Re: [Miase-discuss] MIASE paper - reproducibility

[Stefan H. <sh...@vb...>]

Hello Nicolas,

On Mon, 11 May 2009 16:07:34 +0100 (BST)
"Nicolas Le Novere" <le...@eb...> wrote:

> 
> > I agree with Nicolas that we should ask for reproducibility.
> 
> I think you got me wrong. I actually advocated the opposite. And I
> believed I was reflecting the Auckland consensus, that said MIASE did
> not deal with correctness.
> 
> > Repeating
> > a simulation is insufficient. If a simulation experiment which is
> > described in a MIASE compliant format is allowed to have different
> > results we have not specified anything at least in my opinion.
> 
> Yes, we specified a way to discover the discrepancy, which is exactly
> what a materials and methods is for. Results are described in another
> part of the paper, called ... results. We should encourage the use of
> standard formats to describe numerical results, but I do not believe
> the results themselves are part of a "simulation experiment
> description". And even less the correctness criteria to compare two
> sets of results.
> 

I think we actually agree, I was not precise enough. We need to
distinguish between the use of MIASE and its scope. The scope of MIASE
is to specify repeatable simulations. The use is to determine
reproducibility of scientific results.

Thanks,
Stefan


-- 
Stefan Hoops, Ph.D.
Senior Project Associate
Virginia Bioinformatics Institute - 0477
Virginia Tech
Bioinformatics Facility II
Blacksburg, Va 24061, USA

Phone: (540) 231-1799
Fax:   (540) 231-2606
Email: sh...@vb...