http://net.bio.net/BIOSCI/biosci.FAQ.html (PC Press Internet CD, 03/1996)Newsgroups: bionet.announce Last-modified: 28 February 1995This document supplements the BIOSCI Newsgroups Information Sheet and provides details on how to participate in BIOSCI forums. Both documents are available for anonymous FTP and gopher retrieval (port 70) from net.bio.net [134.172.2.69]. The text version of the FAQ is found in pub/BIOSCI/doc/biosci.FAQ. This document is also available using the World Wide Web at "http://www.bio.net/BIOSCI/biosci.FAQ.html". This document may also be requested by e-mail by sending the command
From: BIOSCI Administrator <biosci-help@net.bio.net> Reply-To: biosci-help@net.bio.net Subject: BIOSCI/bionet Frequently Asked Questions Approved: bionews-moderator@net.bio.net BIOSCI/bionet Frequently Asked Questions (FAQ) ----------------------------------------------
info faq
in the body of an e-mail message addressed to the Internet address
biosci-server@net.bio.netAny text placed on the Subject: line of your message is ignored, so please be sure to put the "info faq" command in the main body of your e-mail message. The FAQ is posted the first of each month to the BIONEWS/bionet.announce newsgroup along with the BIOSCI information sheet and the list of changes to the newsgroups during the preceding month.
BIOSCI messages are distributed without editorial intervention in most cases. Dissemination is by both electronic mail and over Usenet in the form of the "bionet" newsgroups (see below for Usenet details). The contents of the electronic mail distribution is identical to the Usenet news distribution, but we encourage BIOSCI users to access the system through Usenet news software whenever possible. E-mail distributions may eventually be phased out. As of October 1992, 59% of our readers used Usenet news software instead of e-mail.
You may find much more detailed and up to date information concerning Usenet in the news.announce.newusers newsgroup. These articles are also available using anonymous FTP from rtfm.mit.edu [18.181.0.24, but please always reference the hostname rtfm.mit.edu, as IP addresses and canonical names will change in the future, but rtfm.mit.edu will remain correct], in the /pub/usenet/news.announce.newusers directory. You may be specifically interested in the following articles:
Two versions of the BIOSCI info sheet are available, one for the Americas and the Pacific Rim countries, and the second for Europe, Africa, and Central Asia. The former may be requested by e-mail to biosci-help@net.bio.net, while the latter may be requested from biosci@daresbury.ac.uk.
A few guidelines on specific newsgroups:
BIONAUTS/bionet.users.addresses: This newsgroup was designed to help biologists "voyaging" into the new world of electronic networking. This is also the appropriate forum for requesting electronic mail addresses of other biologists if you can not find them in the BIOSCI user address directory (the address directory is described elsewhere in this FAQ). Regarding address requests to BIONAUTS, there are no guarantees that the people in question will respond personally, of course, but someone else might. In addition, this forum can be used for asking questions if you need any help with mail and news software or other aspects of electronic networking, e.g. "What is WAIS, gopher, and all of these other newfangled things that I have been hearing about?" (see another FAQ section for answers to this last question!).
BIONEWS/bionet.announce: This is a moderated newsgroup designed to be low-volume, high content and intended primarily for announcements of interest to most users on the network, e.g., for general announcements such as for scientific meetings, courses, etc. We recommend that ALL participants subscribe to this newsgroup to keep up with the items above and also to receive the latest information about changes to BIOSCI/bionet.
BIOFORUM/bionet.general: BIOFORUM is intended for discussions on topics that do not fit in to any of the specialty newsgroups. If you want to start a new newsgroup, you might begin by trying to raise interest through a discussion in this forum. Be aware that this newsgroup is by design one of the most "chatty" forums in the BIOSCI network.
BIO-JOURNALS/bionet.journals.contents: This newsgroup is not for postings by readers. It is used to distribute the Table of Contents for over 30 biological research journals approximately a week or two in advance of publication (see the latest listing of journals in the FAQ section about the BIO-JOURNALS newsgroup).
BIO-SOFTWARE: Intended for discussions about software in the biological sciences. There are other Usenet newsgroups and mailing lists for questions about word processors, etc., i.e., for general purpose software. BIO-SOFTWARE is intended for discussions about software for biologists. For Usenet users only, please note that there is an accompanying newsgroup bionet.software.sources used for distributing biological software source code and binaries. This service is not available by e-mail.
COMPUTATIONAL-BIOLOGY: This newsgroup is moderated, i.e., postings made to the group are reviewed by a moderator before being distributed.
EMPLOYMENT: These are the posting regulations for EMPLOYMENT/bionet.jobs as formulated by the U.S. National Science Foundation. Readers outside of the U.S. should check with their local network authorities to determine what rules apply to their usage. EMPLOYMENT/bionet.jobs is to be used for the posting of job openings in the biological sciences or professional level jobs that support the work of biological scientists (such as for computer/systems programming/support). There are no restrictions on the content of the postings if these jobs are in the non-profit sector. Individuals regardless of their place of employment may post their CVs/resumes to this newsgroup or simply place a request for work if they are looking for jobs in this area of endeavor. Commercial companies can post jobs intended for professional people in the areas just mentioned provided that the postings are limited to the format described below. Extended commercial job/benefit descriptions and promotional material are not allowed, nor may commercial firms post openings for non-professional positions (if in doubt about the appropriateness of a posting, please check with biosci-help@net.bio.net before proceeding).
SCIENCE-RESOURCES: This newgroup is used solely to distribute funding agency announcements such as the "NIH Guide for Grants and Contracts" and is not to be used for postings by readers.
Most other BIOSCI newsgroups are dedicated to professional discussions in the area defined by the name of the newsgroup. You are free to post anything of interest within the specialty served by the newsgroup. Please note that the lack of face-to-face contact often emboldens some of our readers. While we can wish that everyone learned manners in grade school or at home, please be aware that discussions can sometimes become a bit more heated than a new user might be accustomed to (our readership is usually composed of "sober" Ph.D.s, or so we used to think, but it appears that perhaps economic hard times have taken their toll on sobriety 8-).
NOTE: To understand what 8-) means tilt your head to the left; other variants: :-) and :-(. These symbols try to add emotional connotations to the electrons such as "that's a joke, son!"
Commercial activities on BIOSCI are in general prohibited except as noted below. People at for-profit organizations are free to read all postings made to the BIOSCI/bionet newsgroups, but must ensure that their postings to the newsgroups do not violate our guidelines.
Commercial organizations may post job openings on EMPLOYMENT/bionet.jobs subject to the format restrictions for that group. Commercial job posting format restrictions for the EMPLOYMENT/bionet.jobs newsgroup are described above under the question "Where should I post my messages?" Users who violate these format restrictions consciously risk losing their network access.
BIOSCI readers without any financial connections to a company or a product may discuss and/or post endorsements of a commercial product. However, it is standard Internet practice to include in the posting a disclaimer of any financial interest in the product/company. Note that postings to newsgroups are subject to libel laws. BIOSCI advises readers to think twice before taking potshots at products that they do not like.
BIOSCI users often post general questions about problems that might be solved through the use of a commercial product. It is EXTREMELY IMPORTANT, however, that such general questions not be answered by people affiliated with the product or company that might stand to gain a sale as a result. For example, user X may ask, "Is there a product that will allow me to separate protein A from protein B given the following properties ...?", but, if user Y works at company Z which sells a product that can accomplish this task, user Y does NOT have permission to respond to the question. Responses can only be posted by other scientists who might have experience in solving the problem in question and who do not stand to gain financially by promoting the product in question, i.e., they are not employees, consultants, or connected to the company via other financial ties. As noted above, postings endorsing commercial products should contain a customary disclaimer stating the absence of financial ties of the poster to the product/company.
Commercial companies MAY RESPOND to a public BIOSCI newsgroup if a BIOSCI user asks a question directly about one of their products, e.g., mentions it by name. The response should be limited to a factual answer of the question posed and should avoid any hint of advertising hype. Comparisons with competitors' products should be avoided completely.
Finally, as a general rule, if you are unsure about the appropriateness of your posting, before you post anything please send a copy of what you propose to post to the BIOSCI adminstrator at biosci-help@net.bio.net for review.
BIOSCI will takes steps to terminate network access to any reader who willfully violates our commercial use policies.
If you are using e-mail, first select the newsgroup that you wish to post to and find the mailing address in the BIOSCI info sheet for your region. For example, to post to the METHODS-AND-REAGENTS newsgroup you would use one of the following two addresses depending upon your location:
Address Serving ------- ------- methods@net.bio.net The Americas and Pacific Rim methods@daresbury.ac.uk Europe, Africa, and Central AsiaOnce you have entered the newsgroup mailing address on the To: line of your mail message, the rest of the process is the same as composing and sending any e-mail message. Your message will be automatically distributed to all mail recipients on the list and also distributed by Usenet news.
The BIOSCI information sheet containing the latest list of e-mail addresses for each of the above regions can be requested from biosci@net.bio.net or biosci@daresbury.ac.uk respectively.
Please note that software safeguards in our system which prevent mailing loops also make it difficult to use news software to both crosspost to different newsgroups AND simultaneously mail to all associated mailing lists. If you absolutely must distribute a message to different newsgroups AND their associated mailing lists, the way to do this is to e-mail a separate copy of your message to each newsgroup e-mail posting address. Including multiple mailing addresses on a single e-mail message will not crosspost to all mailing lists. Please be aware that many people read multiple groups by mail and be assured that, if two groups are related, many people who are interested in one will obviously sign up for the other group, too. Before crossposting, be certain that your message is so important that it really warrants sending multiple copies to a large number of people.
The best way to determine the news forum is to look at the line in the mail header that starts with "To:". For example, if you see "To: arab-gen@net.bio.net" or "To: arab-gen@daresbury.ac.uk" then you know that the address for sending a reply to everyone on the newsgroup is "arab-gen@net.bio.net" or "arab-gen@daresbury.ac.uk." The "From:" line in the mail header indicates who sent the message. In most cases, if you want to reply only to the author of the message, use the address on the "From:" line, and, if you want to reply to everyone on the newsgroup, use the address on the "To:" line (but please read the following sections on the BIOSCI-REQUEST address and replying to BIOSCI postings for additional information).
Please note that replies to BIOSCI messages are not automatically sent back to the newsgroup address. The default reply on most mail systems (your local mail configuration may differ) will be to reply to the address that you see on the "From:" line, i.e., only to the person who posted the original message. You must consciously decide to send a copy of your reply to the newsgroup by including the newsgroup posting address in your e-mail response. This default reply (to the original sender only) is an Internet newsgroup standard and is the opposite of that used by the BITNET LISTSERV software (for those who may be familiar with the latter; the Internet standard is designed to minimize wasted network bandwidth, i.e., to avoid the automatic, unthinking posting by many people of the same answer to a particular question).
If you are replying to an e-mail message from BIOSCI, be sure to look carefully at the To: and Cc: lines of your reply message before sending it off. If you want the reply to be PRIVATE, only the address of the person who posted the original message (and perhaps your address and/or that of other individuals) should be on the To: and Cc: address lines. If you want the reply to be PUBLIC, be sure that the newsgroup posting address appears on either the To: or Cc: line of your response. If your mail system is a bit unorthodox and puts the "BIOSCI-REQUEST" address in your response (see the section about BIOSCI-REQUEST above), please be sure to correct this before sending your message (ask your systems administrator how to edit the To: and Cc: lines of your mail messages before sending if you do not know how to do this).
Now that you have read about all of these problems with using e-mail to participate in BIOSCI, why don't you get news software installed at your site and make life easy for yourself instead of using e-mail 8-)!! Let's look at Usenet news next!
Address for tests Location ----------------- -------- biosci@daresbury.ac.uk Europe, Africa, and Central Asia biosci@net.bio.net Americas and the Pacific RimIf you need to test your Usenet news software, please post test messages to the Usenet newsgroup misc.test which was created solely for this purpose.
Please note that all new BIOSCI/bionet newsgroups are announced on BIONEWS/bionet.announce as soon as they are ready for use. If you see this announcement, this means that the BIOSCI staff has tested the group and is (1) sure that it works, and (2) knows that it has propagated to at least some other sites in both North America and Europe. We obviously can not check for propagation to the thousands of sites on Usenet. Depending upon your source of Usenet news, there may be a delay of several days before the newgroup message reaches your site. The announcement of the newsgroup availability, however, is always sent to bionet.announce after the newgroup message has been sent and after system tests have been run.
Administrative Address Location ---------------------- -------- biosci@daresbury.ac.uk Europe, Africa, and Central Asia biosci@net.bio.net Americas and the Pacific Rim
Administrative Address Location ---------------------- -------- biosci@net.bio.net The Americas and Pacific Rim biosci-help@daresbury.ac.uk Europe, Africa, and Central AsiaThe most recent list of BIOSCI newsgroups/mailing addresses and the latest revision of the BIOSCI/bionet FAQ are posted the first of each month on the BIONEWS/bionet.announce newsgroup. You should save these postings for future reference.
telnet quake.think.com
and login in as "wais" to experiment with the software. All of our
WAIS sources (biosci.src, biology-journal-contents.src, and
biologists-addresses.src) may be selected from the menu for searching.
Please also refer to the FAQ section below entitled "Please help me find the e-mail address for Dr. ..."
for additional uses of our WAIS sources. If you are not on the Internet you may search the BIOSCI WAIS archives by e-mail using our WAISMAIL e-mail server. For instructions on using WAISMAIL, please send the message
help
in the body of a mail message addressed to the Internet address
waismail@net.bio.net
and be sure to leave the Subject: line of your message blank.
Detailed instructions will be returned to you automatically. The SERC Daresbury BIOSCI node runs a BIOSCI newsgroups WAIS source called BIOWAIS. This source can also be searched through their gopher client at host s-crim1.dl.ac.uk, port 70.
All the Bionet newsgroup postings since December 1991 are stored for Gopher searching and retrieval and anonymous ftp at ftp.bio.indiana.edu, the IUBIO Archive maintained by Don Gilbert. The directory in the anonymous FTP account is usenet/bionet. This gopher site also contains an outstanding collection of biological software and databases.
Another excellent gopher server is maintained by Dan Jacobson at merlot.gdb.org, port 70. In addition to newsgroup archives, many other information sources of use to biologists are available.
In Europe, Rob Harper runs a full-featured Gopher for biologists at gopher.csc.fi and Reinhard Doelz maintains a biology gopher at gopher.embnet.unibas.edu. The number of "gopher holes" on the network is expanding too rapidly to list them all here.
Note, however, that maintaining such a FAQ is a gargantuan task. We also recommend searching the METHODS archives for keywords through the use of the WAIS and Gopher software as described in the "archives" question above.
In each issue of "Trends in Biochemical Sciences" since November 1993, Dr. Hengen writes a monthly digest column of the METHODS newsgroup. This column highlights topics of special interest which were discussed recently on the newsgroup.
Note that the BIOSCI-REQUEST address at net.bio.net was established to trap daemon bouncers instead of passing them back to the person who posts a message. Unfortunately due to network incompatibilities, the BIOSCI-REQUEST trapping mechanism is often disabled when the bad address is not on the Internet.
When a proposal is received it will be posted on BIONEWS/bionet.announce. A ten day period for discussion on BIOFORUM/bionet.general will follow and precede the call for votes. After the discussion, the person proposing the newsgroup may modify or withdraw the proposal prior to the call for votes. The modified proposal will then be included in a call for votes on BIONEWS/bionet.announce. The proposal must collect 80 YES votes in 30 days and the number of YES votes must exceed the number of NO votes by at least 40 to pass.
BIOSCI management must be informed in advance of any intended efforts to advertise the newsgroup proposal in other forums. While BIOSCI wishes to inform potential users of the creation of newsgroups that might be of interest to them, promotional efforts should be focussed in forums likely to be utilized by professionals in the subject area covered by the newsgroup proposal, and should seek participation in the discussion of the proposal within bionet.general/BIOFORUM rather than promoting separate discussions in other forums to which portions of the BIOSCI readership may not have ready access.
If a proposal is not passed by the readers, there will be a three month period before it can be brought up for another vote.
The mailing lists will be maintained initially only at net.bio.net instead of at both BIOSCI sites. It will be the responsibility of the person who proposes the list to get it up and running within the six month period. They will have to handle promotion; our involvement at BIOSCI at net.bio.net will be limited to creating the list, putting out one announcement about it, and handling subscription requests.
After six months, the list will be put out for discussion and a vote according to our procedures for full-fledged newsgroups above (unless the organizer decides to bow out). If it passes it will become a full-fledged BIOSCI newsgroup at both net.bio.net and daresbury.ac.uk and will also have a parallel Usenet newsgroup. If it fails, the prototype mailing list at net.bio.net will be shut down.
Note that this service does not preclude people who have an idea that has widespread appeal from following our current newsgroup creation policy and going to a vote after a 10 day discussion.
If you have an idea for a prototype newsgroup, please send it to biosci-help@net.bio.net.
The address database is reindexed nightly for WAIS, waismail, and gopher access. If you have access to gopher, connect to net.bio.net to search the database. If you have access to WAIS, please use our WAIS source biologists-addresses.src. If you are not on the Internet, please use our waismail server (send the word "help" to waismail@net.bio.net to get instructions; any text on the Subject: line of your message will be ignored, so put the help command in the body of the mail message.).
Please carefully follow the instructions for completing the form below and return it to either of the following two addresses (whichever is more convenient for you). Thanks in advance for taking the time to complete and return the form.
Addresses for returning forms Location Network ----------------------------- -------- ------- biovote@net.bio.net U.S.A. Internet/BITNET biovote@daresbury.ac.uk U.K. JANET
> To add yourself to the database just point your > gopher client at merlot.gdb.org and select the following: > > --> 15. Searching For Biologists/ > > --> 9. E-mail Addresses of Biosci-Bionet Users/ > > --> 1. Add (or Correct) Your Address to the BIOSCI User Address > Data.. > > > And fill out the form.or Rob Harper's gopher site in Europe as follows:
> Europeans can point their gopher client at gopher.csc.fi and add their > information to the database. All entries will be mailed directly to > Dave for incorporation in a wais source. > > The path to the questionare is as follows. > > ---> 10. Finnish EMBnet BioBox/ > > ---> 8. FAQ Files/ > > FAQ Files > > 1. EMBnet: Information. > 2. EMBnet: Internet resources guide. > 3. A Biologist's Guide to Internet Resources/ > 4. All FAQs (Frequently Asked Questions) Searches and Archives/ > --->5. Bionauts Address Database (questionaire) <TEL>
Please do NOT extend your responses past the end of each line (80 characters).
PLEASE DO NOT alter any of the field identifiers such as "first name:". If you have nothing to enter after a field identifier, PLEASE LEAVE IT - do not delete it even if there is no data on the line in question.
Several lines are provided at the end of the form for comments, but, please adhere to the line length restriction.
On the date: line, please enter the date in the DD-MM-YY format, e.g., 15-05-93 for 15 May 1993. This line will tell others when the information was last updated. Please be sure to include the 0's for single digit days or months, e.g., 15-05-93, not 15-5-93.
Note that the "e-mail network:" line below is for specifying, e.g., "Internet," "BITNET," "EARN," "JANET," or whatever other network that your computer may be on.
If you are uncertain about any field, please feel free to leave it blank, but please DO NOT DELETE the field identifier from the form!
In the first field below, "New information or Update ...", please enter "N" if this is the first time that you have registered in the directory or "U" if you are correcting a listing that you sent to us previously.
The comment: lines may be used for anything that you like but PLEASE DO NOT DELETE THEM FROM THE FORM OR ALTER THEM. One suggested use is to list the names of the newsgroups in which you participate. Please use the MAILING LIST name (see below - the latest version of the list can be requested from biosci@net.bio.net) instead of the Usenet name even if you don't participate by e-mail. WAIS might get confused by the periods in the Usenet names. This allows one to retrieve via WAIS or waismail the list of participants in a particular group.
For example:
comment: ARABIDOPSIS PLANT-BIOLOGY BIONEWS On the comment: lines use these names below -- NOT the Usenet names below MAILING LIST NAME Usenet Newsgroup Name ----------------- --------------------- ACEDB-SOFT bionet.software.acedb AGEING bionet.molbio.ageing AGROFORESTRY bionet.agroforestry ARABIDOPSIS bionet.genome.arabidopsis BIOFORUM bionet.general BIO-INFORMATION-THEORY bionet.info-theory BIONAUTS bionet.users.addresses BIONEWS bionet.announce BIO-JOURNALS bionet.journals.contents BIO-MATRIX bionet.molbio.bio-matrix BIOPHYSICAL-SOCIETY bionet.prof-society.biophysics BIOPHYSICS bionet.biophysics BIO-SOFTWARE bionet.software BIOTHERMOKINETICS bionet.metabolic-reg CELL-BIOLOGY bionet.cellbiol CHLAMYDOMONAS bionet.chlamydomonas CHROMOSOMES bionet.genome.chromosomes COMPUTATIONAL-BIOLOGY bionet.biology.computational CYTONET bionet.cellbiol.cytonet DROSOPHILA bionet.drosophila EMBL-DATABANK bionet.molbio.embldatabank EMPLOYMENT bionet.jobs GDB bionet.molbio.gdb GENBANK-BB bionet.molbio.genbank GENETIC-LINKAGE bionet.molbio.gene-linkage GRASSES-SCIENCE bionet.biology.grasses HIV-MOLECULAR-BIOLOGY bionet.molbio.hiv HUMAN-GENOME-PROGRAM bionet.molbio.genome-program IMMUNOLOGY bionet.immunology INFO-GCG bionet.software.gcg JOURNAL-NOTES bionet.journals.note METHODS-AND-REAGENTS bionet.molbio.methds-reagnts MOLECULAR-EVOLUTION bionet.molbio.evolution MYCOLOGY bionet.mycology NEUROSCIENCE bionet.neuroscience N2-FIXATION bionet.biology.n2-fixation PARASITOLOGY bionet.parasitology PHOTOSYNTHESIS bionet.photosynthesis PLANT-BIOLOGY bionet.plants POPULATION-BIOLOGY bionet.population-bio PROTEIN-ANALYSIS bionet.molbio.proteins PROTEIN-CRYSTALLOGRAPHY bionet.xtallography PROTISTA bionet.protista RAPD bionet.molbio.rapd SCIENCE-RESOURCES bionet.sci-resources STRUCTURAL-NMR bionet.structural-nmr TROPICAL-BIOLOGY bionet.biology.tropical VIROLOGY bionet.virology WOMEN-IN-BIOLOGY bionet.women-in-bio YEAST bionet.molbio.yeastListing newsgroups on the comment: line is optional, of course.
Thanks again for your cooperation!
--------------- please cut here and return portion below --------------- New information or Update to old record (enter N or U): date (DD-MM-YY): first name: middle initial: family name: job title: e-mail address: e-mail network: phone number: FAX number: institution: address1: address2: address3: city: state/province: country: postal code: research interest: research interest: comment: comment: comment: comment: comment:
if (h = instr(s,"net.general")) {
off = h-s;
strncpy(scrbuf,s,off+4);
strcpy(scrbuf+off+4,"followup");
safecpy(scrbuf+off+12,h+11,sizeof(scrbuf));
s = scrbuf;
}
What's going on is that there used to be the convention that
followups to articles in the newsgroup net.general (which doesn't
exist anymore and hasn't for something like 5 years) should be placed
in net.followup. For better or for worse, the rn code attempted to
enforce this convention. What's going on in the above code is that
the string "net.general" in the Newsgroups line of an article being
follow-ed-up to gets changed to "net.followup". Unfortunately, that
means "bionet.general" gets changed to "bionet.followup". I would
suggest simply deleting the above code entirely. I'm not even sure
why it's still there, other than nobody bothered to take it out, and
until bionet.general came around, it never bit anybody.
Old code never dies. It simply gets integrated into the host
genome of the program it's part of waiting for the right environmental
conditions to appear.
--
roy@alanine.phri.nyu.edu (Roy Smith)
Public Health Research Institute
455 First Avenue, New York, NY 10016, USA
"Arcane? Did you say arcane? It wouldn't be Unix if it wasn't arcane!"
+++++++++++++++++++++++
From: Wayne Rindone <wrindone@BBN.COM>
Subject: Another source of bionet.followup problem
Thought you might like to know that there are other potential
reasons for the appearance of the bogus bionet.followup group name. A
couple of months ago, I installed rn 4.4 on my workstation, expecting
that to fix the bionet.followup problem, among other things. I was
very surprised to discover that I still had bionet.followup appearing,
even though it was quite clear there was nothing in the new rn sources
to account for that.
It turned out that the following lines were included in
/usr/local/news/rn/Pnews.header:
case $ng in
*net.general*)
follow=`echo "$ng" | sed 's/net\.general/net.followup/g'`
;;
*)
follow=""
;;
esac
Once these were removed the problem disappeared. I have no idea
if this logic was created locally at BBN or not, or if it came from
elsewhere or had wider dissemination beyond BBN. Although the problem
is solved for me, I have a bad feeling that it will turn up many
places around the world for many years to come.
Feel free to mention Pnews.header as another potential source of
the problem the next time someone asks if you think that helpful.
Wayne Rindone, BBN
+++++++++++++++++++++++
+++++++++++++++++++++++
The problem is indeed in the rn sources, specifically in intrp.c. In
the version I have (intrp.c,v 4.3.2.11 90/12/31 11:47:44 sob Exp),
It's the following code at lines 664-670:
net<1>ftp net.bio.net ### connect to the BIOSCI computer
---------------
Connected to net.bio.net.
220 net.bio.net FTP server (SunOS 4.1) ready.
Name (net.bio.net:kristoff): anonymous ### login as anonymous
---------
331 Guest login ok, send ident as password.
Password: ### enter any password; typically your e-mail address
----------
230 Guest login ok, access restrictions apply.
ftp> ls ### display the directories. sometimes "dir" is used here
--
200 PORT command successful.
150 ASCII data connection for /bin/ls (134.172.2.69,3225) (0 bytes).
bin
dev
etc
lost+found
misc
pub
usr
226 ASCII Transfer complete.
72 bytes received in 0.1 seconds (0.7 Kbytes/s)
ftp> cd pub ### change to the "pub" public directory. Most FTP
------ ### sites place public material in this directory
250 CWD command successful.
ftp> ls ### list the files again. BIOSCI archives are in BIOSCI 8-)
-- ### Be sure to strictly follow upper/lower case in filenames
### when accessing FTP sites running UNIX such as net.bio.net
200 PORT command successful.
150 ASCII data connection for /bin/ls (134.172.2.69,3227) (0 bytes).
BIOSCI
README
doc
dos
mac
unix
vms
226 ASCII Transfer complete.
42 bytes received in 0.05 seconds (0.82 Kbytes/s)
ftp> cd BIOSCI
---------
250 CWD command successful.
ftp> ls
--
200 PORT command successful.
150 ASCII data connection for /bin/ls (134.172.2.69,3228) (0 bytes).
ADDRESSES
AGEING
AGROFORESTRY
ARABIDOPSIS
BIO-INFO
BIO-JOURNALS
BIO-MATRIX
BIO-SOFTWARE
BIOFORUM
BIONEWS
CHROMOSOME-22
COMPUTATIONAL-BIOLOGY
EMBL-DATABANK
EMPLOYMENT
GDB
GENBANK-BB
GENETIC-LINKAGE
HIV-BIOL
HUMAN-GENOME
IMMUNOLOGY
JRNLNOTE
METHDS-REAGNTS
MOLECULAR-EVOLUTION
NEUROSCIENCE
PLANT-BIOLOGY
POPULATION-BIOLOGY
PROTEIN-ANALYSIS
PROTEIN-CRYSTALLOGRAPHY
SCIENCE-RESOURCES
TROPICAL-BIOLOGY
VIROLOGY
WOMENINBIOLOGY
biosci-uk.infosheet
biosci-us.infosheet
biosci.FAQ
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ftp> cd PROTEIN-ANALYSIS ### We want to look at PROTEIN-ANALYSIS archives
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250 CWD command successful.
ftp> ls
--
200 PORT command successful.
150 ASCII data connection for /bin/ls (134.172.2.69,3233) (0 bytes).
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current
226 ASCII Transfer complete.
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ftp> get 9211 ### Retrieve the file for November 1992.
--------
200 PORT command successful.
150 ASCII data connection for 9211 (134.172.2.69,3234) (208763 bytes).
226 ASCII Transfer complete.
local: 9211 remote: 9211
213849 bytes received in 1.4 seconds (1.5e+02 Kbytes/s)
ftp> bye ### End the FTP session. Some systems use quit or exit.
---
221 Goodbye.
Liberal use of the ? key and help at the ftp> prompt will provide
information on other options.
telnet quake.think.com
and logging in as "wais" (lowercase).
The following information is excerpted from the Gopher FAQ. Many questions have been cut out for brevity.
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Common Questions and Answers about the Internet Gopher, a
client/server protocol for making a world wide information service,
with many implementations. Posted to comp.infosystems.gopher and
news.answers every two weeks.
The most recent version of this FAQ can be gotten through gopher, or
via anonymous ftp:
rtfm.mit.edu:/pub/usenet/news.answers/gopher-faq
Those without FTP access should send e-mail to mail-server@rtfm.mit.edu
with "send usenet/news.answers/finding-sources" in the body to find out
how to do FTP by e-mail.
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List of questions in the Gopher FAQ:
Q0: What is Gopher?
Q1: Where can I get Gopher software?
Q2: What do I need to access Gopher?
Q3: Where are there publicly available logins for Gopher?
Q5: Who Develops Gopher Software?
Q12: What is the relationship between Gopher and (WAIS, WWW, ftp)?
Q13: Are papers or articles describing Gopher available?
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Q0: What is Gopher?
A0: The Internet Gopher client/server provides a distributed
information delivery system around which a world/campus-wide
information system (CWIS) can readily be constructed. While
providing a delivery vehicle for local information, Gopher
facilitates access to other Gopher and information servers
throughout the world.
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Q1: Where can I get Gopher software?
A1: via anonymous ftp to boombox.micro.umn.edu. Look in the directory
/pub/gopher
--------------------------------------------------------------------
Q2: What do I need to access Gopher?
A2: You will need a gopher "client" program that runs on your local PC
or workstation
There are clients for the following systems. The directory
following the name is the location of the client on the anonymous
ftp site boombox.micro.umn.edu (134.84.132.2) in the directory
/pub/gopher.
Unix Curses & Emacs : /pub/gopher/Unix/gopher1.03.tar.Z
Xwindows : /pub/gopher/Unix/xgopher1.1a.tar.Z
Macintosh Hypercard : /pub/gopher/Mac_client/
Macintosh Application : /pub/gopher/Macintosh-TurboGopher
DOS w/Clarkson Driver : /pub/gopher/PC_client/
NeXTstep : /pub/gopher/NeXT/
VM/CMS : /pub/gopher/Rice_CMS/ or /pub/gopher/Vienna_CMS/
VMS : /pub/gopher/VMS/
OS/2 2.0 : /pub/gopher/os2/
MVS/XA : /pub/gopher/mvs/
Many other clients and servers have been developed by others, the
following is an attempt at a comprehensive list.
A Macintosh Application, "MacGopher".
ftp.cc.utah.edu:/pub/gopher/Macintosh
Another Macintosh application, "GopherApp".
ftp.bio.indiana.edu:/util/gopher/gopherapp
A port of the UNIX curses client for DOS with PC/TCP
oac.hsc.uth.tmc.edu:/public/dos/misc/dosgopher.exe
A port of the UNIX curses client for PC-NFS
bcm.tmc.edu:/nfs/gopher.exe
A beta version of the PC Gopher client for Novell's LAN Workplace
for DOS
lennon.itn.med.umich.edu:/gopher
A Xwindows/DECwindows client
job.acs.ohio-stat.edu:
Most of the above clients can also be fetched via a gopher client
itself. Put the following on a gopher server:
Type=1
Host=boombox.micro.umn.edu
Port=70
Path=
Name=Gopher Software Distribution.
Or point your gopher client at boombox.micro.umn.edu, port 70 and
look in the gopher directory.
There are also a number of public telnet login sites available.
The University of Minnesota operates one on the machine
"consultant.micro.umn.edu" (134.84.132.4) See Q3 for more
information about this. It is recommended that you run the client
software instead of logging into the public telnet login sites. A
client uses the custom features of the local machine (mouse,
scroll bars, etc.) A local client is also faster.
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Q3: Where are there publicly available logins for Gopher?
A3: Here is a short list, use the site closest to you to minimize
network lag.
Non-tn3270 Public Logins:
Hostname IP# Login Area
------------------------- --------------- ------ -------------
consultant.micro.umn.edu 134.84.132.4 gopher North America
gopher.uiuc.edu 128.174.33.160 gopher North America
panda.uiowa.edu 128.255.40.201 panda North America
gopher.sunet.se 192.36.125.2 gopher Europe
info.anu.edu.au 150.203.84.20 info Australia
gopher.chalmers.se 129.16.221.40 gopher Sweden
tolten.puc.cl 146.155.1.16 gopher South America
ecnet.ec 157.100.45.2 gopher Ecuador
tn3270 Public Logins:
Hostname IP# Login Area
------------------------- --------------- ------ -------------
pubinfo.ais.umn.edu 128.101.109.1 -none- North America
It is recommended that you run the client software instead of
logging into the public login sites. A client uses the
custom features of the local machine (mouse, scroll bars, etc.)
and is local client is also faster.
---------------------------------------------------------------------
Q5: Who Develops Gopher Software?
A5: Gopher was originally developed in April 1991 by the University
of Minnesota Microcomputer, Workstation, Networks Center to help
our campus find answers to their computer questions.
It has since grown into a full-fledged World Wide Information
System used by a large number of sites in the world.
Many people have contributed to the project, too numerous to
count.
The people behind the much of the gopher software can be reached
via e-mail at gopher@boombox.micro.umn.edu, or via paper mail:
Internet Gopher Developers
100 Union St. SE #190
Minneapolis, MN 55455 USA
Or via FAX at:
+1 (612) 625-6817
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Q12: What is the relationship between Gopher and (WAIS, WWW, ftp)?
A12: Gopher is intimately intertwined with these two other systems.
As shipped the Unix gopher server has the capability to:
- Search local WAIS indices.
- Query remote WAIS servers and funnel the results to gopher
clients.
- Query remote ftp sites and funnel the results to gopher
clients.
- Be queried by WWW (World Wide Web) clients (either using
built in gopher querying or using native http querying.
-------------------------------------------------------------------
Q13: Are papers or articles describing Gopher available?
A13: Gopher has a whole chapter devoted to it in :
_The_Whole_Internet_, Ed Kroll, O'Reilly, 1992 (Editors note:
..Great book, go out and buy a bunch!)
Other references include:
_The_Internet_Gopher_, "ConneXions", July 1992, Interop.
_Exploring_Internet_GopherSpace_ "The Internet Society News", v1n2 1992,
(You can subscribe to the Internet Society News by sending e-mail to
isoc@nri.reston.va.us)
_The_Internet_Gopher_Protocol_, Proceedings of the Twenty-Third
IETF, CNRI, Section 5.3
_Internet_Gopher_, Proceedings of Canadian Networking '92
_The_Internet_Gopher_, INTERNET: Getting Started, SRI
International, Section 10.5.5
_Tools_help_Internet_users_discover_on-line_treasures, Computerworld,
July 20, 1992
_TCP/IP_Network_Administration_, O'Reilly.
Balakrishan, B. (Oct 1992)
"SPIGopher: Making SPIRES databases accessible through the
Gopher protocol". SPIRES Fall '92 Workshop, Chapel Hill, North
Carolina.
Tomer, C. Information Technology Standards for Libraries,
_Journal of the American Society for Information Science_,
43(8):566-570, Sept 1992.
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In a nutshell, Mosaic is a "hypertext browser," i.e., an application program that lets you read through the thousands of cross-linked hypertext documents, pictures and sound bites now available on the Internet. A more detailed explanation will be included in a future version of this FAQ. For now, we recommend using FTP to ftp.ncsa.uiuc.edu to pick up a version of Mosaic for your hardware platform. Note that to get the most out of Mosaic, your machine needs a direct and fast Internet connection. 9600 baud links or lower will not be a happy compromise except possibly for browsing plain text documents in some cases.
The second easy route is to post your request to the BIONAUTS/bionet.users.addresses newsgroup managed by Rob Harper. Odds are that you will get a response fairly promptly, but, if not, there are other routes described below.
If the person in question has posted to BIOSCI/bionet or another Usenet newsgroup, they will be listed in the "usenet-addresses" WAIS source. If you are on the Internet, telnet to quake.think.com and login as "wais" (lowercase). After entering your terminal type, select the usenet-addresses source from the list presented to you (use the up-arrow key to get there more quickly since it is near the end of a long list). When the source is highlighted, press the return key and then enter the person's surname at the Keywords: prompt to begin the search. Available commands are listed at the bottom of the screen. When finished, press "s" to return to the source menu and then "q" to quit.
For those who do not have access to the Internet, the usenet-addresses source can also be accessed by e-mail. Please send mail to mail-server@rtfm.mit.edu with "help" in the body of the message in order to receive more information.
Another source of information for finding Internet, but not BITNET, addresses is netfind. Use the command
telnet bruno.cs.colorado.edu
and login as "netfind" without a password. The program is menu-driven
and pretty self-explanatory. Unfortunately it is not available to
people on BITNET. Gopher is also useful in the address search. For example, Dan Jacobson provides access to several directories of biologists at his gopher hole on merlot.gdb.org.
None of the above methods is guaranteed to return you an answer, so you may still have to resort to the telephone or (groan) regular mail to make contact 8-(.
Brookhaven Protein Data Bank bionet.xtallography
PIR or SWISS-PROT bionet.molbio.proteins
NCBI GenBank DataBank bionet.molbio.genbank
EMBL Databank bionet.molbio.embldatabank
Human Genome Database (GDB) bionet.molbio.gdb
Museums and Herbaria bionet.plants, or private inquiry
to beach@huh.harvard.edu
Since staff members of these databases usually monitor the
corresponding newsgroups fairly closely, a posting about a problem on
the appropriate board will usually get a response from someone on a
database staff fairly quickly. Problems that might not be of general
interest or corrections to particular entries should be directed as
follows.
Database address -------- ------- Brookhaven pdb@chm.chm.bnl.gov, pdb@bnlchm.bitnet PIR postmaster@nbrf.georgetown.edu, postmast@gunbrf.bitnet SWISS-PROT bairoch@cmu.unige.ch GenBank update@ncbi.nlm.nih.gov EMBL update@embl-heidelberg.de GDB help@welch.jhu.edu Herbaria beach@huh.harvard.edu
Researchers should submit nucleotide sequence data directly to GenBank or EMBL for assignment of an accession number prior to publication. Derived amino acid sequence data may also be included at the same time. Amino acid sequence data submitted in this way to GenBank, EMBL or DDBJ is eventually passed on to PIR, and need not be submitted separately to PIR. This is done so correct cross-references can be made between nucleotide and protein sequence accession numbers. All other determined amino acid sequences may be submitted directly to PIR when the authors permit their public release prior to publication.
Authors are strongly urged to use the sequence submission software package AUTHORIN to submit their sequence data to the databanks; a free copy (for either the IBM PC or Macintosh) can be obtained by sending your request and regular postal mailing address to:
authorin@ncbi.nlm.nih.gov
Please be sure to specify the IBM or Mac version when sending your request.
Japanese authors who use the NEC 9801 PC should communicate directly with DDBJ, as these machines use a version of DOS that is significantly different enough to render the discs unreadable on MS-DOS computers here. The staff at DDBJ will forward the data to the appropriate databank via electronic mail. DDBJ may be contacted at:
ddbjsubs@flat.nig.ac.jp
The address for GenBank submissions is:
U.S. mail (for submissions on diskette, indicate whether Mac or PC):
GenBank Submissions
National Center for Biotechnology Information
Bldg. 38A, Room 8N-803
8600 Rockville Pike
Bethesda, MD 20894
E-mail submission of new sequences: gb-sub@ncbi.nlm.nih.gov
E-mail submission of updates: update@ncbi.nlm.nih.gov
The address for EMBL submissions is:
EMBL Data Submissions Postfach 10.2209 D-6900, Heidelburg Federal Republic of Germany Telephone (+49) 6221-387-258 Electronic mail: DATASUBS@EMBL-Heidelberg.DEThe address for DDBJ submissions is:
DNA Database of Japan Center for Genetic Information Research National Institute of Genetics 111 Yata Mishima, Shizuoka 411 JAPAN Telephone (+81) 559-75-3651 Electronic mail: ddbjsubs@flat.nig.ac.jpThe address for PIR submissions is:
PIR Submissions National Biomedical Research Foundation 3900 Reservoir Road, NW Washington, DC 20007 U.S.A. Telephone: (202) 687-2121 Electronic mail: FILESERV@GUNBRF.BITNET, FILESERV@NBRF.Georgetown.EDUWhile we would again urge that AUTHORIN be used as the first choice in data submission tools, the GenBank/EMBL/PIR Data Submission Form can be obtained by sending a message consisting of the words
SEND SUBFORMto the PIR FILESERV address. This form can be filled in using any text editor, saved in ASCII (text) format, and mailed electronically or on disk to the databanks.
Please, do not submit data either by electronic mail or on disk in files that are formatted for word processing programs. Such files are almost always unreadable except by systems with the same configuration of computer, operating system and word-processing program. For files sent by disk, either DOS or Mac formatted disks can be used but regular "double density" disks are preferred to "high density" disks.