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Hello Mike

On Wed, 20 May 2009 12:35:09 -0700
"Michael Hucka" <mhucka@caltech.edu> wrote:

> Let me throw out another idea about this.
>
> Suppose (hypothetically speaking :-)) that we were to
> introduce a web service for libSBML [+], and produce a pure
> Java version that is *not* a *complete* reimplementation,
> but instead called on the web service version for certain
> complex operations such as model validation, unit analysis,
> etc. My thinking is that this would address multiple
> problems:
>
> 1) It would permit a pure java implementation
>
> 2) It would do it without incurring the implementation and
> maintenance cost of reproducing the entire libsbml code
> base. There would still be only one code base for some
> of the really hairy bits that are also the most worrisome
> from the standpoint of ensuring identical behavior.
>
> 3) It would also make the pure java deployable smaller in
> size than a full libsbml java implementation would be.
>
> Downsides:
>
> 1) Some of the libsbml functionality in the pure java
> version would require a network connection to use.
> We'd be careful to make them only things that have to be
> deliberately called, not common operations.
>
> 2) It wouldn't solve the problem of having to implement
> Level 3 packages twice. (You wouldn't want to implement
> them only in the libsbml core and then make all of it
> accessible over the web service; the point of the
> approach being proposed here is that *most* of the
> libsbml functionality would be in the pure java client.
> I don't see that L3 packages would not be sufficiently
> heavy to qualify.)
>
> We would have to figure out which operations are most
> worthwhile doing via the web, balancing the size of data
> transfer involved versus the complexity of the code in
> libsbml that would be saved from reimplementation. I also
> have ideas for how to provide a high-availability facility
> for the web service, so that people wouldn't all have to hit
> a single server sitting under my desk at Caltech :-).
>
> This seems like a workable compromise, no?
>
> Can people try to think about the weaknesses and shot holes
> into this scheme? Likewise, if there are some additional
> clever hacks we could do, please mention them. If we're
> going to write a grant proposal to get more developers to do
> this, we'd better know about possible counter-arguments now.
>
> Footnotes:
> [+] Frank Bergmann already provides a web service system
> exposing much of the libSBML API. The web service proposed
> here would admittedly replicate a significant chunk of that.
> However, it would do it in different ways, so it would not
> be an identical system.
>
> MH
>

I think that providing a web service would be great. This would not only
benefit any Java application it would also benefit any other
application able to communicate with web services. It would definitely
ease the deployment problems Oliver is facing. The drawback of the
need to be connected to the Internet is for his Java web start
environment not existent.

Of course it would be nice if we could have some people providing such
a web service for the general public. To spin this further these
services should be registered it in Biomoby ...

Mike I really like that :)

Thanks,
Stefan


--
Stefan Hoops, Ph.D.
Senior Project Associate
Virginia Bioinformatics Institute - 0477
Virginia Tech
Bioinformatics Facility II
Blacksburg, Va 24061, USA

Phone: (540) 231-1799
Fax: (540) 231-2606
Email: shoops@vbi.vt.edu
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