From owner-gdb@net.bio.net Mon Jan 12 22:00:00 1998 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.molbio.gdb Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 13 Jan 1998 02:00:16 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 233 Sender: daemon@net.bio.net Distribution: world Message-ID: <199801131000.CAA17258@net.bio.net> NNTP-Posting-Host: net.bio.net (LAST REVISION: 30-JUL-95) This BIOSCI "miniFAQ" is designed to answer the questions that come up the *most frequently*. The main BIOSCI FAQ (Frequently Asked Questions) is accessible on the World Wide Web at URL http://www.bio.net/. If you can not find an answer to your question in this or other documentation, the BIOSCI technical support staff answers e-mail queries sent to biosci-help@net.bio.net We can only answer questions about the use of the newsgroups and mailing lists. We unfortunately do not have the staff to do Internet information searches or answer scientific questions. Please post those to the appropriate BIOSCI/bionet newsgroups. Contents: -------- 0) BIOSCI NEEDS YOUR SUPPORT!! 1) Using the WWW to access the BIOSCI/bionet newsgroups. 2) What to do about "spams," i.e., junk mail, ads, etc. 3) Examples of subscribing and unsubscribing to the mailing lists. 4) The BIOSCI user address and research interest directory. 0) BIOSCI NEEDS YOUR SUPPORT!! ------------------------------ BIOSCI's government funding has been expended, and we are now operating solely from advertising revenue that we have raised from our Web site at http://www.bio.net/. We need just a few minutes of your time to help us serve you. You can do two important things which will take very little time for you individually and will immensely help us continue to help you. First, please use our WWW system at http://www.bio.net/ to access the archives. You can post or reply to messages via your Web browser as described in item #1 below. Your usage helps attract sponsors. If you contact any of our sponsors, please be sure to thank them for supporting BIOSCI. It is critical for them to get this feedback if they are to continue their sponsorship for the long term. Second, if you work for a company or organization that provides products or services of interest to the biology community, please pass this message on to your marketing or marketing communications department or other appropriate group. Please ask them to help support BIOSCI by sponsoring our Web site and explain the uses and benefits of the system to the biology community. If they are interested, they can then contact us for further information at our tech support address, biosci-help@net.bio.net. 1) Using the WWW to access the BIOSCI/bionet newsgroups. -------------------------------------------------------- As of 10 December 1995, all BIOSCI/bionet full newsgroups are accessible through the World Wide Web (WWW) at URL http://www.bio.net. One can read and reply publicly or privately to both recent postings and archived messages through one's Web browser if it is configured properly to send e-mail. Each newsgroup is equipped with its own WAIS index. The main BIOSCI home page also has access to the BIO-JOURNALS Table of Contents database WAIS index and the BIOSCI user address database described in another item further below. 2) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups), mailing lists, and a hypermail archive at URL http://www.bio.net/. The same postings are distributed on all media (except for a small number of mailing-list-only groups at net.bio.net). Unfortunately it is becoming a despicable practice on the Internet (by a few people out to make a fast buck) to do automated mass postings to thousands of newsgroups and mailing lists. These attempts to grab free advertising are refered to as "spams" in the usual, somewhat boneheaded, net terminology. USENET is more susceptible to this practice, and many spams originate on the USENET groups and then are passed on to the mailing lists. However, spammers also get lists of mailing addresses and hit these too, so neither medium is immune. What should you do personally if you get junk mail? --------------------------------------------------- Just delete it and move on without reading it further. Filing a protest is becoming increasingly useless because spammers are often disguising the addresses where the messages are sent from. Unless you really understand Internet mail systems, your attempt at protest by sending replies to the message will often end up being sent to the address of an innocent person that the spammer is victimizing. What can BIOSCI/bionet do to protect its newsgroups? ---------------------------------------------------- The only solution currently available is to moderate the newsgroup. If this newsgroup is already moderated, then you are in good shape. Moderation protects the USENET distribution from about 95% of the spams that are being sent to date and protects the mailing lists completely. Moderation means, however, that someone has to take the time to review each message before it goes out. We have set up software here that simply allows the moderator to forward to an address at net.bio.net messages that (s)he wishes to have distributed. This takes no more time than that needed to read the message and pass it on, say about 1 min. per message. Most newsgroups currently have a discussion leader who is responsible for their newsgroup. The discussions leaders and their e-mail addresses are listed in the BIOSCI Information Sheet which is available on the Web at http://www.bio.net/. If a newsgroup is being hit with too many junk postings, please contact the discussion leader for that group and see if there is interest in moderating the group. Please do not assume that by simply posting a complaint to the newsgroup itself, anyone on the BIOSCI staff will act on your complaint. With close to 100 newsgroups to run, the BIOSCI staff has to rely on the discussion leaders of each newsgroup to report problems directly to us at biosci-help@net.bio.net. We will moderate any of our newsgroups if the discussion leader tells us that the readership of the group wishes to do so and if a moderator is willing to do the work. For most BIOSCI/bionet groups, this entails only a few minutes of work each day. Moderating a newsgroup will resolve probably 95% of the junk postings on the USENET distribution. Unfortunately there are easy ways for determined spammers to override the moderation mechanism on USENET, but we can protect our e-mail subscribers from unwanted postings if the newsgroup is moderated. You can also access our newsgroups over the WWW at URL http://www.bio.net. While this Web interface will not stop spammers from trying to post to the groups, this will give you yet another way, besides using USENET news, to keep the junk out of your personal mail files. For those of you with local USENET news systems, the Web interface will also give you faster access to new newsgroups and recent postings. 3) Examples of subscribing and unsubscribing to the mailing lists. ------------------------------------------------------------------ PLEASE NOTE: The BIOSCI management does NOT act on subscription/unsubscription requests that are posted improperly to the newsgroups and mailing lists. People who do this only bother everyone on the lists to no avail. Please be sure to follow the proper procedures below. Gory details are in the BIOSCI Information sheets on the Web at http://www.bio.net. Below we give an example utilizing the METHODS-AND-REAGENTS list at both of our two BIOSCI sites: Users in the Americas and Pacific Rim countries who use the BIOSCI ------------------------------------------------------------------ node at computer net.bio.net: ---------------------------- A) Determine the "listname" which is the <=8 character mail address ^^^^^^^^^^^^^ for the group. These can be found in the BIOSCI Info. Sheet. For the METHODS-AND-REAGENTS group the mailing address is methods@net.bio.net. The listname is the portion of the address to the left of the @ sign, i.e., "methods". The listname is used with the "subscribe" and "unsubscribe" commands illustrated below. B) Mail all commands in the body of a mail message addressed to biosci-server@net.bio.net. Do NOT send commands to the newsgroup posting addresses! Leave the Subject: line blank, any text on it will be ignored. C) In the body of your message put one or more of the following commands with an "end" command on the last line, e.g., subscribe methods unsubscribe methods end Do NOT put your e-mail address or other text on these lines. The server only allows you to cancel your subscription if the address on your mail header matches the address on our mailing list. Please ask for help at biosci-help@net.bio.net if your address has changed, e.g., if you know you are on the list but the server tells you that you are not a member. Users in Europe, Africa, and Central Asia who use the BIOSCI node at -------------------------------------------------------------------- computer daresbury.ac.uk (also known as dl.ac.uk): ------------------------------------------------- To subscribe and unsubscribe to/from the BIOSCI lists, you need to specify the full USENET newsgroup name with "bionet-news." prepended. The USENET newsgroup names are listed in the BIOSCI Information sheet on the Web at http://www.bio.net/. For the METHODS-AND-REAGENTS list the USENET newsgroup name is bionet.molbio.methds-reagnts, thus the appropriate commands are sub bionet-news.bionet.molbio.methds-reagnts unsub bionet-news.bionet.molbio.methds-reagnts These commands are included in a message addressed to mxt@dl.ac.uk, NOT to the newsgroup mailing addresses. As usual, include the text in the body of the message as text on the Subject: line is ignored. To unsubscribe from all the lists at the UK node, use unsub bionet-news Please note that if the address in the list is different than the one in your mail message header, you will not be able to unsubscribe by this method. If you have problems, please mail biosci@daresbury.ac.uk. 4) The BIOSCI user address and research interest directory. ----------------------------------------------------------- Please take this opportunity to add your name, address, and research interest information to the BIOSCI User Address Database if you have not already done so. You can fill out the address form directly through our Web page at URL http://www.bio.net/adrform.html. The address database is reindexed nightly for WWW access (the URL is http://www.bio.net/). If you are not directly on the Internet but can reach it by e-mail, please use our waismail server to access the user directory. waismail use is described above. You can also request a user address form by e-mail from biosci-help@net.bio.net. Please check your database entry from time-to-time to see if your address information is still up-to-date. Because of our limited personnel resources, we ask that you resubmit a *complete* form to revise your entry; we only replace complete entries and do not have resources to edit old forms. From owner-gdb@net.bio.net Tue Jan 20 22:00:00 1998 Path: biosci!GDB.ORG!avoltz From: avoltz@GDB.ORG (Amy Voltz) Newsgroups: bionet.molbio.gdb Subject: Termination of GDB - Public Announcement (fwd) Date: 21 Jan 1998 09:42:57 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 116 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Dear Colleagues, The Genome Database project (GDB: http://www.gdb.org), which provides human gene mapping data to human genetics researchers from its base at Johns Hopkins School of Medicine, will soon be ceasing its operations. This action is a consequence of the decision by the project's primary funder, the U.S. Department of Energy's Office of Energy Research, to discontinue GDB funding in order to focus its informatics resources primarily on the results of the sequencing phase of the human genome project. Termination of the GDB project is expected to be completed by July 31, 1998. The database will continue to be made available to the scientific community after that time, but further change to its content will cease. GDB was initially created at Johns Hopkins in 1989 by the Howard Hughes Medical Institute to capture the data from the Human Gene Mapping Library project at Yale. In 1991 the responsibility for funding the project was assumed jointly by the Department of Energy, the National Institutes of Health, and the Japan Science and Technology Agency. A series of mirror sites in many countries helped to insure international access to the data. One of the first major accomplishments of the project was to capture in electronic form much of the information about human genetics and gene mapping accumulated by the scientific community during the two decades prior to the Human Genome Project. These data were reviewed and edited by a worldwide group of volunteer scientists to assure quality, under the auspices of the Human Genome Organization (HUGO). The data included information on human genes, probes, clones, and allele frequencies, and represented the first significant attempt to collect the data necessary to get the Human Genome project under way. During its lifetime GDB provided informatics support for a succession of HUGO-sponsored Human Gene Mapping meetings and Single Chromosome workshops, hosted in a variety of locations around the world. These meetings brought together researchers from many countries to piece together integrated chromosome maps from numerous separate experimental results; the results were then made available to the research community via GDB. GDB pioneered the use of the World-Wide Web as a tool for dissemination of bioinformatics data to the community, which has now become routine. The project was also one of the first to deploy a Java client application (Mapview) to graphically display database query results. In recent years novel algorithms were developed to integrate multiple maps into a single comprehensive chromosome model which could be searched and displayed. By the mid-1990's small-scale mapping was giving way to high resolution whole-genome mapping at a small number of centers, as part of the mapping phase of the Human Genome Project. More recently the focus has shifted again to high-throughput sequencing. As the heyday of traditional mapping has faded, so has the perceived need for a large community database project focussed on maps. The decision has therefore been made to terminate the GDB project. The database will continue to be made available to the scientific community at the same Web address for the forseeable future, though most curation and data acquisition activities will cease before long. It is expected that the international mirror sites will make their own decisions regarding the longer term maintenance and supply of the final GDB release. Human Gene Nomenclature will continue to be curated by Dr. Sue Povey at the University College of London. The OMIM database, which since 1995 has had no formal connection with GDB, will not be affected and will continue to be available through NCBI (http://www.ncbi.nlm.nih.gov/omim). The Computational Bioscience Section (http://compbio.ornl.gov) of the Oak Ridge National Laboratory has agreed to maintain the servers for access to the current copy of GDB after the project ends at Johns Hopkins University. This Section is headed by Dr. Ed Uberbacher, the developer of the widely-used GRAIL eukaryotic gene-finding program. Oak Ridge is the coordinating site for the Genome Annotation Consortium (GAC, http://compbio.ornl.gov/CoLab) project, which is developing software and data systems to assist in assembling and annotating the results of human genome sequencing on an ongoing basis. Having GDB available locally will facilitate the GAC's integration of map data with sequence to produce the annotated reference genomic sequence, which is the ultimate goal of the Human Genome Project. I would like to take this opportunity to applaud the GDB project staff and management for their hard work and creative effort over the 8 year history of the project. I would also like to offer my deepest thanks to the past and present members of both our Quarterly Review Committee and our International Scientific Advisory Committee for their advice and support over the years, and to thank our host institution, the Johns Hopkins School of Medicine. We hope that this decision does not cause any great inconvenience to members of the scientific community. Please send comments or concerns to comments@gdb.org, or fill out the comment form at http://www.gdb.org/shutdown/shutdown.html, which permits comments to be anonymous, if desired. Please be as specific as possible in describing any use of GDB in your research for which no equivalent resource currently exists. These comments will be forwarded to myself and the funding agencies. Funding agency representatives can be contacted directly at the following addresses: Department of Energy: Daniel.Drell@oer.doe.gov Marvin.Frazier@oer.doe.gov National Institutes of Health: Lisa_Brooks@nih.gov The GDB staff can be contacted collectively at gdbstaff@gdb.org. Sincerely, Stanley Letovsky, Ph.D. Director, Genome Database letovsky@gdb.org