Path: utzoo!attcan!utgpu!watserv1!watmath!uunet!tut.cis.ohio-state.edu!zaphod.mps.ohio-state.edu!rpi!ccnysci!phri!roy From: roy@phri.nyu.edu (Roy Smith) Newsgroups: bionet.molbio.genbank Subject: Re: Distributing GenBank with CD ROM Message-ID: <1989Dec13.040237.4701@phri.nyu.edu> Date: 13 Dec 89 04:02:37 GMT References: <8912121303.AA01409@wubios.WUstl.EDU> Sender: news@phri.nyu.edu (News System) Reply-To: roy@alanine.UUCP (Roy Smith) Organization: Public Health Research Institute, NYC Lines: 63 The numbers David Benton gives regarding the genbank distributions are pretty horrifying. The whole concept of getting a stack of 125 floppys twice a year is beyond belief. Not to mention cutting 12,500 of them! There is no doubt that this is a totally untenable way to distribute this information. 5 1600 BPI tapes isn't much better. Not to mention that if it's up to 5 reels at 1600, how much longer can I, with my 6250 drive, be so smug about only having to deal with a single reel? March 90? June 90 at the latest? David hopes that CD will make the 360k floppy distribution obsolete, but is there really much hope that people who havn't managed to get 1.4 Meg (or even 720k) floppy drives yet will shell out $800 or so for a CD drive? Hopefully the Project Officer can be convinced that scheduling an end to the 360k distribution will simply be a good way to give some folks some incentive to upgrade their hardware. Hand in hand with this, of course, would be a commitment from NIH to approve grants for said upgrades. I had no idea that 1-day turnaround was possible for CDs. I was under the impression that it was more like several weeks; I guess I havn't been keeping up with the technology. Given that datum, and the pricing figures supplied by J. Philip Miller, I have to change my opinion about CDs as a distribution medium. It certainly seems like it beats magtape and absolutely puts floppys to shame. I notice that genbank is now available on TK-50s. While I suppose that was a necessity, my feeling on the issue is that it simply panders to DEC's insistence on introducing proprietary tape formats totally incompatible with accepted industry standards. If anybody wants to hear more on that subject, write me privately; most of my thoughts on the TK-50 are best not aired in public. I understand the need to be careful about the design of CD file formats to work with (or is that around?) the timing characteristics of CD drives. I just hope that some way is found to make the raw data on the disk available to people who want it in essentially the same form as it is now. In the past few days, I guess I've thrown a lot of criticism at the genbank folks. I know I've certainly done so in the past. Lest anybody get the wrong idea, I should state that I think the IG folks are doing a pretty good job. Certainly, the state of genbank has improved since IG took over the contract from BBN. Not to mention that the size of the database has grown so much since then so the job is that much harder. Everything possible should be done to make life easier on the keepers of the sacred knowledge. It should be a condition of accepting an NIH or NSF grant that any sequences produced *must* be submitted to genbank in machine readable form. Make it part of the stock "administrative assurances" section of the application. Make it a check-off box on the front page of R01s along with the animal welfare and human subjects, etc. Make it part of the standard instructions to reviewers on study sections to do genbank searches to see if the PI has been naughty or nice. Some way should also be found to twist journals' arms and make them refuse to accept manuscripts if there is any sequence data that hasn't been submitted to genbank. I find it absolutely impossible to believe that there is a single lab in the US (or, for that matter, most of the world) doing sequencing that doesn't at least have a PC clone with a 360k floppy drive. What's so hard about copying the sequence to a floppy and dropping it in the mail? Quick informal poll. How many of you have, in say, the past 6 months, requested that somebody send you a sequence and received a printout of the sequence on paper!? Ah, but I'm preaching to the converted. -- Roy Smith, Public Health Research Institute 455 First Avenue, New York, NY 10016 roy@alanine.phri.nyu.edu -OR- {att,philabs,cmcl2,rutgers,hombre}!phri!roy "My karma ran over my dogma"