Re: If there were a pure Java libSBML ...
20 May '09 01:47
Stefan Hoops wrote:
> Hello Mike,
> 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.
I agreed that it would be hard to require that. But in practice, if
there is not such an extension, the
SBML L3 package will be less used/supported I think.
> 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.
I think, you are exactly speaking about one of the problem here, it is
difficult to make the libsbml bindings works properly.
And you have to compile first (or ask the users to compile) libsbml for
the different platforms before trying to setup the java bindings.
With a pure java implementation, all of that is gone.
> 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.
Wrong assumption here, the jre is often ship with an application to be
sure it is available to run the application and
that the user do not need to do anything else that click a button to
launch and run it properly.
May be Oracle is one of the only one that ship their own JVM in purpose
but it will probably change in the near future.
> 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
> efficient approach.
There is no certainty that this path will be the less time consuming.
> Another often mentioned concern is the ability to deal with large
> models. I think that java is not the ideal way to address this.
Again, an other misconception, most applications dealing with terabytes
of data developed at EBI are written in Perl or Java.
And, the most important point is that java application are tolerant to
errors and reliable and performance is not anymore a problem this days.
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