BIOSCI/BIONET FREQUENTLY ASKED QUESTIONS (FAQ) Newsgroups: bionet.announce Last-modified: 28 February 1995 From: BIOSCI Administrator 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) ---------------------------------------------- This 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 info faq in the body of an e-mail message addressed to the Internet address biosci-server@net.bio.net Any 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. _________________________________________________________________ Contents COMMON QUESTIONS ABOUT BIOSCI/BIONET USAGE * What is BIOSCI and bionet? * What newsgroups are available on BIOSCI/bionet? * Where should I post my messages? * What are the restrictions on commercial activities in the BIOSCI/bionet newsgroups? * How does one post a message? * Should I post my message to more than one newsgroup? * Sorting out mail - which newsgroup did an e-mail message come from? * Why do all of my postings come from "BIOSCI-REQUEST?" * How do I reply to a BIOSCI posting? * What is Usenet? * How can I get news software at my site? * How can I test my news or mail software? * I hear that a new bionet newsgroup was created but why isn't it at my site yet? * A new bionet Usenet group has been created at my site but there are no messages in it. However, I see that messages are being sent out to the mailing list. Why do the contents differ? * How do I request or cancel e-mail subscriptions to BIOSCI newsgroups? * How can I get a list of newsgroups or my subscriptions? * How do I find back issues of BIOSCI postings? * Is there a summary of METHODS-AND-REAGENTS postings? * What journals are available on BIO-JOURNALS? How can one locate articles? * Why are there two BIOSCI sites? * Why have I stopped getting messages? * What should I do about mail error messages that come back when I post? * How does one start a new BIOSCI newsgroup/mailing list? * How can I list my address information in the BIOSCI user directory? * Why didn't my Usenet posting show up elsewhere? * Why are my messages are going to bionet.followup? COMMON QUESTIONS POSTED TO BIOSCI/BIONET NEWSGROUPS * What are all of these references to FTP, WAIS, Gopher, and WWW? * Please help me find the e-mail address for Dr. ... * How do I report a problem in a biological data base? * What about submitting sequence data to GenBank, EMBL, DDBJ or PIR? Other questions to add to this list??? Please send them to biosci-help@net.bio.net. We would also appreciate your sending the answer to the question if possible. All contributions will be gratefully acknowledged by including the author's name along with the answer provided. _________________________________________________________________ Common Questions about BIOSCI/bionet usage WHAT IS BIOSCI AND BIONET? We'll spare you the fascinating historical details and say simply that BIOSCI is a series of freely accessible electronic communication forums (i.e., electronic bulletin boards or "newsgroups") for use by biological scientists worldwide. No fees are charged for the service. The system is intended to promote communication between professionals in the biological sciences. All postings to the newsgroups should be made in that spirit. While the general public may "listen in" to the discussions, these newsgroups are intended primarily for communications between researchers. There are other forums on Usenet such as sci.bio for the asking and answering of biological questions from lay persons. 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: * What_is_Usenet? * What_is_Usenet?__A_second_opinion. * Usenet_Software:_History_and_Sources * How_to_Get_Information_about_Networks * How_to_become_a_Usenet_site * Answers_to_Frequently_Asked_Questions_about_Usenet * Emily_Postnews_Answers_Your_Questions_on_Netiquette * Hints_on_writing_style_for_Usenet Detailed starting information on how to get your site connected to the Internet can be found the file "How_to_Get_Information_about_Networks". _________________________________________________________________ WHAT NEWSGROUPS ARE AVAILABLE ON BIOSCI/BIONET? "THE BIOSCI ELECTRONIC NEWSGROUP NETWORK INFORMATION SHEET" containing the latest list of newsgroups, e-mail posting addresses, and other information about subscribing/unsubscribing, etc., to BIOSCI is posted the first of each month on the BIONEWS/bionet.announce newsgroup along with this FAQ posting. 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. _________________________________________________________________ WHERE SHOULD I POST MY MESSAGES? The list of newsgroups in the BIOSCI info sheet gives a brief description of the purpose of each newsgroup. Please select the appropriate forum for your posting with the newsgroup's purpose in mind. The groups designated as "Scientific Interest Group" are for discussions of professional interest in the area designated by the newsgroup name, i.e., population biology issues should obviously be directed to the POPULATION-BIOLOGY newsgroup. 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). Commercial job posting format The posting should include * job title * one or two line factual description of the position * an e-mail contact address for further information; a regular surface mail address and contact telephone number is also permissible. To repeat, commercial job postings that do not comply with the above format or that are for jobs in areas outside of the range described above are not permissible in this newsgroup. Your cooperation is greatly appreciated. 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!" _________________________________________________________________ WHAT ARE THE RESTRICTIONS ON COMMERCIAL ACTIVITIES IN THE BIOSCI/BIONET NEWSGROUPS? BIOSCI is funded in part by the National Science Foundation (NSF) which supports the Internet in the U.S. with U.S. taxpayer dollars. NSF is responsible for setting Acceptable Use Policy (AUP) for the the NSFNet backbone section of the Internet of which BIOSCI makes extensive use. Because of these reasons, BIOSCI users should adhere to the following guidelines. 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. _________________________________________________________________ HOW DOES ONE POST A MESSAGE? If you use Usenet, run your posting program (e.g., postnews or e.g., use the ":post" command in nn) and follow the prompts. Please check with your local systems administrator for details on using your local news software; general information on Usenet and how to get news software is provided further below but each news program is different. When prompted, enter the appropriate newsgroup name from the list of Usenet names in the BIOSCI info sheet. Be sure to set your news distribution to "world" (or "bionet" if the option is available) if you want your message to be seen by others. Some Usenet systems may default to "local" which means that only people on your local computer will see the message. You can limit the extent of distribution of your message by choosing other distribution options, e.g., "usa" distributes only to the U.S.A. (sometimes! - on occasion these distribution limiting features don't work for a variety of reasons). Usually pressing "?" or "h" at the Distribution: prompt will show you your options. After entering your options, you are usually placed in an editor to compose your message. After saving it and exiting the editor, one typically enters a "send" command to complete the posting process. 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 Asia Once 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. _________________________________________________________________ SHOULD I POST MY MESSAGE TO MORE THAN ONE NEWSGROUP? Generally only ONE copy of a message should be posted to the most appropriate forum. Crossposting the same message to multiple newsgroups can aggravate readers who participate by e-mail. These people will receive multiple copies of a message if they are on the mailing lists for the groups that receive the crosspostings. 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. _________________________________________________________________ SORTING OUT MAIL - WHICH NEWSGROUP DID AN E-MAIL MESSAGE COME FROM? If you use Usenet news software, all messages are sorted by newsgroup so there is no problem identifying the source. If you receive BIOSCI postings in your mail file, all postings are funneled into your one mail file merely by chronological order of posting and you must be a little discerning to follow discussions. 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). _________________________________________________________________ WHY DO ALL OF MY POSTINGS COME FROM "BIOSCI-REQUEST?" Unfortunately some mail systems make all BIOSCI postings appear to come from someone named "BIOSCI-REQUEST." The BIOSCI-REQUEST@net.bio.net address was established to trap mailing error messages ("bouncers"). The address is not normally seen by BIOSCI readers in the messages that they receive. Unfortunately some proprietary (read "VMS") and other oddball mail systems misread the information used to transmit Internet e-mail messages and may end up putting the BIOSCI-REQUEST address on the From: line in the mail that you may receive. If this happens at your site and you want to reply to a message, please use either the newsgroup address on the To: line of the message or try to find the author's e-mail address elsewhere in the message (people often append this at the end of their text in their "signature"). If you send a message back to BIOSCI-REQUEST@net.bio.net, the BIOSCI managers at net.bio.net will be the only ones who will see it (we will try to forward it to the appropriate newsgroup, but would appreciate it if you would determine the correct address yourself first). _________________________________________________________________ HOW DO I REPLY TO A BIOSCI POSTING? If you are using news software, there are usually two types of reply commands. One command sends a private reply to the author of the original posting; the second sends a "followup" posting to everyone on the newsgroup. Press ? or h in your news software to find these commands. They are often noted by "r" and "R" or "r" and "f" respectively. 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! _________________________________________________________________ WHAT IS USENET? Usenet (short for Users Network) is an electronic bulletin board network which utilizes various public domain versions of the "netnews" software for message transmission. The software can operate over physical networks ranging from as simple as a telephone UUCP link (via modem) to networks as sophisticated as the Internet. Netnews has been optimized to transmit messages without loss and also to avoid possible mail loops and other errors which plague simple electronic mail "broadcasting." We strongly encourage our users to adopt netnews software at their sites as soon as possible. News software also keeps messages segregated into their respective newsgroups, making it easier to follow the thread of a discussion. If you only use e-mail, messages from all of the newsgroups to which you subscribe will be sent to your one personal e-mail address and will be mixed in with each other and with your other personal messages. This is obviously a suboptimal means of organizing messages. With news software, you can browse the discussion topics easily, read what you want and discard the rest. Why subject yourself to having to page through a disorganized mail file message-by-message unless you really have no other choice?? News software makes the use of BIOSCI pleasant and efficient. It's time to get your organization "into the 20th Century" before it turns into the 21st Century! _________________________________________________________________ HOW CAN I GET NEWS SOFTWARE AT MY SITE? Contact biosci-help@net.bio.net for information on getting started with Usenet. News software can be obtained free of charge from anonymous FTP sources. Note, however (yes, here's the unfortunate catch), that news software should be installed and maintained by a trained systems administrator in most cases; it is not a task for a computer novice. You can find detailed information about Usenet 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: * What_is_Usenet? * What_is_Usenet?__A_second_opinion. * Usenet_Software:_History_and_Sources * How_to_Get_Information_about_Networks * How_to_become_a_Usenet_site _________________________________________________________________ HOW CAN I TEST MY NEWS OR MAIL SOFTWARE? Please DO NOT post test messages to any of the BIOSCI/bionet Usenet newsgroups. If you are unsure about whether or not your mail is working, please send test mail messages to either of our two administrative addresses, but NOT to newsgroup mailing addresses: Address for tests Location ----------------- -------- biosci@daresbury.ac.uk Europe, Africa, and Central Asia biosci@net.bio.net Americas and the Pacific Rim If 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. _________________________________________________________________ I HEAR THAT A NEW BIONET NEWSGROUP WAS CREATED BUT WHY ISN'T IT AT MY SITE YET? This could happen for a variety of reasons. When we create a new Usenet newsgroup, a "newgroup" message is sent out from net.bio.net to news administrators at Usenet sites around the world. Many sites are configured so that such newgroup messages are acted upon automatically and the group is established without human intervention. However, due to the growing volume of Usenet newsgroups, many sites have turned off automatic newgroup creation and require human intervention to create a new Usenet group in response to a newgroup message. If you know from reading BIONEWS/bionet.announce or from contacting the BIOSCI staff at biosci-help@net.bio.net that a new bionet newsgroup should be in existance, please contact your local news administrator and ask them if they acted on the newgroup message. Newgroup messages can sometimes be simply overlooked by the news administrator and sometimes they may not be received if a Usenet site upstream on the net from you had a problem and did not pass on the message. Please let your news adminstrator know that a bionet "checkgroup" message is posted on the first of each month to bionet.announce. Your news administrator can use the contents of that message to update your local list of bionet Usenet newsgroups. 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. _________________________________________________________________ A NEW BIONET USENET GROUP HAS BEEN CREATED AT MY SITE BUT THERE ARE NO MESSAGES IN IT. HOWEVER, I SEE THAT MESSAGES ARE BEING SENT OUT TO THE MAILING LIST. WHY DO THE CONTENTS DIFFER? If you experience the problem above, please contact your local news administrator and have them check with the site that sends you your bionet Usenet news feed. We explained in a question above that new Usenet newsgroups are created in response to a "newgroup" message which is sent out to all Usenet news administrators. It is possible that your news administrator acted on the message to create the group, but that the site which sends you bionet Usenet news did not. Having your Usenet news administrator contact the administrator at the upstream site can usually resolve the problem. If you have a problem getting a reliable bionet Usenet news feed, please contact biosci-help@net.bio.net. _________________________________________________________________ HOW DO I REQUEST OR CANCEL E-MAIL SUBSCRIPTIONS TO BIOSCI NEWSGROUPS? Instructions for subscribing and unsubscribing to the BIOSCI newsgroups by e-mail are included in the BIOSCI info sheet which can be obtained from either of the following two addresses: Administrative Address Location ---------------------- -------- biosci@daresbury.ac.uk Europe, Africa, and Central Asia biosci@net.bio.net Americas and the Pacific Rim _________________________________________________________________ HOW CAN I GET A LIST OF NEWSGROUPS OR MY SUBSCRIPTIONS? Simply send a request to your appropriate BIOSCI distribution site: Administrative Address Location ---------------------- -------- biosci@net.bio.net The Americas and Pacific Rim biosci-help@daresbury.ac.uk Europe, Africa, and Central Asia The 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. _________________________________________________________________ HOW DO I FIND BACK ISSUES OF BIOSCI POSTINGS? The BIOSCI node at net.bio.net maintains the entire collection of BIOSCI/bionet messages. They are available via WAIS (biosci.src and biology-journal-contents.src), Gopher (net.bio.net port 70), anonymous ftp from net.bio.net [134.172.2.69], and Mosaic/WWW (URL is gopher://net.bio.net/). Contact biosci-help@net.bio.net for further help. If you are on the Internet but do not have WAIS software running locally, try 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. _________________________________________________________________ IS THERE A SUMMARY OF METHODS-AND-REAGENTS POSTINGS? Yes. A FAQ for the METHODS newsgroup was created by Paul Hengen of Frederick Cancer Research and Development Center. It can be obtained via anonymous FTP from net.bio.net in pub/BIOSCI/METHDS-REAGNTS/METHODS.FAQ or from ftp.ncifcrf.gov in pub/methods/FAQlist. 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. _________________________________________________________________ WHAT JOURNALS ARE AVAILABLE ON BIO-JOURNALS? HOW CAN ONE LOCATE ARTICLES? The following journals appear regularly as of 6/28/94. This list is constantly expanding and the latest copy can be requested from biosci-help@net.bio.net. * Anatomy & Embryology * Applied Microbiology and Biotechnology * Applied and Environmental Microbiology * Binary * CABIOS * Cell and Tissue Research * Chromosoma * Clinical Chemistry * Current Genetics * EMBO Journal * European Journal of Biochemistry * European Journal of Physiology * Experimental Brain Research * Histochemistry * Human Genetics * IEEE Engineering in Medicine and Biology * Immunogenetics * Journal of Bacteriology * Journal of Biological Chemistry * Journal of Comparative Physiology B: Biochemical, Systemic, and Environmental Physiology * Journal of Membrane Biology * Journal of Molecular Evolution * Journal of Virology * MGG - Molecular and General Genetics * Mammalian Genome * Microbial Releases * Molecular Microbiology * Molecular and Cellular Biology * Nucleic Acids Research * Plant Cell Reports * Planta * Protein Science * Roux's Archives of Developmental Biology * Seminars in Cancer Biology * Seminars in Cell Biology * Seminars in Developmental Biology * Seminars in Immunology * Seminars in the Neurosciences * Seminars in Virology * TAG - Theoretical and Applied Genetics Table of Contents for the journals above are available for FTP from net.bio.net in pub/BIOSCI/BIO-JOURNALS and also for searching and retrieval by Gopher from net.bio.net, port 70. One can use either gopher or WAIS to search the WAIS source biology-journal-contents.src at net.bio.net and retrieve individual article references from the journals above. This can be accessed through WAIS, WAISMAIL, gopher, and Mosaic as described in the FAQ section entitled "How do I find back issues of BIOSCI postings?" _________________________________________________________________ WHY ARE THERE TWO BIOSCI SITES? Originally there were four BIOSCI distribution sites (nodes), but due to administrative complexities, the number of nodes was scaled back to two. Although 99% of you never have to pay for any BIOSCI messages, rest assured that network resources are not free and should not be squandered. We established BIOSCI distribution sites on each side of the Atlantic to minimize network e-mail traffic. For example, if a message is posted to the U.S. site, only one copy is sent on to the U.K. site via netnews software, not by mail before being "exploded" for mail distribution to all of the final e-mail destinations on the "other side of the pond." This is more efficient than sending hundreds of copies of the same message across the Atlantic. A trade-off for this efficiency is slightly increased complexity in the distribution network, i.e., the mailing lists for each newsgroup are split between two sites. In the past BIOSCI experienced sporadic problems with "bounced" mail, but the reduction in the number of BIOSCI distribution sites and the implementation of U.S. to U.K. message transfer via news rather than by e-mail has eliminated this problem. Everyone would be better served if Usenet news was used exclusively, and we have the eventual elimination of e-mail subscriptions as a long term goal. Currently, however, too many biologists still have no other means of access to BIOSCI other than through e-mail. _________________________________________________________________ WHY HAVE I STOPPED GETTING MESSAGES? If your computer or network connection is down, mail sent to your address will "bounce" back to the sender of the message and often to the BIOSCI-REQUEST address at net.bio.net. Given the number of people using BIOSCI around the world, this can become quite a problem, so we have to take prompt action to eliminate troublesome addresses from our mailing lists. Offending addresses are "commented out" of the mailing lists. If your system is down, there may be no way to reach you, so it is your responsibility to contact your BIOSCI distribution site and request reinstatement if you notice a lapse in distribution. There is an automatic reminder system at net.bio.net in the U.S. that sends a message to all "commented out" addresses on the mailing lists at net.bio.net each Monday for three weeks. After that if no response is received to biosci-help@net.bio.net, the bad addresses are completely removed from the mailing lists. _________________________________________________________________ WHAT SHOULD I DO ABOUT MAIL ERROR MESSAGES THAT COME BACK WHEN I POST? It is not uncommon when posting a mail message to a newsgroup to receive an error message from a "mailer daemon." Don't panic!! The devil is not in the employ of BIOSCI! It is a rare day when every single computer and e-mail address in the world is functional. Mail systems are programmed to alert you if mail does not go through to a particular address which could be on any of our BIOSCI lists. Rest assured that your message was received by the vast majority of readers. You may either just delete these "bouncers" or send them on to your local BIOSCI distribution node (in most cases we will probably be aware of them already). It is not uncommon to receive one or two bouncers for any e-mail posting that you make. Note once again that if everyone used news software and if we didn't have to bridge so many incompatible e-mail networks to bring the biology community together, we wouldn't have to deal with this problem. 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. _________________________________________________________________ HOW DOES ONE START A NEW BIOSCI NEWSGROUP/MAILING LIST? BIOSCI's goal is to promote the use of electronic communications among biologists and we are here to assist you in establishing new forums at no charge. There are currently two options - create a full newsgroup or a prototype (mailing lists only): For full-fledged BIOSCI newsgroup status (also see "prototype" rules below) Proposals for new groups must contain a statement of purpose for the group and the name of a person designated as discussion leader unless the group is in the service category such as METHODS, EMPLOYMENT, etc. Discussion leaders are responsible for ensuring that a reasonable level of activity is sustained on the newsgroup (see Newsgroup Termination Policy below). The discussion leader can also propose the creation of moderated newsgroups if he/she agrees to serve as moderator (this requires access to Usenet news software at the moderator's site). Proposals should be sent to biosci-help@net.bio.net. 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. Newsgroup Termination Policy Any group with less than 52 msgs in the previous calendar year will be put on notice by posting an announcement to the newsgroup (not to bionet.announce) that it faces cancellation. It can be reprieved if 80 readers respond within two weeks (this policy will be stated in the termination announcement). It then has two months to reach a usage level of one message per 3 days or else it will be abolished. Appeals to the BIOSCI management about high content albeit low volume on the group will be considered. Newsgroups for Professional Societies in Biology BIOSCI will create a moderated newsgroup in the bionet.prof-society domain without voter approval for any professional society in the biological sciences which has a membership of at least 500. Smaller groups must go through the regular BIOSCI/bionet newsgroup creation process. Because these groups are not discussion forums, they will be exempted from the 52 message per year minimum posting limit and would only be discontinued if the society in question no longer wishes to use them. If usage seems extremely low on any group in the bionet.prof-society domain, the BIOSCI/bionet staff will contact the society in question and ensure that the newsgroup is still wanted. BIOSCI "prototype" newsgroup creation policy We will be happy to establish and administer a straight mailing list without an associated Usenet newsgroup for a six month trial period for anyone that wants to try to form a new electronic community in the biological sciences (We stress that the topics are limited to professional communications though.). 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. _________________________________________________________________ HOW CAN I LIST MY ADDRESS INFORMATION IN THE BIOSCI USER DIRECTORY? Below is the address form that we would like each reader of the BIOSCI/bionet newsgroups to complete and return if you would like to be listed in our database. The database serves as a directory that enables biologists, who are currently using (or even just reading) the BIOSCI newsgroups, to look up e-mail addresses and other information about our users. 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 Making Sure That Your Information Is Current This notice will be mailed bimonthly to each newsgroup. You should check your database entry from time-to-time to see if your address information is still up-to-date. Using Gopher to complete the form If you don't want to use a text editor, you can also use Dan Jacobson's gopher site to fill out the address database form as follows. Otherwise skip this section on gopher and proceed to the instructions for filling out the form below. > 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) Important Instructions - Please Read Carefully Please enter all responses after the : on each line, leaving one (1) blank space after the : (i.e., before the start of your text). 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.yeast Listing 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: _________________________________________________________________ WHY DIDN'T MY USENET POSTING SHOW UP ELSEWHERE? Your local Usenet software may have defaulted to "local" distribution. If this option is selected, only other readers of the bionet newsgroups on your local computer will see your posting. If you want your message to be delivered to all BIOSCI/bionet readers, please be sure to specify "world" or "bionet" when prompted for the Distribution:. Generally, if you press "?" or "h" when prompted, you will see your options for controlling the distribution of your messages on Usenet. If your message does not reach one of the two BIOSCI nodes in the U.S. or the U.K. it will not be distributed to people who participate in BIOSCI by e-mail. _________________________________________________________________ WHY ARE MY MESSAGES ARE GOING TO BIONET.FOLLOWUP? This is a problem that might plague users of older versions of the "rn" newsreading program when they try to reply to messages on BIOFORUM/bionet.general. bionet.followup is a non-existent newsgroup. In the "good old days" there was a newsgroup called "net.general" and replies to net.general were posted to "net.followup." Unfortunately the Usenet name of the BIOFORUM newsgroup, bionet.general, contains the text "net.general" as a subset. Older versions of news software can latch on to this text string and redirect replies to bionet.general messages to bionet.followup. If you are plagued by this problem, please call the following fixes, provided by Roy Smith and Wayne Rindone, to the attention of your local systems manager: +++++++++++++++++++++++ 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: 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 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 +++++++++++++++++++++++ _________________________________________________________________ Common questions posted to BIOSCI/bionet newsgroups WHAT ARE ALL OF THESE REFERENCES TO FTP, WAIS, GOPHER, AND WWW/MOSAIC? FTP FTP stands for File Transfer Protocol and is a method for transmitting files at high speed over the Internet. There are also e-mail servers at various BITNET sites which provide e-mail access to FTP archives. Send the word "HELP" to BITFTP@PUCC.BITNET for details. A sample session of using FTP to access the BIOSCI archives follows. Keyboard input is underlined. ### highlights comments about the procedure. 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 226 ASCII Transfer complete. 562 bytes received in 0.1 seconds (5.5 Kbytes/s) ftp> cd PROTEIN-ANALYSIS ### We want to look at PROTEIN-ANALYSIS archives ------------------- 250 CWD command successful. ftp> ls -- 200 PORT command successful. 150 ASCII data connection for /bin/ls (134.172.2.69,3233) (0 bytes). 8912 9001 9002 9003 9004 9005 9006 9007 9008 9009 9010 9011 9012 9101 9102 9103 9104 9105 9106 9107 9108 9109 9110 9111 9112 9201 9202 9203 9204 9205 9206 9207 9208 9209 9210 9211 current 226 ASCII Transfer complete. 225 bytes received in 0.12 seconds (1.8 Kbytes/s) 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. WAIS WAIS stands for Wide Area Information Server. WAIS software allows information to be stored at many sites around the Internet in to a particular format. Computers running WAIS software can query these sources remotely using a standard protocol. Free software is available for many popular hardware platforms, but requires some systems expertise to install. Now that you know how to use FTP (above), you can use anonymous ftp to think.com and cd to the "wais" directory for software and more information. A public WAIS account is accessible to Internet users by using the command telnet quake.think.com and logging in as "wais" (lowercase). Gopher Gopher is both a user-friendly interface to the FTP program described above and a network searching tool similar to WAIS (which can also utilize WAIS information sources). Gopher software is available as described below for many platforms; TurboGopher on the Macintosh is especially slick! Don Gilbert (gilbertd@silver.ucs.indiana.edu) at ftp.bio.indiana.edu runs the excellent IUBIO Gopher Hole with many services of use to biologists, including search and retrieval of GenBank entries and BIOSCI/bionet newsgroup postings among many other information resources. Dan Jacobson (danj@gdb.org) runs an excellent gopher server at merlot.gdb.org with software, database, news, and government information archives. In Europe Rob Harper (harper@finsun.csc.fi) has set up a similar gold mine of information at gopher.csc.fi. Please see the section on searching the BIOSCI archives for other useful gopher sites. The following information is excerpted from the Gopher FAQ. Many questions have been cut out for brevity. ---------------------------------------------------------------------- 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. ------------------------------------------------------------------- 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? ------------------------------------------------------------------- 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. ------------------------------------------------------------------- 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. --------------------------------------------------------------------- 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 --------------------------------------------------------------------- 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. ------------------------------------------------------------------- WWW/Mosaic The World-Wide Web (WWW) has become the latest hot network item, especially since the advent of the Mosaic software from the National Center for Supercomputing Applications at the University of Illinois. 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. _________________________________________________________________ PLEASE HELP ME FIND THE E-MAIL ADDRESS FOR DR. ... If you can not get this information by calling the person in question, there are several other resources that can be of help. As of May 1993, BIOSCI at net.bio.net began running a BIOSCI user address directory which can be accessed through gopher to net.bio.net or via WAIS or waismail. The WAIS source is called biologists-addresses.src and is updated daily. See the FAQ section entitled "How do I find back issues of BIOSCI postings?" for information on WAIS and waismail access. Instructions for using the address source are included in the waismail help file which can be retrieved by sending the word "help" to waismail@net.bio.net (leave the Subject: line of your message blank.) 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-(. _________________________________________________________________ HOW DO I REPORT A PROBLEM IN A BIOLOGICAL DATA BASE? (answer contributed by Dr. John Garavelli of PIR) 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 _________________________________________________________________ WHAT ABOUT SUBMITTING SEQUENCE DATA TO GENBANK, EMBL, DDBJ OR PIR? (answer contributed by Dr. John Garavelli of PIR) 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.DE The 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.jp The 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.EDU While 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 SUBFORM to 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.