[Vp-reproduce-subgroup] [EXT] Re: [Vp-integration-subgroup] Fletcher & Osborne's Seven Challenges (Re: White paper Revisions)

[James Osborne]

Indeed the 6th Challenge is

"*how to develop standards and benchmarks for multicellular implementation
comparison*."

Which ties very well with the aims of the subgroup (and the white paper)
but there's only a few paragraphs on it in the paper due to space.

As the focus of this paper was multicellular simulations the main point was
the need for a set of "standard" multicellular problems which would allow
benchmarking of methods and or tools but also provide a basis for
specification as you would need to specify these standard problems with no
ambiguity allowing reproducibility.

James


On Tue, May 4, 2021 at 10:08 PM Jacob Barhak <jacob.barhak at gmail.com> wrote:

> * External email: Please exercise caution *
> ------------------------------
> Thanks William,
>
> This is nice work with a lot of overlap to our focus areas.
>
> Both authors are now on this mailing list.
>
> I personally liked the reference to HPC,  although I did not see mention
> of newer tools to solve the problem.
>
> I also liked how they called SBML a specification rather than a standard.
> This is the correct way to address it.
>
>           Jacob
>
>
> On Tue, May 4, 2021, 06:22 William Waites <wwaites at ieee.org> wrote:
>
>> "Seven challenges in the multiscale modeling of multicellular tissues",
>> Fletcher & Osborne
>> https://onlinelibrary.wiley.com/doi/full/10.1002/wsbm.1527
>>
>> CHALLENGE 1: MODEL CONSTRUCTION
>> CHALLENGE 2: MODEL CALIBRATION
>> CHALLENGE 3: NUMERICAL SOLUTION
>> CHALLENGE 4: SOFTWARE AND HARDWARE IMPLEMENTATION
>> CHALLENGE 5: MODEL VALIDATION
>> CHALLENGE 6: DATA/CODE STANDARDS AND BENCHMARKS
>> CHALLENGE 7: COMPARING MODELING ASSUMPTIONS AND APPROACHES
>>
>>
>>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.simtk.org/pipermail/vp-reproduce-subgroup/attachments/20210505/dd1a2aca/attachment.html>