Don.Gilbert@IUBio.Bio.Indiana.Edu (Don Gilbert) (08/22/90)
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@CSHLAB.BITNET: prefers unix Roy Smith, Public Health Research Institute, New York, NY: has unix, likes mac networks, discusses pros of mac network, cons of unix administration. 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 migration. 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 migration. 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 computing. 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, Australia: both vms and unix are needed now, Sun is unix machine of choice, more good comments. ---------- -- Don Don.Gilbert@iubio.bio.indiana.edu biology dept., indiana univ., bloomington, in 47405, usa