science software (mol biol/biochem/biology) under Linux

zinc zinc at zifi.genetics.utah.edu
Fri Oct 4 17:41:22 EST 1996


-----BEGIN PGP SIGNED MESSAGE-----

howdy folks,

i'm attempting to compile a list of software that either people have
claimed runs under Linux or that is known to run under Linux for the
people at Caldera (Caldera is Ray Noorda's ( of Novell fame ) new
company).

here is my list so far.  if people have additions i'd love to have
them.  it would be nice if you could include a brief description or a
URL pointing to a web page with a description.  also, a URL for the
source or binary executable would be super..

thanks,

- -patrick finerty
biochem grad student, u of utah

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

a lot of these are in FORTRAN so how well they compile is probably due
to how good the fortran support on a system is...

=======
something called VMD (Visual Molecular Dynamics) is almost ported: 
http://www.ks.uiuc.edu/Research/vmd/ 
=======
Molden
fortran source, got it from

ftp://ftp.caos.kun.nl/pub/molgraph/molden

=======
RasMol
available on sunsite, also available here:

it _is_ possible to compile this for 16 bpp display, i've done it and
used it a lot myself.  you just have to change the Makefile to use
- -DSIXTEENBIT instead of -DEIGHTBIT or -DTHIRTYTWOBIT
=======

XtalView

also in fortran (crystallographers love fortran).  have to sign a
license to get source but not for binaries...

http://www.sdsc.edu/CCMS/Packages/XTALVIEW/

it looks like binaries are avail for Linux...(according to the above
page)
=======
WhatIf

http://swift.embl-heidelberg.de/whatif/

licensed for a small fee to academics...

=======
Procheck

http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html

obtain source from:
ftp://128.40.46.11/pub/procheck/tar3_4/procheck.tar.Z 

this is more fortran fun and games.  it seems to compile almost but i
haven't tried to use it yet...

=======
MOPAC
i searched all over for this - couldn't find the source!  only a ton
of damned html manuals.  a post to bionet.software is in order...

=======
i heard the GAMESS programs compile under Linux but i did not try them
as you have to go through a little effort to get them...

GAMESS-US
http://www.msg.ameslab.gov/GAMESS/dist.menu.html
site license is free to everyone but must sign a form... 


GAMESS-UK
http://gserv1.dl.ac.uk/CCP/CCP1/gamess.html
=======

Entrez/Cn3D from ncbi

database searching tools (for remote database queries)

the ncbi package...

linux binary of the network database search tools:
ftp://ncbi.nlm.nih.gov/blast/network/blast2/

this requires the network Entrez program to be configured, get a linux
binary here:  ftp://ncbi.nlm.nih.gov/entrez/network/linux.tar.Z

=======
fasta	ftp.virginia.edu/pub/fasta/fasta30t6.shar.Z
used default makefile but changed THR_CC= to be blank.

   THR_CC=

   then  make sall
=======


RNA folding related software:

Viena RNA package:
compiles fine under Linux but Makefile needs tweaking (hell, i managed
to get it to work...)

ftp://ftp.itc.univie.ac.at/pub/RNA/ViennaRNA-1.1b.tar.gz

=======
naview 

this compiles fine under Linux

http://www.ibc.wustl.edu/~zuker/ref/BRUR88.html

ftp://snark.wustl.edu/pub/naview.tar.Z
===========================================================================

- -- 
"Those that give up essential liberty to obtain a little temporary
 safety deserve neither liberty nor safety." -- Benjamin Franklin (1773)
			  finger for PGP key
zifi runs LINUX 2.1.1  -=-=-=WEB=-=-=->  http://zifi.genetics.utah.edu

-----BEGIN PGP SIGNATURE-----
Version: 2.6.2
Comment: Processed by Mailcrypt 3.4, an Emacs/PGP interface

iQCVAwUBMlWSjk3Qo/lG0AH5AQGg6AQAqOXjcYV7EIcv7E1jqVp8z0mOP1+nJMYo
5Yu1gZVfPcjGTQJOFay25kGtLy0fnVJzmLwSQUDQ/r5iLTxnf0kZ4JIDST9Hxz1H
oSjLvYY39HS6YLjCShioGeXLOEz9FiU1bxVvGj+5fXdhflrwFvMcqEyPumuc+qD6
/6Evc5wjeyk=
=vOTi
-----END PGP SIGNATURE-----




More information about the Bio-soft mailing list