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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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