[Cdk-devel] Re: Chemical Semantic Web and Thanks

[E.L. W. <eg...@us...>]

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On Wednesday 08 December 2004 11:51, Eugen Leitl wrote:
> It's noticeable that the pharma industry is
> a consumer of our efforts but has not contributed anything in return and
> continues to pay for overpriced software products that do not use modern
> methodology.=20

Since CDK is licensed LGPL, it can be embedded in proprietary software.
And because if this CDK is used in such software, and we did have=20
contributions from companies back into CDK. For example, the important=20
UniversalIsomorphismTest (isomorphism, mcss...) was contributed by
Ixelis (http://www.ixelis.com/).

> "Open source is unfair to commercial developers"
> I think this attitude is particularly strong in the US and perhaps German=
y.
> The idea is that public funding should not be used to compete against
> commercial organisations. As Mike Ashburner replied, most Open software in
> bioinformatics is written by people on short term contracts often with no
> possibility of extension. I know that made contributors to these lists do
> not have jobs. I developed much of CML when I was unemployed after being
> made redundant from Glaxo.

Same for me. Most my opensource work is not even part of my PhD, and all do=
ne=20
in free hours! Totally unpaid work.

Another argument I would like to put into this discussion:
In the Netherlands big companies often have reduced taxes, or a special=20
agreement on the taxes they have to pay, while they make very much use of t=
he=20
countries infrastructure. This is IMHO some form of public funding.

The "Open source is unfair to commercial developers" argument is also rathe=
r=20
unfair itself: most opensource licenses do *not* disallow embedding in=20
proprietary software! E.g. the LGPL (see earlier) and the BSD license. So=20
companies can directly benefit from many opensource projects without that=20
costing them anything.

> I would be more (slightly) more sympathetic to this view if the chemical
> software industry provided anything substantial to the community. I know =
of
> no support for Open efforts from the chemical software industry other than
> a very undersupported effort to get an Open Management Group spec for
> chemistry. I was invited to contribute CML as the core of this spec, but
> even then it was made clear that I would not even have my (foreign) travel
> expenses paid - even though I had no job.

As said, some chemoinformatics companies break with this habit.

> Meanwhile - when you are hacking the latest set of bugs at 0200 in the
> morning, take heart - it really is appreciated - and yes - the day of Open
> Source for "chemistry" is dawning. In fact I think the centre of gravity =
of
> chemical software development is starting to shift towards bioscience [and
> materials] so that people will simply refer to the informatics of small
> molecules as "bioinformatics"

Let's use molinformatics from now on... (short for molecular informatics). =
I=20
used this term already in the CDK presentation at the CIC meeting, and will=
=20
start using it as much as possible.
Because what we do is deal with molecular information, small molecules=20
(chemoinformatics) and larger molecules (bioinformatics).

Egon

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e.w...@sc...
PhD-student on Molecular Representation in Chemometrics
Radboud University Nijmegen
http://www.cac.science.ru.nl/people/egonw/
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