, it could be necessary for some 
simulations to provide some additional parameters to the integrator. 
Relative and absolute tolerance settings can make a significant 
difference to the results obtained, and a maximum internal time step is 
often essential to avoid missing a stimulus for cardiac models.

I haven't thought about the next point at all really, but Andrew's IVOI 
(Independent Variable of Integration) could possibly be done using the 
nested simulation proposal. Since setValue can change any model 
variable, you could adapt Frank's example implementing a uniform time 
course with nestedSimulation to vary whatever variable happened to be 
the IVOI.

It is my impression that the intended semantics of setValue is to 
perform an immediate change of the referenced variable, and allow it to 
vary if simulation of the model under the originalTask causes this. Is 
this correct? For my application, I will require to be able to impose 
boundary conditions, e.g. by clamping certain state variables to 
different values for different periods of simulation. I think this would 
be best achieved by a model change, supplying new MathML etc. with a 
parameter which can be set in a setValue.

The main limitation in SED-ML currently for my work is the support for 
post-processing. As I understand it, the data generators implicitly act 
on an array of values (or multiple arrays of the same length if they 
take multiple inputs), applying the same operation to each element of 
the array and producing an output array of the same length. However, I 
want to be able to specify post-processing such as:

    * gradient of one variable with respect to another (not necessarily
      time)
    * take the value of a variable at a specific time (optionally with
      interpolation if this wasn't an output point)
    * return the peak value of a variable (optionally after a specified
      time)
    * calculate action potential duration and restitution relations
      (which link the action potential duration to the previous
      diastolic interval)

I haven't yet figured out an elegant way of specifying these however 
(except as Matlab code...). I will also need to be able to use the 
output of one post-processing step as the input to another, which I 
believe bears some relation to chaining simulations. So this whole topic 
can probably wait for a future version of SED-ML!

As always, I'd be very interested to hear people's opinions on these ideas.

Best wishes,
Jonathan

Frank Bergmann wrote:
> Hello
>
>   
>> I think... I need some sample code to see what you're doing :-) Would you
>> mind posting an example (if you have any available)?
>>
>>     
>
> What I posted before was the basic idea I had. I did not yet implement this
> approach, but it will be in LibSedML by the time of the hackathon, if more
> people find it of interest. (Otherwise I just have to hide it in the
> annotation section). After your mail I went ahead and posted more detail
> here: 
>
> http://frank-fbergmann.blogspot.com/2010/03/nested-simulation-experiments.ht
> ml
>
> I hope this helps, 
> Best
> Frank
>
>   
>> Thanks a lot,
>> Dagmar
>>
>>
>> Frank Bergmann wrote:
>>     
>>> Hello all,
>>>
>>> First of all thank you so much Dagmar for reviving this list. It is
>>> good to see the ball moving again.
>>>
>>> I've been working with SED-ML extensively over the last months. The
>>> biggest concern of mine has always been the way that SED-ML is
>>>       
>> structured.
>>     
>>> Currently, whenever we want to exchange a new simulation experiment,
>>> we need to add a new class to SED-ML. (And no, the AnySimulation class
>>> will not be exchangeable, so it should be dropped as soon as
>>> possible). That also means that each time a class is added to SED-ML
>>> everyone else has to start implementing support for it. This is a sure
>>> way for SED-ML to fail as standard!
>>>
>>> Back in Waiheke last year we tried to resolve that issue by adding the
>>> Range classes to the existing simulation experiments like TimeCourse.
>>> And it did sound good back then. However, thinking on how to implement
>>> it and, perhaps more importantly, how to apply it to other simulation
>>> experiments, it proved hard to do. This concept only translates into a
>>> triple amount of work for the implementers of the SED-ML format.
>>>
>>> And so here my proposal. Let us go back to the roots. By defining
>>> simple primitives, for a simulation step, bringing the model to steady
>>> state, and changing values, we can finally arrive at a truly
>>> extendable standard that is also easy to implement. I've placed my
>>>       
>> thoughts online:
>>     
>>> http://precedings.nature.com/documents/4257/version/1
>>>
>>> Bergmann, Frank. A Simple Nested Simulation for SED-ML. Available from
>>> Nature Precedings <http://dx.doi.org/10.1038/npre.2010.4257.1> (2010)
>>>
>>>
>>> Let me know what you think,
>>> Best
>>> Frank
>>>
>>>
>>> ----------------------------------------------------------------------
>>> -------- Download Intel&#174; Parallel Studio Eval Try the new
>>> software tools for yourself. Speed compiling, find bugs proactively,
>>> and fine-tune applications for parallel performance.
>>> See why Intel Parallel Studio got high marks during beta.
>>> http://p.sf.net/sfu/intel-sw-dev
>>> _______________________________________________
>>> SED-ML-discuss mailing list
>>> SED...@li...
>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>>
>>>       
>>
>>     
> ----------------------------------------------------------------------------
> --
>   
>> Download Intel&#174; Parallel Studio Eval Try the new software tools for
>> yourself. Speed compiling, find bugs proactively, and fine-tune
>>     
> applications
>   
>> for parallel performance.
>> See why Intel Parallel Studio got high marks during beta.
>> http://p.sf.net/sfu/intel-sw-dev
>> _______________________________________________
>> SED-ML-discuss mailing list
>> SED...@li...
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>     
>
>
> ------------------------------------------------------------------------------
> Download Intel&#174; Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-
>   

[SED-ML-discuss] Remote attendance of SED-ML session at the hackathon

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

Hello all,

we will have a SED-ML break-out session during the upcoming 
biomodels.net/SBML hackathon in Seattle starting from Saturday 
http://sbml.org/Events/Hackathons/The_2010_SBML-BioModels.net_Hackathon.

Mike Hucka was so kind to organise video live feed for all break out 
sessions, including the SED-ML one. In case you would like to join the 
sessions, but are will not be able to attend the meeting, please check 
the web site for further information on how to join remotely:

http://sbml.org/Events/Hackathons/The_2010_SBML-BioModels.net_Hackathon/Live_feed

Best,
Dagmar

Re: [SED-ML-discuss] Proposing a Nested Simulation Experiment

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

  Maybe to explain better - I  was recently at a talk from our Biopepa  
(www.biopepa.org) colleagues who have recently implemented various  
sorts of 'experiment' functionality to alter models  in various ways  
and compare the results, but use a non-XML based model representation.  
So I was thinking that setting values based on an 'identifiable  
element'  rather than XPath would extend the range of models whose  
experiments could be described in SED-ML to include all models that  
have identifiers (although at the expense of the complete flexibility  
Xpath gives you to alter a model in any way)

Richard

> Hello All,
>
> sorry I have been away for the last couple of days.
>
> the motivation with the proposal for the setValue function was made   
> so that different changes could be applied for each iteration of the  
>  nested experiment. This basically allows us to perform loop   
> operations (such as in 'for' or 'while' loops). I'm perfectly fine   
> with determining the target of the setValue by an XPath expression,   
> I was just worried that really for many cases we won't have one,   
> such as for time in the case of SBML models, that is why I think it   
> is fine to extend it by additional keywords.
>
> So with the nested task + setValue + oneStep + steadyState the aim   
> was to broaden the range of Simulation Experiments that can be   
> encoded with SED-ML. This already allows for any time course   
> simulation, (1-D, 2-D..., N-D) (steady state) parameter scans. And   
> any kinds of pulse experiments. And that without having to define a   
> new simulation class each time.
>
> But we don't have to stop here ... we could have a more general   
> function like the one you are suggesting as subclass for the   
> setValue one. I'm just not sure how you would parameterize it. ...   
> The setValue class would take the value of the current range and   
> through that either apply or calculate a change for a value. I'm not  
>  sure how you would parameterize your example of removing reactions   
> ... If I were to remove a reaction I would probably do that as   
> before by creating a changed model with the reaction removed, and   
> then apply the nested simulation to it.
>
> But maybe I'm misunderstanding your intentions
>
> cheers
> Frank
>
>
> On Mar 30, 2010, at 7:32 AM, Richard Adams wrote:
>
>>
>> Frank,
>>  I read your proposal on your blog - with the 'setValue' function,
>> are you thinking that is a way of manipulating the model without
>> constraining it to be XML based? So long as a parameter /variable is
>> identifiable, tools capable of accepting a model in a particular
>> format would still be able to manipulate it.
>>
>> I guess this would preclude sweeping structural changes applied to an
>> XML model that can be done with Xpath (removing a reaction, for
>> example) but is the increase in generality for simple cases of value
>> manipulation worth considering?
>>
>> Best wishes
>>
>> Richard
>>
>>
>>
>>
>>
>>> Hello Andrew:
>>>
>>>>
>>>> A few comments. I think that dealing with 'time' is probably one of the
>>>> biggest weaknesses in this approach. You wrote:
>>>> "We could make it convention, that if this is not defined, then the
>>>> models time parameter is changed".
>>>> Firstly, as soon as we talk about time, we lose generality; I suggest
>>>> 'independent variable of integration' or a similar term. I'll refer to
>>>> it as 'IVOI' here.
>>>>
>>>
>>> Given the frequent use of integration over time, I think we can
>>> justify having this class. But I'm open to introduce your IVOI as a
>>> more general case. Though I'm afraid many tools will not be able to
>>> handle IVOI.
>>>
>>>> Secondly, modern DAE / IDA solvers take adaptive steps in their IVOI,
>>>> rather than fixed steps. Your proposal seems to not allow adaptive
>>>> step-sizes - rather, it forces the user to specify the step size on
>>>> 'OneStep'.
>>>>
>>>
>>> Definitely, what the oneStep is meant to describe is how far you
>>> would like to simulate until your next output point. How many steps
>>> the integrator internally takes would be independent of this.
>>>
>>>> => Parameters controlling the internal stepping. For example, allowing
>>>> for an optional maximum step size to control errors and ensure that the
>>>> solver finds features like stimulation pulses.
>>>
>>> Again, the one step approach only tells you when you want your next
>>> output point, this can be controlled through the range element on
>>> the nested simulation experiment.
>>>
>>>> => Parameters controlling which data is reported. Some simulations will
>>>> want to report every internal step, while in others, reporting this data
>>>> will produce more data than is required.
>>>
>>> This will be defined through the data generators that are defined,
>>> just as in the current approach.
>>>
>>>> The above is implemented in CellML Simulation Metadata and the CellML
>>>> API and OpenCell extensions to it (this metadata focuses entirely on
>>>> 'time' course experiments at present, but does that one task better than
>>>> anything proposed for SEDML to date).
>>>>
>>>
>>> Great! ... so which tools can i download to experiment with it? it
>>> would be good to test exchange of simulation experiments that way.
>>>
>>> best
>>> Frank
>>>
>>>> Best wishes,
>>>> Andrew
>>>>
>>>>>
>>>>> Bergmann, Frank. A Simple Nested Simulation for SED-ML. Available from
>>>>> Nature Precedings <http://dx.doi.org/10.1038/npre.2010.4257.1> (2010)
>>>>>
>>>>>
>>>>> Let me know what you think,
>>>>> Best
>>>>> Frank
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> Download Intel&#174; Parallel Studio Eval
>>>>> Try the new software tools for yourself. Speed compiling, find bugs
>>>>> proactively, and fine-tune applications for parallel performance.
>>>>> See why Intel Parallel Studio got high marks during beta.
>>>>> http://p.sf.net/sfu/intel-sw-dev
>>>>> _______________________________________________
>>>>> SED-ML-discuss mailing list
>>>>> SED...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Download Intel&#174; Parallel Studio Eval
>>>> Try the new software tools for yourself. Speed compiling, find bugs
>>>> proactively, and fine-tune applications for parallel performance.
>>>> See why Intel Parallel Studio got high marks during beta.
>>>> http://p.sf.net/sfu/intel-sw-dev
>>>> _______________________________________________
>>>> SED-ML-discuss mailing list
>>>> SED...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Download Intel&#174; Parallel Studio Eval
>>> Try the new software tools for yourself. Speed compiling, find bugs
>>> proactively, and fine-tune applications for parallel performance.
>>> See why Intel Parallel Studio got high marks during beta.
>>> http://p.sf.net/sfu/intel-sw-dev
>>> _______________________________________________
>>> SED-ML-discuss mailing list
>>> SED...@li...
>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>>
>>>
>>
>>
>>
>> --
>> Dr Richard Adams
>> Software Development Team Leader,
>> Centre For Systems Biology Edinburgh
>> University of Edinburgh
>> Tel: 0131 650 8285
>> email : ric...@ed...
>>
>> --
>> The University of Edinburgh is a charitable body, registered in
>> Scotland, with registration number SC005336.
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Download Intel&#174; Parallel Studio Eval
>> Try the new software tools for yourself. Speed compiling, find bugs
>> proactively, and fine-tune applications for parallel performance.
>> See why Intel Parallel Studio got high marks during beta.
>> http://p.sf.net/sfu/intel-sw-dev
>> _______________________________________________
>> SED-ML-discuss mailing list
>> SED...@li...
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
>
> ------------------------------------------------------------------------------
> Download Intel&#174; Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
>



-- 
Dr Richard Adams
Software Development Team Leader,
Centre For Systems Biology Edinburgh
University of Edinburgh
Tel: 0131 650 8285
email : ric...@ed...

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

Re: [SED-ML-discuss] Proposing a Nested Simulation Experiment

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

Hello All, 

sorry I have been away for the last couple of days. 

the motivation with the proposal for the setValue function was made so that different changes could be applied for each iteration of the nested experiment. This basically allows us to perform loop operations (such as in 'for' or 'while' loops). I'm perfectly fine with determining the target of the setValue by an XPath expression, I was just worried that really for many cases we won't have one, such as for time in the case of SBML models, that is why I think it is fine to extend it by additional keywords. 

So with the nested task + setValue + oneStep + steadyState the aim was to broaden the range of Simulation Experiments that can be encoded with SED-ML. This already allows for any time course simulation, (1-D, 2-D..., N-D) (steady state) parameter scans. And any kinds of pulse experiments. And that without having to define a new simulation class each time. 

But we don't have to stop here ... we could have a more general function like the one you are suggesting as subclass for the setValue one. I'm just not sure how you would parameterize it. ... The setValue class would take the value of the current range and through that either apply or calculate a change for a value. I'm not sure how you would parameterize your example of removing reactions ... If I were to remove a reaction I would probably do that as before by creating a changed model with the reaction removed, and then apply the nested simulation to it. 

But maybe I'm misunderstanding your intentions

cheers
Frank


On Mar 30, 2010, at 7:32 AM, Richard Adams wrote:

> 
> Frank,
>  I read your proposal on your blog - with the 'setValue' function,  
> are you thinking that is a way of manipulating the model without  
> constraining it to be XML based? So long as a parameter /variable is  
> identifiable, tools capable of accepting a model in a particular  
> format would still be able to manipulate it.
> 
> I guess this would preclude sweeping structural changes applied to an  
> XML model that can be done with Xpath (removing a reaction, for  
> example) but is the increase in generality for simple cases of value  
> manipulation worth considering?
> 
> Best wishes
> 
> Richard
> 
> 
> 
> 
> 
>> Hello Andrew:
>> 
>>> 
>>> A few comments. I think that dealing with 'time' is probably one of the
>>> biggest weaknesses in this approach. You wrote:
>>> "We could make it convention, that if this is not defined, then the
>>> models time parameter is changed".
>>> Firstly, as soon as we talk about time, we lose generality; I suggest
>>> 'independent variable of integration' or a similar term. I'll refer to
>>> it as 'IVOI' here.
>>> 
>> 
>> Given the frequent use of integration over time, I think we can   
>> justify having this class. But I'm open to introduce your IVOI as a   
>> more general case. Though I'm afraid many tools will not be able to   
>> handle IVOI.
>> 
>>> Secondly, modern DAE / IDA solvers take adaptive steps in their IVOI,
>>> rather than fixed steps. Your proposal seems to not allow adaptive
>>> step-sizes - rather, it forces the user to specify the step size on
>>> 'OneStep'.
>>> 
>> 
>> Definitely, what the oneStep is meant to describe is how far you   
>> would like to simulate until your next output point. How many steps   
>> the integrator internally takes would be independent of this.
>> 
>>> => Parameters controlling the internal stepping. For example, allowing
>>> for an optional maximum step size to control errors and ensure that the
>>> solver finds features like stimulation pulses.
>> 
>> Again, the one step approach only tells you when you want your next   
>> output point, this can be controlled through the range element on   
>> the nested simulation experiment.
>> 
>>> => Parameters controlling which data is reported. Some simulations will
>>> want to report every internal step, while in others, reporting this data
>>> will produce more data than is required.
>> 
>> This will be defined through the data generators that are defined,   
>> just as in the current approach.
>> 
>>> The above is implemented in CellML Simulation Metadata and the CellML
>>> API and OpenCell extensions to it (this metadata focuses entirely on
>>> 'time' course experiments at present, but does that one task better than
>>> anything proposed for SEDML to date).
>>> 
>> 
>> Great! ... so which tools can i download to experiment with it? it   
>> would be good to test exchange of simulation experiments that way.
>> 
>> best
>> Frank
>> 
>>> Best wishes,
>>> Andrew
>>> 
>>>> 
>>>> Bergmann, Frank. A Simple Nested Simulation for SED-ML. Available from
>>>> Nature Precedings <http://dx.doi.org/10.1038/npre.2010.4257.1> (2010)
>>>> 
>>>> 
>>>> Let me know what you think,
>>>> Best
>>>> Frank
>>>> 
>>>> 
>>>> ------------------------------------------------------------------------------
>>>> Download Intel&#174; Parallel Studio Eval
>>>> Try the new software tools for yourself. Speed compiling, find bugs
>>>> proactively, and fine-tune applications for parallel performance.
>>>> See why Intel Parallel Studio got high marks during beta.
>>>> http://p.sf.net/sfu/intel-sw-dev
>>>> _______________________________________________
>>>> SED-ML-discuss mailing list
>>>> SED...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>> 
>>> 
>>> ------------------------------------------------------------------------------
>>> Download Intel&#174; Parallel Studio Eval
>>> Try the new software tools for yourself. Speed compiling, find bugs
>>> proactively, and fine-tune applications for parallel performance.
>>> See why Intel Parallel Studio got high marks during beta.
>>> http://p.sf.net/sfu/intel-sw-dev
>>> _______________________________________________
>>> SED-ML-discuss mailing list
>>> SED...@li...
>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>> 
>> 
>> ------------------------------------------------------------------------------
>> Download Intel&#174; Parallel Studio Eval
>> Try the new software tools for yourself. Speed compiling, find bugs
>> proactively, and fine-tune applications for parallel performance.
>> See why Intel Parallel Studio got high marks during beta.
>> http://p.sf.net/sfu/intel-sw-dev
>> _______________________________________________
>> SED-ML-discuss mailing list
>> SED...@li...
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>> 
>> 
> 
> 
> 
> -- 
> Dr Richard Adams
> Software Development Team Leader,
> Centre For Systems Biology Edinburgh
> University of Edinburgh
> Tel: 0131 650 8285
> email : ric...@ed...
> 
> -- 
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
> 
> 
> 
> ------------------------------------------------------------------------------
> Download Intel&#174; Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

Re: [SED-ML-discuss] Proposing a Nested Simulation Experiment

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

Frank,
  I read your proposal on your blog - with the 'setValue' function,  
are you thinking that is a way of manipulating the model without  
constraining it to be XML based? So long as a parameter /variable is  
identifiable, tools capable of accepting a model in a particular  
format would still be able to manipulate it.

I guess this would preclude sweeping structural changes applied to an  
XML model that can be done with Xpath (removing a reaction, for  
example) but is the increase in generality for simple cases of value  
manipulation worth considering?

Best wishes

Richard





> Hello Andrew:
>
>>
>> A few comments. I think that dealing with 'time' is probably one of the
>> biggest weaknesses in this approach. You wrote:
>> "We could make it convention, that if this is not defined, then the
>> models time parameter is changed".
>> Firstly, as soon as we talk about time, we lose generality; I suggest
>> 'independent variable of integration' or a similar term. I'll refer to
>> it as 'IVOI' here.
>>
>
> Given the frequent use of integration over time, I think we can   
> justify having this class. But I'm open to introduce your IVOI as a   
> more general case. Though I'm afraid many tools will not be able to   
> handle IVOI.
>
>> Secondly, modern DAE / IDA solvers take adaptive steps in their IVOI,
>> rather than fixed steps. Your proposal seems to not allow adaptive
>> step-sizes - rather, it forces the user to specify the step size on
>> 'OneStep'.
>>
>
> Definitely, what the oneStep is meant to describe is how far you   
> would like to simulate until your next output point. How many steps   
> the integrator internally takes would be independent of this.
>
>> => Parameters controlling the internal stepping. For example, allowing
>> for an optional maximum step size to control errors and ensure that the
>> solver finds features like stimulation pulses.
>
> Again, the one step approach only tells you when you want your next   
> output point, this can be controlled through the range element on   
> the nested simulation experiment.
>
>> => Parameters controlling which data is reported. Some simulations will
>> want to report every internal step, while in others, reporting this data
>> will produce more data than is required.
>
> This will be defined through the data generators that are defined,   
> just as in the current approach.
>
>> The above is implemented in CellML Simulation Metadata and the CellML
>> API and OpenCell extensions to it (this metadata focuses entirely on
>> 'time' course experiments at present, but does that one task better than
>> anything proposed for SEDML to date).
>>
>
> Great! ... so which tools can i download to experiment with it? it   
> would be good to test exchange of simulation experiments that way.
>
> best
> Frank
>
>> Best wishes,
>> Andrew
>>
>>>
>>> Bergmann, Frank. A Simple Nested Simulation for SED-ML. Available from
>>> Nature Precedings <http://dx.doi.org/10.1038/npre.2010.4257.1> (2010)
>>>
>>>
>>> Let me know what you think,
>>> Best
>>> Frank
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Download Intel&#174; Parallel Studio Eval
>>> Try the new software tools for yourself. Speed compiling, find bugs
>>> proactively, and fine-tune applications for parallel performance.
>>> See why Intel Parallel Studio got high marks during beta.
>>> http://p.sf.net/sfu/intel-sw-dev
>>> _______________________________________________
>>> SED-ML-discuss mailing list
>>> SED...@li...
>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>
>>
>> ------------------------------------------------------------------------------
>> Download Intel&#174; Parallel Studio Eval
>> Try the new software tools for yourself. Speed compiling, find bugs
>> proactively, and fine-tune applications for parallel performance.
>> See why Intel Parallel Studio got high marks during beta.
>> http://p.sf.net/sfu/intel-sw-dev
>> _______________________________________________
>> SED-ML-discuss mailing list
>> SED...@li...
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
>
> ------------------------------------------------------------------------------
> Download Intel&#174; Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
>



-- 
Dr Richard Adams
Software Development Team Leader,
Centre For Systems Biology Edinburgh
University of Edinburgh
Tel: 0131 650 8285
email : ric...@ed...

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

Re: [SED-ML-discuss] SED-ML roadmap

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

Frank Bergmann wrote:

> Maybe we can also get the organization of SED-ML sorted out soon. I'm sure
> having editors for the spec and an better way to submit proposals would help
> this format to develop faster.

Frank, I am more than sympathetic to that idea. And as soon as the first 
public version of SED-ML is out, there will be a round of election for 
editors etc. I believe that such a move at the moment would actually slow 
down the process. The coverage of the initial SED-ML has been decided 
straight from the beginning in Okinawa. The structure has been described in 
CMSB 2008. What we are doing now, and the "we" includes anyone wanting to 
participate, is to write down this structure in a very precise 
specification, that we can bring to Seattle for hacking.

Meanwhile, nothing preclude to discuss SED-ML Level 1 Version x (x>1) and 
Level y (y>1).

-- 
Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome-Trust
Genome Campus, Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521
Fax:468,Skype:n.lenovere,AIM:nlenovere,MSN:nle...@ho...(NOT email)
http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/, @lenovere

Re: [SED-ML-discuss] How to resolve models

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

On Mar 8, 2010, at 3:16 PM, Nicolas Le novère wrote:

> Fine, but I still do not understand why we need to specify anything. If you 
> provide an archive that contains the SED-ML description and the models 
> needed, you can call the models in the SED-ML file using the URIs 
> "model1.xml", "model2.xml" etc.

Oh I agree, there is not much to specify ... the hope would be to register a mime type for it, specify what the contents could be and perhaps how you identify the simulation experiment description to run in this archive ... richard at one time proposed to have a manifest file there as well ... these kinds of things. 

Frank