Re: [SOSlib-devel] spatial dimension zero

[Rainer M. <ra...@tb...>]

>> can a compartment of dimension zero have a size?
>
> No
>
>>
>> would we currently handle such structures correctly, at least
>> for fixed compartment sizes?
>
> I don't see why not

Mhm, I guess we might get an error for Compartment_getValue, because at 
the moment I think we treat all compartments as a constant having a size. 
E.g. all ODEs are automatically divided by the compartment size.

Is the stochastic test suite with such models available yet?

Rainer


On Tue, 20 Jun 2006, Andrew Finney wrote:

> Rainer
>
>> do you know of any examples of models with a compartment with
>> spatialDimension zero or hasOnlySubstanceUnits true?
>>
>
> Darren Wilkinson created a stoctastic test suite which consists of
> models
> of this form.  They should operate correctly in a deterministic
> simulator as well.
>
>> can a compartment of dimension zero have a size?
>
> No
>
>>
>> would we currently handle such structures correctly, at least
>> for fixed compartment sizes?
>
> I don't see why not
>
> yours Andrew
>
>> -----Original Message-----
>> From: Rainer Machne [mailto:ra...@tb...]
>> Sent: 20 June 2006 15:48
>> To: Andrew Finney
>> Cc: SOSlib Development
>> Subject: Re: [SOSlib-devel] variable compartment bug: example[Scanned]
>>
>>
>>>>> The units of the species are of the form substance/size units
>>
>>> "The units of the species are of the form substance/size
>> units (i.e.,
>>> concentration units, using a broad definition of
>> concentration) if the
>>> compartment's spatialDimensions is non-zero and
>> hasOnlySubstanceUnits
>>> has the value ``false''. The units of the species are of the form
>>> substance if spatialDimensions is zero or hasOnlySubstanceUnits has
>>> the value ``true''. The units of substance are those defined in the
>>> substanceUnits, and the size units are those given in the
>>> spatialSizeUnits field."
>>> ...
>>
>> oops, i guess it was some freudian process that blinded me to
>> the continuation of this sentence :)
>>
>> do you know of any examples of models with a compartment with
>> spatialDimension zero or hasOnlySubstanceUnits true?
>>
>> can a compartment of dimension zero have a size?
>>
>> would we currently handle such structures correctly, at least
>> for fixed compartment sizes?
>>
>> BTW, there are several models with variable compartments in
>> the test suite, all in the group rulesForParametersAndCompartments.
>>
>> Could it be that SOSlib only succeeded because the program
>> used to generate tested results also does it wrong?
>>
>> Rainer
>>
>>
>> On Tue, 20 Jun 2006, Andrew Finney wrote:
>>
>>> Rainer
>>>
>>>>>> of course you have to check if the species in your kinetic
>>>> law have
>>>>>> dimension conc or substance!
>>>>>> sbml allows the usage of both, doesn't it?
>>>>>
>>>>> See section 4.6.4 here
>>>>>
>>>>
>> http://sbml.org/specifications/sbml-level-2/version-1/html/sbml-level
>>>> -
>>>>> 2.html#SECTION00046000000000000000
>>>>>
>>>>> "
>>>>> The units of the species are of the form substance/size units
>>>>>
>>>>> ...
>>>>>
>>>>> The units of the species are used in the following ways:
>>>>>
>>>>> ...
>>>>>    * The species identifier has these units when it appears as a
>>>>> numerical quantity in a mathematical formula expressed in MathML
>>>>> (discussed in Section 3.6.3).
>>>>> "
>>>>>
>>>>> So i guess, the units of species in math expressions are
>> always in
>>>>> concentrations!
>>>>>
>>>
>>> WRONG
>>>
>>> They are either substance or concentration units depending on the
>>> attributes of the species element.
>>>
>>> "The units of the species are of the form substance/size
>> units (i.e.,
>>> concentration units, using a broad definition of
>> concentration) if the
>>> compartment's spatialDimensions is non-zero and
>> hasOnlySubstanceUnits
>>> has the value ``false''. The units of the species are of the form
>>> substance if spatialDimensions is zero or hasOnlySubstanceUnits has
>>> the value ``true''. The units of substance are those defined in the
>>> substanceUnits, and the size units are those given in the
>>> spatialSizeUnits field."
>>> ...
>>>
>>> "The units of the species are used in the following ways:
>>>
>>>
>>> The species initialConcentration field has these units (see Section
>>> 4.6.3).
>>>
>>> The species identifier has these units when it appears as a
>> numerical
>>> quantity in a mathematical formula expressed in MathML
>> (discussed in
>>> Section 3.6.3).
>>>
>>> The math field of an AssignmentRule structure determining
>> the species'
>>> quantity (see Section 4.8.2) has these units.
>>>
>>> In RateRule structures that set the rate of change of the species'
>>> quantity (Section 4.8.3), the units on the rule's math
>> field are the
>>> units of the species divided by the built-in time units. "
>>>
>>> yours Andrew
>>>
>>>
>>>
>>>
>>>> -----Original Message-----
>>>> From: sbm...@li...
>>>> [mailto:sbm...@li...] On
>> Behalf Of
>>>> Rainer Machne
>>>> Sent: 20 June 2006 15:26
>>>> To: Stefan Mueller
>>>> Cc: sbm...@li...
>>>> Subject: Re: [SOSlib-devel] variable compartment bug:
>>>> example[Scanned]
>>>>
>>>>
>>>>
>>>> This
>>>>
>>>>> current ODE: d[S1]/dt = f(S1, S2, ...) / V planned ODE: d
>> S1 /dt =
>>>>> f(S1, S2, ...)
>>>>
>>>> should of course be
>>>>
>>>> current ODE: d[S1]/dt = f([S1], [S2], ...) / V planned ODE: d
>>>> S1 /dt = f([S1], [S2], ...)
>>>>
>>>>
>>>> On Tue, 20 Jun 2006, Rainer Machne wrote:
>>>>
>>>>> stefan
>>>>>
>>>>>
>>>>>>> divide k by V(0) and the whole kinetic law again by V^2 for 2nd
>>>>>>> order reactions
>>>>>>
>>>>>> yes.
>>>>>> and that's exactly the same what you are planning, if you
>>>> want to use
>>>>>> conc ans subst in parallel.
>>>>>> only the point of conversion differs.
>>>>>
>>>>> not really. i wasn't planning any conversion of the math,
>>>> except for:
>>>>>
>>>>> current ODE: d[S1]/dt = f(S1, S2, ...) / V planned ODE: d
>> S1 /dt =
>>>>> f(S1, S2, ...)
>>>>>
>>>>> then we have two data->value arrays, let's say
>>>>>
>>>>> data->odeValues = S1, S2, S3, etc.
>>>>> and
>>>>> data->concValues = [S1], [S2], [S3] etc.
>>>>>
>>>>>
>>>>> The first array `odeValues' corresponds to the SUNDIALS
>>>> values in NVector y.
>>>>> The second array `concValues' will be used in evaluateAST, for
>>>>> evaluation the math.
>>>>>
>>>>>
>>>>> This would be equivalent of course, with just replacing
>> all [S1] in
>>>>> all math expressions with S1/volume, and only using one array
>>>>> data->odeValues
>>>>>
>>>>> While the latter approach might be easier to implement it has a
>>>>> probably the not so small drawback, that for each species
>>>> in each math
>>>>> expression the evaluation needs one more operation, i.e.
>>>> the division,
>>>>> while this division could be done only once for each
>>>> species whenever
>>>>> data->odeValues is updated (i.e. e.g. in the
>>>> SOSlib/SUNDIALS funciton f).
>>>>>
>>>>> However, this might still only be correct, if compartments are
>>>>> determined by assignment rules.
>>>>> If they are determined by rate rules, then the replacement
>>>> S1 -> S1/V
>>>>> would also be required for constructing the jacobi matrix.
>>>>>
>>>>>> of course you have to check if the species in your kinetic
>>>> law have
>>>>>> dimension conc or substance!
>>>>>> sbml allows the usage of both, doesn't it?
>>>>>
>>>>> See section 4.6.4 here
>>>>>
>>>>
>> http://sbml.org/specifications/sbml-level-2/version-1/html/sbml-level
>>>> -
>>>>> 2.html#SECTION00046000000000000000
>>>>>
>>>>> "
>>>>> The units of the species are of the form substance/size units
>>>>>
>>>>> ...
>>>>>
>>>>> The units of the species are used in the following ways:
>>>>>
>>>>> ...
>>>>>    * The species identifier has these units when it appears as a
>>>>> numerical quantity in a mathematical formula expressed in MathML
>>>>> (discussed in Section 3.6.3).
>>>>> "
>>>>>
>>>>> So i guess, the units of species in math expressions are
>> always in
>>>>> concentrations!
>>>>>
>>>>> Rainer
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>>
>>>>>> i mean, every species is in a well-defined compartment, isn't it?
>>>>>> so you can use the formula [S]=S/V whenever you want...
>>>>>>
>>>>>> i would eliminate conc as early as possile, but that's a
>> matter of
>>>>> taste.
>>>>>
>>>>>
>>>>>
>>>>> On Tue, 20 Jun 2006, Stefan Mueller wrote:
>>>>>
>>>>>> hi rainer!
>>>>>>
>>>>>>> stefan
>>>>>>>
>>>>>>>>> Currently the ODE would be:
>>>>>>>>>
>>>>>>>>> d[S1]/dt = k1 * [S1] / V1
>>>>>>>>
>>>>>>>> this is not valid for variable compartments.
>>>>>>>
>>>>>>> i said that it's invalid for variable compartments some
>>>> lines below:
>>>>>>>>> which is only valid for constant compartments V1 and V2.
>>>>>>>>
>>>>>>>> please don't use it for comparison!
>>>>>>>
>>>>>>> it's not used for comparison, but it is the current
>>>> implementation
>>>>>>> in SOSlib!
>>>>>>
>>>>>> i said this just to avoid any additional misunderstanding.
>>>>>> the whole topic seems to be quite confusing...
>>>>>>
>>>>>>>>> At least for the second ODE, depending in two different
>>>> volumes,
>>>>>>>>> the conversion to ODEs depending on substance instead of
>>>>>>>>> concentration is not as simple as
>>>>>>>>>
>>>>>>>>>> dS1/dt = k * [S1] * [S2] / V(0) * V = k/V(0) * S1 * S2 / V
>>>>>>>>
>>>>>>>> why dou you refer to this law for a reaction of order 2?
>>>>>>>
>>>>>>> sorry, at first i wanted to make the second reaction in
>> V2 of 2nd
>>>>>>> order, e.g.,
>>>>>>>
>>>>>>> in V2:
>>>>>>> S2 + S3 -> P: k2*[S2]*[S3]
>>>>>>>
>>>>>>>>> as your example before,
>>>>>>>>> but for S2 I get:
>>>>>>>>>
>>>>>>>>> dS2/dt = k1/V1(0) * S1/V1 * V2  -  k2/V2(0) * S2
>>>>>>>>>
>>>>>>>>> Right?
>>>>>>>>
>>>>>>>> no!
>>>>>>>> dS2/dt = k1/V1(0) * S1 - k2/V2(0) * S2 it's as simple as that!
>>>>>>>> (since dS2/dt = -dS1/dt as far as reaction S1->S2 is
>> concerned.)
>>>>>>>> that's the advantage of kinetic laws (and consequently
>> odes) for
>>>>>>>> substances!
>>>>>>>
>>>>>>> of course! sorry, i got quite confused obviously.
>>>>>>>
>>>>>>> and for the above second order reaction in V2 it would be:
>>>>>>>
>>>>>>>   dS2/dt = k1/V1(0) * S1 - k2/V2(0) * S1 * S3 / V2
>>>>>>>
>>>>>>> Right this time?
>>>>>>
>>>>>> yes :)
>>>>>>
>>>>>>>>> Thus I would really have to check the type of reaction
>>>> and edit a
>>>>>>>>> lot of kinetic laws before constructing the ODEs.
>>>>>>>>
>>>>>>>> the above example shows that this is not necessary.
>>>>>>>> maybe there are other examples...
>>>>>>>
>>>>>>> so you say, we could convert kinetic laws that don't explicitly
>>>>>>> contain the volume by simply differentiating these
>> three cases and
>>>>>>>
>>>>>>>>>> order 1:
>>>>>>>>>> S1->junk: k*[S1]
>>>>>>>>>> dS1/dt = k * [S1] / V(0) * V = k/V(0) * S1
>>>>>>>
>>>>>>> divide k by V(0) for 1st order reactions
>>>>>>>
>>>>>>>>>> order 2:
>>>>>>>>>> S1+S2->bla: k*[S1]*[S2]
>>>>>>>>>> dS1/dt = k * [S1] * [S2] / V(0) * V = k/V(0) * S1 * S2 / V
>>>>>>>
>>>>>>> divide k by V(0) and the whole kinetic law again by V^2 for 2nd
>>>>>>> order reactions
>>>>>>>
>>>>>>>>>> order 3:
>>>>>>>>>> S1+S2+S3->wow: k*[S1]*[S2]*[S3]
>>>>>>>>>> dS1/dt = k * [S1] * [S2] * [S3] / V(0) * V = k/V(0) *
>>>> S1 * S2 *
>>>>>>>>>> S3 /
>>>>>>>
>>>>>>> V^2
>>>>>>>
>>>>>>> divide k by V(0) and the whole kinetic law again by V^2 for 2nd
>>>>>>> order reactions
>>>>>>
>>>>>> yes.
>>>>>> and that's exactly the same what you are planning, if you
>>>> want to use
>>>>>> conc ans subst in parallel.
>>>>>> only the point of conversion differs.
>>>>>>
>>>>>> i mean, every species is in a well-defined compartment, isn't it?
>>>>>> so you can use the formula [S]=S/V whenever you want...
>>>>>>
>>>>>> i would eliminate conc as early as possile, but that's a
>>>> matter of taste.
>>>>>>
>>>>>>> but there are also enzymatic reactions, with in often
>>>> quite complex
>>>>>>> kinetic laws. we would really have to do unit checking,
>>>> recognizing
>>>>>>> the implemented reaction mechanisms etc.
>>>>>>
>>>>>> of course you have to check if the species in your kinetic
>>>> law have
>>>>>> dimension conc or substance!
>>>>>> sbml allows the usage of both, doesn't it?
>>>>>>
>>>>>>> also, we don't really know in which compartment
>> reactions happen,
>>>>>>> but could just try to get this information from the
>>>> reactants' compartments.
>>>>>>
>>>>>> this does not matter, for 2 reasons:
>>>>>>
>>>>>> 1. if the kinetic law is specified correctly (including the
>>>>>> compartment size), e.g. A+B->C: k*V*[A]*[B], the the
>>>> compartment size
>>>>>> is considered automatically.
>>>>>>
>>>>>> 2. the conversion [S]=S/V does not depend on reactions,
>>>> but only on
>>>>>> species (and their compartments).
>>>>>>
>>>>>>> so i guess, it would be much easier to
>>>>>>>
>>>>>>> a) use ODEs for substances but dependent on
>>>> concentrations, here the
>>>>>>> only thing we need to do is to leave out the compartment
>>>> division at
>>>>>>> the end of Species_odeFromReactions and have a double
>>>> bookkeeping of
>>>>>>> amounts and concentrations
>>>>>>
>>>>>> to my taste, double book keeping is dangerous and produces
>>>> overhead.
>>>>>>
>>>>>>> and
>>>>>>>
>>>>>>> b) just ignore WRONG models that have a variable
>> compartment but
>>>>>>> don't have the compartment explicitly in their kinetic laws (or
>>>>>>> check for such cases and issue an error);
>>>>>>>
>>>>>>> isn't it an issue of correct model writing rather then
>>>> correct model
>>>>>>> solving?
>>>>>>
>>>>>> i agree.
>>>>>>
>>>>>>> However, another problem might be that to calculate in amounts
>>>>>>> rather then in concentrations also changes the use of absolute
>>>>>>> errors and maybe also the general the performance of the
>>>> integrator, i guess. ??
>>>>>>
>>>>>> abs errors might change, but that's not an issue.
>>>>>> rel errors should stay the same.
>>>>>> (in one-compartment models everything is just multiplied by the
>>>>>> volume.)
>>>>>>
>>>>>>> maybe we will have to really implement both in parallel,
>>>>>>
>>>>>> i hope not :)
>>>>>>
>>>>>>> * ODEs for concentrations/time if no variable
>> compartments are in
>>>>>>> the model
>>>>>>> * ODEs for ammounts/time if any compartment is variable
>>>>>>>
>>>>>>> ?
>>>>>>>
>>>>>>> Rainer
>>>>>>
>>>>>> maybe we discuss the next round via telephone :)
>>>>>>
>>>>>> cheers, s
>>>>>>
>>>>>>
>>>>>>>>> Thus I think it just doesn't work with kinetic laws
>> that don't
>>>>>>>>> include the compartment explicitly!
>>>>>>>>
>>>>>>>> i don't know exactly what you mean.
>>>>>>>> of course kinetic laws with explicit compartment are
>>>> "nicer", but
>>>>>>>> you can always transform any kinetic law to a "nice" one...
>>>>>>>>
>>>>>>>>> But if they include the compartment we can write ODEs for
>>>>>>>>> substances but have concentrations in the right hand
>>>> side of the
>>>>>>>>> ODEs. We then just need to a second array for the
>>>> concentrations, as discussed before.
>>>>>>>>
>>>>>>>> if we still use concentrations is a separate problem,
>>>> independent
>>>>>>>> of which we discussed until now.
>>>>>>>> it's a matter of taste, if we eliminate the
>> concentrations  from
>>>>>>>> the kinetic laws and get a (possibly nonlinear)
>>>> dependence on the
>>>>>>>> compartments OR if we keep concentrations and always
>> have linear
>>>>>>>> dependence on the comp.
>>>>>>>>
>>>>>>>>> Rainer
>>>>>>>>
>>>>>>>> cheers,
>>>>>>>> stefan.
>>>>>>>>
>>>>>>>>> On Mon, 19 Jun 2006, Stefan Mueller wrote:
>>>>>>>>>> let me summarize:
>>>>>>>>>> kinetic laws have units substance/time, and they depend on
>>>>>>>>>> concentrations or substances.
>>>>>>>>>>
>>>>>>>>>> we SHOULD write down odes for substances, and we COULD
>>>> eliminate
>>>>>>>>>> concs completely.
>>>>>>>>>> (of course, we would have to convert initial concs to
>>>>>>>>>> substances.)
>>>>>>>>>>
>>>>>>>>>> in any case, odes for substances depend on the
>>>> compartment size
>>>>>>>>>> (linearly or according to the order of the reaction):
>>>>>>>>>>
>>>>>>>>>> order 1:
>>>>>>>>>> S1->junk: k*[S1]
>>>>>>>>>> dS1/dt = k * [S1] / V(0) * V = k/V(0) * S1
>>>>>>>>>>
>>>>>>>>>> order 2:
>>>>>>>>>> S1+S2->bla: k*[S1]*[S2]
>>>>>>>>>> dS1/dt = k * [S1] * [S2] / V(0) * V = k/V(0) * S1 * S2 / V
>>>>>>>>>>
>>>>>>>>>> order 3:
>>>>>>>>>> S1+S2+S3->wow: k*[S1]*[S2]*[S3]
>>>>>>>>>> dS1/dt = k * [S1] * [S2] * [S3] / V(0) * V = k/V(0) *
>>>> S1 * S2 *
>>>>>>>>>> S3 /
>>>>>>>>>> V^2
>>>>>>>>>>
>>>>>>>>>> ...
>>>>>>>>>>
>>>>>>>>>> if the kinetic laws included the compartment
>>>> explicitly (which is
>>>>>>>>>> desirable), we would have the following situation:
>>>>>>>>>>
>>>>>>>>>> order 1:
>>>>>>>>>> S1->junk: r*[S1]*V
>>>>>>>>>> dS1/dt =  r * [S1] * V= r * S1
>>>>>>>>>>
>>>>>>>>>> order 2:
>>>>>>>>>> S1+S2->bla: r*[S1]*[S2]*V
>>>>>>>>>> dS1/dt = r * [S1] * [S2] * V= r * S1 * S2 / V
>>>>>>>>>>
>>>>>>>>>> order 3:
>>>>>>>>>> S1+S2+S3->wow: r*[S1]*[S2]*[S3]*V
>>>>>>>>>> dS1/dt = r * [S1] * [S2] * [S3] * V = r * S1 * S2 * S3 / V^2
>>>>>>>>>>
>>>>>>>>>> as stated earlier, odes for substances have got another
>>>>>>>>>> advantage. for the compartment size we could use
>> either a rate
>>>>>>>>>> rule or an assignment
>>>>>>>>>> rule: dV/dt = f(t, V, ...)
>>>>>>>>>> or
>>>>>>>>>> V= f(t, V, ...)
>>>>>>>>>>
>>>>>>>>>> cheers,
>>>>>>>>>> stefan.
>>>>>>>>>>
>>>>>>>>>> Am Montag 19 Juni 2006 11:17 schrieb Stefan Mueller:
>>>>>>>>>>> andrew:
>>>>>>>>>>>
>>>>>>>>>>> for the SBML system
>>>>>>>>>>> 	S1 in C
>>>>>>>>>>> 	S1->junk : k * [S1]
>>>>>>>>>>> 	dC/dt = 1
>>>>>>>>>>>
>>>>>>>>>>> the right math is:
>>>>>>>>>>> 	dS1/dt = k * [S1] / C(0) * C
>>>>>>>>>>> 	dC/dt = 1
>>>>>>>>>>> with initial cond:
>>>>>>>>>>> 	S1(0) = [S1](0) * C(0)
>>>>>>>>>>> 	C(0)
>>>>>>>>>>>
>>>>>>>>>>> notation:
>>>>>>>>>>> 	S1 ... substance
>>>>>>>>>>> 	[S1] ... conc
>>>>>>>>>>>
>>>>>>>>>>> the "proposed solution" (who proposed this?) has the right
>>>>>>>>>>> units, but is wrong otherwise... :)
>>>>>>>>>>>
>>>>>>>>>>> as rainer and me already discussed, everything
>> would be much
>>>>>>>>>>> clearer, if the kinetic law included the compartment
>>>> explicitly:
>>>>>>>>>>> 	S1 in C
>>>>>>>>>>> 	S1->junk : C * r * [S1]
>>>>>>>>>>> 	dC/dt = 1
>>>>>>>>>>>
>>>>>>>>>>> with:
>>>>>>>>>>> 	r ... the "real" chemical rate constant.
>>>>>>>>>>>
>>>>>>>>>>> rainer:
>>>>>>>>>>>
>>>>>>>>>>> chemists always knew that rate constants are not
>>>> constant with
>>>>>>>>>>> respect to pH, T, ... as a physicist i have to be fair! :)
>>>>>>>>>>>
>>>>>>>>>>> to conclude: the math is not really tricky.
>>>>>>>>>>> odes for substances are better suited to handle
>> both multiple
>>>>>>>>>>> and variable compartments. of course, we have to
>> take care of
>>>>>>>>>>> many implementation details...
>>>>>>>>>>>
>>>>>>>>>>> cheers,
>>>>>>>>>>> stefan.
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> sbmlsolver-devel mailing list
>>>>>>>>>> sbm...@li...
>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/sbmlsolver-devel
>>>>>>>>>
>>>>>>>>> _______________________________________________
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