Menu
▾
▴
Re: [SED-ML-discuss] Nested Proposal v2
|
From: Richard A. <ric...@ed...> - 2012-02-07 23:52:50
|
I agree with Jonathan on this - if a nested simulation can handle a
uniform time course, by specifying the range to use 'time' as a
target, why not go the whole hog and get rid of UniformTimeCourse? The
concept in l1v1 of a task relating a simulation and a model, while
elegant, seems rather obsolete by this proposal.
The advantages of being able to define simulations independently of a
model seem outweighed by the benefits of using Frank's primitive-based
approach, to my mind.
Since the nestedSimulation can use XPath to identify the model
variables that will be altered , it is already tied to a model - so
perhaps it could use a model reference directly, rather than relating
to a model via a Task.
How about renaming nestedSimulation to 'simulationTask'. A base
simulationTask can then refer to a model, or to another
simulationTask - ultimately this will lead to a 'base task' that will
point to a model element.
Here is an example of what I mean based on Frank's 1D parameter scan
example:
Note that
a) UniformTimeCourse is replaced by a simulationTask.
b) 'Tasks' are removed altogether.
c) A simulation task can refer to another task ('originalTask') or a
model.
d) Variables in DataGenerators now refer to simulationTasks rather
than 'Tasks'.
In a nested set of simulationTasks, the outermost one should always
refer to a SED-ML model element.
<?xml version="1.0" encoding="utf-8"?>
<sedML level="1" version="1" xmlns="http://sed-ml.org/">
<listOfSimulationTasks>
<simulationTask id="utc" resetModel="false"
model="model1" range="timestep">
<algorithm kisaoID="KISAO:0000019" />
<ranges>
<uniformRange id="timestep" start="0" end="20"
numberOfPoints="1000" />
</ranges>
<changes>
<setValue target="urn:sedml:symbol:time" range="timestep">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> timeStep </ci>
</math>
</setValue>
</changes>
</simulationTask>
<simulationTask id="nested1" resetModel="true"
originalTask="utc" range="current">
<ranges>
<vectorRange id="current">
<value>8</value>
<value>4</value>
<value>0.4</value>
</vectorRange>
</ranges>
<changes>
<setValue
target="/sbml:sbml/sbml:model/sbml:listOfParameters/
sbml:parameter[@id='J0_v0']"
range="current">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> current </ci>
</math>
</setValue>
</changes>
</simulationTask>
</listOfSimulationTasks>
<listOfModels>
<model id="model1" language="urn:sedml:language:sbml"
source="http://libsedml.svn.sourceforge.net/viewvc/libsedml/trunk/Samples/models/oscli.xml
" />
</listOfModels>
<listOfDataGenerators>
<dataGenerator id="time1" name="time">
<listOfVariables>
<variable id="time" name="time" taskReference="nested1"
target="time" />
</listOfVariables>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> time </ci>
</math>
</dataGenerator>
<dataGenerator id="J0_v0_1" name="J0_v0">
<listOfVariables>
<variable id="J0_v0" name="J0_v0" taskReference="nested1"
target="/sbml:sbml/sbml:model/sbml:listOfParameters/
sbml:parameter[@id='J0_v0']" />
</listOfVariables>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> J0_v0 </ci>
</math>
</dataGenerator>
<dataGenerator id="S1_1" name="S1">
<listOfVariables>
<variable id="S1" name="S1" taskReference="nested1"
target="/sbml:sbml/sbml:model/sbml:listOfSpecies/
sbml:species[@id='S1']" />
</listOfVariables>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> S1 </ci>
</math>
</dataGenerator>
<dataGenerator id="S2_1" name="S2">
<listOfVariables>
<variable id="S2" name="S2" taskReference="nested1"
target="/sbml:sbml/sbml:model/sbml:listOfSpecies/
sbml:species[@id='S2']" />
</listOfVariables>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> S2 </ci>
</math>
</dataGenerator>
</listOfDataGenerators>
<listOfOutputs>
<plot2D id="plot1" name="Timecourse (Oscli) (for v0 = 8, 4, 0.4)">
<listOfCurves>
<curve id="curve1" logX="false" logY="false"
xDataReference="time1" yDataReference="S1_1" />
<curve id="curve2" logX="false" logY="false"
xDataReference="time1" yDataReference="S2_1" />
</listOfCurves>
</plot2D>
</listOfOutputs>
</sedML>
One other suggestion: in the current nestedSimulations, inner loops
are not reusable - they are defined with respect to the outer
simulations. How about
being able to define 1D parameter scans independently, which could be
combined together simply, e.g.,
<nestedSimulationTask>
<simulationTaskRef refid="paramscan1"/>
<simulationTaskRef refid="paramscan2"/>
</nestedSimulationTask>
indicating a combination of two tasks to produce a 2D scan? I.e.,
each task is defined 'one-dimensionally' but can be composed into N-
dimensional simulations by linear combination.
Finally one other benefit of the nested simulation approach in
general, to include in the proposal ( I think it's been mentioned in
discussions) is that it will no longer be
necessary to use SBML Events to encode time dependent changes to
parameters in SBML - a vector range of time values. This will be
really useful to reduce the pollution of model databases with
structurally identical models differing only in runtime setup.
Cheers
Richard
On 7 Feb 2012, at 11:43, Jonathan Cooper wrote:
> Hi Frank & everyone,
>
> I'm afraid I've not properly read the most recent emails on this
> thread
> yet, as I've been away on holiday. However I made some notes on the
> proposal on my journey out which hopefully will be useful, so I'm
> sending them now, and will go through the discussion later this week
> hopefully.
>
> On the topic of nesting tasks (rather than simulations) - I think this
> does make more sense, as the nesting references a task, and this
> shouldn't be done from a simulation. Also you need to change model
> variables when looping, so need the model reference that a task gives
> you. It'd be nice to have some more flesh on the ideas in Nicolas'
> second email on this sub-topic.
>
> This approach has the potential advantage that a nested task wouldn't
> have/need an algorithm element. However, tasks have a modelReference
> which also seems redundant. What would happen if the reference task
> referenced a different model? Could the modelReference be disallowed
> for
> this subclass? (The hierarchy would need tweaking a little to do
> this.)
>
>
> I have a few other queries/suggestions on the proposal.
>
> 1) I think it should be possible to use the nested features to
> specify a
> timecourse simulations. This isn't obvious or neat at present, which
> suggests that improvement should be possible.
>
> For instance, oneStep currently specifies the step value, but this
> would
> more naturally live in a range on the nested task (and would avoid
> having to make it optional to account for steady-state). So perhaps a
> better approach is to move towards parameterised simulation
> entities, so
> that (analogous to setting a model variable) you can set a parameter
> on
> a simulation object? This could link quite nicely with the
> algorithmParameter proposal for specifying simulation parameters. Then
> you could, for instance, set the "end time" for a oneStep of an ODE
> solver.
>
> For specifying the target of such a set, I don't really like the
> idea of
> XPath into the SED-ML document - it just looks ugly to me. Since we
> already have globally unique IDs within SED-ML, using those seems
> tidier.
>
> 2) It's not clear in the current proposal whether changes are
> applied at
> the start or end of each iteration; I assume (and suggest) start. It
> would also be nice to be able to apply a change at the start/end of a
> whole nested simulation/task.
>
> 3) Passing in range values. The various suggestions in the proposal
> all
> seem a little clunky. Since ranges have globally unique IDs, could we
> make all ranges in the simulation/task implicitly accessible using
> this
> ID as a variable name? Since the ID space is shared across all object
> types, it can't conflict with a variable or parameter. The same
> feature
> could be used to avoid needing an index attribute in a
> functionalRange,
> and would make it easier to combine multiple ranges in other ways (a
> functionalRange could sum 2 ranges, for instance, or different
> variables
> could be set based on different ranges).
>
> Best wishes,
> Jonathan
>
> On 19/01/2012 07:17, Frank T. Bergmann wrote:
>> Hello,
>>
>> As many of you know early in 2010 I proposed a simple nested
>> simulation
>> experiment for SED-ML. Of course that was well before the SED-ML
>> spec was
>> released. Since then I listened to your feedback and made
>> adjustments. With
>> the start of the new year it is time to get the Nested Simulation
>> Proposal
>> for SED-ML ready for wide-spread adoption. I believe nested
>> simulations are
>> vital for SED-ML so that we can cover a much larger variety of
>> simulation
>> experiments.
>>
>> I've taken these past weeks to fully flesh out all the details and
>> the
>> document is now available from Nature Proceedings:
>>
>> http://precedings.nature.com/documents/4257/version/2
>>
>> Unlike the last version this time there is a full description of each
>> element along with examples. If you only have a couple of seconds,
>> have a
>> look at my blog where you see the examples:
>>
>> http://frank-fbergmann.blogspot.com/2012/01/sed-ml-nested-simulation-proposa
>> l-v2.html
>>
>> Or try the SED-ML Web Tools, that I updated to be able to simulate
>> the
>> nested experiment:
>>
>> http://sysbioapps.dyndns.org/SED-ML_Web_Tools/
>>
>> I look forward to your feedback!
>>
>>
>> Best
>> Frank
>>
>>
>> ------------------------------------------------------------------------------
>> Keep Your Developer Skills Current with LearnDevNow!
>> The most comprehensive online learning library for Microsoft
>> developers
>> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3,
>> MVC3,
>> Metro Style Apps, more. Free future releases when you subscribe now!
>> http://p.sf.net/sfu/learndevnow-d2d
>> _______________________________________________
>> SED-ML-discuss mailing list
>> SED...@li...
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
> ------------------------------------------------------------------------------
> Keep Your Developer Skills Current with LearnDevNow!
> The most comprehensive online learning library for Microsoft
> developers
> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3,
> MVC3,
> Metro Style Apps, more. Free future releases when you subscribe now!
> http://p.sf.net/sfu/learndevnow-d2d
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
Dr Richard Adams
Centre For Systems Biology Edinburgh
University of Edinburgh
Tel: 0131 651 9019
email : ric...@ed...
Web: http://csbe.bio.ed.ac.uk/adams.php
*** Places available on CSBE modelling course April 2012 ***
see http://www.csbe.ed.ac.uk/news-events/event/course-details
--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
|
