[Joelib-devel] Re: [QSAR-devel] Toxicity predictions with lazar and predictive toxicology book

[Joerg K. W. <we...@in...>]

Hi Christoph Helma,
Hi Matthew Stahl,
Hi Warren DeLano,
Hi Geoff Hutchinson,

so you are finished with your post doc, right ? :-) And unfortunately 
your announcement is not uncritical and all flaming discussions can be 
send directly to me or to the QSAR, JOELib or Openbabel lists.
Until now I am a scientist, so I am not really interested in license 
dicussions. And nonetheless I think it is my liability and curse as 
administrator to open this discussion. Sorry, Christoph but you are the 
first after the open source publications of Warren and Matthew, and 
software has in your case a long history called OELib.

1. Christoph, it would be nice, if you can submit some references to 
both lists, if you are too busy I can do this. Maybe the ILP or fuzzy 
key papers and/or the link to the challenge web page.

2. As shown at page http://www.predictive-toxicology.org/lazar/form.php 
you are using OpenBabel and JOELib. The guys of the 
http://www.compumine.se/adme/adme.jsp web page uses also JOELib for 
example purpose.
Please beware that both tools are GPL, so beware of your commercial 
interests. So, every source code derived and *based* on OpenBabel and 
JOELib must be GPL, too. If your prediction source code is independent 
of both packages I am fine with your tools. Otherwise, I recommend you 
to switch to OEChem of EyesOpen, it should be really similar to 
OpenBabel http://www.eyesopen.com/ or to Marvin from ChemAxxon.

So, I do not want to be a killjoy, but please check for possible GPL 
violations. And I agree with the critic of M. Stahl, one of the 
developers of OELib (JOELib and OpenBabel predecessor), that it is 
dangerous for commercial partners to use GPLed open source, but its good 
for creating a standard (against to which commercial partners can test 
their products) and to work with in academia. If you are interested in 
consultant work, there should be no problem at all!
Otherwise EyesOpen has the copyrights on the chemical expert systems and 
algorithms derived from OELib. And this should not be forgotten.

Kind regards, Joerg

P.S.: Sorry, again, for being uncomfortable, it's IMHO my responsibility 
as administrator.

> Apologies if you receive multiple copies of this message!
> ========================================================
> 
> The lazar system for free online predictions of toxic activities is now
> available at http://www.predictive-toxicology.org/lazar/! You can use a
> webinterface to draw chemical structures and to obtain predictions for
> rodent (rat and mice) carcinogenicity and Salmonella mutagenicity. Further
> toxicity endpoints will be available in the future.
> 
> At the same time I want to take the opportunity to announce the new book
> "Predictive Toxicology" that I have edited. It covers state-of-the
> art techniques, databases, application areas and the most important
> predictive toxicology programs. "Predictive Toxicology" has been published
> by Marcel Dekker/CRC Press.
> 
> If you are interested in confidential predictions, batch predictions
> or the development of modules for new endpoints, please contact
> he...@in....
> 
> If you want to receive also in the future information about new lazar
> developments, please subscribe to the lazar-announce mailinglist at
> http://www.predictive-toxicology.org/mailman/listinfo/lazar-announce.
> 
> If you have questions or comments concerning the lazar system,
> please post them to the lazar-discussion mailinglist at
> http://www.predictive-toxicology.org/mailman/listinfo/lazar-discussion.
> 
> If you want to discuss predictive toxicology topics in general,
> please use the the predictive-toxicology mailinglist at
> http://www.predictive-toxicology.org/mailman/listinfo/predictive-toxicology.
> 
> 
> Best regards,
> Christoph Helma
> ==
> :: in silico toxicology
> :: he...@in...
> :: www.in-silico.de
> 
> 
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-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de
--
Never mistake motion for action.
                                     (E. Hemingway)

Never mistake action for meaningful action.
                                (Hugo Kubinyi,2004)