zinc wrote:
>> -----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,
>
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)
> finger for PGP key
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