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

J jhp20 at cus.cam.ac.uk
Sun Oct 6 17:16:28 EST 1996


zinc wrote:
> 
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> 
> 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,
> 


Hi,

I was also thinking to make such a list to make a web page later
under the name of Linux for Biology. I hope you will keep the
list and announce later for the community.

Cheers,

Jong





> - -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)
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> zifi runs LINUX 2.1.1  -=-=-=WEB=-=-=->  http://zifi.genetics.utah.edu
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