Catalog of Molecular Biology programs

Patricia Rodriguez-Tome pat at genethon.fr
Fri Nov 5 10:59:52 EST 1993


(the english version is at line : 43)

	Le CEPH-Fondation Jean Dausset et Genethon, avec le soutien du projet
	ReSIG (Reseaux de Serveurs Informatiques pour les Genomes) mettent en
	place un catalogue des logiciels d'interet general dans le champ de la
	biologie et de la genetique moleculaire. 

	Ce catalogue devrait contenir, a terme, la majorite des programmes
	existants (academiques, serveurs de traitement, commerciaux).
	L'accent est mis plus particulierement sur les environnments
	multi-utilisateurs orientes reseaux (eg. UNIX, VAX/VMS,
	IBM370/VM).  Ce catalogue ne peut etre maintenu a jour qu'avec
	l'aide de la communaute :  auteurs des programmes,
	administrateurs des archives et utilisateurs.  Nous serions
	heureux de recevoir vos corrections, commentaires et annonces
	de nouveaux logiciels aux adresses suivantes :

	- Patricia.Rodriguez-Tome at genethon.fr
	- Dominique.Caterina at genethon.fr

	Dans un premier temps les domaines retenus sont les suivants :

	- l'analyse de sequence (version 1.0)
	- la phylogenie (version 1.0)
	- l'analyse de liaisons genetiques (version 2.0)
	- l'acquisition des donnees experimentales, en particulier traitements
	d'images. (version 3.0)

	D'autres domaines seront pris en compte ulterieurement, mais
	ou s'arrete la biologie moleculaire?

	Le catalogue des bases de donnees disponibles est maintenu par
	Amos Bairoch (bairoch at cmu.unige.ch) sur expasy.unige.ch .

	Merci a tous pour votre cooperation
	et Enjoy it!

	Patricia Rodriguez-Tome
	CEPH - GENETHON 
	Patricia.Rodriguez-Tome at genethon.fr

=========================================================================
(english)

With the support of the RESIG project (Networks of computer servers for
Genomes),  the CEPH-Fondation-Jean-Dausset and Genethon have been
collecting a software  directory of general interest in molecular
biology and genetics.  In the long run, such a directory ought to
contain most of the existing programmes (from  academic, processing
servers to commercial programmes), with some emphasis on
network-oriented multi-user environments (eg UNIX, VAX/VMS).

This directory cannot  be up-to-date without the help of the computer
community, that is to say the programme  authors, archive
adminsitrators and end-users.

Thus, any corrections, comments and announcements of new software would
be mostly welcome at the following addresses :

 - Patricia.Rodriguez-Tome at genethon.fr 
 - Dominique.Caterina at genethon.fr

At first, the areas taken into account are as follows :
	 - sequence analysis (release 1.0) 
         - phylogeny (release 1.0) 
         - linkage analysis (release 2.0) 
         - experimental data acquisition, 
           specially image processing (release 3.0)


Subsequently, other areas will be taken into account, but where does
molecular biology  stop ? 

The directory of available databases is maintained by Amos Bairoch
(bairoch at cmu.unige.ch) on expasy.unige.ch 

Thank you very much for your cooperation and Enjoy it !
	Patricia Rodriguez-Tome
	CEPH - GENETHON 
	Patricia.Rodriguez-Tome at genethon.fr

 -----------------------------------------------------------------------------

	USAGE :


	Cette premiere version, encore experimentale et incomplete est
	disponible sur le serveur de genethon avec les procedures
	suivantes :
        The first release, which is still experimental and uncomplete, is
        available on genethon's  server with the following procedures :
		
	ftp anonyme sur ftp.genethon.fr pub/resig/catalogue/bio-catal.1.0
					pub/resig/catalogue/bio-catal.1.0.resume

					=========
	gopher a (at) gopher.genethon.fr :
		1. About Genethon's Gopher
		2. Biblio/
	  -->	3. Bio Catalog/
			1. Bio Catalog (Thanks)
			2. Bio Catalog release 1.0 (resume)
			3. Bio Catalog release 1.0
			4. Bio Catalog release 1.0 <?>

					===========
	WAIS : le texte a ete indexe, et la source est :
		the text is indexed, and the source is :
	(:source
	:version 3
        :ip-name "wais-server.genethon.fr"
        :tcp-port 210
        :database-name "bio-catal"
        :cost 0.00
	:cost-unit :free
        :maintainer "Patricia.Rodriguez-Tome at genethon.fr"
        :description "Server created with Wais release 8 b5 (BIO) on Nov 2 1993
         The files of type para used in the index were:
         /gopher-data/bio_catal/bio-catal.1.0
         This is the indexed version of CEPH-GENETHON catalogue
	 for Molecular Biology programs.
         "  
         )

					=============
	World Wide Web : (tres bientot - very soon)

	URL: http://www.genethon.fr:80/genethon_fr.html   (en francais)
        URL: http://www.genethon.fr:80/genethon_en.html   (in english)

					=============
				

	REMERCIEMENTS:

	La premiere edition de ce catalogue a ete realisee par compilation des
	multiples documents disponibles sur l'Internet, completes par
	des communications personnelles d'experts du domaine.
	Nous tenons a remercier tous ceux qui, meme involontairement, nous
	ont prete leur concours.

	Toute erreur dans ce catalogue est notre faute, non la leur.

	ACKNOWLEDGEMENTS :

	The first edition of this directory comes from the compilation
	of various documents available on Internet and has been
	completed by personal communications from experts of each
	field.
	We would like to thank all the people who have cooperated, even
	unintentionally.


Lists :
------
NAME    List of molecular biology email servers
AUTHOR  Amos Bairoch / Dept. Medical Biochemistry / University of Geneva
ADDRESS Dept. Medical Biochemistry / University of Geneva, Switzerland
ADDRESS bairoch at cmu.unige.ch

NAME    List of molecular biology FTP servers for databases and software
AUTHOR  Amos Bairoch 
ADDRESS Dept. Medical Biochemistry / University of Geneva, Switzerland
ADDRESS bairoch at cmu.unige.ch

NAME    Catalogue des programmes 
AUTHOR  Philippe Dessen
ADDRESS Service de BioInformatique/ CNRS INSERM, France
ADDRESS dessen at gnome.inserm-vjf.fr

NAME	BIRCH
AUTHOR  
ADDRESS University of Manitoba, Canada

NAME    UNIX Molecular Biology Software on EMBL File Server
AUTHOR
ADDRESS EMBL, Germany
ADDRESS nethelp at embl-heidelberg.de

NAME    VMS Molecular Biology Software on EMBL File Server
AUTHOR 
ADDRESS EMBL, Germany
ADDRESS nethelp at embl-heidelberg.de

NAME    GENBANK SOFTWARE CLEARINGHOUSE
AUTHOR  Dave Kristofferson
ADDRESS Intelligenetics, Inc. USA
ADDRESS kristoff at net.bio.net

NAME    References for DNA seq.....
NAME    (article in the News)
AUTHOR  Sanjay Nayar <snayar at NEXT3.CS.UMR.EDU>
ADDRESS USA

NAME    Reviews of Seq Analysis Progs
NAME	(article in bionet.software)
AUTHOR  Harry Mangalam 
ADDRESS Dept of Biocomputing / The Salk Institute , USA
ADDRESS mangalam at salk-sgi.sdsc.edu

NAME    List of phylogenie programs
AUTHOR  Joe Felsenstein
ADDRESS Dept. of Genetics, Univ. of Washington, USA
ADDRESS joe at genetics.washington.edu 




FTP sites :
----------
ORGANISM : European biology Molecular Laboratory
NAME     : EMBL Anonymous Ftp Server
ADDRESS  : ftp.embl-heidelberg.de (192.54.41.33)
ADDRESS  : Germany

ORGANISM : Indiana University / Biology Department
NAME     : IuBio archive for biology
ADDRESS  : ftp.bio.indiana.edu (129.79.224.25)
ADDRESS  : USA

ORGANISM : University of Houston
NAME     : University of Houston Gene-Server
ADDRESS  : ftp.bchs.uh.edu (129.7.2.43)
ADDRESS  : USA

ORGANISM : National Institute of Genetics (NIG) (Japan)
NAME     : National Institute of Genetics ftp server
ADDRESS  : ftp.nig.ac.jp (133.39.16.66)
ADDRESS  : Japan

ORGANISM : National Center for Biotechnology Information (NCBI)
ADDRESS  : ncbi.nlm.nih.gov (130.14.20.1)
ADDRESS  : USA

ORGANISM : Dept. of Genetics, Univ. of Washington
ADDRESS  : evolution.genetics.washington.edu (128.95.12.41)
ADDRESS  : USA

ORGANISM :
ADDRESS  : anthro.utah.edu (128.110.192.93)
ADDRESS  : USA

ORGANISM :
ADDRESS  :  ftp.cs.utoronto.ca (128.100.3.6 or 128.100.1.105)
ADDRESS  : Canada

ORGANISM : University of Manitoba
ADDRESS  : ccu.umanitoba.ca (130.179.16.8)
ADDRESS  : Canada

ORGANISM : University of Geneva Switzerland
ADDRESS  : expasy.hcuge.ch (129.195.254.61)
ADDRESS  : Switzerland

ORGANISM : New Mexico State University
ADDRESS  : haywire.nmsu.edu (128.123.001.032)
ADDRESS  : USA

ORGANISM : NCI/FCRDC
ADDRESS  : ncifcrf.gov (129.43.2.10)
ADDRESS  : USA

ORGANISM : University of Virginia
ADDRESS  : uvaarpa.virginia.edu (128.143.2.7)
ADDRESS  : USA

ORGANISM : Department of Molecular biology / Massachussetts General Hospital
ADDRESS  : frodo.mgh.harvard.edu (132.183.190.10)
ADDRESS  : USA

ORGANISM : Department of Mathematics / Stanford University
ADDRESS  : gnomic.stanford.edu (36.120.0.19)
ADDRESS  : USA

ORGANISM : Molecular Biology Computer Research Resource (MBCRR)
ADDRESS  : mbcrr.harvard.edu (134.174.51.4)
ADDRESS  : USA

ORGANISM : New England BioLabs (NEB)
ADDRESS  : vent.neb.com (192.138.220.2)
ADDRESS  : USA

ORGANISM : Intelligenetics Inc.
ADDRESS  : net.bio.net (134.172.2.69)
ADDRESS  : USA

ORGANISM :
ADDRESS  : groucho.cs.psu.edu (130.203.2.12)
ADDRESS  : USA


-- 
-------------------------------------------------------------
Patricia RODRIGUEZ-TOME       Genethon
Internet : pat at genethon.fr
-------------------------------------------------------------



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