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[cellml-discussion] unit conversion


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  • From: m.cooling at auckland.ac.nz (Mike Cooling)
  • Subject: [cellml-discussion] unit conversion
  • Date: Tue, 3 Jun 2008 11:25:49 +1200
Does it strike anyone else as inconsistent that 'moles' are a unit when
moles are just a scaling factor? Like dozen. Maybe they should be
implemented using 'multiplier' or similar rather than a base unit.

For example, I could have a mole of amps. I couldn't have a second of amps.



-----Original Message-----
From: cellml-discussion-bounces at cellml.org
[mailto:cellml-discussion-bounces at cellml.org] On Behalf Of James Lawson
Sent: Tuesday, 3 June 2008 11:07 a.m.
To: Erik B
Cc: cellml-discussion at cellml.org
Subject: Re: [cellml-discussion] unit conversion

Thanks Erik,

I managed to fix the issue before receiving your email, but this clears
things up for me very concisely. I would venture to say that the reason that
so many CellML models in the CellML repository do not pass Jsim's units
checking is not because of CellML, or any tools used to create CellML
models. Rather it is often because the models themselves contain unit
inconsistencies. It does not help that units are irrelevant to most
modelling tools, but I think the modelling community is starting to raise
the bar with regards to this issue. Unfortunately it is often quite
difficult to 'fix' inappropriate units (both quantitatively and
qualitatively,) in a model without breaking it.

FYI I've uploaded the model in question, which now runs in Jsim, COR and
PCEnv, at:
http://www.cellml.org/models/sachse_moreno_abildskov_2008_version02

The 'auto' setting for the integrator in Jsim will not run the model - the
CVode integrator must be selected manually.

Kind regards,
James Lawson

Erik Butterworth wrote:
> On Thu, 29 May 2008, Andrew Miller wrote:
>
>> I think James had something more along the lines of:
>> I_inter_fibro = 10^6 * (V_fibro - V) / R_mf (where 10^6 is marked as
>> a dimensionless number).
>>
>> In this case the intention of the modeller is that the expression
>> being equated to I_inter_fibro is already in nanoamps, and this will
>> give the correct results in PCEnv and COR, I believe.
>>
>> I agree that it would be better modelling practice to mark 10^6 as
>> being in units nanoamps per milliamps, and in this case PCEnv and COR
>> will give correct results of 1E6 nanoamperes (and I presume also JSim?).
>
> Short answer: yes.
>
> Long answer: JSim has two unit conversion modes, on and off. With
> conversion on, the simplest correct formation in MML is
>
> 1. I_inter_fibro = (V_fibro - V) / R_mf;
>
> With unit conversion off, the simplest correct formation is:
>
> 2. I_inter_fibro = 10^6 * (V_fibro - V) / R_mf;
>
> With either unit conversion on or off, a dimensionalized constant
> will produce correct results, at the expense of conciseness:
>
> 3. I_inter_fibro = (10^6 nanoamp/milliamp) * (V_fibro - V) / R_mf;
>
> To be compatible with (my understanding of) the CellML units spec,
> JSim's CellML -> MML converter creates MML with unit conversion on.
> However, due the the historically large (although perhaps decreasing)
> number of CellML models that didn't pass JSim unit balance, the JSim
> WWW site provides (for CellML models not passing unit balance) an
> "imperfect" MML translation with unit conversion off. This allows the
> models to be compiled and run, even if they may need conversion factor
> editing. Even if the CellML model doesn't pass JSim unit balance, it
> would still run correctly if all needed conversion factors were in the
> CellML in form #3 above.
>
> Hope this helps,
>
> Erik B.
>
>
>
>>
>> At least my reading of the CellML specification is that tools should
>> not be automatically inserting conversion factors like this when
>> processing CellML models, although they may optionally warn the user
>> that a conversion factor may be missing and / or offer to insert it
>> for them.
>>
>> Best regards,
>> Andrew
>>
>>>
>>> Erik Butterworth butterw at u.washington.edu 206-685-2007
>>>
>>> On Thu, 29 May 2008, Andrew Miller wrote:
>>>
>>>> Date: Thu, 29 May 2008 11:29:50 +1200
>>>> From: Andrew Miller <ak.miller at auckland.ac.nz>
>>>> To: James Lawson <j.lawson at auckland.ac.nz>
>>>> Cc: James Lawson <j.lawson at auckland.ac.nz>,
>>>> butterw at u.washington.edu
>>>> Subject: Re: unit conversion
>>>>
>>>> James Lawson wrote:
>>>>> Hi Andrew, Justin,
>>>>>
>>>>> Thanks for your help. Basically, I've had to multiply a current by
>>>>> a scaling factor of 1 million to get the model to run in PCEnv. It
>>>>> was made in Jsim and worked fine, but now I have a model that will
>>>>> run in PCEnv but not Jsim. Do you guys have any idea about what I
>>>>> could do to get it running in both? Would showing you the model
>>>>> help? I could email the Jsim guys and ask them if I knew what to
>>>>> ask.. It seems like Jsim doesn't really convert nanoamps into
>>>>> 10e-6 amps and work with the value from there, whereas PCEnv does.
>>>>> Would this be right?
>>>>>
>>>>> Basically the issue that I have addressed is that units for the
>>>>> variables in the equation for I_inter_fibro aren't dimensionally
>>>>> equivalent:
>>>>>
>>>>> The equation is: I_inter_fibro =(V_fibro - V) / R_mf
>>>>>
>>>>> Where I_inter_fibro is in nanoamperes, V_fibro and V are in
>>>>> millivolts and R_mf is in ohms. So the equation says that nanoamps
>>>>> = millivolts / ohms. Thus I have changed the equation to say
>>>>> I_inter_fibro = 1e+06 * (V_fibro - V) / R_mf
>>>> Hi James,
>>>>
>>>> What are the units on the 1E6 scaling factor? If you put them in
>>>> nanoamps_per_milliamp or something like that, then I think all
>>>> software should do the right thing. Automatically inserting the
>>>> conversion factor is not the correct software behaviour however; at
>>>> most software should be flagging the problem and helping the user
>>>> to insert the factor if they decide there is an actual problem.
>>>>
>>>> Best regards,
>>>> Andrew
>>>>
>>>>>
>>>>> So at the moment I do not know how to get the model to run in both
>>>>> PCEnv and Jsim. What I'll do is upload a variant of the model to
>>>>> the repository with different curation notes, but ideally I should
>>>>> be able to get one model that runs in both environments. This
>>>>> looks like it might be a pretty persistent problem unfortunately.
>>>>>
>>>>> Thanks,
>>>>> James
>>>>>
>>>>> Andrew Miller wrote:
>>>>>> James Lawson wrote:
>>>>>>> Hi guys,
>>>>>>>
>>>>>>> I was wondering if you might be able to help me out with a
>>>>>>> curation issue. I've been working on a model that was tested in
>>>>>>> Jsim that just wasn't producing the right results in PCEnv.
>>>>>>> Finally I figured out that it was something to do with the
>>>>>>> magnitude of a current being out by a factor of a million -
>>>>>>> milli to nano. So obviously this is something to do with unit
>>>>>>> conversions being applied in one tool and not the other. I was
>>>>>>> under the impression that it was Jsim that doesn't apply units
>>>>>>> conversions and PCEnv and COR that do - am I right here? I'm
>>>>>>> worried that having fixed the model under PCEnv, I've broken it
>>>>>>> under Jsim. Could you guys please explain here?
>>>>>>>
>>>>>>> I do have JSim on my computer but I'm unable to figure out how
>>>>>>> to import a CellML file into it and run it.
>>>>>> PCEnv carries out units conversions at the connections (so if you
>>>>>> cannot something in millimol/L to something in nanomol/L it will
>>>>>> convert for you; this is what the CellML specificatin requires).
>>>>>> COR doesn't do this, and instead gives an error if you try to
>>>>>> connect variables in diffferent units. I've heard that some
>>>>>> versions of JSim try to actually change the maths to insert
>>>>>> conversion factors in at the equation level - but I believe this
>>>>>> is usually turned off.
>>>>>>
>>>>>> Best regards,
>>>>>> Andrew
>>>>>
>>>>
>>>>
>>
>>




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