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Hi Mike,

Did you get convincing reasons as to why the current JNI approach is
unsatisfactory?

IMHO I'm not sure of any shortcomings in the current approach (apart
from the 64-bit Mac nonsense that I keep complaining about, and also
have no idea how one would use libsbml in an applet). Would the
benefits of doing this outweigh the non-trivial downsides?

Cheers,

Neil.

Neil Swainston
Experimental Officer

Manchester Centre for Integrative Systems Biology
Manchester Interdisciplinary Biocentre
University of Manchester
Manchester M1 7DN
England

On 18 May 2009, at 21:18, Michael Hucka wrote:

> In the recent libSBML survey, people frequently asked for a
> pure Java implementation. We're considering it. Developing
> it would be a non-trivial undertaking and have serious
> maintenance implications, for example because we would have
> two separate code bases to deal with. We have some ideas
> for how to avoid rewriting some of the more complex parts,
> but here are some issues we don't know what to do about:
>
> 1) When libSBML 5 is introduced with its modular extension
> mechanism to support SBML Level 3 packages, and we
> request other developers to provide implementations of L3
> packages, would people have to provide *both* a regular
> implementation (including a SWIG interface definition for
> Java) and a pure Java implementation? If not, then who
> will implement the other version?
>
> 2) Level 3 package support should come with validation code,
> so that libSBML can do validation on models that include
> the given L3 package. The validator built into libSBML
> will likely be modularized to support extensions for L3
> packages. Will developers who implement support for L3
> packages also have to provide validator code in *both*
> C/C++ and pure Java form, if a pure Java version of
> libSBML exists?
>
> We'd like your opinions on what to do.
>
> MH
> P.S. If you haven't already done so, please do the survey:
> http://sbml.org/SBML_Projects/Development/LibSBML_survey_2009
>
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