Hi Warran,
thanx for this discussion start on open source chemoinformatics.
I printed your article in Drug Discovery Today (feb 2005) yesterday, but have
not read it yet...
On Thursday 5 May 2005 07:00, Warren DeLano wrote:
> > Look! Jmol is mentioned in this ad. (As if Jmol were competing!)
>
> Wavefunction is doing a smart thing by making it crystal clear why
> SpartanModel outpaces Jmol and Chime in various ways at the present time.
But not all arguments are valid... let's resummarize it (I left out Chime as I
am not familiar with that product enough):
SpartanModel Jmol
Commerial yes no(t yet)
molecular modeling yes viewer
calculation engine yes no
molecular database yes yes (via dadml)
structure builders yes no
PDB reading yes yes
Spartan output reading sure only partial
Spartan db of structures yes Zinc db has optimized structs
Compatible with WinXP,OS/X yes yes (*)
Compatible with Linux no? yes
No internet requires yes yes
Afforable yes yes
Extra tools (red box) yes partial
*) somethimes problems: this is where companies add value: support!
I think Jmol comes out quite competable :)
> For now, their case is strong.
Agreed. We don't have an inline database (we provide the internet as database
via the DADML plugin), and we don't have a model builder.
> But if you extrapolate out a few years
> given current progress in open-source, I think their concerns are
> thoroughly justified. With the possible exception of quantum codes,
> virtually all of the functionality in SpartanModel already exists in
> open-source. It is just that no one has yet had the time or motivation to
> tie all those diverse codes together into a usable tool capable of meeting
> real-world needs.
>
> Could some one do it? Of course! But would it be right or good to do so?
> Now that's less clear... At $30/copy, it is not like Wavefunction is
> trying to rip people off -- heck a plastic chemistry set costs about the
> same, doesn't it? If they can make a profit at those prices, then I think
> they should be congratulated, not obviated -- at least not immediately.
> Consider...
Agreed. I that providing this extra value is where the open source chemistry
market will have to find its funding too.
> How would you feel learning in a couple of years that Jmol has cost X
> number of people their jobs across the industry due to a precipitous
> collapse of revenue streams for molecular viewers?
Don't think this will happen. Jmol is just a viewer, and if it did, the worked
with companies with bad market knowledge... molecular viewers have been
around for many years now, and there's little 'unique selling point' there.
Unless you can provide special features, like press print quality rendering
etc...
> Let's imagine that
> ChemAxon, Accelrys, Wavefunction, Schrodinger, Cache, OpenEye, Tripos, and
> Astex all continue to spend millions on developing their own proprietary
> viewer architectures, can't make a dime, and end up having to lay off
> developers because Jmol is free, open-source, and adequate to meet market
> needs? Would that be a good thing?
Counter question. A company that spends millions on something they know has
little added value... Would that be a good thing?
> Probably, given the overall positive
> societal impact of a standard, ubiquitious, free, and open-source molecular
> viewer. But in the mean time, it will be tough for those developers and
> their families!
I agree that chemoinformatician have a tough choice... or do something
different than chemoinformatics software development, or start up/join a
chemo software company...
And what about those chemoinformaticians that chose the first option, and do
what they like to do (programming chemoinformatics) in that non-working
hours ?!?! Should those stop just because someone else went for the second
option?
Anyway, I do appreciate your discussion of their situation... I'm exploring my
options for after my PhD too now...
> Of course, that is just business. New technologies create and destroy
> markets all the time, and society benefits hugely overall.
Yes, it's called innovation :)
> But the
> difference here with open-source is that we developers really do have the
> ability to reshape markets "in our spare time". We have that power, and we
> wield it volitionally, and therefore I suggest that we should consciously
> acknowledge and be aware of how our creations impact those around us.
What about the other way around? How much does the commercial chemoinformatics
world realize that they are holding back by not open sourcing *old*
technologies, like an open source 3D builders, etc... algorithms that have
become so important in daily research...
> Bob, of course we compete -- we compete on terms the traditional
> competition cannot hope to meet, and if and when we are about to utterly
> destroy a proprietary product's ability to succeed in a given space, then I
> think we should have a good reason for doing so.
Open source is an important reason already, I think!
Let the companies decide where the true value is in their software, and make
the parts without value open source, and let's joint forces! The CDK is LGPL,
explicitely allowing embedding in proprietary software! Jmol is LGPL,
explicitely allowing embedding in proprietary software!
They should not spend millions on a viewer if they can already download it
from the internet! And likewise for people who might get fired next year...
SpartanModel value is not in the viewer! It's in the QM software and in the
database, and in the builder... in the support they provide to get it all
working in the target platforms,
> Even when we have such a
> reason, I see nothing wrong with letting the competition know what's
> coming, exercising a little restraint with respect to deployment, and
> helping those poor souls reach higher ground before the tsunami hits. It's
> just not fair, otherwise. ;)
Sure they have the right to compare, even if they do it suboptimal... And as
often said: "Even bad publicity is publicity" :) Maybe it's just a shame that
they did not add our URL.
I do want to remark, however, that Jmol fills a niche that the commercial
companies forgot to (intentionally or not) fill: scriptable cross
platform/cross browser visiualisation of molecular data.
If they would have listened to what users needed, they would have filled the
niche, and Jmol would not be what it is now.
Egon
--
[EMAIL PROTECTED]
PhD student on Molecular Representation in Chemometrics
Radboud University Nijmegen
http://www.cac.science.ru.nl/people/egonw/
GPG: 1024D/D6336BA6
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