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Nicolas Le Novere wrote:
> The SBML community has know little b for a while since they first came to
> us, a long time ago, saying roughly "we're much better than you, and we do
> everything in a simpler way, understandable by users".
>
> I think (and this is a personal opinion, that does NOT reflect the opinion
> of the SBML editors as a whole) this is a worthwhile effort, but
> completely different than SBML and CellML.
>
> 1) In general, the terser a language is, the more fuzzy but the harder to
> interpret it is. If the SBML spec is so long and complicated, it is
> because one of our goal is to ensure that everyone interpret an SBML
> description exactly the same way. That bears a lot of consequences on
> units etc. Terse is good. Unambiguous is better (if you want to exchange
> and integrate)
>

Software code can also be terse and unambiguous, and can be exchanged with
others to be integrated into one's software. A software language must also
be interpreted the exact same way between different interpreters, or users
are not going to be interested in using the non-standard interpreters
(usually, anyway). I can see the same objectives accomplished with little b
just as well, provided that the model code was written with unambiguity in
mind.

> 2) I am not sure LISP is a good *description* language. And we need to
> separate description of the model structure from description of the
> simulation. SBML and CellML are not programming language.
>

I think this can be done with a programming language. A modeler could define
a set of files as the description of the model structure, and build a
different set of files for the description of the simulation, then the
completed models can be assembled together.

Naturally, SBML and CellML were never meant to be programming languages from
the beginning. XML based languages have other types of advantages over
lisp-based languages, naming the great number of tools able to interpret XML
files, interoperability with XML/RDF for a variety of metadata capabilities,
and many more. I see it as a case of two different class of langauges with
different objectives in mind...

> Again this is a personal feeling. At the end I guess the only criteria is
> the usefullness for the scientific community.
>

... and both types will have their niche where they will be widely used in
the community.

Just a couple cents from a software programmer.

Tommy.

>> Hi all,
>>
>> Has anyone encountered this before?
>>
>> http://www.littleb.org/
>>
>> The little b project is an effort to provide an open source
>> <http://www.opensource.org/> language which allows scientists to build
>> mathematical models <http://en.wikipedia.org/wiki/Mathematical_model> of
>> complex systems. The initial focus is systems biology
>> <http://en.wikipedia.org/wiki/Systems_biology>. The goal is to stimulate
>> widespread sharing and reuse of models.
>>
>> The little b language is designed to allow biologists to build models
>> quickly and easily from shared parts, and to allow theorists to program
>> new ways of describing complex systems. Currently, libraries have been
>> developed for building ODE
>> <http://en.wikipedia.org/wiki/Differential_equation> models of molecular
>> networks in multi-compartment systems such as cellular epithelia.
>>
>> Little b is based in Common Lisp and contains mechanisms for rule-based
>> reasoning, symbolic mathematics and object-oriented definitions. The
>> syntax is designed to be terse and human-readable to facilitate
>> communication. The environment is both interactive and compilable.
>>
>> Kind regards,
>> James
>>
>> _______________________________________________
>> cellml-discussion mailing list
>> cellml-discussion at cellml.org
>> http://www.cellml.org/mailman/listinfo/cellml-discussion
>>
>
>

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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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