"The Scientist" is looking for the best freeware and shareware

Harry Mangalam mangalam at uci.edu
Fri May 26 11:35:52 EST 1995


In article <finnD93Jnz.4Ey at netcom.com>, finn at netcom.com (Robert Finn) wrote:

> For an article in "The Scientist" I am looking for suggestions for the best
> freeware and shareware programs of special interest to life scientists.  I'm
> looking for everything from statistics packages to molecular modeling to
> sequence matching, etc.  Please post here or send me e-mail describing
> your favorite freeware and shareware, where to obtain it, and why it's so
> great.  I'm also looking for suggestions for the best sites on the Internet
> to obtain science-related software.
> 
> Please e-mail me at finn at netcom.com.  I am a free-lance science writer,
> based in Long Beach, California, and a frequent contributor to "The
> Scientist," which is described as "The newspaper for the life sciences
> professional."

Hmmmm, that's one guaranteed to start fights! There are a number of
extraordinary free and shareware programs available.  You might try
Pedro's Biomolecular Research Tools:
http://www.public.iastate.edu/~pedro/research_tools.html
 (itself an excellent example of usefully organized information)  for a
wealth of descriptive pointers.  However, if you're looking for personal
recommendations, here are some of my favorites, either because of
abilities or ease of use or both:  Apologies to the many notable ones I
left out.

Mac:
----
Fetch - by Jim Matthews; free to academics, $25 to others. The standard
Mac FTP Client.  Simple, easy to use, intuitive, bookmarkable, etc. Get it
at most Mac Archives
(ftp://ftp.hawaii.edu//mirrors/info-mac/comm/tcp/fetch-212.hqx).  More
info can be got at fetch at dartmouth.edu

MacMelvyl - by Kent Gardner.  Freeware.  Mac interface to Melvyl, the
University of California's computerized library system, notable for its
scope, power, and incredibly ugly interface.  MacMelvyl hides the ugliness
and allows its power to be used easily by mere humans. Home is:
ftp://ftp.mic.ucla.edu//pub/mac/macmelvyl

DNA Strider - by Christian Marck. $200 shareware.  One of the first and
still one of the best DNA analysis programs.  It lacks the noisy frills
and many of the desirable features of commercial pkgs, but none have come
close to matching it for speed, and elegance of interface.  It is the only
Mac pkg that's really usable on a Mac SE and the only one that I'd use on
an hour to hour basis at my bench. Author is a reclusive type.  No public
email or phone.  Only way to contact him is via mail or fax.

Dr. Christian Marck
Service de Biochimie et de Genetique Moleculaire
Bat. 142 Centre d'Etudes de Saclay
91191 GIF-SUR-YVETTE      CEDEX        FRANCE
fax: (33 1) 69 08 47 12


NIH Image - Wayne Rasband; Freeware (Pascal source code also freely
available). An astonishing, commerical grade image analysis pkg.  Power
Mac native code speeds many operations into the workstation class.  No Mac
owner should buy any image analysis program without cheching this out
first.  Lots of add-ins and extras at the ftp site. (many sites, but home
is: ftp://zippy.nimh.nih.gov//pub/nih-image/)

NCSA Telnet - many people. Freeware.  The standard Mac terminal emulator. 
So easy it diappears. (ftp://ftp.ncsa.uiuc.edu//Telnet/Mac/Telnet2.7)

Alpha - Pete Keleher. $25 shareware.  A text editor based on Ousterhout's
tcl scripting language that comes with custom setups for just about any
kind of file (HTML, TeX, Perl, C/C++, Fortran, Pascal, tcl, you name it,
and is further almost infinitely customizable via tcl.  Also has keyboard
macros, many unixy tools, can be used as the external editor for MacPerl,
Think C, Metrowerks, etc. Carried in many Mac Archives, but home is:
http://www.cs.umd.edu/~keleher/alpha.html

OzTeX - by Andrew Trevorrow. Mac interface to TeX.  Strange that 2 such
"opposing" technologies could be made to work together so well.  If you
must TeX, OzTeX!  (many sites, including:
ftp://ftp.hawaii.edu//mirrors/info-mac/text/oztex-18.hqx; note many other
files also needed)

Newswatcher - John Norstad.  Free. The best newsreader available on any
platform for any price. Period. (ftp://ftp.acns.nwu.edu/pub/newswatcher/)

lpdaemon - by Caspar Boon.  Utility that allows unix workstations to print
to Postscript laserwriters on Mac networks.  Great little utility. 
(Relatively) easy to set up, very robust on my Macs, handles only
postscript, but with postscript wrappers available (lptops, nenscript) on
almost every unix machine, it easily handles PS'ed text as well.  I have a
script that makes using it as easy as typing "netprint". (Many sites,
including
ftp://ftp.hawaii.edu//mirrors/info-mac/comm/tcp/lp-daemon-34.hqx)

SeqApp - by Don Gilbert.  A Jekyll/Hyde application.  Annoyingly, almost
uselessly buggy but still 2 or 3 generations ahead of the pack, with
builtin POPmailer (mail your gripes to the author from within the
program), gopher, access to Internet services, multiple/single sequence
editor, extensible, etc.  Currently being ported to a multiple platforms
as SeqPUP. (ftp://ftp.bio.indiana.edu//molbio/seqapp
or
ftp://ftp.bio.indiana.edu//molbio/seqpup)


Windows/DOS (Don't use it much, so I can't be of much use here)

RNAFold - by Ole Matzura.  A true Windows program allowing RNA folding
based on algorithms of M. Zuker and J. McCaskill, using the Win32s patch. 
Impressive that it could be done at all much less done so nicely.
http://broccoli.mfn.ki.se/rnadraw/rnadraw.html 


Unix:
Linux - Amazing 32-bit FREE unix clone that converts a DOS-hobbled Pentium
into a SPARC-beater workstation, by Linus Torvalds, and a host of Internet
volunteers.  Xwindows via XFree86 (included), NFS, multitasking, protected
memory, disk caching in the OS, the GNU tools, Lan Manager compatibility,
and progressively, commercial applications, including Word Perfect,
Spreadsheets, Databases, etc. Shrinkwrapped versions probably available at
many computer shops for ~$20. Try this one to start with:
http://www.cs.uiowa.edu:80/~phenning/Linux/

Setor - by Steven Evans.  Free to academics for a signature. SGI only. A
3D Molecular visualization aid that makes full use of the SGI 3D
hardware.  Can change just about any viewing parameter to do incredible
visualizations of molecules (Ribbons, helices, custom coloring of
residues, binding lights to residues for emphasis, measurements, side by
side and Crystal Eyes stero.  Comes bundled with setorplot/posterplot
which allows interactive display and modification of vector-based
molecular diagrams such as molscript (by Per Kraulis) produces.  Write to
Steve (elmo at nrcbsa.bio.nrc.ca) for agreement.

Sculpt - by Mark Surles.  Once Free, now $ware with very friendly academic
discount.  SGI/Cray only.  AMAZING molecular modeler that allows
interactive manipulation and modification of proteins (and other small
molecules) with exceptionally easy to use interface.  Performs near real
time manipulation WITH MINIMIZATION on a surprisingly large proteins (with
ability to freeze/thaw parts of protein).  The demo pkg itself is an
education in itself.  Display end runs on an SGI IRIS, the compute end can
run on the same machine, on a multiprocessor SGI Challenge or Cray.
(http://www.cts.com/~isigen/)

Multiplatform (of special note!)

RASMOL, by Roger Sayle - 3D molecular Viewer for Mac, Windows and X
windows - extraordinary job. (many sites carry it; home is at
ftp://ftp.dcs.ed.ac.uk/pub/rasmol/)

Acedb (and variants), original by Jean Thierry-Mieg and Richard Durbin. 
An Xwindow and now Mac version of a genome database with multiple views
into the genome.  Available in forms to support the Genome projects of C
elegans, Saccharomyces, many others.  Write to the authors for latest
versions and projects: Jean Thierry-Mieg (CNRS, France)
mieg at kaa.cnrs-mop.fr and Richard Durbin (MRC, UK) rd at mrc-lmb.cam.ac.uk


Mosaic, Netscape, etc.  - the programs that made (destroyed?) the WWW and
the Internet.  The usual places

Eudora - by Steve Dorner, others.  Now $ware as well as freeware (freeware
version lags the $ware version by several revs).  (Arguably) the best
POPmail client available. ftp://ftp.qualcomm.com//quest/mac/eudora and 
 ftp://ftp.qualcomm.com//quest/windows/eudora

Readseq - by Don Gilbert. Sequence format interconverter.
(ftp://ftp.bio.indiana.edu//molbio/readseq/)

Perl - by Larry Wall.  Extraordinary scripting language for Mac, DOS,
unix. If you have to program, try this first.  All major FTP sites.

tcl/tk - by John Ousterhout.  Another extraordinary scripting language and
X window interface builder. (for unix - ftp://ftp.cs.berkeley.edu//ucb/tcl
for Mac - see Alpha home page above)


Of Special Note: Don Gilbert, 
                 BioComputing Office 
                 Biology Department, Indiana University
                 Bloomington, IN  47405   USA

   Don has been in the forefront of innovative software development for
years, contributing significantly to the establishment, enhancement, and
promotion of gopher, wais, Flybase, the Mac and now multiplatform software
development.  His many software contributions (Readseq, Seqapp/Seqpup,
Gopherapp/Gopherpup, loopdloop, IUBIO extensions to WAIS, 1st wais
interface to Genbank and other biological databases, and landmark IUBIO
gopher/ftp server) have addressed and advanced the efficient use of
computers in the life sciences and have been copied, inspired, or
incorporated into many of the commercial applications that are now
available.  Indeed, probably one of the major phrases that the support
people for the major commercial molecular biology packages have come to
dread is "Well, Don Gilbert does it like this for free - why can't you?" 

Cheers
Harry
-- 
Harry J Mangalam, Microbiology and Molecular Genetics, UC Irvine,
      Irvine, CA, 92717, (714) 824-4824, fax (714) 824 8598
                 --- knowledge is fractal ---
            http://hornet.mmg.uci.edu/~hjm/hjm.html
  Computational Biology..SGI..Woodworking..Bicycling..Linux..WWW 




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