A question that I posed on the bionet.software newsgroup recently is:
Could everyone who has an opinion on what the most powerful &/or most
popular multi-user system for molecular biology will be in the next 5
years, please reply to me?
My thanks to those who took the time to answer -- many of whom are in the
positions of aquiring, administering and programming for these multi-user
computers in molecular biology. The responses are quite useful to me and
I hope to others looking to the future of molbio computing. This was not
an unbiased survey -- my opinions colored the question and the Bionet
newsgroup is widely distributed thru the Usenet of Unix computers. It is
also distributed outside of Usenet, however.
Of 17 responses, about 15 saw Unix as the current or near future leader
for multi-user systems. Most respondents now use a Unix system. Of those
using VMS, some are migrating to Unix, and some are using it only to run
specific software such as GCG.
I asked this question with the implicit assumption that some form of
large, multi-user computers would remain a necessity for molecular
biologists in the near future. Several respondents corrected or
challenged this assumption by discussing mac/pc networks as a replacement
for multi-user computers, or at least to use in a majority of data
analyses. My opinion remains that large, non-personal computers will
continue in the forseable future as essential to molecular biology. They
are often now, and will increasingly become compute servers, offering raw
computing power to networked users who will use them, but in a
microcomputer environment. Examples are the search servers provided by
GenBank and EMBL, and one mentioned by Alex Reisner.
My plan now is to look for a Sun SparcStation or Silicon Graphics Iris to
add a Unix, RISC computer to our local VMS microVax. I also tested the
real-world performance of a Sun 4/330 rated at 20 MIPS versus Iubio rated
at 0.5 MIPS. Using Joe FelsensteinUs DNAML on 18 species of 128 base
strands of aligned 5S rRNA, IuBio took 33 hours and the SUN took less than
2 hours. IuBio cost us around $55K a couple years back. A 16 MIPS
SparcStation 330 will cost us about $25K.
The full text of these responses should be quite useful to anyone faced
with similar decisions about their future multi-user computing platforms.
The complete text can be obtained by anonymous ftp to
iubio.bio.indiana.edu, directory [Archive.Help] as TUnix-in-MolBio.txtU,
or ask me for an e-mailing of this. Summary of responses:
douglas prasher, woods hole oceanographic inst:
has unix, plans for unix, uses IG suite, MASE, Phylip
Joe Felsenstein, Dept. of Genetics, Univ. of Washington, Seattle:
has DECstation, DEC and Sun are main workstation contenders, Unix with
X-windows mouse/window interface is the portable route of the future.
stern at CSHLAB.BITNET:
Roy Smith, Public Health Research Institute, New York, NY:
has unix, likes mac networks, discusses pros of mac network, cons of unix
Ross Smith, Cell Biology, NYU Medical Center:
has vms, plans for vms or vms/unix convergence.
Joe Smith, U. of Pennsylvania, Dept. of Biochem. and Biophysics:
has unix, plans for unix.
Henry Ford (@gdr.bath.ac.uk):
has unix, plans for unix, thinks european data bases are planning unix
Bob Woodman (@hpuxa.ircc.ohio-state.edu):
has unix, likes OS/2 networks.
John Cargill, Ontario Cancer Institute, Toronto:
has mixed vms and unix, plans for unix; unix is rougher around edges,
harder for system management; several helpful comments for vms->unix
Paul Schneeman, Computing Services, UCDavis:
has DECstations, vms and unix, prefers vms; comments support vms over unix.
Una Smith, Princeton Univ.:
has unix, supports what works best for software, likes micro networks and
Rick Westerman, Biochemistry, Purdue University:
has unix and vms, prefers unix or mac/pc network.
Sue Funk, Chemical Abstracts Service, Columbus, OH:
has unix and vms, prefers unix but uses vms for the GCG software.
Dan Davison, dept. of biochem. & biophys. sci., univ. of Houston:
Mike Cherry, Massachusetts General Hospital, Boston:
sees unix dominating in future, but with mac/pc networks as main user
front end. Has thoughtful comments on future of molecular biology
Alex Reisner, Sydney University:
has GCG running on unix Sun SPARC Server now, prefers Sun SPARC for future.
Tony Kyne, Walter and Eliza Hall Institute of Medical Research, Victoria,
both vms and unix are needed now, Sun is unix machine of choice, more good
Don.Gilbert at iubio.bio.indiana.edu
biology dept., indiana univ., bloomington, in 47405, usa