International response to our T32 web pages


Message-id: <199603122308.AA19762@hermes.rus.uni-stuttgart.de>
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Date: Tue, 14 Mar 95 00:12:45 -0800
From: c.heppel@studbox.uni-stuttgart.de
To: gammel@Physik.TU-Muenchen.DE
Subject: veralteter link

euer link zu webcrawler ist veraltet.
der neue heisst: http://webcrawler.com/
ansonsten ist die serch-engine seite echt gut.
claus

Thanks, has been considered

From: LiDIA (Thomas P.) 
Date: Mon, 15 Apr 1996 18:02:43 +0200 (MET DST)
Message-Id: <199604151602.SAA19658@voyager.cs.uni-sb.de>
To: gammel@Physik.TU-Muenchen.DE
Subject: LiDIA Mail - Announcement

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

                         ANNOUNCEMENT

                            LiDIA

           A library for computational number theory

  Copyright (c) 1994, 1995, 1996 by the LiDIA Group - Version 1.2

                Universit"at des Saarlandes
                Fachbereich 14 - Informatik
                 Lehrstuhl Prof. Buchmann
                    Postfach 151150
                  D - 66041 Saarbr"ucken

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

CONTENTS
@@@@@@@@

1) ABSTRACT
2) LiDIA GROUP
3) CONTENTS OF THIS RELEASE
   3.1 What is new?
   3.2 What is in work?
4) HOW TO GET AND INSTALL LiDIA
   4.1) FTP procedure
   4.2) Unpacking procedure
   4.3) Installation procedure (short version) 
   4.4) Calling a test program
   4.5) Installation procedure (long version) 
5) NOTE
   4.1) Send an email
   4.2) Be a part of it 
6) LiDIA GOES TO DARMSTADT
7) ACKNOWLEDGEMENTS

1) ABSTRACT 
@@@@@@@@@@@

LiDIA is a *powerful C++ library* for computational number theory
which provides a collection of *highly optimized implementations*
of  various   multiprecision   data   types   and  time-intensive
algorithms.  LiDIA  is  developed  by  the  LiDIA  Group,  at the
Universit"at  des  Saarlandes  and  it  is *free* for educational
purposes. The current version runs on 

o alpha, sparc7, sparc8, mips, intel(paragon), hp, cray c90, rs6k

with the following compilers

o g++-2.6.x, g++-2.7.x, cfront-3.01, HP C++, MIPS C++, xlC, Sun's
  acc, Watcom v.10, Borland-4.x

on the following operating systems

o SunOS, Solaris, OSF/1, OS/2, AIX-3.2.5, IRIX-5.2, Linux, FreeBSD,
  HP-UX9.05, MacOS (*), Windows 95 (**)

supporting the object file formats

o a.out, ELF

(*) At  the  moment  there  is no automatic way to build LiDIA on
    the  Mac.  We have built LiDIA manually using the CodeWarrior
    C/C++  compiler,  version 7.  The corresponding project files
    will be released soon.

(**) with some modifications (contact lidia@cs.uni-sb.de for more
     information).

For  a more detailed description of LiDIA's design and features we 
refer to the manual.

2) LiDIA GROUP 
@@@@@@@@@@@@@@

At the moment the LiDIA Group consists of the following people:

Werner Backes         F-D Berger         Ingrid Biehl
Johannes Buchmann     John Cremona       Sascha Demetrio
Thomas Denny          Kurt Huwig         Thorsten Lauer
Frank Lehmann         Markus Maurer      Oliver Morsch
Andreas M"uller       Volker M"uller     Stefan Neis
Thomas Papanikolaou   Sachar Paulus      Nigel Smart
Victor Shoup          Thomas Sosnowski   Patrick Theobald
Damian Weber          Susanne Wetzel

Old Members
^^^^^^^^^^^
Oliver van Sprang     Ren'e Weiskircher

3) CONTENTS OF THIS RELEASE
@@@@@@@@@@@@@@@@@@@@@@@@@@@

3.1) What is new?
^^^^^^^^^^^^^^^^^

The current  version of LiDIA (1.2) is a major  release. It follows
the  beta-tested  version 1.2.0b released on 26th of February  1996
by  registered  LiDIA users. Most of the work was done in extending
the package and in improving stability and performance.

o the  factorization  class  now  includes an implementation of the
  self-initializing version of the multipolynomial quadratic sieve.
  With  this method LiDIA is now able to factor integers of size 75
  digits  (max).  For  example, a 50-digit number with two 25-digit
  prime factors is now factored in 16 minutes on a sparc20.

o new  template  vectors  and matrices have been included, unifying
  matrices and lattices.

o new template implementation of Laurent power series and univariate
  polynomials.

o a  memory  manager  is now included providing 4 modi which can be
  chosen  at  compile time: malloc (using the system's memory mana-
  ger malloc/free), dentzer (using a buddy-algorithm combined with
  free-list storage), boehm (Boehm's garbage collector) and default
  (no memory manager at all).

3.2) What is in work?
^^^^^^^^^^^^^^^^^^^^^

o In beta testing

  - Finite fields GF(2^n), GF(2^p)
  - Generic multivariate rational function arithmetic
  - Gr"obner bases
  - Factoring in F_p[x] (Shoup's algorithms)

  (pre-releases of these packages available on request)

o In work

  - Porting of John Cremona's elliptic curve package
  - Discrete logarithms using COS
  - Symbolic computation package
  - Invariants of number fields
  - Counting points on elliptic curves over |F_p, p > 3
  - Incoprorating PoSSo's Customizable Memory Manager into LiDIA 
  - LiDIA development environment (support for configuring, (remote)
    control version, editing, compiling, running and debugging of
    LiDIA programs)

4) HOW TO GET AND INSTALL LiDIA
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@

4.1) FTP procedure
^^^^^^^^^^^^^^^^^^
LiDIA is available by anonymous ftp from

             crypt1.cs.uni-sb.de:/pub/systems/LiDIA
             ftp.cs.uni-sb.de:/pub/LiDIA
	     unix.hensa.ac.uk:/mirrors/LiDIA

If you have ncftp you can get LiDIA by simply typing

     ncftp crypt1.cs.uni-sb.de:/pub/systems/LiDIA/LiDIA.tgz

else use the following ftp session. With > we denote the commands
you have to type in. // denotes a short explanation.

> ftp crypt1.cs.uni-sb.de          // connect  to  the ftp server  
> anonymous                        // your     login         name
>          // your password is your email
                                   // address.  PLEASE  give  the 
				   // correct email address. 
> cd pub/systems/LiDIA             // the  directory  where LiDIA
                                   // resides 
> binary                           // set  binary  mode  for data
                                   // transfer
> get README                       // get   the    README    file
> get COPYRIGHT                    // get   the    COPYRIGHT file
> get LiDIA.tgz                    // get      the        package
> bye                              // disconnect

This session  will  get the files README, COPYRIGHT and LiDIA.tgz
and  will place them in the current directory (from now on called 
UNPACKDIR).

4.2) Unpacking procedure
^^^^^^^^^^^^^^^^^^^^^^^^
Now typing in

               gunzip -c LiDIA.tgz | tar xvf -

will  create  a  directory  named  LiDIA;  in this directory the 
following files/directories should exist:

UNPACKDIR/LiDIA:

Readme     bugs/           doc/           lib/      makefile.os2 
bin/       config/         include/       makefile          src/

Readme ............................................... this file
bin ........... holds LiDIA's applications files (see make appl) 
lib .................. holds LiDIA's library and thr primes file
config ...................... contains the configuration scripts
doc .......... contains LiDIA's documentation in various formats
include ............................ holds LiDIA's include files
makefile ............................. for UNIX, Linux, AIX, ... 
makefile.os2 ..................................... for OS/2 only
src ............................................ LiDIA's sources

4.3) Installation procedure (short version)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
In the UNPACKDIR/LiDIA directory type

STEP 1.         make configure

and  answer  the  questions  of  the `configure' script. You will
be  asked  for the installation path of LiDIA (this is by default
/usr/local).  Please  enter  an  existing  path on which you have
write  permission, since this is neccessary by the `make install'
command below. If your machine produces objects in the ELF format
you should also edit the file 

		LiDIA/config/CONFIG

and replace the line

		ASFLAGS = -DUMMY

with 
		ASFLAGS = -DHAVE_ELF

Solaris  users  should  also  define  -DSOLARIS after the default
CFLAGS and CXXFLAGS (if this is not already guessed by the confi-
gure script). After this type

STEP 2.         make

to build the library and (optionally)

STEP 2a.        make appl

to create the applications which test the classes and demonstrate
their  use.  Finally,  if  and  only  if  you have not chosen the 
current path as installation path, type

STEP 3.         make install

to  install  the  library  of  LiDIA (libLiDIA.a) and the include
files on your system. If you want to change the installation path
please  rerun  STEP 1  before   calling  `make install'.  LiDIA's 
library is installed by default on

                /usr/local/lib/LiDIA/$host-cpu/$cpp/libLiDIA.a

where host-cpu is  determined  by  the  command `config.guess' of
the  GNU  software and $cpp is the C++ compiler used (in this way
you  are  allowed  to  create  multiple  libraries   produced  by
different  compilers  on the same machine). LiDIA's include files
are installed by default on

                /usr/local/include/LiDIA

and finally LiDIA's binaries are installed on

		/usr/local/bin/LiDIA/$host-cpu/$cpp

4.3) Calling a test program
^^^^^^^^^^^^^^^^^^^^^^^^^^^
To call a test program, change to the directory 

                UNPACKDIR/LiDIA/bin/$host-cpu/$cpp

by simply typing

		cd UNPACKDIR/LiDIA/bin/$host-cpu/$cpp

The  applications in this directory, try to test all functions of
the  LiDIA  classes.  They are succesful, if they do not print an 
error message.

4.4) Installation procedure (long version) 
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Please read the chapter `Installing' in the manual

                UNPACKDIR/LiDIA/doc/manual/lidiaman.ps

5) NOTE
@@@@@@@

5.1) Send an email
^^^^^^^^^^^^^^^^^^
After  having  installed   LiDIA,  please send us an email saying
that  you have done so. This enables us to inform you about bugs,
bug fixes, new version, etc.

If you successfully installed LiDIA please tell us so  If you had
no  success  at  all  and  this  is likely to be a bug  in LiDIA,
(including  incomplete / incorrect documentation), please report.
Note that we will  probably  not  be able  to reconstruct  a  bug
without  a detailed description. The format suggested in the file
`bug_reports.form'  in  the  LiDIA/bugs directory should  be  the
guide for all bug reports.  Approved bugs will be included in the
file `bugs' which also resides in the LiDIA/bugs directory. You
can send your suggestions, enhancements, etc to

                     lidia@cs.uni-sb.de

Please, send bug reports (and fixes) to

                   lidia-bugs@cs.uni-sb.de

5.2) Be a part of it 
^^^^^^^^^^^^^^^^^^^^
We would also appreciate all sorts of feedback,  bug reports  and
bug  fixes,  enhancements,  contributions  etc. At this point one
short  note  (answering  the  question  posed frequently by LiDIA
users):

For  programs  contributed  to LiDIA the copyright remains to the
author.  However,  once a program is contributed to LiDIA and  is
released  for  the public with LiDIA it is not possible to remove
it from the package, since users may have built their work on top
of it.  LiDIA's policy is to put the author's name in the manual,
the  source code and in the announcement of the corresponding re-
lease.  For  more  details, please read the file COPYRIGHT in the
main distribution directory.

6) LiDIA GOES DARMSTADT
@@@@@@@@@@@@@@@@@@@@@@@

The LiDIA Group will move to Darmstadt (about 40km from Frankfurt)
by  the  end of the year, following Prof. J. Buchmann.  Until  the
movement  is completed, the user support (a team of 6 programmers)
will remain in  Saarbr"ucken.

We will inform you more precisely on this in about one month.

7) ACKNOWLEDGEMENTS
@@@@@@@@@@@@@@@@@@@

I would like to thank in the name of the LiDIA Group all users who
have  up-loaded,  installed and beta-tested LiDIA in this short a-
mount of time.

LiDIA  profits  from  user contributions and various public domain
software packages:  special  thanks  to  Arjen  Lenstra  and  Paul
Leyland  for  freelip-1.0,  Ralf  Dentzer   for   libI and the GNU
project for their superb software. LiDIA's development environment
uses GNU tools extensively. 

Thanks  also to Hans-J. Boehm and Alan J. Demers for the gc memory
manager. 

Last  but  not  least,  I  would  like  to thank my colleagues John
Cremona (Exeter University)  and Nigel P. Smart (University of Kent
at Canterbury) for many useful comments and discussions.

Best to all of you,

	Thomas Papanikolaou (TP)

-------------------------------------------------------------------
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message with the subject of "help" to lidiaadm@cs.uni-sb.de.

Thanks, has been considered in link list


Message-id: <199604151118.HAA01189@Arl-Mail-Svc-1.compuserve.com>
Content-type: text/plain
Date: Mon, 15 Apr 1996 07:18:57 -0400 (EDT)
From: 100651.3330@compuserve.com
To: gammel@Physik.TU-Muenchen.DE
Subject: lesbarkeit


Sorry guys,

aber eure Seite ist praktisch nicht lesbar: gr|ne links auf einem blau schraffierten hintergrund.....

Gr|_e,
Thomas aus frankfurt

Thanks, has been considered

Message-Id: <3192592B.200C@eng.sun.com>
Date: Thu, 09 May 1996 13:44:27 -0700
From: Erik Guttman 
Organization: Sun Microsystems
Mime-Version: 1.0
To: gammel@Physik.TU-Muenchen.DE
Subject: problem downloading matpack
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Hi Berndt, 

I found out about matpack from altavista.
I gather that I am not one of many, as the
cgi counter says I am visitor 2.  I had a
pretty hard time downloading the mattgz 
split files.  The bandwidth between you and
me is pretty meager (ungefaehr 1.4kbs).  I
also got partial copies (1.307 kb for mattgz.aa
and 1.249 kb for mattgz.ac) which made recon-
struction impossible till I figured it out.
(I have a very fast link to the net.  Do you?)

I am eager to mine your sources for the algo-
rithms that I read about on your web pages.

As I am only the 2nd visitor and I found out
about this through altavista, I wanted to let
you know I am using it.  I hope you intended
it to be found.  Thanks for putting it up there!

Erik Guttman
eguttman@eng.sun.com

Thanks for informing me

Sender: toli@samson.CHEM.UIC.EDU
Message-Id: <319D9D15.167E@samson.chem.uic.edu>
Date: Sat, 18 May 1996 02:49:09 -0700
From: Anatoli Krassavine 
Organization: U. of Illinois at Chicago
Mime-Version: 1.0
To: gammel@Physik.TU-Muenchen.DE
Subject: addition to Scientific Internet Resources list
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit

Dear Dr. Gammel,

  Here is one more link which you could consider interesting to add to
your Scientific Internet Resources list.

 http://mc.ioc.ac.ru/mc2/viewer/index.htm

  Awarded the Coveted COOL Rating by Gamelan and Rated TOP 5% WebApplet
by JARS.

  ChemSymphony is a platform independent set of interactive JAVA applets
that allows 3-D molecular structures to be easily incorporated into HTML
documents. The system understands most of the common file formats. The
structures can be manipulated in real time, rendered in a variety of
styles, and edited by the user. Other functionality includes the ability
to browse through databases of chemical structures as well as
interfacing to computational programs.

  ChemSymphony offers easy and attractive way for new generation of
Java-enabled browsers bring molecular modeling into hypertext documents
used in both research and the class room.

                         Sincerely yours,
                             Toly

-- 
______________________________________________________________________
Anatoli O. Krassavine    \ My ChemSymphony applet is awarded the 
kras@nmr1.ioc.ac.ru      / coveted COOL rating by GAMELAN and TOP 5%
toli@samson.chem.uic.edu \ WebApplet by JARS!
                         / http://mc.ioc.ac.ru/mc.htm
                         \ http://www.ch.ic.ac.uk/java/chemviewer/
______________________________________________________________________
Looking for hiring: Java/Java Script/Perl/CGI programming & 
^^^^^^^^^^^^^^^^^^  WWW site design
______________________________________________________________________
Program which works properly 90% of the time is 100% useless!
______________________________________________________________________

Thanks, has been considered in the scientific index

Received:  from dragonfly.wolfram.com
	by srv.cip.physik.tu-muenchen.de with SMTP id AA02694
	for  (5.67a/IDA-1.5/bs04);
	Thu, 23 May 1996 01:57:49 +0200
Received: (from root@localhost) by dragonfly.wolfram.com (8.7.5/8.7.3) id RAA22452; Wed, 22 May 1996 17:52:08 -0500 (CDT)
Date: Wed, 22 May 1996 17:52:08 -0500 (CDT)
Message-Id: <199605222252.RAA22452@dragonfly.wolfram.com>
From: rcwalter@wolfram.com (Rick Walter)
To: gammel@Physik.TU-Muenchen.DE
Subject: Link request
Precedence: Bulk

While surfing the web, I came across your page that contains links to other
sites:

http://www.physik.tu-muenchen.de/lehrstuehle/T32/scientific_abc.html

I'd like to know if you'll provide a link to Wolfram Research
(http://www.wolfram.com/). Our site contains a sophisticated scientific
visualization gallery, interactive demo, and MathReader, a free utility for
reading Mathematica documents. There's a lot of information about
Mathematica and related applications that would greatly complement the
other links on your page.

I appreciate your help and look forward to hearing from you soon.

Rick Walter (rcwalter@wolfram.com)
Wolfram Research

Thanks, has been considered in the scientific and commercial index


Received:  from zeke.phys.chemie.tu-muenchen.de
	by srv.cip.physik.tu-muenchen.de with SMTP id AA20481
	for  (5.67a/IDA-1.5/bs04);
	Tue, 11 Jun 1996 10:32:36 +0200
Received: by zeke.phys.chemie.tu-muenchen.de (920330.SGI/910805.SGI)
	for gammel@physik.tu-muenchen.de id AA24673; Tue, 11 Jun 96 10:32:35 +0200
Date: Tue, 11 Jun 96 10:32:35 +0200
From: eckhard@zeke.phys.chemie.tu-muenchen.de (Eckhard Waterstradt)
Message-Id: <9606110832.AA24673@zeke.phys.chemie.tu-muenchen.de>
To: gammel@Physik.TU-Muenchen.DE
Subject: zeke

Lieber Webmaster,
  die URL der WWW ZEKE Homepage hat sich geaendert. Sie lautet nun:
http://www.chemie.tu-muenchen.de/zeke/
Koennten sie bitte in Ihrer Seite mit der URL:
http://www.physik.tu-muenchen.de/lehrstuehle/T32/scientific_abc.html
den entsprechenden Link unter ZEKE Server aendern.
mit freundlichen Gruessen
                          Eckhard Waterstradt

Updated now

From: dunbrack@cmpharm.ucsf.edu
Message-Id: <199606270025.RAA04877@tolliver.ucsf.edu>
Subject: Backbone-dependent rotamer library website
To: gammel@Physik.TU-Muenchen.DE
Date: Wed, 26 Jun 1996 17:25:45 -0700 (PDT)
Cc: dunbrack@cmpharm.ucsf.edu (roland dunbrack)
Mime-Version: 1.0
Content-Type: text/plain; charset=US-ASCII
Content-Transfer-Encoding: 7bit

To the person who maintains the Scientific Internet Resources Alphabetical
at Uni-Muenchen (gammel@physik.tu-muenchen.de):

Thank you for including my website on your list of resources.
I have changed updated and changed the site significantly
in the last few weeks.  It has moved to the following address:

	http://www.cmpharm.ucsf.edu/~dunbrack.

In your alphabetical list, perhaps it ought to go
under "Backbone-dependent..." rather than under
my first name.

I've attached an announcement of the site that I sent
out to current users last weekend.

Thank you,

Roland Dunbrack
dunbrack@cmpharm.uscf.edu

******************************************************************

				June 22, 1996

Dear Colleague,

The backbone-dependent rotamer library is now available on the World
Wide Web at

	http://www.cmpharm.ucsf.edu/~dunbrack

The Backbone-Dependent Rotamer Library Webpage includes
backbone-independent and backbone-dependent rotamer libraries, a
program for making sidechain conformation predictions from input phi
and psi values and for evaluating the rotamers and chi angles of a
preliminary x-ray, NMR, or model structure in comparison to the
experimental distributions of rotamers and chi angles in the Protein
Databank. The site also presents in detail a description of local
steric interactions that influence sidechain rotamer and chi angle
choice and includes graphical representations of the
backbone-independent and backbone-dependent rotamer libraries
developed by Dunbrack and Karplus annotated to show where local steric
interactions affect rotamer and chi angle populations.

The January 1996 version of the library is now available. It contains
393 chains from the PDB of resolution 2.0 A or better and less than
50% homology with other chains in the set. It will be updated
regularly (every few months). This is 3 times larger than the original
library (March 1992).

Everything described in the Webpage is also available by anonymous ftp at 

	ftp.cmpharm.ucsf.edu

in the file /pub/bbdep96/bbdep96.Jan.tar.gz.

You can register for the BBDEP e-mailing list on the Website for
updates on the the library and programs for using it.  We plan to add
a homology modeling program soon for placing sidechains on a backbone,
eliminating steric clashes, and producing an output PDB file.

Any questions, please do not hesitate to contact me.

Roland L. Dunbrack, Jr.
Departments of Pharmaceutical Chemistry 
   and Cellular and Molecular Pharmacology
University of California, San Francisco
San Francisco CA 94143-0450

Email: dunbrack@cmpharm.ucsf.edu

Link has been updated

Institute T32 ,

author et al., Updated 19.5.1996

Send us suggestions for improvements and updates: gammel@physik.tu-muenchen.de,