Summary: Unix vs. other multiuser computers?

Don Gilbert Don.Gilbert at IUBio.Bio.Indiana.Edu
Tue Aug 21 17:42:03 EST 1990

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.

prefers unix

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 
Iris computer.

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:
prefers unix

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

Don.Gilbert at iubio.bio.indiana.edu    
biology dept., indiana univ.,  bloomington, in 47405, usa  

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