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My own $0.02, as another software developer and an old Lisp
hacker myself (and of course, everything I say here is
purely personal opinion).

TY> I think this can be done with a programming language.

Yup, you can exchange programs as your "model description",
and people did essentially that for a few decades. (They
still do even today, especially when the model is, e.g.,
MATLAB code.) There are at least two reasons why people are
trying to move away from that:

1) The system interpreting the description must implement
the entire programming language interpreter. Little b,
for example, needs Lisp underneath it. But regardless of
whether your description requires Lisp or not, it's a
nontrivial requirement. It reduces your ability to share
the model on the one hand, and the size of your willing
audience on the other.

2) The essence of what you're trying to model becomes lost.
It is no longer a description of the domain phenomena
(here, biological mechanisms), and instead becomes tied
up with artifacts of the simulation/analysis framework.

(I'm sorry if that seems obvious and I'm missing your
point!)

TY> XML based languages have other types of advantages
TY> over lisp-based languages, naming the great number of
TY> tools able to interpret XML files, interoperability
TY> with XML/RDF for a variety of metadata capabilities,
TY> and many more.

I'm not sure if you're saying this, but just to be clear,
XML is *not* a programming language. It's merely a
serialization format. One could use ASN.1, or Google's
Protocol Buffers, or any of another of others.

MH

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• [cellml-discussion] little b - shared models built from reusable parts, James Lawson, 07/25/2008
  • [cellml-discussion] little b - shared models built from reusable parts, Catherine Lloyd, 07/25/2008
  • [cellml-discussion] little b - shared models built from reusable parts, Nicolas Le Novere, 07/26/2008
    • [cellml-discussion] little b - shared models built from reusable parts, Tommy Yu, 07/26/2008
      • [cellml-discussion] little b - shared models built from reusable parts, Michael Hucka, 07/29/2008
        • [cellml-discussion] little b - shared models built from reusable parts, Tommy Yu, 07/29/2008

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