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Path: senator-bedfellow.mit.edu!enterpoop.mit.edu!biosci!NET.BIO.NET!kristoff From: kristoff@NET.BIO.NET (David Kristofferson) Newsgroups: bionet.announce Subject: BIOSCI Newsgroups Information Message-ID: <9304010901.AA09238@net.bio.net> Date: 1 Apr 93 09:01:02 GMT Sender: kristoff@net.bio.net Distribution: bionet Lines: 324 Approved: bionews-moderator@genbank.bio.net ---------------------------------------------------------------------- THE BIOSCI ELECTRONIC NEWSGROUP NETWORK INFORMATION SHEET ---------------------------------------------------------------------- This is the BIOSCI information sheet for the Americas and Pacific Rim countries. If you are located in Europe, Africa, or Central Asia, please request that version of the BIOSCI information sheet by sending e-mail to the Internet address: biosci@net.bio.net. New users of BIOSCI/bionet may want to read the "Frequently Asked Questions" or "FAQ" sheet for BIOSCI. The FAQ provides details on how to participate in these forums and is available for anonymous FTP from net.bio.net [134.172.2.69] in pub/BIOSCI/biosci.FAQ. It may also be requested by sending e-mail to biosci@net.bio.net (use plain English for your request). The FAQ is also posted on the first of each month to the newsgroup BIONEWS/bionet.announce immediately following the posting of the BIOSCI information sheet. ---------------------------------------------------------------------- Introduction ------------ The BIOSCI newsgroup network was developed to allow easy worldwide communications between biological scientists who work on a variety of computer networks. By having distribution sites or "nodes" on each major network, BIOSCI allows its users to contact people around the world without having to learn a variety of computer addressing tricks. Any user can simply post a message to his/her regional BIOSCI node and copies of that message will be distributed automatically to all other subscribers on all of the participating networks, including the Internet, USENET, BITNET, EARN, NETNORTH, HEANET, and JANET. E-mail Subscription Requests and other Information -------------------------------------------------- If you need to receive BIOSCI messages by e-mail, please send all subscription requests, subscription cancellations, or any other questions about using BIOSCI to the Internet address biosci@net.bio.net As your request will be read by a human, there is no need for special syntax in your message. Simply select the newsgroups from the list below to which you would like to subscribe. ********************************************************************** DO NOT, REPEAT, DO NOT POST SUBSCRIPTION REQUESTS DIRECTLY TO ANY OF THE NEWSGROUP ADDRESSES. PLEASE USE ONLY THE ADDRESS biosci@net.bio.net Your posting could go to several thousand people. Supposing that each person spends a couple of seconds to figure out that you did this, before they go on to the next message. You will have wasted the equivalent of several hours of one person's time, not to mention the computer time and disk storage that are wasted. ********************************************************************** PLEASE NOTE THAT IF YOU HAVE ACCESS TO USENET NEWS YOU DO NOT NEED AN E-MAIL SUBSCRIPTION!! Simply read and post to the newsgroups in the "bionet" newsgroup heirarchy using your USENET news software (e.g., readnews, rn, vnews, ANU-NEWS, postnews). WE STRONGLY ENCOURAGE ALL INTERESTED USERS TO EXPLORE GETTING USENET NEWS SOFTWARE AT YOUR SITE. THE SOFTWARE IS IN THE PUBLIC DOMAIN, AND YOU WILL FIND IT MUCH MORE CONVENIENT THAN SUBSCRIBING TO NEWSGROUPS BY E-MAIL. Please consult your systems manager or contact biosci@net.bio.net for assistance if needed. Canceling E-mail Subscriptions ------------------------------ ********************************************************************** AS WE NOTED ABOVE, PLEASE DO NOT SEND CANCELLATION NOTICES TO THE NEWSGROUP E-MAIL POSTING ADDRESSES. PLEASE USE ONLY THE ADDRESS biosci@net.bio.net FOR CANCELLATION NOTICES. ********************************************************************** If you have subscribed to a newsgroup and are now leaving an institution or changing your e-mail address, it is IMPERATIVE that you send a note to biosci@net.bio.net and cancel your subscription! Non-existent addresses or overflowing mailboxes cause computer mail programs to send back "daemon" messages which might bother everybody on the newsgroup. We will immediately remove any address causing such a problem, but would prefer it if you would notify us in advance as a courtesy to the rest of the user community. Interruption of E-mail Service ------------------------------ It is our policy to remove any address from our mailing lists which becomes inaccessible and causes mail to bounce back to the sender. This might happen to you if your local computer or network fails for a significant period of time. If you notice that you are no longer receiving BIOSCI postings, it may be because your address was removed for the above reason. It will be necessary for you to contact biosci@net.bio.net and resubscribe. Please see BIOSCI FAQ II, mentioned at the beginning of this document, for more details on how BIOSCI handles addresses which reject mail. List of BIOSCI Newsgroups ------------------------- NEWSGROUP NAME TOPIC -------------- ----- AGEING Discussions about ageing research AGROFORESTRY Discussions about agroforestry research ARABIDOPSIS Newsgroup for the Arabidopsis Genome Project BIOFORUM Discussions about biological topics for which there is not yet a dedicated newsgroup BIOLOGICAL-INFORMATION- THEORY-AND-CHOWDER-SOCIETY Applications of information theory to biology BIONAUTS Question/answer forum for help using electronic networks, locating e-mail addresses, etc. BIONEWS ** General announcements of widespread interest to biologists BIO-JOURNALS Tables of Contents of biological journals BIO-MATRIX Applications of computers to biological databases BIO-SOFTWARE Information on software for the biological sciences CHROMOSOME-22 Mapping and Sequencing of Human Chromosome 22 COMPUTATIONAL-BIOLOGY ** Mathematical and computer applications in biology EMBL-DATABANK Messages to and from the EMBL database staff EMPLOYMENT Job opportunities in biology (see BIOSCI FAQ *before* posting commercial job openings) GDB Messages to and from the Genome Data Bank staff GENBANK-BB Messages to and from the GenBank database staff GENETIC-LINKAGE Newsgroup for genetic linkage analysis HIV-MOLECULAR-BIOLOGY Discussions about the molecular biology of HIV HUMAN-GENOME-PROGRAM NIH-sponsored newsgroup on human genome issues IMMUNOLOGY Discussions about research in immunology JOURNAL-NOTES Practical advice on dealing with professional journals METHODS-AND-REAGENTS Requests for information and lab reagents MOLECULAR-EVOLUTION Discussions about research in molecular evolution NEUROSCIENCE Discussions about research in the neurosciences N2-FIXATION Discussion about biological nitrogen fixation PLANT-BIOLOGY Discussions about research in plant biology POPULATION-BIOLOGY Discussions about research in population biology PROTEIN-ANALYSIS Discussions about research on proteins and messages for the PIR and SWISS-PROT databank staffs. PROTEIN-CRYSTALLOGRAPHY Discussion about crystallography of macromolecules and messages for the PDB staff RAPD Discussions about Randomly Amplified Polymorphic DNA SCIENCE-RESOURCES Information from/about scientific funding agencies TROPICAL-BIOLOGY Discussions about research in tropical biology VIROLOGY Discussions about research in virology WOMEN-IN-BIOLOGY Discussions about issues concerning women biologists ** Note that newsgroups flagged with ** are moderated, i.e., postings are directed to a moderator (editor) who later forwards messages (possibly edited or condensed) to the newsgroup. Posting Messages to Newsgroups ------------------------------ The lists below include the addresses for posting messages and also the names of the corresponding UNIX USENET newsgroups. Messages can either be posted into the USENET newsgroups using "postnews" or similar software or they can be submitted by electronic mail to the mailing addresses given below. In most cases, messages are posted directly to the newsgroups without editorial intervention. USENET users who use the "postnews" or similar software on their local computer should be sure to set the message distribution to "world" or "bionet" or else your message may not be distributed beyond your local computer. USENET newsgroups are read using, e.g., the "readnews," "rn," or "vnews" software on UNIX systems. USENET news software is in the public domain and is available for most UNIX systems. A public domain USENET news software package named ANU-NEWS is also available for VAX/VMS systems. Your local BIOSCI node can point you towards acquiring the software for use on your computer system. Those who use e-mail to post messages should send their mail to the following Internet addresses in the USA: NEWSGROUP NAME Mailing Address -------------- ---------------- AGEING ageing@net.bio.net AGROFORESTRY ag-forst@net.bio.net ARABIDOPSIS arab-gen@net.bio.net BIOFORUM bioforum@net.bio.net BIO-INFORMATION-THEORY + bio-info@net.bio.net BIONAUTS bio-naut@net.bio.net BIONEWS ** bionews@net.bio.net BIO-JOURNALS bio-jrnl@net.bio.net BIO-MATRIX biomatrx@net.bio.net BIO-SOFTWARE bio-soft@net.bio.net CHROMOSOME-22 chrom-22@net.bio.net COMPUTATIONAL-BIOLOGY ** comp-bio@net.bio.net EMBL-DATABANK embl-db@net.bio.net EMPLOYMENT biojobs@net.bio.net GDB gdb@net.bio.net GENBANK-BB genbankb@net.bio.net GENETIC-LINKAGE gen-link@net.bio.net HIV-MOLECULAR-BIOLOGY hiv-biol@net.bio.net HUMAN-GENOME-PROGRAM gnome-pr@net.bio.net IMMUNOLOGY immuno@net.bio.net JOURNAL-NOTES jrnlnote@net.bio.net METHODS-AND-REAGENTS methods@net.bio.net MOLECULAR-EVOLUTION mol-evol@net.bio.net NEUROSCIENCE neur-sci@net.bio.net N2-FIXATION n2fix@net.bio.net PLANT-BIOLOGY plantbio@net.bio.net POPULATION-BIOLOGY pop-bio@net.bio.net PROTEIN-ANALYSIS proteins@net.bio.net PROTEIN-CRYSTALLOGRAPHY xtal-log@net.bio.net RAPD rapd@net.bio.net SCIENCE-RESOURCES sci-res@net.bio.net TROPICAL-BIOLOGY trop-bio@net.bio.net VIROLOGY virology@net.bio.net WOMEN-IN-BIOLOGY womenbio@net.bio.net + full name is BIOLOGICAL-INFORMATION-THEORY-AND-CHOWDER-SOCIETY ** Note that newsgroups flagged with ** are moderated, i.e., postings are directed to a moderator (editor) who later forwards messages (possibly edited or condensed) to the newsgroup. List of USENET newsgroups ------------------------- BIOSCI messages are distributed on the following USENET newsgroups in the "bionet" heirarchy. Contents of the USENET newsgroups and the e-mail distributions listed above are the same, i.e., messages sent in by e-mail are also forwarded to USENET and messages posted to USENET newsgroups are also distributed to e-mail subscribers. NEWSGROUP NAME USENET Newsgroup Name -------------- --------------------- 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 BIO-SOFTWARE bionet.software CHROMOSOME-22 bionet.genome.chrom22 COMPUTATIONAL-BIOLOGY ** bionet.biology.computational EMBL-DATABANK bionet.molbio.embldatabank EMPLOYMENT bionet.jobs GDB bionet.molbio.gdb GENBANK-BB bionet.molbio.genbank GENETIC-LINKAGE bionet.molbio.gene-linkage HIV-MOLECULAR-BIOLOGY bionet.molbio.hiv HUMAN-GENOME-PROGRAM bionet.molbio.genome-program IMMUNOLOGY bionet.immunology JOURNAL-NOTES bionet.journals.note METHODS-AND-REAGENTS bionet.molbio.methds-reagnts MOLECULAR-EVOLUTION bionet.molbio.evolution NEUROSCIENCE bionet.neuroscience N2-FIXATION bionet.biology.n2-fixation PLANT-BIOLOGY bionet.plants POPULATION-BIOLOGY bionet.population-bio PROTEIN-ANALYSIS bionet.molbio.proteins PROTEIN-CRYSTALLOGRAPHY bionet.xtallography RAPD bionet.molbio.rapd SCIENCE-RESOURCES bionet.sci-resources TROPICAL-BIOLOGY bionet.biology.tropical VIROLOGY bionet.virology WOMEN-IN-BIOLOGY bionet.women-in-bio + full name is BIOLOGICAL-INFORMATION-THEORY-AND-CHOWDER-SOCIETY ** Note that newsgroups flagged with ** are moderated, i.e., postings are directed to a moderator (editor) who later forwards messages (possibly edited or condensed) to the newsgroup. BIOSCI "prototype" newsgroups ----------------------------- To assist areas of research in developing their own electronic communication forums, BIOSCI at net.bio.net will set up on request a mailing list *without* an associated USENET newsgroup. The mailing list is created only at net.bio.net, the U.S. BIOSCI node, and all subscription requests must be sent to biosci@net.bio.net regardless of one's geographical location. There is no charge for this or any other BIOSCI service, as usual. This procedure waives the rule that requires each new newsgroup proposal to be put to a vote of the readership first (see BIOSCI/bionet FAQ II, mentioned at the beginning of this document, for details on creating new full-fledged newsgroups and prototype newsgroups). Each mailing list ("prototype newsgroup") must have a scientist volunteer to serve as its discussion leader. The prototype newsgroup has six months to build up its readership after which time it is put out for a vote for full newsgroup status (i.e., to have both a mailing list *and* parallel USENET newsgroup created at both BIOSCI nodes in the U.S. and U.K.). If you are interested in establishing such a forum for your research specialty, please contact biosci@net.bio.net. The current prototype newsgroups are listed below. Please send subscription requests to biosci@net.bio.net and NOT to the newsgroup posting addresses. Prototype newsgroups are *not* archived, so please be sure to save any messages that you may want to refer to again. Posting Address Purpose --------------- ------- autoseqs@net.bio.net Discussions about automated DNA sequencing btk-mca@net.bio.net Discussions about biothermal kinetics FURTHER QUESTIONS??? Please address them to biosci@net.bio.net. Inflating: BIONET.INF <to console> Path: senator-bedfellow.mit.edu!enterpoop.mit.edu!gatech!udel!wupost!uwm.edu!biosci!net.bio.net From: kristoff@net.bio.net (Dave Kristofferson) Newsgroups: bionet.announce Subject: BIOSCI/bionet Frequently Asked Questions Message-ID: <Apr.1.01.03.02.1993.9393@net.bio.net> Date: 1 Apr 93 09:03:03 GMT Sender: kristoff@net.bio.net Lines: 1522 Approved: bionews-moderator@net.bio.net BIOSCI/bionet Frequently Asked Questions (FAQ) ---------------------------------------------- (last revised - 3/10/93) This document describes the general purpose and uses of the BIOSCI/bionet newsgroups and provides details on how to participate in these forums. It is available for anonymous FTP from net.bio.net [134.172.2.69] in pub/BIOSCI/biosci.FAQ. This document may also be requested by e-mail to biosci@net.bio.net (use plain English - this is not a server address). It 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. The FAQ is also posted monthly to the USENET newsgroup news.answers and is archived along with other USENET newsgroup FAQs at pit-manager.mit.edu [18.172.1.27]. Contents -------- Common Questions about BIOSCI/bionet usage ------------------------------------------ * What is BIOSCI and bionet? * What newsgroups are available on BIOSCI/bionet? * Who are the discussion leaders for the various newsgroups? * Where (and how many times) should I post my messages? * How does one post a message? * How do I find back issues of BIOSCI postings? * Is there a summary of METHODS-AND-REAGENTS postings? * What is USENET? * How can I get news software at my site? * How do I request or cancel e-mail subscriptions to BIOSCI newsgroups? * How can I get a list of newsgroups or my subscriptions? * Why are BIOSCI e-mail subscription requests not processed by machine? * Why are there two BIOSCI sites? * How does one know to which newsgroup a message was posted? * What is the "BIOSCI-REQUEST" address? * Why have I stopped getting messages? * I posted a message and got back an error message from a daemon!! * How does one start a new BIOSCI newsgroup/mailing list? * What journals are available on BIO-JOURNALS? How can one locate articles? * 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 --------------------------------------------------- * How do I report a problem in a biological data base? * What about submitting sequence data to GenBank, EMBL, DDBJ or PIR? * Please help me find the e-mail address for Dr. ... * What are all of these references to FTP, WAIS, Gopher, and WWW? Other questions to add to this list??? Please send them to biosci@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. BIOSCI messages are distributed without editorial intervention in most cases. Dissemination is by normal electronic mail and also 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. We provide a summary about USENET further below. More detailed information has been collected from the USENET newsgroup news.announce.newusers and placed in two files in the pub/BIOSCI directory in the anonymous FTP area on net.bio.net [134.172.2.69]. The file "usenet.info" contains the following articles: How to become a USENET site USENET Software: History and Sources What is Usenet? How to Get Information about Networks The file "usenet.info2" contains Answers to Frequently Asked Questions about Usenet Emily Postnews Answers Your Questions on Netiquette Hints on writing style for Usenet Another file in the same directory entitled "internet.info" provides starting information on how to get your site connected to the Internet. Any or all of these files may be requested by e-mail to biosci@net.bio.net. What newsgroups are available on BIOSCI/bionet? ----------------------------------------------- This is the list of the mailing lists and the corresponding USENET newsgroup names as of 12/92. A posting of the latest list of newsgroups and other information about subscribing/unsubscribing, etc., to BIOSCI (the "BIOSCI info sheet") 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@net.bio.net, while the latter may be requested from biosci@daresbury.ac.uk. MAILING LIST NAME USENET Newsgroup Name ----------------- --------------------- 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 BIO-SOFTWARE bionet.software CHROMOSOME-22 bionet.genome.chrom22 COMPUTATIONAL-BIOLOGY ** bionet.biology.computational EMBL-DATABANK bionet.molbio.embldatabank EMPLOYMENT bionet.jobs GDB bionet.molbio.gdb GENBANK-BB bionet.molbio.genbank GENETIC-LINKAGE bionet.molbio.gene-linkage HIV-MOLECULAR-BIOLOGY bionet.molbio.hiv HUMAN-GENOME-PROGRAM bionet.molbio.genome-program IMMUNOLOGY bionet.immunology JOURNAL-NOTES bionet.journals.note METHODS-AND-REAGENTS bionet.molbio.methds-reagnts MOLECULAR-EVOLUTION bionet.molbio.evolution NEUROSCIENCE bionet.neuroscience PLANT-BIOLOGY bionet.plants POPULATION-BIOLOGY bionet.population-bio PROTEIN-ANALYSIS bionet.molbio.proteins PROTEIN-CRYSTALLOGRAPHY bionet.xtallography SCIENCE-RESOURCES bionet.sci-resources TROPICAL-BIOLOGY bionet.biology.tropical VIROLOGY bionet.virology WOMEN-IN-BIOLOGY bionet.women-in-bio + full name is BIOLOGICAL-INFORMATION-THEORY-AND-CHOWDER-SOCIETY ** Note that newsgroups flagged with ** are moderated, i.e., postings are directed to a moderator (editor) who later forwards messages (possibly edited or condensed) to the newsgroup. NEWSGROUP NAME TOPIC -------------- ----- AGEING Discussions about ageing research AGROFORESTRY Discussions about agroforestry research ARABIDOPSIS Newsgroup for the Arabidopsis Genome Project BIOFORUM Discussions about biological topics for which there is not yet a dedicated newsgroup BIOLOGICAL-INFORMATION- THEORY-AND-CHOWDER-SOCIETY Applications of information theory to biology BIONAUTS Question/answer forum for help using electronic networks, locating e-mail addresses, etc. BIONEWS ** General announcements of widespread interest to biologists BIO-JOURNALS Tables of Contents of biological journals BIO-MATRIX Applications of computers to biological databases BIO-SOFTWARE Information on software for the biological sciences CHROMOSOME-22 Mapping and Sequencing of Human Chromosome 22 COMPUTATIONAL-BIOLOGY ** Mathematical and computer applications in biology EMBL-DATABANK Messages to and from the EMBL database staff EMPLOYMENT Job opportunities GDB Messages to and from the Genome Data Bank staff GENBANK-BB Messages to and from the GenBank database staff GENETIC-LINKAGE Newsgroup for genetic linkage analysis HIV-MOLECULAR-BIOLOGY Discussions about the molecular biology of HIV HUMAN-GENOME-PROGRAM NIH-sponsored newsgroup on human genome issues IMMUNOLOGY Discussions about research in immunology JOURNAL-NOTES Practical advice on dealing with professional journals METHODS-AND-REAGENTS Requests for information and lab reagents MOLECULAR-EVOLUTION Discussions about research in molecular evolution NEUROSCIENCE Discussions about research in the neurosciences PLANT-BIOLOGY Discussions about research in plant biology POPULATION-BIOLOGY Discussions about research in population biology PROTEIN-ANALYSIS Discussions about research on proteins and messages for the PIR and SWISS-PROT databank staffs. PROTEIN-CRYSTALLOGRAPHY Discussion about crystallography of macromolecules and messages for the PDB staff SCIENCE-RESOURCES Information from/about scientific funding agencies TROPICAL-BIOLOGY Discussions about research in tropical biology VIROLOGY Discussions about research in virology WOMEN-IN-BIOLOGY Discussions about issues concerning women biologists ** Note that newsgroups flagged with ** are moderated, i.e., postings are directed to a moderator (editor) who later forwards messages (possibly edited or condensed) to the newsgroup. Who are the discussion leaders for the various newsgroups? ---------------------------------------------------------- Most scientific specialty newsgroups (except for a few created several years ago) have individuals who are responsible for stimulating discussion on the newsgroup. General purpose forums such as METHODS-AND-REAGENTS do not have discussion leaders. If a group that you are interested in does not seem to have much activity recently, please contact the discussion leader and ask why 8-). NEWSGROUP NAME Discussion Leader and their e-mail address -------------- ------------------------------------------ AGEING Sydney Shall (bafa1@central.sussex.ac.uk) AGROFORESTRY Gerry Lawson (F_GJL@vaxa.nerc-bush.ac.uk) ARABIDOPSIS Chris Somerville (21847CRS@msu.edu) BIOFORUM None BIOLOGICAL-INFORMATION- THEORY-AND-CHOWDER-SOCIETY Tom Schneider (toms@ncifcrf.gov) BIONAUTS Rob Harper (harper@convex.csc.fi) BIONEWS ** David Kristofferson (kristoff@net.bio.net) BIO-JOURNALS David Kristofferson (kristoff@net.bio.net) BIO-MATRIX Dan Davison (davison@uh.edu) BIO-SOFTWARE None CHROMOSOME-22 Robert L. Nussbaum (nussbaum@a1.mscf.upenn.edu) COMPUTATIONAL-BIOLOGY ** Phil J. Curtiss (curtiss@umiacs.umd.edu) EMBL-DATABANK None (datalib@embl-heidelberg.de) EMPLOYMENT None GDB Kerryn Brandt (kab@welchgate.welch.jhu.edu) GENBANK-BB Dennis Benson (benson@ncbi.nlm.nih.gov) GENETIC-LINKAGE Steve Bryant (s_bryant@icrf.ac.uk) HIV-MOLECULAR-BIOLOGY Mika Salminen (msalminen@nphi.fi) HUMAN-GENOME-PROGRAM Jane Peterson (jp2@cu.nih.gov) IMMUNOLOGY Donald Forsdyke (forsdyke@qucdn.queensu.ca) JOURNAL-NOTES Donald Forsdyke (forsdyke@qucdn.queensu.ca) METHODS-AND-REAGENTS None MOLECULAR-EVOLUTION Dan Davison (davison@uh.edu) NEUROSCIENCE Vincent A Mazzarella (vamg6792@uxa.cso.uiuc.edu) PLANT-BIOLOGY Tony Travis (ajt@rri.sari.ac.uk) POPULATION-BIOLOGY None PROTEIN-ANALYSIS Amos Bairoch (BAIROCH@cmu.unige.ch) and John Garavelli (garavelli@nbrf.georgetown.edu) PROTEIN-CRYSTALLOGRAPHY Morten Kjeldgaard (morten@oase.kemi.aau.dk) SCIENCE-RESOURCES David Kristofferson (kristoff@net.bio.net) TROPICAL-BIOLOGY Matti Nummelin (saarikko@cc.helsinki.fi) VIROLOGY Robert Coelen (robert@arbo.microbiol.uwa.oz.au) WOMEN-IN-BIOLOGY Cassandra Smith (cls@buenga.bu.edu) Where (and how many times) should I post my messages? ----------------------------------------------------- The list of newsgroups above 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. 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. A few guidelines on some of the other 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 (no guarantees they'll respond personally, of course, but someone else might; e-mail directory services still leave much to be desired). 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 below 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 by opening up a discussion in this forum. BIO-JOURNALS/bionet.journals.contents: This newsgroup is not for postings by readers. It is used to distribute the Table of Contents for the following journals approximately a week or two in advance of publication: Anatomy & Embryology Applied Microbiology and Biotechnology Applied and Environmental Microbiology CABIOS* Cell and Tissue Research Chromosoma Current Genetics EMBO Journal* European Journal of Biochemistry European Journal of Physiology Experimental Brain Research Histochemistry Human Genetics 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 TAG - Theoretical and Applied Genetics 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. You can post messages without editorial intervention to other BIOSCI/bionet newsgroups. 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 kristoff@net.bio.net *before* proceeding). Commercial job posting format: ----------------------------- The posting should include o job title o one or two line factual description of the position o 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 I used to think 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!" How does one post a message? ---------------------------- If you use USENET, run your posting program and follow the prompts (e.g., postnews, 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). Enter the appropriate newsgroup from the list of USENET names (above) when prompted. 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. Usually pressing "?" or "h" at the Distribution: prompt will show you your options. If you are using e-mail, first select the newsgroup that you wish to post to from the list above and find the mailing address. The latest list of mailing addresses is found in the BIOSCI information 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 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. 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) and anonymous ftp from net.bio.net [134.172.2.69]. Gopher retrieval will also be available soon. Contact biosci@net.bio.net for further help. If you do not have WAIS software running locally, but do have access to the Internet, try telnet quake.think.com and login in as "wais" to experiment with the software. Both of our WAIS sources, biosci.src and biology-journal-contents.src, may be selected from the menu for searching. All the Bionet newsgroup postings since December 1991 are stored for Gopher searching and retrieval and anonymous ftp archive at ftp.bio.indiana.edu, the IUBIO archive maintained by Don Gilbert. The ftp directory in the anonymous account is usenet/bionet. 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 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. 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." It is for this reason that 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. How can I get news software at my site? --------------------------------------- Contact biosci@net.bio.net for information on getting started with USENET. News software can be obtained free of charge from anonymous FTP sources. The file "usenet.info" available by anonymous FTP from net.bio.net in pub/BIOSCI contains the following articles: How to become a USENET site USENET Software: History and Sources What is Usenet? How to Get Information about Networks How do I request or cancel e-mail subscriptions to BIOSCI newsgroups? --------------------------------------------------------------------- If you have access to USENET news software, then YOU DO NOT NEED AN E-MAIL SUBSCRIPTION! Only those people who need to receive postings by e-mail must request to be added to the mailing lists. USENET users can simply read the various bionet newsgroups using their news software. If your site has USENET news but does not get the bionet newsgroups, please request help by sending a message to biosci@net.bio.net. For those who need e-mail subscriptions or who want to cancel current e-mail subscriptions, please send a request to one of the following addresses. Please choose the site that serves your location. Simply pick the newsgroup(s) from the list above that you wish to subscribe to and request that your address be added to the chosen mailing lists. Please use plain English; no special message syntax is required in your subscription or cancellation request. Address Serving ------- ------- biosci@net.bio.net The Americas and Pacific Rim biosci@daresbury.ac.uk Europe, Africa, and Central Asia ****If you are changing e-mail addresses****, please be sure to send a message to your appropriate biosci address above and request that your subscriptions be changed or canceled!! How can I get a list of newsgroups or my subscriptions? ------------------------------------------------------- As with any other subscription correspondence, simply send a request to your appropriate BIOSCI distribution site: Address Serving ------- ------- biosci@net.bio.net The Americas and Pacific Rim biosci@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. Why are BIOSCI e-mail subscription requests not processed by machine? --------------------------------------------------------------------- To date the daily volume of BIOSCI subscription requests is small and can typically be handled in under 15 minutes a day. We have preferred to handle requests through the use of semi-automated scripts at the two BIOSCI distribution nodes instead of requiring our readers to learn a special syntax for processing subscriptions automatically. Use of the newsgroups is rapidly growing, however, so we are taking steps to provide automated subscription handling in the future. 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. How does one know to which newsgroup a message was posted? ---------------------------------------------------------- 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 and you must be a little discerning. 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. If you want to reply only to the author of the message, use the address on the "From:" line. If you want to reply to everyone on the newsgroup, use the address on the "To:" line. Please note that replies to BIOSCI messages are *not* automatically sent back to the newsgroup address. The default reply will be (in most cases, your local mail configuration might alter this) 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). What is the "BIOSCI-REQUEST" address? ------------------------------------- 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). 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@net.bio.net, the bad addresses are completely removed from the mailing lists. I posted a message and got back an error message from a 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: 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@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. 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@net.bio.net. What journals are available on BIO-JOURNALS? How can one locate articles? -------------------------------------------------------------------------- The following journals appear regularly. This list will be expanded in 1993. Applied and Environmental Microbiology CABIOS EMBO Journal Journal of Bacteriology Journal of Biological Chemistry Journal of Virology Molecular and Cellular Biology Molecular Microbiology Nucleic Acids Research Table of Contents for the journals above are available for FTP from net.bio.net in pub/BIOSCI/BIO-JOURNALS. One can use the WAIS source biology-journal-contents.src at net.bio.net to retrieve individual article references from the journals above. If you do not have WAIS software running locally, but do have access to the Internet, try telnet quake.think.com and login in as "wais" to experiment with the software. Both of our WAIS sources, biosci.src and biology-journal-contents.src, may be selected from the menu for searching. 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 <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 ---------------------------------------------------------------------- Common questions posted to BIOSCI/bionet newsgroups *************************************************** 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@net.bio.net 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: GenBank Submissions Mail Stop K710 Los Alamos National Laboratory Los Alamos, NM 87545 U.S.A. Telephone: (505) 665-2177 Electronic mail: gb-sub@life.lanl.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. 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 at least three other resources that can be of help. The easiest 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 two 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@pit-manager.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. 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-(. What are all of these references to FTP, WAIS, Gopher, and WWW? --------------------------------------------------------------- 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 internet.info usenet.info usenet.info2 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. In Europe Rob Harper (harper@finsun.csc.fi) has set up a similar gold mine of information at gopher.csc.fi. 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: pit-manager.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 --- The World-Wide Web is yet another network information tool. You can experiment with WWW if you have Internet access by using the command telnet info.cern.ch This will take you automatically into the WWW software on this host computer. Choosing menu item 3 displays the following information: WORLD WIDE WEB The WorldWideWeb (W3) is a wide-area hypermedia[1] information retrieval initiative aiming to give universal access to a large universe of documents. Everything there is online about W3 is linked directly or indirectly to this document, including an executive summary[2] of the project, Mailing lists[3] , Policy[4] , November's W3 news[5] , Frequently Asked Questions[6] . What's out there?[7] Pointers to the world's online information, subjects[8] , W3 servers[9] , etc. Help[10] on the browser you are using Software Products[11] A list of W3 project components and their current state. (e.g. Line Mode[12] ,Midas[13], Viola[14] , NeXTStep[15] , Servers[16] , Tools[17] , Mail robot[18] , Library[19] ) Technical[20] Details of protocols, formats, program internals etc Bibliography[21] Paper documentation on W3 and references.