[Joelib-devel] QSAR

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

Dear Nina Nikolova,
Dear All,

please reply also to the JOELib mailing list and ... i've already
published three papers about QSAR and our group has it's main focus on
data mining and optimization algorithms, so i think i've some experience
in this area, too.
http://www-ra.informatik.uni-tuebingen.de/

I've read your QSAR 'similarity review'-paper. Excellent !!!
Furthermore i've already submitted a paper about critiziing a missing
standard
for the chemical expert systems and all folowing steps, like descriptor
calculation, atom type assignment, ...

Descriptor import is no problem with JOELib, e.g. MOE, MolConnZ, Petra,
...
BTW, i do not like not transparent programs, like Dragon although their
book is excellent ...

Machine learning suites: Weka, YACC, Matlab, R, ... all fine ! For Weka
and
Matlab you can ask me, i've implemented interfaces and using them heavily.
R is similar and a long time ago i've used the interface under Java very
shortly ... we're matlab based !

The JOELib IDE has already basic statistic and entropy interfaces !!!
A student of mine has extended the Weka-DataMining Model for Molecules, i
recommend to use this data model ! Main interest is to use also user
defined similarity metrics for clustering !
BTW, the JOELib-Weka version contains also some add-on packages !

For CML and descriptors i've already started a HTML page discussion at,
please
reply to CDK and JOELib discussion lists:
http://www-ra.informatik.uni-tuebingen.de/mitarb/wegner/private/cml/cmlAndDescriptors.htm

Please discuss things heavily and avoid inventing the wheel twice ...

Kind regards, Joerg

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
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