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BIOSCI/bionet Frequently Asked Questions (FAQ)

Newsgroups: bionet.announce
Last-modified:  mostly 9 December 1999; partial update June 2006
 
From: BIOSCI Administrator <biosci-help@net.bio.net> Reply-To: biosci-help@net.bio.net Subject: BIOSCI/bionet Frequently Asked Questions BIOSCI/bionet Frequently Asked Questions (FAQ) ----------------------------------------------
This document supplements the BIOSCI Newsgroups Information Sheet and provides details on how to participate in BIOSCI forums. Both documents are available for anonymous FTP and web retrieval from net.bio.net. The text version of the FAQ is found in pub/BIOSCI/doc/biosci.FAQ. This document is also available using the World Wide Web at http://www.bio.net/docs/biosci.FAQ.html.


Contents

Common Questions about BIOSCI/bionet usage

Common questions posted to BIOSCI/bionet newsgroups

Other questions to add to this list??? Please send them to biosci-help@net.bio.net. We would also appreciate your sending the answer to the question if possible. All contributions will be gratefully acknowledged by including the author's name along with the answer provided.


Common Questions about BIOSCI/bionet usage

What is BIOSCI and bionet?

We'll spare you the fascinating historical details and say simply that BIOSCI is a series of freely accessible electronic communication forums (i.e., electronic bulletin boards or "newsgroups") for use by biological scientists worldwide. No fees are charged for the service. The system is intended to promote communication between professionals in the biological sciences. All postings to the newsgroups should be made in that spirit. While the general public may "listen in" to the discussions, these newsgroups are intended primarily for communications between researchers. There are other forums on Usenet such as sci.bio for the asking and answering of biological questions from lay persons.

BIOSCI messages are distributed without editorial intervention in most cases. Dissemination is by both electronic mail and over Usenet in the form of the "bionet" newsgroups (see below for Usenet details). The contents of the electronic mail distribution is identical to the Usenet news distribution, but we encourage BIOSCI users to access the system through Usenet news software whenever possible. E-mail distributions may eventually be phased out. As of October 1992, 59% of our readers used Usenet news software instead of e-mail.

You may find much more detailed and up to date information concerning Usenet in the news.announce.newusers newsgroup. These articles are also available using anonymous FTP from rtfm.mit.edu, in the /pub/usenet/news.announce.newusers directory. You may be specifically interested in the following articles:

Detailed starting information on how to get your site connected to the Internet can be found the file "How_to_Get_Information_about_Networks".


What newsgroups are available on BIOSCI/bionet?

"THE BIOSCI ELECTRONIC NEWSGROUP NETWORK INFORMATION SHEET" containing the latest list of newsgroups, e-mail posting addresses, and other information about subscribing/unsubscribing, etc., to BIOSCI is posted the first of each month on the BIONEWS/bionet.announce newsgroup along with this FAQ posting.

Two versions of the BIOSCI info sheet are available, one for the Americas and the Pacific Rim countries, and the second for Europe, Africa, and Central Asia. The former may be requested by e-mail to biosci-help@net.bio.net, while the latter may be requested from biosci@hgmp.mrc.ac.uk.


Where should I post my messages?

The list of newsgroups in the BIOSCI info sheet gives a brief description of the purpose of each newsgroup. Please select the appropriate forum for your posting with the newsgroup's purpose in mind. The groups designated as "Scientific Interest Group" are for discussions of professional interest in the area designated by the newsgroup name, i.e., population biology issues should obviously be directed to the POPULATION-BIOLOGY newsgroup.

A few guidelines on specific newsgroups:

A thumbnail description for each Bionet group is listed at http://www.bio.net/, the Bionet main website. Find in the Charters folder, details for most newsgroups on the desired discussion topics.

BIONEWS/bionet.announce: This is a moderated newsgroup designed to be low-volume, high content and intended primarily for announcements of interest to most users on the network, e.g., for general announcements such as for scientific meetings, courses, etc. We recommend that ALL participants subscribe to this newsgroup to keep up with the items above and also to receive the latest information about changes to BIOSCI/bionet.

BIOFORUM/bionet.general: BIOFORUM is intended for discussions on topics that do not fit in to any of the specialty newsgroups. If you want to start a new newsgroup, you might begin by trying to raise interest through a discussion in this forum. Be aware that this newsgroup is by design one of the most "chatty" forums in the BIOSCI network.

BIO-SOFTWARE: Intended for discussions about software in the biological sciences. There are other Usenet newsgroups and mailing lists for questions about word processors, etc., i.e., for general purpose software. BIO-SOFTWARE is intended for discussions about software for biologists. For Usenet users only, please note that there is an accompanying newsgroup bionet.software.sources used for distributing biological software source code and binaries. This service is not available by e-mail.

COMPUTATIONAL-BIOLOGY: This newsgroup is moderated, i.e., postings made to the group are reviewed by a moderator before being distributed.

EMPLOYMENT: These are the posting regulations for EMPLOYMENT/bionet.jobs as formulated by the U.S. National Science Foundation. Readers outside of the U.S. should check with their local network authorities to determine what rules apply to their usage. EMPLOYMENT/bionet.jobs is to be used for the posting of job openings in the biological sciences or professional level jobs that support the work of biological scientists (such as for computer/systems programming/support). There are no restrictions on the content of the postings if these jobs are in the non-profit sector. Individuals regardless of their place of employment may post their CVs/resumes to this newsgroup or simply place a request for work if they are looking for jobs in this area of endeavor. Commercial companies can post jobs intended for professional people in the areas just mentioned provided that the postings are limited to the format described below. Extended commercial job/benefit descriptions and promotional material are not allowed, nor may commercial firms post openings for non-professional positions (if in doubt about the appropriateness of a posting, please check with biosci-help@net.bio.net before proceeding).

Commercial job posting format

The posting should include 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.

Most other BIOSCI newsgroups are dedicated to professional discussions in the area defined by the name of the newsgroup. You are free to post anything of interest within the specialty served by the newsgroup. Please note that the lack of face-to-face contact often emboldens some of our readers. While we can wish that everyone learned manners in grade school or at home, please be aware that discussions can sometimes become a bit more heated than a new user might be accustomed to (our readership is usually composed of "sober" Ph.D.s, or so we used to think, but it appears that perhaps economic hard times have taken their toll on sobriety 8-).

NOTE: To understand what 8-) means tilt your head to the left; other variants: :-) and :-(. These symbols try to add emotional connotations to the electrons such as "that's a joke, son!"


How does public Bionet impact personal privacy?

BIOSCI/Bionet reflects and facilitates the science community's passion for public discourse to arrive at truths in an open manner that all can see and review. You should use Bionet in this spirit, and be prepared to share your views, questions and answers in a publicly visible manner. While anonymous postings are not discarded out of hand, moderators and readers expect some knowledge of the author to understand the import of your message. As a discussion or question asker, you should be prepared to provide knowledge of who you are. This is in line with general Usenet established practice. One can learn more about Usenet accepted usage from related links.

Bionet news and discussion has been archived for public use since its inception in the 1980s, with archives available for rereading and searching via the Internet search engines, Yahoo, Google, and others. The Bionet archives provide important references to science discussions and knowledge to many scientists and lay people.

Those who read and respond to your discussion have expectations of knowing who they are interacting with. If you are concerned with personal privacy please read here:

"The fact that opinions shared in Usenet newsgroups are ... like little bylined editorials published in one of the most widely read newspapers on Earth, is not news." Your Thoughts: A Permanent Public Record, Wired, 1998
"... privacy discourages information sharing between individuals which in turn can lead to mistrust and intolerance amongst people and perpetuate false information. If information can be shared widely then facts can generally be verified through many different sources and there are less chances of inaccuracies." wikipedia/Privacy
* The major issue is that of credibility. The other readers will probably take you more seriously and it is easier to build a genuine reputation around a true identity. Anonymous postings are ignored more readily than overt ones.
* Asking for help and advice on the Usenet? You'll get it more readily if the readers know who is asking.
Anonymous Usenet posting, another view

Bionet and other Usenet groups are archived at various placed around the 'Net, including Google. One needs to understand from the nature of Bionet, Usenet and public science discussions that personal privacy is at odds with use of these public discussion groups.

As Google and the related search engines have become a common tool to discover the Internet presence of people, usually for various good uses, some of Bionet's contributors who did not fully understand these issues request editing and removal of posts from the public archives. The Bionet staff will accept such requests (see email address above), and are understanding of the importance of personal privacy issues. We cannot however promise to act on such requests, due to both the public policy that is an integral part of Bionet and Usenet, and limited resources to manage such requests. We ask that requestors have an understanding and accept that this public policy is a long standing part of science discourse and Bionet.

As noted in the first FAQ item, Bionet is for biology science discussion. Personal issues including requests for medical advice, legal advice, and such are not desired topics, and are among those where personal privacy is likely to become important to the requestor. Caveat emptor, you should be aware before you make use of Bionet groups whether your questions are suited to a public forum.

To those who ask for removal or edits of their public postings, please consider this analogy: one places a classified ad in the New York Times newspaper, then years later asks that all public libraries with archived copies of the Times remove this ad. Differences between this case and Bionet postings are that one received the value of Bionet's public news distribution for free, and Google may not yet be searching newspaper archives. Bionet has published these archives, and notices of these regularly since 1992 at bionet.announce in the BIOSCI/bionet Frequently Asked Questions; see e.g. http://groups.google.com/group/bionet.announce/browse_frm/month/1993-01


What are the restrictions on commercial activities in the BIOSCI/bionet newsgroups?

BIOSCI is funded in part by the National Science Foundation (NSF) which supports the Internet in the U.S. with U.S. taxpayer dollars. NSF is responsible for setting Acceptable Use Policy (AUP) for the the NSFNet backbone section of the Internet of which BIOSCI makes extensive use. Because of these reasons, BIOSCI users should adhere to the following guidelines.

Commercial activities on BIOSCI are in general prohibited except as noted below. People at for-profit organizations are free to read all postings made to the BIOSCI/bionet newsgroups, but must ensure that their postings to the newsgroups do not violate our guidelines.

Commercial organizations may post job openings on EMPLOYMENT/bionet.jobs subject to the format restrictions for that group. Commercial job posting format restrictions for the EMPLOYMENT/bionet.jobs newsgroup are described above under the question "Where should I post my messages?" Users who violate these format restrictions consciously risk losing their network access.

BIOSCI readers without any financial connections to a company or a product may discuss and/or post endorsements of a commercial product. However, it is standard Internet practice to include in the posting a disclaimer of any financial interest in the product/company. Note that postings to newsgroups are subject to libel laws. BIOSCI advises readers to think twice before taking potshots at products that they do not like.

BIOSCI users often post general questions about problems that might be solved through the use of a commercial product. It is EXTREMELY IMPORTANT, however, that such general questions not be answered by people affiliated with the product or company that might stand to gain a sale as a result. For example, user X may ask, "Is there a product that will allow me to separate protein A from protein B given the following properties ...?", but, if user Y works at company Z which sells a product that can accomplish this task, user Y does NOT have permission to respond to the question. Responses can only be posted by other scientists who might have experience in solving the problem in question and who do not stand to gain financially by promoting the product in question, i.e., they are not employees, consultants, or connected to the company via other financial ties. As noted above, postings endorsing commercial products should contain a customary disclaimer stating the absence of financial ties of the poster to the product/company.

Commercial companies MAY RESPOND to a public BIOSCI newsgroup if a BIOSCI user asks a question directly about one of their products, e.g., mentions it by name. The response should be limited to a factual answer of the question posed and should avoid any hint of advertising hype. Comparisons with competitors' products should be avoided completely.

Finally, as a general rule, if you are unsure about the appropriateness of your posting, before you post anything please send a copy of what you propose to post to the BIOSCI adminstrator at biosci-help@net.bio.net for review.

BIOSCI will takes steps to terminate network access to any reader who willfully violates our commercial use policies.


How does one post a message?

If you use Usenet, run your posting program (e.g., postnews or e.g., use the ":post" command in nn) and follow the prompts. Please check with your local systems administrator for details on using your local news software; general information on Usenet and how to get news software is provided further below but each news program is different. When prompted, enter the appropriate newsgroup name from the list of Usenet names in the BIOSCI info sheet. Be sure to set your news distribution to "world" (or "bionet" if the option is available) if you want your message to be seen by others. Some Usenet systems may default to "local" which means that only people on your local computer will see the message. You can limit the extent of distribution of your message by choosing other distribution options, e.g., "usa" distributes only to the U.S.A. (sometimes! - on occasion these distribution limiting features don't work for a variety of reasons). Usually pressing "?" or "h" at the Distribution: prompt will show you your options. After entering your options, you are usually placed in an editor to compose your message. After saving it and exiting the editor, one typically enters a "send" command to complete the posting process.

If you are using e-mail, first select the newsgroup that you wish to post to and find the mailing address in the BIOSCI info sheet for your region. For example, to post to the METHODS-AND-REAGENTS newsgroup you would use one of the following two addresses depending upon your location:

Address                               Serving
-------                               -------
methods@net.bio.net                   The planet Earth
Once you have entered the newsgroup mailing address on the To: line of your mail message, the rest of the process is the same as composing and sending any e-mail message. Your message will be automatically distributed to all mail recipients on the list and also distributed by Usenet news.

The BIOSCI information sheet containing the latest list of e-mail addresses for each of the above regions can be requested from biosci@net.bio.net or biosci@hgmp.mrc.ac.uk respectively.


Should I post my message to more than one newsgroup?

Generally only ONE copy of a message should be posted to the most appropriate forum. Crossposting the same message to multiple newsgroups can aggravate readers who participate by e-mail. These people will receive multiple copies of a message if they are on the mailing lists for the groups that receive the crosspostings.

Please note that software safeguards in our system which prevent mailing loops also make it difficult to use news software to both crosspost to different newsgroups AND simultaneously mail to all associated mailing lists. If you absolutely must distribute a message to different newsgroups AND their associated mailing lists, the way to do this is to e-mail a separate copy of your message to each newsgroup e-mail posting address. Including multiple mailing addresses on a single e-mail message will not crosspost to all mailing lists. Please be aware that many people read multiple groups by mail and be assured that, if two groups are related, many people who are interested in one will obviously sign up for the other group, too. Before crossposting, be certain that your message is so important that it really warrants sending multiple copies to a large number of people.


Sorting out mail - which newsgroup did an e-mail message come from?

If you use Usenet news software, all messages are sorted by newsgroup so there is no problem identifying the source. If you receive BIOSCI postings in your mail file, all postings are funneled into your one mail file merely by chronological order of posting and you must be a little discerning to follow discussions.

The best way to determine the news forum is to look at the line in the mail header that starts with "To:". For example, if you see "To: arab-gen@net.bio.net" or "To: arab-gen@hgmp.mrc.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@hgmp.mrc.ac.uk." The "From:" line in the mail header indicates who sent the message. In most cases, if you want to reply only to the author of the message, use the address on the "From:" line, and, if you want to reply to everyone on the newsgroup, use the address on the "To:" line (but please read the following sections on the BIOSCI-REQUEST address and replying to BIOSCI postings for additional information).

Please note that replies to BIOSCI messages are not automatically sent back to the newsgroup address. The default reply on most mail systems (your local mail configuration may differ) will be to reply to the address that you see on the "From:" line, i.e., only to the person who posted the original message. You must consciously decide to send a copy of your reply to the newsgroup by including the newsgroup posting address in your e-mail response. This default reply (to the original sender only) is an Internet newsgroup standard and is the opposite of that used by the BITNET LISTSERV software (for those who may be familiar with the latter; the Internet standard is designed to minimize wasted network bandwidth, i.e., to avoid the automatic, unthinking posting by many people of the same answer to a particular question).


Why do all of my postings come from "BIOSCI-REQUEST?"

Unfortunately some mail systems make all BIOSCI postings appear to come from someone named "BIOSCI-REQUEST." The BIOSCI-REQUEST@net.bio.net address was established to trap mailing error messages ("bouncers"). The address is not normally seen by BIOSCI readers in the messages that they receive. Unfortunately some proprietary (read "VMS") and other oddball mail systems misread the information used to transmit Internet e-mail messages and may end up putting the BIOSCI-REQUEST address on the From: line in the mail that you may receive. If this happens at your site and you want to reply to a message, please use either the newsgroup address on the To: line of the message or try to find the author's e-mail address elsewhere in the message (people often append this at the end of their text in their "signature"). If you send a message back to BIOSCI-REQUEST@net.bio.net, the BIOSCI managers at net.bio.net will be the only ones who will see it (we will try to forward it to the appropriate newsgroup, but would appreciate it if you would determine the correct address yourself first).


How do I reply to a BIOSCI posting?

If you are using news software, there are usually two types of reply commands. One command sends a private reply to the author of the original posting; the second sends a "followup" posting to everyone on the newsgroup. Press ? or h in your news software to find these commands. They are often noted by "r" and "R" or "r" and "f" respectively.

If you are replying to an e-mail message from BIOSCI, be sure to look carefully at the To: and Cc: lines of your reply message before sending it off. If you want the reply to be PRIVATE, only the address of the person who posted the original message (and perhaps your address and/or that of other individuals) should be on the To: and Cc: address lines. If you want the reply to be PUBLIC, be sure that the newsgroup posting address appears on either the To: or Cc: line of your response. If your mail system is a bit unorthodox and puts the "BIOSCI-REQUEST" address in your response (see the section about BIOSCI-REQUEST above), please be sure to correct this before sending your message (ask your systems administrator how to edit the To: and Cc: lines of your mail messages before sending if you do not know how to do this).

Now that you have read about all of these problems with using e-mail to participate in BIOSCI, why don't you get news software installed at your site and make life easy for yourself instead of using e-mail 8-)!! Let's look at Usenet news next!


What is Usenet?

Usenet (short for Users Network) is an electronic bulletin board network which utilizes various public domain versions of the "netnews" software for message transmission. The software can operate over physical networks ranging from as simple as a telephone UUCP link (via modem) to networks as sophisticated as the Internet. Netnews has been optimized to transmit messages without loss and also to avoid possible mail loops and other errors which plague simple electronic mail "broadcasting." We strongly encourage our users to adopt netnews software at their sites as soon as possible. News software also keeps messages segregated into their respective newsgroups, making it easier to follow the thread of a discussion. If you only use e-mail, messages from all of the newsgroups to which you subscribe will be sent to your one personal e-mail address and will be mixed in with each other and with your other personal messages. This is obviously a suboptimal means of organizing messages. With news software, you can browse the discussion topics easily, read what you want and discard the rest. Why subject yourself to having to page through a disorganized mail file message-by-message unless you really have no other choice?? News software makes the use of BIOSCI pleasant and efficient. It's time to get your organization "into the 20th Century" before it turns into the 21st Century!


How can I get news software at my site?

Contact biosci-help@net.bio.net for information on getting started with Usenet. News software can be obtained free of charge from anonymous FTP sources. Note, however (yes, here's the unfortunate catch), that news software should be installed and maintained by a trained systems administrator in most cases; it is not a task for a computer novice. You can find detailed information about Usenet using anonymous FTP from rtfm.mit.edu [18.181.0.24, but please always reference the hostname rtfm.mit.edu, as IP addresses and canonical names will change in the future, but rtfm.mit.edu will remain correct], in the /pub/usenet/news.announce.newusers directory. You may be specifically interested in the following articles:

How can I test my news or mail software?

Please DO NOT post test messages to any of the BIOSCI/bionet Usenet newsgroups. If you are unsure about whether or not your mail is working, please send test mail messages to either of our two administrative addresses, but NOT to newsgroup mailing addresses:

Address for tests                    Location
-----------------                    --------
biosci@net.bio.net                   the planet Earth
If you need to test your Usenet news software, please post test messages to the Usenet newsgroup misc.test which was created solely for this purpose.


I hear that a new bionet newsgroup was created but why isn't it at my site yet?

This could happen for a variety of reasons. When we create a new Usenet newsgroup, a "newgroup" message is sent out from net.bio.net to news administrators at Usenet sites around the world. Many sites are configured so that such newgroup messages are acted upon automatically and the group is established without human intervention. However, due to the growing volume of Usenet newsgroups, many sites have turned off automatic newgroup creation and require human intervention to create a new Usenet group in response to a newgroup message. If you know from reading BIONEWS/bionet.announce or from contacting the BIOSCI staff at biosci-help@net.bio.net that a new bionet newsgroup should be in existance, please contact your local news administrator and ask them if they acted on the newgroup message. Newgroup messages can sometimes be simply overlooked by the news administrator and sometimes they may not be received if a Usenet site upstream on the net from you had a problem and did not pass on the message. Please let your news adminstrator know that a bionet "checkgroup" message is posted on the first of each month to bionet.announce. Your news administrator can use the contents of that message to update your local list of bionet Usenet newsgroups.

Please note that all new BIOSCI/bionet newsgroups are announced on BIONEWS/bionet.announce as soon as they are ready for use. If you see this announcement, this means that the BIOSCI staff has tested the group and is (1) sure that it works, and (2) knows that it has propagated to at least some other sites in both North America and Europe. We obviously can not check for propagation to the thousands of sites on Usenet. Depending upon your source of Usenet news, there may be a delay of several days before the newgroup message reaches your site. The announcement of the newsgroup availability, however, is always sent to bionet.announce after the newgroup message has been sent and after system tests have been run.


A new bionet Usenet group has been created at my site but there are no messages in it. However, I see that messages are being sent out to the mailing list. Why do the contents differ?

If you experience the problem above, please contact your local news administrator and have them check with the site that sends you your bionet Usenet news feed. We explained in a question above that new Usenet newsgroups are created in response to a "newgroup" message which is sent out to all Usenet news administrators. It is possible that your news administrator acted on the message to create the group, but that the site which sends you bionet Usenet news did not. Having your Usenet news administrator contact the administrator at the upstream site can usually resolve the problem. If you have a problem getting a reliable bionet Usenet news feed, please contact biosci-help@net.bio.net.


How do I request or cancel e-mail subscriptions to BIOSCI newsgroups?

See the unsubscribe section for lists at http://www.bio.net/biomail/listinfo/ {listname}

How can I get a list of newsgroups or my subscriptions?

See the subscription options section for lists at http://www.bio.net/biomail/listinfo/ {listname}

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 accessible via the World Wide Web at http://www.bio.net/archives.html. The archives are sorted by date, and you can search each group individually.

All the Bionet newsgroup postings since December 1991 are stored for Gopher searching and retrieval and anonymous ftp at ftp.bio.indiana.edu, the IUBIO Archive maintained by Don Gilbert. The directory in the anonymous FTP account is usenet/bionet. This site also contains an outstanding collection of biological software and databases.


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 ftp.ncifcrf.gov in pub/methods/FAQlist.

Note, however, that maintaining such a FAQ is a gargantuan task. We also recommend searching the METHODS archives for keywords as described in the "archives" question above.

In each issue of "Trends in Biochemical Sciences" since November 1993, Dr. Hengen writes a monthly digest column of the METHODS newsgroup. This column highlights topics of special interest which were discussed recently on the newsgroup.


What journals are available on BIO-JOURNALS? How can one locate articles?

// obsolete :( //

Why are there two BIOSCI sites?

Actually, there aren't any more. Skip a paragraph:

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.

As of December 1999, there's only a single node, at the HGMP Resouyrce Center in Hinxton, near Cambridge, England. The previous paragraph is historical.

As of June 2005, Bionet/BIOSCI has moved to IUBio Archive, Indiana University, Bloomington, Indiana.


Why have I stopped getting messages?

If your computer or network connection is down, mail sent to your address will "bounce" back to the sender of the message and often to the BIOSCI-REQUEST address at net.bio.net. Given the number of people using BIOSCI around the world, this can become quite a problem, so we have to take prompt action to eliminate troublesome addresses from our mailing lists. Offending addresses are "commented out" of the mailing lists. If your system is down, there may be no way to reach you, so it is your responsibility to contact your BIOSCI distribution site and request reinstatement if you notice a lapse in distribution. There is an automatic reminder system at net.bio.net in the U.S. that sends a message to all "commented out" addresses on the mailing lists at net.bio.net each Monday for three weeks. After that if no response is received to biosci-help@net.bio.net, the bad addresses are completely removed from the mailing lists.


What should I do about mail error messages that come back when I post?

It is not uncommon when posting a mail message to a newsgroup to receive an error message from a "mailer daemon." Don't panic!! The devil is not in the employ of BIOSCI! It is a rare day when every single computer and e-mail address in the world is functional. Mail systems are programmed to alert you if mail does not go through to a particular address which could be on any of our BIOSCI lists. Rest assured that your message was received by the vast majority of readers. You may either just delete these "bouncers" or send them on to your local BIOSCI distribution node (in most cases we will probably be aware of them already). It is not uncommon to receive one or two bouncers for any e-mail posting that you make. Note once again that if everyone used news software and if we didn't have to bridge so many incompatible e-mail networks to bring the biology community together, we wouldn't have to deal with this problem.

Note that the BIOSCI-REQUEST address at net.bio.net was established to trap daemon bouncers instead of passing them back to the person who posts a message. Unfortunately due to network incompatibilities, the BIOSCI-REQUEST trapping mechanism is often disabled when the bad address is not on the Internet.


How does one start a new BIOSCI newsgroup/mailing list?

BIOSCI's goal is to promote the use of electronic communications among biologists and we are here to assist you in establishing new forums at no charge. There are currently two options - create a full newsgroup or a prototype (mailing lists only):

For full-fledged BIOSCI newsgroup status (also see "prototype" rules below)

Proposals for new groups must contain a statement of purpose for the group and the name of a person designated as discussion leader unless the group is in the service category such as METHODS, EMPLOYMENT, etc. Discussion leaders are responsible for ensuring that a reasonable level of activity is sustained on the newsgroup (see Newsgroup Termination Policy below). The discussion leader can also propose the creation of moderated newsgroups if he/she agrees to serve as moderator (this requires access to Usenet news software at the moderator's site). Proposals should be sent to biosci-help@net.bio.net.

When a proposal is received it will be posted on BIONEWS/bionet.announce. A ten day period for discussion on BIOFORUM/bionet.general will follow and precede the call for votes. After the discussion, the person proposing the newsgroup may modify or withdraw the proposal prior to the call for votes. The modified proposal will then be included in a call for votes on BIONEWS/bionet.announce. The proposal must collect 80 YES votes in 30 days and the number of YES votes must exceed the number of NO votes by at least 40 to pass.

BIOSCI management must be informed in advance of any intended efforts to advertise the newsgroup proposal in other forums. While BIOSCI wishes to inform potential users of the creation of newsgroups that might be of interest to them, promotional efforts should be focussed in forums likely to be utilized by professionals in the subject area covered by the newsgroup proposal, and should seek participation in the discussion of the proposal within bionet.general/BIOFORUM rather than promoting separate discussions in other forums to which portions of the BIOSCI readership may not have ready access.

If a proposal is not passed by the readers, there will be a three month period before it can be brought up for another vote.

Newsgroup Termination Policy
Any group with less than 52 msgs in the previous calendar year will be put on notice by posting an announcement to the newsgroup (not to bionet.announce) that it faces cancellation. It can be reprieved if 80 readers respond within two weeks (this policy will be stated in the termination announcement). It then has two months to reach a usage level of one message per 3 days or else it will be abolished. Appeals to the BIOSCI management about high content albeit low volume on the group will be considered.

Newsgroups for Professional Societies in Biology
BIOSCI will create a moderated newsgroup in the bionet.prof-society domain without voter approval for any professional society in the biological sciences which has a membership of at least 500. Smaller groups must go through the regular BIOSCI/bionet newsgroup creation process. Because these groups are not discussion forums, they will be exempted from the 52 message per year minimum posting limit and would only be discontinued if the society in question no longer wishes to use them. If usage seems extremely low on any group in the bionet.prof-society domain, the BIOSCI/bionet staff will contact the society in question and ensure that the newsgroup is still wanted.

BIOSCI "prototype" newsgroup creation policy

We will be happy to establish and administer a straight mailing list without an associated Usenet newsgroup for a six month trial period for anyone that wants to try to form a new electronic community in the biological sciences (We stress that the topics are limited to professional communications though.).

The mailing lists will be maintained initially only at net.bio.net instead of at both BIOSCI sites. It will be the responsibility of the person who proposes the list to get it up and running within the six month period. They will have to handle promotion; our involvement at BIOSCI at net.bio.net will be limited to creating the list, putting out one announcement about it, and handling subscription requests.

After six months, the list will be put out for discussion and a vote according to our procedures for full-fledged newsgroups above (unless the organizer decides to bow out). If it passes it will become a full-fledged BIOSCI newsgroup at both net.bio.net and hgmp.mrc.ac.uk and will also have a parallel Usenet newsgroup. If it fails, the prototype mailing list at net.bio.net will be shut down.

Note that this service does not preclude people who have an idea that has widespread appeal from following our current newsgroup creation policy and going to a vote after a 10 day discussion.

If you have an idea for a prototype newsgroup, please send it to biosci-help@net.bio.net.


How can I list my address information in the BIOSCI user directory?

// obsolete :( //

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

What are all of these references to FTP, WAIS, Gopher, and WWW/Mosaic?

FTP

FTP stands for File Transfer Protocol and is a method for transmitting files at high speed over the Internet. There are also e-mail servers at various BITNET sites which provide e-mail access to FTP archives. Send the word "HELP" to BITFTP@PUCC.BITNET for details. A sample session of using FTP to access the BIOSCI archives follows. Keyboard input is underlined. ### highlights comments about the procedure.

net<1>ftp net.bio.net     ### connect to the BIOSCI computer
      ---------------
Connected to net.bio.net.
220 net.bio.net FTP server (Version wu-2.6.0(1) Fri Oct 22 14:11:53 BST 1999) ready.
Name (net.bio.net:kristoff): anonymous     ### login as anonymous
                             ---------
331 Guest login ok, send your complete e-mail address 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 Opening ASCII mode data connection for /bin/ls (134.172.2.69,3225)
total 10
bin
dev
etc
pub
usr
226 ASCII Transfer complete.
271 bytes received in 0.024 seconds (10.96 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> dir     ### list the files again.  BIOSCI archives are in BIOSCI 8-)
     --     ### Be sure to strictly follow upper/lower case in filenames
            ### when accessing FTP sites running UNIX such as net.bio.net
200 PORT command successful.
150 ASCII data connection for /bin/ls (134.172.2.69,3227) (0 bytes).
BIOSCI
README
doc
dos
mac
unix
vms
226 ASCII Transfer complete.
42 bytes received in 0.05 seconds (0.82 Kbytes/s)
ftp> cd BIOSCI
     ---------
250 CWD command successful.
ftp> ls
     --
200 PORT command successful.
150 ASCII data connection for /bin/ls (134.172.2.69,3228) (0 bytes).
ADDRESSES
AGEING
AGROFORESTRY
ARABIDOPSIS
BIO-INFO
BIO-JOURNALS
BIO-MATRIX
BIO-SOFTWARE
BIOFORUM
BIONEWS
CHROMOSOME-22
COMPUTATIONAL-BIOLOGY
EMBL-DATABANK
EMPLOYMENT
GDB
GENBANK-BB
GENETIC-LINKAGE
HIV-BIOL
HUMAN-GENOME
IMMUNOLOGY
JRNLNOTE
METHDS-REAGNTS
MOLECULAR-EVOLUTION
NEUROSCIENCE
PLANT-BIOLOGY
POPULATION-BIOLOGY
PROTEIN-ANALYSIS
PROTEIN-CRYSTALLOGRAPHY
SCIENCE-RESOURCES
TROPICAL-BIOLOGY
VIROLOGY
WOMENINBIOLOGY
biosci-uk.infosheet
biosci-us.infosheet
biosci.FAQ
226 ASCII Transfer complete.
562 bytes received in 0.1 seconds (5.5 Kbytes/s)
ftp> cd PROTEIN-ANALYSIS   ### We want to look at PROTEIN-ANALYSIS archives
     -------------------
250 CWD command successful.
ftp> ls
     --
200 PORT command successful.
150 ASCII data connection for /bin/ls (134.172.2.69,3233) (0 bytes).
8912
9001
9002
9003
9004
9005
9006
9007
9008
9009
9010
9011
9012
9101
9102
9103
9104
9105
9106
9107
9108
9109
9110
9111
9112
9201
9202
9203
9204
9205
9206
9207
9208
9209
9210
9211
current
226 ASCII Transfer complete.
225 bytes received in 0.12 seconds (1.8 Kbytes/s)
ftp> get 9211     ### Retrieve the file for November 1992.
     --------
200 PORT command successful.
150 ASCII data connection for 9211 (134.172.2.69,3234) (208763 bytes).
226 ASCII Transfer complete.
local: 9211 remote: 9211
213849 bytes received in 1.4 seconds (1.5e+02 Kbytes/s)
ftp> bye     ### End the FTP session.  Some systems use quit or exit.
     ---
221 Goodbye.
Liberal use of the ? key and help at the ftp> prompt will provide information on other options.

WAIS

WAIS stands for Wide Area Information Server. It allowed sophisticated search and retrieval, but the WWW has made it wither and die.

Gopher

Gopher provided a user friendly front end to wais, ftp, and other information sources, but again has been largely superceded by the World Wide Web.

WWW/Mosaic

The World-Wide Web (WWW) has become the latest hot network item. It's now so prevalnet in the public psyche that it's probably not worth us trying to explain what it is, because by the time you read this, it'll probably be out of date.


Please help me find the e-mail address for Dr. ...

If you can not get this information by calling the person in question, there are several other resources that can be of help. As of May 1993, BIOSCI at net.bio.net began running a BIOSCI user address directory which can be accessed through gopher to net.bio.net or via WAIS or waismail. The WAIS source is called biologists-addresses.src and is updated daily. See the FAQ section entitled "How do I find back issues of BIOSCI postings?" for information on WAIS and waismail access. Instructions for using the address source are included in the waismail help file which can be retrieved by sending the word "help" to waismail@net.bio.net (leave the Subject: line of your message blank.)

The second easy route is to post your request to the BIONAUTS/bionet.users.addresses newsgroup managed by Rob Harper. Odds are that you will get a response fairly promptly, but, if not, there are other routes described below.

If the person in question has posted to BIOSCI/bionet or another Usenet newsgroup, they will be listed in the "usenet-addresses" WAIS source. If you are on the Internet, telnet to quake.think.com and login as "wais" (lowercase). After entering your terminal type, select the usenet-addresses source from the list presented to you (use the up-arrow key to get there more quickly since it is near the end of a long list). When the source is highlighted, press the return key and then enter the person's surname at the Keywords: prompt to begin the search. Available commands are listed at the bottom of the screen. When finished, press "s" to return to the source menu and then "q" to quit.

For those who do not have access to the Internet, the usenet-addresses source can also be accessed by e-mail. Please send mail to mail-server@rtfm.mit.edu with "help" in the body of the message in order to receive more information.

Another source of information for finding Internet, but not BITNET, addresses is netfind. Use the command

        telnet bruno.cs.colorado.edu
and login as "netfind" without a password. The program is menu-driven and pretty self-explanatory. Unfortunately it is not available to people on BITNET.

Gopher is also useful in the address search. For example, Dan Jacobson provides access to several directories of biologists at his gopher hole on merlot.gdb.org.

None of the above methods is guaranteed to return you an answer, so you may still have to resort to the telephone or (groan) regular mail to make contact 8-(.


How do I report a problem in a biological data base?

(answer contributed by Dr. John Garavelli of PIR)

Brookhaven Protein Data Bank    bionet.xtallography
PIR or SWISS-PROT               bionet.molbio.proteins
NCBI GenBank DataBank           bionet.molbio.genbank
EMBL Databank                   bionet.molbio.embldatabank
Human Genome Database (GDB)     bionet.molbio.gdb
Museums and Herbaria            bionet.plants, or private inquiry
                                  to beach@huh.harvard.edu
Since staff members of these databases usually monitor the corresponding newsgroups fairly closely, a posting about a problem on the appropriate board will usually get a response from someone on a database staff fairly quickly. Problems that might not be of general interest or corrections to particular entries should be directed as follows.

Database      address
--------      -------
Brookhaven    pdb@chm.chm.bnl.gov, pdb@bnlchm.bitnet
PIR           postmaster@nbrf.georgetown.edu, postmast@gunbrf.bitnet
SWISS-PROT    bairoch@cmu.unige.ch
GenBank       update@ncbi.nlm.nih.gov
EMBL          update@embl-heidelberg.de
GDB           help@welch.jhu.edu
Herbaria      beach@huh.harvard.edu

What about submitting sequence data to GenBank, EMBL, DDBJ or PIR?

(answer contributed by Dr. John Garavelli of PIR)

Researchers should submit nucleotide sequence data directly to GenBank or EMBL for assignment of an accession number prior to publication. Derived amino acid sequence data may also be included at the same time. Amino acid sequence data submitted in this way to GenBank, EMBL or DDBJ is eventually passed on to PIR, and need not be submitted separately to PIR. This is done so correct cross-references can be made between nucleotide and protein sequence accession numbers. All other determined amino acid sequences may be submitted directly to PIR when the authors permit their public release prior to publication.

Authors are strongly urged to use the sequence submission software package AUTHORIN to submit their sequence data to the databanks; a free copy (for either the IBM PC or Macintosh) can be obtained by sending your request and regular postal mailing address to:

        authorin@ncbi.nlm.nih.gov

Please be sure to specify the IBM or Mac version when sending your request.

Japanese authors who use the NEC 9801 PC should communicate directly with DDBJ, as these machines use a version of DOS that is significantly different enough to render the discs unreadable on MS-DOS computers here. The staff at DDBJ will forward the data to the appropriate databank via electronic mail. DDBJ may be contacted at:

        ddbjsubs@flat.nig.ac.jp
The address for GenBank submissions is:
   U.S. mail (for submissions on diskette, indicate whether Mac or PC):
                GenBank Submissions
                National Center for Biotechnology Information
                Bldg. 38A, Room 8N-803
                8600 Rockville Pike
                Bethesda, MD 20894

   E-mail submission of new sequences:  gb-sub@ncbi.nlm.nih.gov

   E-mail submission of updates:        update@ncbi.nlm.nih.gov
The address for EMBL submissions is:
	EMBL Data Submissions
	Postfach 10.2209
	D-6900, Heidelburg
	Federal Republic of Germany
	Telephone (+49) 6221-387-258
	Electronic mail: DATASUBS@EMBL-Heidelberg.DE
The address for DDBJ submissions is:
	DNA Database of Japan
	Center for Genetic Information Research
	National Institute of Genetics
	111 Yata
	Mishima, Shizuoka 411
	JAPAN
	Telephone (+81) 559-75-3651
	Electronic mail:  ddbjsubs@flat.nig.ac.jp
The address for PIR submissions is:
	PIR Submissions
	National Biomedical Research Foundation
	3900 Reservoir Road, NW
	Washington, DC  20007
	U.S.A.
	Telephone: (202) 687-2121
	Electronic mail:  FILESERV@GUNBRF.BITNET, FILESERV@NBRF.Georgetown.EDU
While we would again urge that AUTHORIN be used as the first choice in data submission tools, the GenBank/EMBL/PIR Data Submission Form can be obtained by sending a message consisting of the words

	SEND SUBFORM
to the PIR FILESERV address. This form can be filled in using any text editor, saved in ASCII (text) format, and mailed electronically or on disk to the databanks.

Please, do not submit data either by electronic mail or on disk in files that are formatted for word processing programs. Such files are almost always unreadable except by systems with the same configuration of computer, operating system and word-processing program. For files sent by disk, either DOS or Mac formatted disks can be used but regular "double density" disks are preferred to "high density" disks.


Send comments to us at archive@iubio.bio.indiana.edu