Shareware and Freeware for Science

[Robert Horton]

cathyom at TIAC.COM ("Catherine O'Malley") wrote:

: I am constructing a home page to facilitate the efforts of working
: scientists who want to locate tools for common tasks. 

There are a huge number of free- and semi-free tools out there, but a
personal list of the ones you find most useful can help overcome the
info-overload. This may help you get started:

General lists:

* The European Bioinformatics Institute's BioCatalog, "a software
directory of general interest in molecular biology and genetics," can
be found at http://www.ebi.ac.uk/biocat/biocat.html

* Links to "over 80 sites around the world that archive software and
data for Biologists which you can browse through":
 http://www.gdb.org/Dan/softsearch/biol-links.html

* And, of course, Pedro's Biomolecular Research Tools at
http://www.public.iastate.edu/~pedro/research_tools.html These are
mostly (all?) links to on-line resources, rather than programs you
download to use on your PC. This is a June 1995 update: I think Pedro
had to go write his thesis or something.

The Big Biosoftware Archive Sites are at EMBL and Indiana U:

* Indiana University:
gopher://fly.bio.indiana.edu:70/11/IUBio-Software%2bData

* The "Searching for Software and Data" page at
http://fire.clarkson.edu/doc/html/htut.html lets you search throught
the European Molecular Biology Laboratories (EMBL) software archives.
The links to literature references are "really experimental", but it's
a great idea.

* a gopher front to search both archives, plus a long list of other
servers, is found at gopher://merlot.gdb.org:70/11/softsearch/bio

Selected really cool programs and their homepages:

* Entrez: http://atlas.nlm.nih.gov:5700/Entrez/  from the National
Center for Biotechnology Information <http://www.ncbi.nlm.nih.gov/>

* NIH Image home page: ftp://zippy.nimh.nih.gov/pub/nih-image/

* RasMol (#-D molecular image viewer for Mac, Win, and Unix) :
ftp://ftp.dcs.ed.ac.uk/home/ftp/pub/rasmol/

* PHYLIP home page:
http://evolution.genetics.washington.edu/phylip.html Maintained by Joe
Felsenstein of the University of Washington
<joe at genetics.washington.edu>. The page entitled "PHYLOGENY PROGRAMS
AVAILABLE ELSEWHERE"
<http://evolution.genetics.washington.edu/phylip/software.html> reviews
a lot of free and commercial programs, and points you to other
collections of phylogenetic programs (these include sequence alignment
programs).

* SeqPup sequence analysis package by Don Gilbert:
http://iubio.bio.indiana.edu/1/IUBio-Software%2bData/molbio/seqpup/

Database searching:

* the Baylor College of Medicine Search Launcher
http://kiwi.imgen.bcm.tmc.edu:8088/search-launcher/launcher.html "is an
on-going project to organize molecular biology-related search and
analysis services available on the WWW by function by providing a
single point-of-entry for related searches "


---
Robert M. Horton
http://134.84.47.3                                       Have a :) day

"Scotty, try flushing the radioactive waste into the ventilation system!"