Hi David, I haven't been using Jsim, I've mainly been using PCEnv. It is my understanding that I can't use Jsim yet, from what others have told me, but I haven't checked that out myself.
Regarding the star system, I agree it is confusing. I'm just using it because it's there. If you have any ideas on a more robust way on presenting curation status to users, I'm all ears. I agree unit checks are really essential to properly validating a model, but often there doesn't seem to be a way of getting everything to check out. For example, take this relatively simple model that I've just fixed. I've given it two stars because it nicely reproduces the figures in the paper it comes from. However, when I run Jonathan Cooper's validator on it, the following result comes up: "[EMAIL PROTECTED]:~/Desktop/tools/JC$ python validator.py ~/Desktop/goldbeter3.cellml Validating file /people/jlaw060/Desktop/goldbeter3.cellml against CellML 1.0 Error checking units: Operator plus requires its operands to have dimensionally equivalent units; dimensionless and first_order_rate differ Context: 1st expression in the 1st math element in component M XPath: /*[1]/*[4]/*[8]/*[1]/*[3]/*[2]/*[3] Error checking units: Operator plus requires its operands to have dimensionally equivalent units; dimensionless and first_order_rate differ Context: 1st expression in the 1st math element in component X XPath: /*[1]/*[5]/*[8]/*[1]/*[3]/*[2]/*[3] Unrecognised namespaces used: http://cellml.org/tmp-documentation http://imc.org/vCard/3.0# http://www.cellml.org/metadata/simulation/1.0# File is NOT valid CellML 1.0" The first equation it has a problem with is: d(M)/d(time) = V1 * M_ / (K1 + M_) - V2 * M / (K2 + M) where it doesn't like adding K1 to M_ (or K2 to M,) which have units "per minute" (first order rate) and "dimensionless" (fraction of concentration of:activated enzyme / total enzyme,) respectively. Because of the way this model is built, getting the units to match would require drastically remaking it, and I don't think I'd know how to do it. I have some ideas, but only because this is a particularly simple model, with 3 differential equations and two algebraic expressions. In a larger model I would have absolutely no idea where to start. So what is the solution to this? Only code up models in CellML that are perfect? Because technically, this model isn't valid CellML Kind regards, James David Nickerson wrote: > Hi all, > > I am just after a bit of clarification on the use of the stars with the > models in the model repository. As I understand the model curation (from > http://www.cellml.org/repository-info/info), one star means the model is > at curation level 1, two stars for level 2, and three for level 3 > curation. For the model simulation tools, there is one star if the model > loads in and runs, 2 if the model gives the right results, and 3 stars > if the results have been rigorously verified. > > The first question I have is if the stars next to the "Standard" link > represent the model curation level while those next to specific tools > correspond to the running of simulations of that model with that tool? > In other words, it is not very obvious what all the stars are implying > when looking at a model's page in the repository. > > Looking at the models with two stars (thanks to Tommy's new filter tool > on the main page), I see they generally have two stars for Standard, > PCEnv and COR but no stars for JSim. If the "Standard" stars do reflect > the curation level of the model, then my second question is how are the > units are being checked (as required for level 2 curation) without using > JSim? I was under the impression that JSim was the only tool capable of > throughly checking all the units for consistency in a model, but perhaps > there is something else? And if so, should it not also be displayed > along with PCEnv, COR, and JSim? > > > Thanks, > David. > _______________________________________________ cellml-discussion mailing list [email protected] http://www.cellml.org/mailman/listinfo/cellml-discussion
