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[cellml-discussion] Initial units assignment


Chronological Thread 
  • From: jonathan.cooper at comlab.ox.ac.uk (Jonathan Cooper)
  • Subject: [cellml-discussion] Initial units assignment
  • Date: Mon, 16 Apr 2007 12:20:59 +0100
On Mon, Apr 16, 2007 at 03:44:18PM +0800, David Nickerson wrote:
> Hi all,
>
> The subject of units and associated issues has been popping up quite a
> bit lately, and a lot of the current problems are mainly due to
> publication of models without full dimensional annotation and/or errors
> in the initial encoding of a model into CellML. From my experiences, I
> have found that when a model is accurately and completely units balanced
> from inception to completion, then a lot of the issues with units are
> not apparent.
>
> In order to help overcome the initial hurdle in assigning units to
> variables when the reference source my not be complete in regard to
> units, Erik Butterworth of JSim fame has proposed quite a neat solution.
> Currently, as part of the units checking in JSim, JSim will try to
> assign units to variables whose units are not assigned. This process is
> reasonably accurate assuming there is a base of variables whose units
> are correctly assigned. In this example (in MML syntax):
>
> real A mm;
> real B sec;
> real C;
> real D = A/(B+C);
>
> JSim would assign C units of sec (to match B), and assign D units
> of mm/sec (to match A/(B+C)).
>
> This feature can currently be used by coding up models in MML first and
> then grabbing the generated units for use in the CellML encoding - a
> fairly awkward process. What Erik is proposing is:
>
> "One possible project would be for JSim to read in CellML files which
> might be missing unit assignment, and add them in as necessary. JSim
> could then either proceed with modeling, or write out the unit enhanced
> CellML and exit. This approach would probably take a few weeks on this
> end (assuming I can budget the time), but I could consider it if your
> team thinks they'd like to work with such a tool and integrate into the
> CellML archival process."
>
> I am trying to determine if there would be enough interest from CellML
> model authors to make it worthwhile pursuing such a project? Anyone
> interested please speak up :-)

I'm not a model author, but I do find this interesting. Is there any
documentation available on how JSim does this?

Jonathan.

--
Jonathan Cooper MSN: msn at jonc.me.uk www: jonc.me.uk/

If you don't know where you are going, you can never get lost. - Herb Cohen


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