Could we perhaps consider built-in scaling factors for CellML 1.2?
That way could still support the SI units but just that one of them (mole)
is as a scaling factor which is what it is as far as I can see.
We might also include built-in scaling factors for converting between
prefixes. For example if I have
a variable A in nanomolar and another B in micromolar I might want to say:
A = 1e3 * B
One way to do this is to define a scaling factor unit say (in CORspeak)
def unit nanospermicro from
unit liter {pref: nano};
unit liter {pref: micro, expo:-1};
enddef;
and then have
A = 1e3 {nanospermicro} * B.
Which is slightly clunky.
(I think the use of 'liter' above should also be replaced with
'dimensionless', but that is a different issue).
We could also include dozen, which would aid the bakery-modelling community
too ;).
-----Original Message-----
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Peter Hunter
Sent: Tuesday, 3 June 2008 11:35 a.m.
To: CellML Discussion List
Subject: Re: [cellml-discussion] unit conversion
Hi Mike,
I agree - but there they are in the SI base unit list see
http://physics.nist.gov/cuu/Units/units.html
so probably 150 years too late to do much about it!
Cheers,
Peter
Mike Cooling wrote:
> 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: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of James
> Lawson
> Sent: Tuesday, 3 June 2008 11:07 a.m.
> To: Erik B
> Cc: cellml-discussion@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 [EMAIL PROTECTED] 206-685-2007
>>>>
>>>> On Thu, 29 May 2008, Andrew Miller wrote:
>>>>
>>>>> Date: Thu, 29 May 2008 11:29:50 +1200
>>>>> From: Andrew Miller <[EMAIL PROTECTED]>
>>>>> To: James Lawson <[EMAIL PROTECTED]>
>>>>> Cc: James Lawson <[EMAIL PROTECTED]>,
>>>>> [EMAIL PROTECTED]
>>>>> 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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