1515151515 1515151515 1515151515 1515151515 1515 1515 1515 1515151515 1515 1515 1515 151515151515 15151515 1515151515 15151515 151515151515 15151515 1515 1515 1515 15151515 1515 1515 1515 1515 1515 1515 1515 1515 1515 1515 1515 1515151515 1515 1515151515 1515151515 1515 1515 1515151515 1515 1515151515 1515151515 1515 1515 No 15 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% INDEPENDANT NEWSLETTER PRODUCED AT HELSINKI UNIVERSITY, FINLAND << EDITED BY ROBERT HARPER >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% This edition of BioBit deals with GOS (GenBank On-line Service). Originally I wanted to do a session with Dave Kristofferson using IRC which is an INTERNET RELAY CHAT just to show that chatting is possible on Internet as well as on Bitnet. In actual fact we did have one IRC session between Finland and the USA, but a full example session will have to wait until a later date. Perhaps the scientific user community is still not ready for IRC. Just before Christmas the BIONET computer resource came to a halt, and GenBank On-line Service was the pheonix that was born out of the ashes. (Nice mythological reference there ED). I was interested to know what the change from BIONET to GOS would mean in practical terms, hence this short interview. Here are the questions that I posed. Questions:- **** GOS ***** 1) How does GOS compare to BIONET? 2) Has the changeover caused any confusion amongst users? 3) What is the most recent development in database distribution? **** Electronic Communications and Bulletin Boards (Newsgroups) **** 1) How does GOS view the BIOSCI Bboards? 2) How would you like to see the Bboards develop? 3) What are the problems that exist with Bboards? **** Connection by Public Data Network or by Internet **** 1) If I am on Internet can I FTP into GOS? 2) Do I pay anything to get into GOS? 3) Is anonymous FTP possible? 4) What other "free" services does GOS offer? **** More information **** 1) Where can one get more information about GOS? 2) E-mail address? 3) Postal address? It also seems that the word BIONET has been burned into the conciousness of networkers in the life sciences since references are still being made to the BIONET Bboards... and even the name of BIONET is still retained in the Usenet newsgroups even though BIONET as a functional entity really does not exist anymore. (Have you noticed that LISTSERV people talk about "Lists", Usenet folk have invented "Newsgroups", and BIONET people refer to "Bboards", when basically they are talking about the same thing.) The correct term to use when refering to the network for life scientists is BIOSCI, since this covers the European nodes, namely those nodes at DARESBURY, BMC and IRLEARN. But I suppose that the name BIONET will stick in the memory and become the stuff that legends spring from... and besides it would be such a hasssle to convert everything on Usenet from BIONET to BIOSCI. Anyway enough of this preamble, let's get on with the questions. > Questions:- > **** GOS > 1) How does GOS compare to BIONET? The main software in use on BIONET was the IntelliGenetics software. This is still available on the on-line service but all costs of providing access to that software now have to be born by the user instead of being defrayed by the NIH. Some of the other aspects of BIONET such as the contributed academic software and the contributed databases are gone (except for FASTA/TFASTA which are still available), but these features were not used as extensively as the IG software and their loss may not be a major inconvenience to the user community. However, on the plus side, BIONET was limping along on an old DEC 2065 computer which we had a very hard time getting funds to replace. The GenBank On-line Service has a very fast Solbourne superminicomputer with four 20 MIPS processors (compared to about one 1.5 MIPS processor for the Dec 20). (This information should be of special interest to Dr. Stephen "GCG" Clark :-) ED) Although disk I/O and other factors also contribute to the overall speed of program execution, it is safe to say that the sluggish response on BIONET should be a thing of the past (at least until the databases mushroom quite a bit more and the user community reaches even larger numbers than on BIONET (937)). Another important plus is the availability of the latest data from GenBank, EMBL, and GenPept (a database of translated coding regions from GenBank). These databases are updated on-line on a daily basis. The regular quarterly releases of the SWISS-PROT database are also available. All of these are searchable (for entry retrieval) by the very fast IRX program from the National Library of Medicine. Access to electronic communications remains unchanged from BIONET and a new newsgroup about the HUMAN-GENOME-PROGRAM has been added to the BIOSCI set. Finally, the GenBank On-line Service is now open to commercial users whereas previously we were restricted to providing access only for non-profit users. > 2) Has the changeover caused any confusion amongst users? I'm sure that it has caused some since everything didn't come together until the last minute, i.e., just a few weeks before BIONET was terminated. Application and information packets were sent to all BIONET users so hopefully the confusion has abated. > 3) What is the most recent development in database distribution? The latest GenBank daily updates are distributed via the USENET newsgroup bionet.molbio.genbank.updates. Public domain software produced in collaboration with Roy and Ross Smith and colleagues is available for offloading these files. The software extracts the data from the news distribution and converts it into a useable format. The software is available for UNIX machines by anonymous FTP from: goober.phri.nyu.edu (128.122.136.10). Software for VMS is available by MAILSERVer from MAILSERV@NYUMED.BITNET or MAILSERV@mcclb0.med.nyu.edu with a single line in the body of the message reading "SEND NIGHTLY.1" The distribution is VMS_SHAREd. > *** Electronic Communications and Bulletin Boards (Newsgroups) > 1) How does GOS view the BIOSCI Bboards? We are continuing on in our previous capacity as a BIOSCI node. Users on GOS use the "vnews" USENET news software for reading BIOSCI and other USENET newsgroups. This is very convenient and easy to use > 2) How would you like to see the Bboards develop? I hope that the HUMAN-GENOME-PROGRAM newsgroup leads to an expanded role for BIOSCI in communications among scientists in this area. After all of the smoke clears and everything is in place for GOS my first item is to get back together with various journal editors and increase the number of Table of Contents submissions to BIO-JOURNALS. > 3) What are the problems that exist with Bboards? The main technical difficulty is the necessity to bridge a number of different mail programs on different networks while avoiding mail loops and error messages. This has been overcome to a large extent, but not completely. Ideally I would like to see the uniform adoption of USENET news software by all sites thus eliminating the need for BIOSCI nodes and effectively putting us out of a large part of our job. I don't hesitate to add that the communications software needs to be made more user-friendly too, although it is not as bad as a few people like to make out. The new on-line service manual (free with the subscription) shows how simple it is to use e-mail and newsreading software. The main human problem is still increasing people's awareness of the existence and utility of BIOSCI. I am very optimistic that this goal will be met over the next several years with a little bit of patience and perseverance. > **** Connection by Public Data Network or by Internet > 1) If I am on Internet can I FTP into GOS? Yes. Our host is GENBANK.BIO.NET. > 2) Do I pay anything to get into GOS? Yes, but there are also some free services. I can't use the network for distributing prices. This information is included in our application packets which can be requested by sending one's regular postal address (snail mail, not e-mail) to: gos@genbank.bio.net There are two types of accounts, class I and class II. Class I provides access to all of the GOS features except for the IntelliGenetics software. Class II, for an additional fee, provides class I access plus access to the IntelliGenetics software. There are also limits on connect hours for the initial fee and an hourly charge for extra time unlike on BIONET. Since the NIH is underwriting considerably less of the service than it did for BIONET, it is necessary for us to pay for more of the costs with increased user fees. > 3) Is anonymous FTP possible? Yes. The latest sequence data can be retrieved by anonymous ftp to genbank.bio.net. The old BIONET contributed software is still in place although we can no longer devote resources to supporting this. Before BIONET went under, as you well know, we transferred copies to both EMBL and the University of Houston who have included these programs on their software servers. Spencer Yeh on BIONET as well as Ranier Fuchs and Dan Davison devoted a lot of effort in making sure that what had been created was not lost. > 4) What other "free" services does GOS offer? Free limited-time sessions over Telenet to retrieve GenBank and EMBL entries with IRX. Free e-mail FASTA database searches and retrieval of hits by locus name or accession number. To get information on this, send a message containing just the word HELP (no subject line) to search@genbank.bio.net. > **** More information > 1) Where can one get more information about GOS? Just send a request for an application to gos@genbank.bio.net and we'll promptly send one out to you. We need a regular full postal address from potential applicants. The application packet fully describes the service features and prices. > 2) E-mail address? Same as the above > 3) Postal address? GenBank On-line Service c/o IntelliGenetics 700 E. El Camino Real Mountain View, CA 94040 USA Phone: 415-962-7364 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % Robert Harper % Internet: HARPER@CC.HELSINKI.FI % % Helsinki University % Earn/Bitnet HARPER@FINUHA.BITNET % % Finland % Tel:358-0-7085300 Fax:358-0-7085011 % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -=ROB=- % These opinions are shareware... if you like them send $5 % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%