Catherine Lloyd wrote:

Hi Andrew and RandallThis has gone beyond a curation question... Can one of you pleaseexplain daes to Lucian and also how OpenCell handles them?

In a CellML model, if you have two equations: f(x, y, z, a, b, c) = g(x, y, z, a, b, c) h(x, y, z, a, b, c) = i(x, y, z, a, b, c)

`then this means that both equations in the model are true simultaneously`

`(CellML is declarative, not procedural).`

`The CellML Integration Service included with the CellML API currently`

`handles this case by using the Levenberg-Marquardt non-linear`

`optimisation algorithm to look for a solution to`

(f(x, y, z, a, b, c) - g(x, y, z, a, b, c))^2 = 0 (h(x, y, z, a, b, c) = i(x, y, z, a, b, c))^2 = 0

`It will satisfy as many of x, y, z, a, b, and c as possible using other`

`equations first.`

Work is also in progress towards supporting IDA. Best wishes, Andrew

That would be much appreciated - Thank you :) Best wishes Catherine Begin forwarded message:*From: *Lucian Smith <lpsm...@spod-central.org<mailto:lpsm...@spod-central.org>>*Date: *11 March 2010 9:01:27 AM*To: *Catherine Lloyd <c.ll...@auckland.ac.nz<mailto:c.ll...@auckland.ac.nz>>*Subject: **Re: Haugh 2004b* Aha, thanks! So, I don't know anything about differential algebraicequations, and I'm afraid the wikipedia page about it is opaque to me.But the loop in question occurs with a couple 'Assignment rules' (asthey're known in SBML), with the first variable depending on the secondvariable, and the second depending on the first. Is the claim that ifthesystem is set up correctly, there is always a set of variables such thatthose assignment rules will both be satisfiable? And that thisrelates todifferential algebraic equations somehow? Or does OpenCell simplyexecutethe first in each iteration based on the previous iteration's values, and then execute the second based on those results? (We're probably moving away from curation questions at this point...) Thanks for the assistance! And I'm glad you appreciated the follow-up post--I had been hoping to get at least a little bit of discussion out of it, but I'll settle for a thanks ;-) -Lucian* Catherine Lloyd <c.ll...@auckland.ac.nz<mailto:c.ll...@auckland.ac.nz>> [2010-03-10 01:15] writes:Hi Lucian Yes, it's a curation question :) OK, so Haugh_2004 has this curation statement:This CellML model runs in both COR and OpenCell. The units have beenchecked and they are consistent. The CellML model may recreate theresults of the original published model but there is no simplevalidation method as there are no "concentration against time" figuresin the paper. The CellML model is based on equations A1a, A1b, A1c,A1d and A1e from the Appendix. Parameter values were taken from table1 in the paper and were also supplied through correspondence with theoriginal model author.I checked the model in COR and in OpenCell and it runs fine in both. HOWEVER, Haugh_2004b has this statement:This CellML model runs in OpenCell (but not COR due to the presence ofdifferential algebraic equations). The units have been checked andthey are consistent. The CellML model may recreate the results of theoriginal published model but there is no simple validation method asthere are no "concentration against time" figures in the paper. TheCellML model is based on equations A2-A5 from the Appendix (steadystate model). Parameter values were taken from table 1 in the paperand were also supplied through correspondence with the original modelauthor.COR reports an error similar to your tool - that the model has"circular arguments". OpenCell can handle differential algebraicequations though so the model runs in OpenCell - but whether or not itmakes any sense we don't know as there were no results figures in thepublished paper to compare the CellML to.Regarding the stars - this is an unfortunate problem in PMR2 that weare aware about - we can only assign a star rating once in a modelexposure - regardless of how many different models there may be.Tommy knows this and hopefully it will be fixed in the not too distantfuture.I hope this makes some sense - please let me know if it doesn't orif you need more information.Also thank you for your feedback post-meeting - I spotted it on cellmldiscuss when I got back to work on Monday.Best wishes Catherine On 10/03/2010, at 12:41 PM, Lucian Smith wrote:So, I have a question that essentially amounts to a curationquestion (Ithink), so I figured I'd ask you directly instead of the list. ButI amhappy to ask the list if you think that would be better! When translating the model haugh_2004b.cellml from http://models.cellml.org/exposure/4ce2912573256c6a5483da117ed26d9e my software found an error: The definition of 'C' in component 'C'includes a variable 'R', and the the definition of 'R' in component'R'includes a variable 'C'. Then there is a connection between C.C andR.C,and between R.R and C.R. Which I *think* should end up with anoverdetermined model. In all other cases when I've found such aloop, ifI look at the model's curation status, it will say something like"thismodel is overdetermined". But this has a two-star curation, andclaimsthere are no problems (of this nature, at least). So is there notactually a problem and my software thinks there is, or is there aproblemthat is not mentioned in the curation paragraph? Or was the modelchangedsince its last curation? Or is the curation paragraph about haugh2004.txt, and not haugh2004b.txt? Thanks! -Lucian

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