Path: utzoo!utgpu!watserv1!watmath!uunet!shelby!apple!bionet!kristoff From: kristoff@genbank.bio.net (David Kristofferson) Newsgroups: bionet.molbio.genbank Subject: Re: ANONYMOUS FTP FROM BITNET Keywords: Internet Message-ID: Date: 3 Oct 90 23:58:11 GMT References: <9009290610.AA23614@genbank.bio.net> <1990Sep30.043924.19653@nlm.nih.gov> <1990Oct3.195352.5977@nlm.nih.gov> Organization: GenBank Online Service Lines: 90 My earlier response to Dr. States' message, while possibly appearing to be personal, was actually the result of the straw being dropped on the camel's back. I apologize to David that he was in the unfortunate position of having dropped that straw. His reply was a model of forebearance. However, what I am concerned about is not the attitude of any one individual, but a sequence of events which is continuing to occur, mainly outside of these newsgroups, of which this one small incident is just the latest manifestation. If this was an isolated statement I would never have taken the time to reply in the intensity or at the length that I did. I agree completely that "a lively and open discussion depends on all parties feeling free to post their opinions," but one can only compromise so far for the sake of gentility. I intend to be "gentlemanly" only as long as advantage is not taken of that forebearance, as has occurred in my past experiences. I emphasize that this is not an personal accusation against Dr. States, but a general pronouncement to all concerned. In the context of a simple comment about FASTA-MAIL, I realize that the readership may think that these words may border on the absurd, but I can assure you that much larger computing issues are on the agenda. As I stated in my last message, our real concern here is with issues to be decided in the next two years that will affect the future direction of biological computing. Now to return to details and comment on the following: > The turn around time for FASTA-MAIL is dependent on both the response > time of the server itself and the network handling the electronic mail > transactions. My comments were made in the context of a discussion of > the latter. As Dave Kristofferson points out, at a site like NIH, > where E-mail is handled by INTERNET, the turn around time can be pretty > good. There are, however, sites where E-mail processing is handled as > a low priority batch process. If you are dependent on one of those > sites, you may see a dramatic improvement in E-mail mediated services > by getting onto INTERNET. > There is no doubt that e-mail transfer would be faster from our site to other Internet sites rather than to, e.g., JANET, but it is also true that sites which are not on the Internet would be completely cut off from using an interactive, TCP/IP based system. FASTA-MAIL is accessible to people on virtually any major network. I will also suggest that the effect of e-mail delays on other networks may not always be as great as suggested above. While it is the case that the transatlantic BITNET gateways have become extremely congested at times, I have received reports of excellent FASTA-MAIL turnaround times from many non-Internet sites, not only in the U.S. but overseas as well. For example, in the U.K. a user on JANET reported a 15 minute turnaround time to get the results back of a protein search. I invite others to tell us of their experiences, either positive or negative. Of course, if the network or our machine goes down, a delay would occur until the access was restored, but note that this would affect both e-mail and interactive access equally. The facts are the following. Our computer takes about ten minutes (plus or minus one depending on the load) to do a search of 1000 bases against all of Genbank 64. It takes about 1.5 minutes to do a search of 1000 amino acids against all of SWISS-PROT 14. FASTA provides the search time as part of its output. Any additional time is due to transit. Users can utilize this information themselves to decide if the network is unduly affecting them. I have never received any evidence that FASTA-MAIL tooks "days" unless there was an extreme malfunction on the network or with the computer system. I suggest that in terms of turnaround time the difference is not a big issue. On the other hand, if someone wanted to design some nice user-friendly software that would reside on a PC or Mac (which were, e.g., etherneted in to a gateway to the network) and provide an interactive interface to FASTA or BLAST on another machine with a comprehensive up-to-date database somewhere else on the Internet (which is what I assume Dr. States is alluding to), this would be a great help to people who have PC's and Mac's with such a network connection. Such a suggestion could be made without having to mention FASTA-MAIL which is not obsoleted by such software. Had the suggestion been made in this context, much of this discussion would have been kept on a lower key. I would also venture to suggest that this idea has not occurred in only one place. As usual, the question of who does it usually gets down to either who has the funding or who expects to be able to make money by selling it. No one place has the sole monopoly on the talent. -- Sincerely, David Kristofferson, Ph.D. GenBank Manager kristoff@genbank.bio.net