lamoran@gpu.utcs.utoronto.ca (L.A. Moran) (02/19/91)
Brian R. Smith writes,
"Yes, there are platforms that do not (or cannot) support X. I don't
mean to sound snobbish, but I think they'll fall by the wayside.
(Even if you get a Mac or PC X server, you still can't run a program
on the Mac/PC and display on another X server - it's only a one-way
support.) And, if they are replaced by Unix machines, many
departments are going to HAVE to hire an experienced system
administrator to care for and feed them. Even if workstation
manufacturers manage to put a workable system administration layer
over Unix (as NeXT is trying to do), the underlying software still
must be understood."
This opinion seems to be shared by Chris Dow who is also a fan of X-windows
and UNIX.
I use PC's and Mac's. They are quite sufficient for all of my molecular
biology needs so I find it quite puzzling to read comments such as those
expressed on this newsgroup. Most of us do not need to manipulate complex
structures in three dimensions - this is the only reason that I can think of
to purchase an expensive workstation and software that is so complex that
I would need to hire an expert just to run it.
Perhaps Brian Smith or Chris Dow could explain what kind of applications they
are referring to when they make such claims. Do they think that a MAJORITY
of molecular biologists should purchase expensive workstations that run
UNIX and X-windows? If so, why?
-Larry Moran
Dept. of Biochemistrydow@presto.ig.com (Christopher Dow) (02/19/91)
In article <1991Feb18.170310.2344@gpu.utcs.utoronto.ca>, lamoran@gpu.utcs.utoronto.ca (L.A. Moran) writes: > > > Brian R. Smith writes, > > "Yes, there are platforms that do not (or cannot) support X. I don't > mean to sound snobbish, but I think they'll fall by the wayside. > (Even if you get a Mac or PC X server, you still can't run a program > on the Mac/PC and display on another X server - it's only a one-way > support.) And, if they are replaced by Unix machines, many > departments are going to HAVE to hire an experienced system > administrator to care for and feed them. Even if workstation > manufacturers manage to put a workable system administration layer > over Unix (as NeXT is trying to do), the underlying software still > must be understood." > > This opinion seems to be shared by Chris Dow who is also a fan of X-windows > and UNIX. > > > Perhaps Brian Smith or Chris Dow could explain what kind of applications they > are referring to when they make such claims. Do they think that a MAJORITY > of molecular biologists should purchase expensive workstations that run > UNIX and X-windows? If so, why? Obviously, I haven't made myself clear on this issue. I beleive that unix is an extrememly powerful system which has the potential to make more sophisticated, and, ultimately, more useful programs available to the user. At this point, however, I find that unix is far to difficult to manage, and therefore, IntelliGenetics has a commitment to writing software for _all_ major platforms, as evidenced by our poster at _Genome Sequencing II_. Also, please note that a SparcStation IPC costs _much_ less than an equivalently configured Mac II fx, so I don't think one can call unix workstations expensive, they are just a top-of-the-line-type computer. > > -Larry Moran > Dept. of Biochemistry Chris Dow IntelliGenetics Software Engineer 700 East El Camino Real icbmnet: 37 22' 39" N, 122 3' 32" W Mountain View, Ca. 94040 dow@presto.ig.com (415) 962-7320
BROE@AARDVARK.UCS.UOKNOR.EDU (Bruce Roe) (02/19/91)
I will conceed that the time has come for me to get into the world of UNIX, not for any other reason than a series of programs which would help us out greatly is only available on a SparkStation running X-windows. Since my laboratory is populated with Mac's, and a few IBM PC clones, I've been very interested in the recent debate. Frank Kolakowski writes: >There are several reasons to use Unix. And a few more to use X-Windows. >Most of these reasons stem of the ability of machines with >these features to do multiple things at once, with reasonable throughput. >Alas not every lab needs a Unix workstation, but most would really >benefit if they did. > First costs of hardware: > Macs are not cheap but neither are workstations > For about $10,000 you can get a workstation > of modest means to do most of the things you want to > do in molecular biology or biochemistry. > > This workstation will allow n individuals to access > the "same" files at the same time. > > 3 macs and a laser printer is a whole lot more > than 1 workstation, 1 laser printer and a few dumb > terminals. > Do not the above statements need clarification? Seems to me the price comparisons depend on which Sun or Mac you're comparing. > Next multiple "jobs": > In our lab we would like to have the ability to > search GenBank, write a manuscript and > analyze data by more than one person simultaneously. > > With your mac or PC first you probably dial up to > a campus wide facility to do the database search > since multiple databases are not such a good idea. > While you are doing that, it is difficult to do > anything else. > > With X and Unix, you could open up a window, > run telnet, and do your search, while you have your > wordprocessor running in another window, and a graph of > your latest experiment in a third. > Sorry Frank, but I disagree. Your e-mail was received in the VersaTermPro window on my MacIIcx with 2 page monitor, while I was working on a manuscript in a MicroSoft Word window and printing a figure just created with MacDraw in another window. Oh yes, I also was running a GenBank search in Batch on our VAX. I'm running MultiFinder with Mac OS version 6.05 and although it is not "true" multiprocessing, it works just fine. My question is "Why do I have to learn an operating system?" I have no idea of how the Mac OS works, but do know that it is easy to use, has a very short learning curve and uses routines from the Mac Toolbox. I've even programmed in C and FORTRAN on the Mac, used toolbox calls and written real live Mac applications. Ifyou tell me that it's the same as X-windows or similar than that's fine, I can learn that. But your 2 arguments above are way off........ It seems to me there are 2 good reasons for getting into a Unix environment. 1. You're forced to because that's the only system on which your favorate programs will run on. 2. You want more mips for your $, because for under $20 K you can get a SparkStation with 16 meg RAM and blow the socks off your Mac, VAX or whatever. (DOS is so outdated it's not worth discussing) Another reason is multi users, but why bother when the VAX is there. Yet another reason is that you were a CS major, learned C and love Unix. Fine, but who is going to learn the Unix OS in my lab? Guess it will be Me. "Is it time to do Molecular Biology yet Daddy" "No son, it's time to learn Unix" Sigh............................................ Best to one and all, **************************************************************************** * Professor of Chemistry and Biochemistry Dept. of Chem. and Biochem. * * INTERNET: BROE@aardvark.ucs.uoknor.edu University of Oklahoma * * BITNET: BROE@uokucsvx 620 Parrington Oval, Rm 208 * * AT&TNET: 405-325-4912 or 405-325-7610 Norman, Oklahoma 73019 * * FAXnet: 405-325-6111 * ****************************************************************************
lfk@eastman1.mit.edu (Lee F. Kolakowski) (02/19/91)
On 18 Feb 91 17:03:10 GMT, lamoran@gpu.utcs.utoronto.ca (L.A. Moran) said: > Brian R. Smith writes, >> "Yes, there are platforms that do not (or cannot) support X. I don't >> mean to sound snobbish, but I think they'll fall by the >> wayside. (Even if you get a Mac or PC X server, you still >> can't run a program on the Mac/PC and display on another X >> server - it's only a one-way support.) And, if they are >> replaced by Unix machines, many departments are going to HAVE >> to hire an experienced system administrator to care for and >> feed them. Even if workstation manufacturers manage to put a >> workable system administration layer over Unix (as NeXT is >> trying to do), the underlying software still must be >> understood." > This opinion seems to be shared by Chris Dow who is also a fan of X-windows > and UNIX. And many other people.. > I use PC's and Mac's. They are quite sufficient for all of my > molecular biology needs so I find it quite puzzling to read comments > such as those expressed on this newsgroup. Most of us do not need to > manipulate complex structures in three dimensions - this is the only > reason that I can think of to purchase an expensive workstation and > software that is so complex that I would need to hire an expert just > to run it. There are several reasons to use Unix. And a few more to use X-Windows. Most of these reasons stem of the ability of machines with these features to do multiple things at once, with reasonable throughput. Alas not every lab needs a Unix workstation, but most would really benefit if they did. First costs of hardware: Macs are not cheap but neither are workstations For about $10,000 you can get a workstation of modest means to do most of the things you want to do in molecular biology or biochemistry. This workstation will allow n individuals to access the "same" files at the same time. 3 macs and a laser printer is a whole lot more than 1 workstation, 1 laser printer and a few dumb terminals. Next multiple "jobs": In our lab we would like to have the ability to search GenBank, write a manuscript and analyze data by more than one person simultaneously. With your mac or PC first you probably dial up to a campus wide facility to do the database search since multiple databases are not such a good idea. While you are doing that, it is difficult to do anything else. With X and Unix, you could open up a window, run telnet, and do your search, while you have your wordprocessor running in another window, and a graph of your latest experiment in a third. > Perhaps Brian Smith or Chris Dow could explain what kind of > applications they are referring to when they make such claims. Do > they think that a MAJORITY of molecular biologists should purchase > expensive workstations that run UNIX and X-windows? If so, why? It is incorrect that if you have a workstation you must do crystallography or analysis of structures. But, if you wanted to with a Unix box and X, you could. Further, the notion that it is difficult to run a unix system is only partially correct. There is a lot of information about Unix available, if you need to know something you can find it. Having looked at the internals of a Mac, I would hesitate to say that the same is true. Further, research is about breaking new ground. So sure you don't want to spend enough time to get a CS degree in order to write a grant, but Unix has progressed very far from that, and in the next few years, may be light years from the notion that Unix is hard. The second part about research is that you want to maximize your time (that is true about almost every thing else too). Unix and X allow you to be more productive. If you want to send mail to a colleague, send it, don't login to another system to do it. Well, I'll stop now, but this could go on and on. Computers are research tools. If your research does not need to do anything more than write papers and grants, a PC or Mac is all you need. Any more than that, get a unix machine. -- Frank Kolakowski ======================================================================= |lfk@athena.mit.edu or lfk@eastman1.mit.edu or kolakowski@wccf.mit.edu| | Lee F. Kolakowski M.I.T. | | Dept of Chemistry Room 18-506 | | 77 Massachusetts Ave. Cambridge, MA 02139 | | AT&T: 1-617-253-1866 #include <disclaimer.h> | ======================================================================= ||Desert Storm - Lasers have made this the cleanest *dirty war* ever.|| =======================================================================
biegansk@cs.umn.edu (Paul Bieganski) (02/19/91)
In article <9102182122.AA02187@genbank.bio.net> BROE@AARDVARK.UCS.UOKNOR.EDU (Bruce Roe) writes: >... >> run telnet, and do your search, while you have your >> wordprocessor running in another window, and a graph of >> your latest experiment in a third. >> > >Sorry Frank, but I disagree. Your e-mail was received in the VersaTermPro >window on my MacIIcx with 2 page monitor, while I was working on a manuscript >in a MicroSoft Word window and printing a figure just created with MacDraw >in another window. Oh yes, I also was running a GenBank search in Batch >on our VAX. I'm running MultiFinder with Mac OS version 6.05 and although >it is not "true" multiprocessing, it works just fine. Try this: establish a connection to a database/search engine running on a Cray, _paste_ a sequence-object into a sequence editor running on a Sparc, paste part of that sequence into an primer design tool running on a Sun 3/50. All on the same screen, NO text paste/copy involved (i.e. you have a networked, hardware independent inter-client communication protocol). I don't want to get into a holly war - I would just like to point out that there is MUCH more to X/Unix then 'windows' (!) - i.e. the general concept of networked compute-servers, which allow for easy integration of software running on different machines in different locations - without having to hardwire all possible interactions into each and every piece of software. > >My question is "Why do I have to learn an operating system?" I have no >idea of how the Mac OS works, but do know that it is easy to use, has a >very short learning curve and uses routines from the Mac Toolbox. I've >even programmed in C and FORTRAN on the Mac, used toolbox calls and written >real live Mac applications. Ifyou tell me that it's the same as X-windows >or similar than that's fine, I can learn that. But your 2 arguments above >are way off........ > >It seems to me there are 2 good reasons for getting into a Unix environment. >1. You're forced to because that's the only system on which your favorate > programs will run on. >2. You want more mips for your $, because for under $20 K you can get a > SparkStation with 16 meg RAM and blow the socks off your Mac, VAX or > whatever. (DOS is so outdated it's not worth discussing) > >Another reason is multi users, but why bother when the VAX is there. >Yet another reason is that you were a CS major, learned C and love Unix. >Fine, but who is going to learn the Unix OS in my lab? Guess it will be >Me. > > "Is it time to do Molecular Biology yet Daddy" > "No son, it's time to learn Unix" "How do we do molecular biology, Daddy ?" :-) (Re: excellent article by Gilbert in Nature). Again - no flames, PLEASE ! All I'm trying to point out is that this discussion is not (should not ?) be about what's better - Macs/PCs or X/UNIX, but about facilities any modern molecular biology lab should have (more and more of them being computational in nature). Happy searches ! -Paul ============================================================================== | Paul Bieganski | biegansk@cs.umn.edu | | ============================================================================== -- ============================================================================== | Paul Bieganski | biegansk@cs.umn.edu | | ==============================================================================
dtinker@gpu.utcs.utoronto.ca (David Tinker) (02/19/91)
In Article <1991Feb18.170310.2344@gpu.utcs.utoronto.ca>, lamoran@gpu.utcs.utoronto.ca (L.A. Moran) writes: >> Brian R. Smith writes, >> >> "Yes, there are platforms that do not (or cannot) support X. I don't >> mean to sound snobbish, but I think they'll fall by the wayside. >> .... > > This opinion seems to be shared by Chris Dow who is also a fan of X-windows >and UNIX. > > I use PC's and Mac's. They are quite sufficient for all of my molecular > biology needs so I find it quite puzzling to read comments such as those > expressed on this newsgroup. Most of us do not need to manipulate complex > structures in three dimensions - this is the only reason that I can think of > to purchase an expensive workstation and software that is so complex that > I would need to hire an expert just to run it. Well you're both right! First of all, the most common mistake of novices in the computer world, as we all know, is failure to analyse requirements before proceeding with implementation. This applies to the purchase of hardware/software as well as to writing programs. As a person with some reputation for knowledgeabity about micro-computers, I'm sometimes approached for advice by students who intend to purchase a personal computer - it's common to find they haven't really thought about what they plan to use it for! So Larry is correct in thinking about applications first, platform second. On the other hand ... there is technological advance: while technology is not an end in itself, it does have the effect of putting power in people's hands. There is a nice quote at the beginning of "MS-DOS Developer's Guide" by Angermeyer et al (Sams, 1989): > He felt like somebody had taken the lid off life and let him look > at the works > ... Dashiell Hammett, "The Maltese Falcon" Computers can do this. I can do things with my PC-AT clone I wouldn't have even thought of doing before they were available. But I just had a note from my son who works in plant genetics and has just acquired a Sun SPARC station. He notes that programs which took 10 minutes to run on an AT without a math processor, run in 10 seconds on the Sun (these are BIG programs!). It's probably obvious which kind of desktop computer I'd prefer! What now seems fantastically remote and difficult will in the near future be considered a routine tool. Does anybody still use a TTY43? -- ! David O. Tinker / Department of Biochemistry / University of Toronto / ! ! TORONTO, Ontario, Canada M5S 1A8 / Voice: (416) 978-3636 / ! ! UUCP: dtinker@gpu.utcs.utoronto.ca / BITNET: dtinker@vm.utcs.utoronto.ca ! -----------------------------------------------------------------------------
frist@ccu.umanitoba.ca (02/20/91)
Some comments on the recent recent thread concerning the plusses and minuses of X/Unix vs. MacOS. 1) UNIX IS NOT HARD TO LEARN! The thing that annoys me most is the underlying assumption that you have to be a computer whiz to use Unix. This is not because Unix is any harder to learn than any other operating system, (it's easier than most) but that Macintosh propogated the (IMHO) counterproductive idea that you shouldn't have to read any documentation to use a computer. This is like saying you shouldn't have to know anything about electricity to run a gel, or shouldn't have to know anything about DNA polymerases to do PCR. I contend that learning to use Unix is less difficult than learning to drive a car. The reason that many people have trouble with computer operating systems is that they don't take the time to read a book, or take a short course (eg. most computer service centers on university campuses will offer short courses requiring one or two afternoons.) To become a competent Unix user, all you need to learn is: a) A core of about 15 commands. b) How to use the online help in situations where the core won't suffice. c) How to use a text editor. The new X-platforms usually give you a nice screen editor that any Mac-user could easily figure out. Otherwise, it is necessary to plod along with the vi or emacs editor. d) How to use the mailer. Again, on the X-platforms, that is now as simple as any of the Macintosh mailers. e) How to organize your files in directories. 2) UNIX IS BECOMMING STANDARDIZED; MACINTOSH IS PROPRIETARY. This should speak for itself. 3) MACINTOSH DELIBERATELY MAKES IT HARD TO DO ANYTHING SOPHISTICATED. EVEN MANY SIMPLE TASKS/FEATURES ARE NON-EXISTENT IN MAC-OS. The thing for which I can't forgive Steve Jobs is that he deliberately emasculated MacOS. Let me explain what I mean. Stipulated, it's nice to create an operating system that anybody can use. However, it was NOT necessary to remove all of the features necessary to do things like programming, easily creating and editing datafiles, reference to files by name, or direct movement from directory to another. Let me take these things in order: a) PROGRAMMING. Because of the need for rapidly making changes in programs, specifying compiler options, linking, Make-ing etc., you can't just buy a compiler for a Macintosh. Instead, you have to buy (and learn how to use) something like the MPW Workbench, which creates what is essentially an internal operating system in which you do all of the programming steps. In cases in which your program is too big (ie. most of the time) you can't even test it within the environment, but you have to go out to the main environment (if you have enough memory). Ironically, these programmers' environments are usually patterned after Unix! b) What if you have a sequence in one format, and the next program you want to use requires a different format? (Say, a 1 or 2 at the end of the sequence to indicate topololgy.) Under Unix, you enter the vi (or other) editor, jump to the end, add a character, and quit. In Macintosh, you have to traverse the directory tree to your copy of MacWrite (or whatever), click on the cute icon, find your file by clicking through the filelist, import your ASCII file, make your change, export your file, and click back through the directory tree to where your datafile is. The point is YOU CAN'T MAKE QUICK CHANGES IN DATAFILES. c) Oh, there's another problem. Now, to use your program, you can't just execute it by typing its name, but you have to click through the directory tree, find the program, and click on it. Now, you have to open a directory window, find the datafile, click on it... In Unix, I simply go to the subdirectory containing particular sequence or other files, type the name of the program, and go. If I need a second sequence or other datafile while the program is running, and can't remember the name, I just open another window, go browse through the directory until I find the one I want (no harder than browsing through a directory bar on the Mac) and now that I have the filename in front of me, I can type it ( or maybe even paste it) in response to the prompt. I don't need to know where the programs are, so I can concentrate on the data. d) REFERENCE TO FILES BY NAME. If you dig real deep, you can discover that Macintosh OS does, in fact support tree-structured directory names (eg. /usr/home/bill/seq) but these are NOT accessible through the normal operating system. Programming languages usually (grudgingly)let you access these names, but it is not encouraged. Furthermore, names must be fully qualified. Relative pathnames (eg ../../rest_enz) are not part of MacOS. Neither are environment variables, (easy ways to specify distant directories) or a host of other conveniences that make Unix powerful. And while we`re at it... e)MACINTOSH PROVIDES NO SIMPLE WAY TO TYPE OR PRINT THE CONTENTS OF A FILE. In Unix, you can view a file with more (or less), or head, tail, or cat. This gives you a quick way to see what's in it. To print a file, use lpr. To do any of these things in Mac, you have to enter a word processor (eg MacWrite) import the file, and print it or examine it from there. f) How about shell scripts (.bat files in DOS). There is no such thing on the Mac. Again, I pose the question: Why did Macintosh have to eliminate all of the features that make an operating system truely useful? They had to have had these things in-house, or they couldn't have written the thing in the first place. They DELIBERATELY make it as hard as possible to use anything other than what has been specifically provided. 4) THE OVERHEAD ASSOCIATED WITH UNIX workstations. There are two kinds: system administration, and costs. At present, if you have your own Unix workstation, you have to do a certain amount of system administration. NeXT has probably done the best job of giving you a turnkey system that requires a minimal amount of work in getting the system going and keeping it going. Hopefully, the other manufacturers will follow suit in automating the administration overhead. The second issue is cost. Yes, a SUN Sparcstation is more expensive than a MacSE, but that's not a fair comparison. Although I never seriously contemplated buying a Mac, I did find that to approximate the power of the Sparcstation that I ended up buying, an equivalently-configured MacII would have cost MORE. I am not advocating that everyone should have a Sparcstation. Rather, the best approach is for each department or large working group to have a workstation, and for each individual to buy an X-terminal (~$2000) or a client workstation (such as a SUN-SLC). Now, we are talking about the individual having hardware for processing, and sharing programs and diskspace (both of which save $$). In addition to saving money, this concept also means that only one or a few people in the department has to know enough to perform systems administration functions. 5) YOU DO NOT HAVE TO GIVE UP MOUSE-DRIVEN GRAPHICS AND EASY-TO-USE WORD PROCESSING IN UNIX. There are perfectly good products for all of the really popular tasks available for Unix systems. In some cases, the same programs are available as on PC's or Mac's (eg. WordPerfect) CONCLUSION There are very good reasons why computer operating systems are written the way they are. Nobody ever wrote an operating system with the intention of making it hard for people to learn. They wrote them to be versatile and powerful. A chain saw is powerful too, but you need to learn a few things before you can use it. I wish to reiterate that there doesn't have to be a tradeoff between having a system that is straightforward to use, and yet versatile enough to let you use it creatively. I think that in the near future, the X-platforms will do a very good job of redefining the way people use computers for their work. But there will have to be some learning on the part of those wishing to take advantage of it. I have now satisfyingly vented my spleen. Thank you for your indulgence. =============================================================================== Brian Fristensky | What can literature do against the pitiless Department of Plant Science | onslaught of naked violence? Let us not for- University of Manitoba | get that violence does not and cannot flourish Winnipeg, MB R3T 2N2 CANADA | by itself; it is inevitably intertwined with frist@ccu.umanitoba.ca | LYING... Lies can stand up against much in Office phone: 204-474-6085 | world, but not against art. FAX: 204-275-5128 | Alexander Solzhenitsyn, NOBEL LECTURE ===============================================================================