I think we are all missing the underlying point in this discussion. Maybe I'm 
ideological, but developing open source is a method to contribute the community 
and allow others to contribute back. It is not about competition, and it 
disappoints me that we sometimes enter into these discussions of using one open 
source solution over another, while we should be working to use them all 
together. I think the answer to the question of getting Jmol running on iOS and 
in browsers on Android isn't why use iOS or who will pay, but rather, how do we 
best work together to get a satisfactory solution in place using the open 
source tools available.

We are developing the ChemDoodle Web Components (open source HTML5/WebGL 
toolkit for scientific graphics and informatics) for a number of reasons, one 
being as a complement to Jmol (not to replace it). We have a strong focus on 
aesthetic graphics and we are doing our best to match all the functionality of 
Jmol. The GLmol project is also impressive, and we are currently working to 
include parts of it as LGPL plugins to the ChemDoodle Web Components so users 
only need a single library for their functionality without the dependencies of 
the cumbersome third party libraries that GLmol requires.

To clarify Henry's quote about the ChemDoodle Web Components:

"its core javascript functionality is open source) although a different model 
operates here (much of the advanced functionality is actually server side, and 
hence requires the user to have access to that server, and of course also be in 
online mode, ie it may eat up into any data plan you might have on eg your 
iPad)"

While it is true that a lot of advanced functionality is server based, this is 
only true of very advanced algorithms, and all the great graphics and 
interaction are in the core library. The choice to use a server is for a number 
of reasons:

1. There is very complex functionality from our desktop software that we extend 
for free for academic use.
2. Some functionality is very cpu intensive and can be done much faster through 
AJAX and a fast server than directly in Javascript.
3. A lot of legacy code exists that would be very inconvenient to port to 
Javascript. Using AJAX allows us to use the same code with the ChemDoodle Web 
Components. We are trying to figure out the best way to include Jmol on the 
backend as well, so Jmol users will be able to access the same functionality.
4. The criticism that one will run through a data plan quickly is a bit 
exaggerated, you would literally have to load thousands of huge PDB files. The 
rest of the functionality will not consume a significant amount of bandwidth. 
The reason iPad 3 users are running through data plans quickly is because they 
are playing high definition movies.

So, I think that with the tools available, we have the opportunity to work 
together to get the functionality users want on all devices with the tools that 
they are comfortable with. We are more than open to discussion if anyone wants 
to contact us, feel free to contact me directly.

Finally, a few selfish plugs:

The ChemDoodle Web Components running on iOS and Android - 
http://www.ichemlabs.com/1375
iChemLabs and Inkling partnership - 
http://www.sfgate.com/cgi-bin/article.cgi?f=/g/a/2012/03/15/prweb9281945.DTL
ChemDoodle Web Components ranked higher than Angry Birds - 
http://www.netmagazine.com/features/20-webgl-sites-will-blow-your-mind

Kevin Theisen
President, iChemLabs



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