Subject: Summary: Biological class libraries

From: Walter Koppensteiner <[email-masked]>
Date: Wed, 09 Jul 1997 16:26:31 +0200

Hi,

here is a summary of class libraries and other object oriented
approaches to biopolymer representation.

------------------------------------------------------
Thanks to all CCL members how sent replies:
	Konrad Hinsen <[email-masked]>
	Gerald Loeffler <[email-masked]>
	Joe Talafous <[email-masked]>
	Lutz Ehrlich <[email-masked]>
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Molecular Mechanics Toolkit: 
    Phyton
    http://starship.skyport.net/crew/hinsen/mmtk.html
    program library for molecular modelling applications
    
Bioperl Project:
    Perl
    http://www.techfak.uni-bielefeld.de/bcd/Perl/Bio/welcome.html
    handling of biosequence and alignment data
    current modules: Bio::PreSeq and Bio::UnivAln
    
bioWidgets Consortium:
    java
    http://fruitfly.berkeley.edu/biowidgets/
    graphical displays of genome data
     
NAMD/VMD:
    C++
    http://www.ks.uiuc.edu/Research/vmd/
    Molecular Dynamics and visulatization of biomolecules
    
Open Molecule Foundation (OMF)
    Java
    http://www.ch.ic.ac.uk/omf/
    several java class libraries and related stuff
    
PDBlib:
    C++
    http://www.sdsc.edu/pb/pdblib/pdblib.html
    class library is designed for representing macromolecular structure
    
JaMBW: Java Molecular Biology Workbench
    Java
    http://www.embl-heidelberg.de/JaMBW/
    
Birkbeck Bioinformatics Class Library
    C++
    http://www.cryst.bbk.ac.uk/classlib/
    object-oriented software library for use by the bioinformatics and
    molecular modelling communities
    
SCL (Sequence Class Library):
    C++
    http://Molbiol.grumed.fu-berlin.de/scl/
    C++ class library for sequence analysis in molecular biology
    
OTF (Object Technology Framework):
    C++
    http://www.cgl.ucsf.edu/home/otf/
    C++ classes for biochemical application developers
    
Democritos:
    C++
    http://gserv1.dl.ac.uk/CBMT/democ/HOME.html
    C++ classes for bioinformatics and computational chemistry

molbio++:
    C++
    ftp://golgi.harvard.edu/pub/robinson
    ftp://ftp.ebi.ac.uk/pub/software/unix
    C++ library for molecular biosequence analysis

Best wishes,
Walter
-- 
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Walter Koppensteiner                                           
                                            
University of Salzburg
Center of Applied Molecular Engineering

Jakob Haringer Strasse 3           Phone: +43-662-8044-5794
A-5020 Salzburg, Austria           Email: [email-masked]
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