One thing is bugging me: I'll illustrate by means of an example:
We would be inferring that the set fluxes consists of only the elements
{f1,f2,f3} from the three statements: f1 in fluxes, f2 in fluxes, f3 in
fluxes.
But if fluxes={f1,f2,f3,f4,f5}, that would still be consistent with the
-discussion] Using proposed CellML 1.2 features to
create more re-usable metabolic models
Hi all,
To aid in working out what features we should include in CellML 1.2, I
have been looking into one of the major difficulties with creating
re-usable metabolic models at the moment: that to compute
First just to check that in the the connection elements 'flux' should
be 'fluxes'? For example, 'substance_a' component contains no variable
'flux', I assume you meant the set_of_lambda_of_real 'fluxes'?
I think I like this! When will it be released? ;-P
I don't know enough about the lambda
Michael Cooling wrote:
First just to check that in the the connection elements 'flux' should
be 'fluxes'? For example, 'substance_a' component contains no variable
'flux', I assume you meant the set_of_lambda_of_real 'fluxes'?
Thanks for pointing that out - it is hard to validate
because if connections don't have directionality, then it makes no
sense in the language to say
that a connection is from A to B, as opposed to from B to A, and we
wouldn't want to force users to duplicate information and provide both
Oops I didn't mean to imply directionality. I shouldn't
Michael Cooling wrote:
because if connections don't have directionality, then it makes no
sense in the language to say
that a connection is from A to B, as opposed to from B to A, and we
wouldn't want to force users to duplicate information and provide both
Oops I didn't mean to
Michael Cooling wrote:
if both state variables have the same initial values and
rates (which they would...
why should they have the same initial values? I agree if they did then
it makes
no difference to the correctness of the model but it seems very possible to
create a model of
If two models contradict each other (such as by each stating a
initial value for concentrations of the same species, or a different
mechanism for the exact same reaction), then this contradiction has
to be fixed before the models can be composed.
It's not just about composition - during
Hi all,
To aid in working out what features we should include in CellML 1.2, I
have been looking into one of the major difficulties with creating
re-usable metabolic models at the moment: that to compute a derivative,
you need to know all the fluxes, but when a model is extended, new
fluxes
