Re: [Miase-discuss] MIASE paper

[Dagmar K. <da...@eb...>]

Hej David,

thanks a lot for your comments. The tracking of changes worked very 
well, I should have found all of your comments. I have some remaining 
remarks:

1) "What is not in the scope of Miase"
Currently we say that "output descriptions" are not in scope, but of 
course you were right that we are mentioning some output information 
like step sizes, so I changed it to "Graphical output descriptions" as 
you suggested (just to let you know).

2) "Whether or not the simulation result matches reality and whether or 
not an experiment can be conducted on a certain model will neither be 
described nor tested."
You argued that a description is tied to a certain model or number of 
models which makes the comment on scope irrelevant, i.e. whether an 
experiment can be run on the model. But I think what is meant here is to 
point out that there is no validation of whether or not it does make 
sense to run the simulation on the referenced model.

3) Rules
1.B. "If the model is not encoded in a standard format, then the model 
code must be made available to the user."
You said that: "having a model encoded in a standard format doesn't 
imply that it is freely available. Perhaps might be better to state that 
model descriptions must be MIRIAM compliant?"
You are right in the sense that there are cases where models are encoded 
in a standard format, but they are still not available... But I think 
the rule was not addressing the distribution policy...
I am wondering if not the statement in 1. "...All models used in the 
experiment must be named and contain a reference to a model source." 
might be sufficient?
Maybe it would make sense to change it to "a reference to a freely 
available model source". (If we want to force that at all)
I actually think that people who do not want to share their models might 
not want to share their simulation experiments neither ;-)

One more thing here, we should not enforce the use of MIRIAM. We should 
only recommend people to refer to MIRIAM compliant models, if possible.

4) The Repressilator example
You suggested to do "a cell physiology type example as something more 
familiar to the CellML community. Perhaps something along the lines of 
calculating APDs in a parameter scan?"
The more example we have, the better. And the more diverse the even more 
better.
So, if you volunteer to set up the example :-) ... I would not say no :-)
(BTW, Viji is currently doing an example that includes post-processing 
of the output. )

5) Discussion
By "The sole annotation of models is not sufficient to promote reuse of 
existing biological knowledge." I meant "the annotation of the models 
alone is not sufficient, you also need to information on the simulation 
as well". Maybe I could actually change it to "The annotation of 
\models\ only"...

That's all that remained unclear.
Thanks again for the comments.
They'll be included in the next paper update :-)
Dagmar


David Nickerson wrote:
> Hi Dagmar,
>
> Sorry to be out of touch for the last few weeks, but I have finally
> had a chance to go through the manuscript. I have attached my modified
> version - hopefully all the tracking/comments etc work :) Now to look
> into those discussion points...
>
>
> Cheers,
> David.