I think you are addressing 2 different issues here. The first is
whether its is desirable/feasible to provide a pure java version of
libsbml. Whereas the second is whether official extension need to
provide libsbml support.
I think the later is easier to decide. The reality is that we can not
enforce it, especially not the constant maintenance of such a support
library. Thus the existence of an libsbml extension for SBML packages
as a requirement for an official SBML L3 package should not be made.
Regarding the pure Java support. In another thread you said that
portability would be a benefit of such an implementation. My personal
experience is that the gain is minimal. We have less problems compiling
the C++ version of libsbml on any platform as to getting it to work
with the different java installation. In theory the latter should be
trivial but it is not. A pure java implementation will face similar
problems. This is why most larger java based application ship with
their own particular java version.
In a world with unlimited resources a pure java implementation is
nevertheless desirable. But we have limited resources and I would
prefer to spend them on increasing the reliability and improving the
java bindings or making them more java like. This seems to me a far more
Another often mentioned concern is the ability to deal with large
models. I think that java is not the ideal way to address this.
Stefan Hoops, Ph.D.
Senior Project Associate
Virginia Bioinformatics Institute - 0477
Bioinformatics Facility II
Blacksburg, Va 24061, USA