Archive-name: biology/guide Last-modified: 17 April 1993 Version: 1.2 A Biologist's Guide to Internet Resources Version 1.2, 17 April 1993 Recent important changes are noted with "*" and those new to this version are noted with "+" in the margin of the table of contents. As ever, comments and suggestions for additional material are more than welcome. Archive keepers: I could really use help fleshing out section 3.2 !! Una Smith Department of Biology smith-una@yale.edu Yale University New Haven, Connecticut 06511 -*- 0. Contents 1. Conditions of Use + 2. Networking 1. Some Mind-Boggling Statistics + 2. Netiquette + 3. Usenet *+ 1. Newsgroups of Special Interest 2. The Bionet and Bit.listserv Domains * 3. Other Biology Domains *+ 4. Sources of Information 4. Listserver Mailing Lists 1. Commands 2. Archives 3. Gateways into Usenet *+ 5. Other Mailing Lists *+ 6. Newsletters * 7. Directories 3. Information Archives * 1. Bibliographies *+ 2. List of Archives 1. Online Help * 2. Search Engines + 3. Software Archives 4. Access Tools 1. Telnet 2. Anonymous Ftp 3. Gopher 4. Archie 5. Veronica 6. WAIS 7. The Web 4. Commercial Services *+ 5. Useful and Important FAQs + 1. What's a FAQ and where can I get one? + 2. Does anyone have an e-mail address for X? 3. How do I find a good graduate program? 4. Where can I get old newsgroup/mailing list articles? 5. Where can I find biology-related job announcements? + A. Assorted Listserver Mailing Lists + B. Bibliography + C. Contributors -*- 1. Conditions of Use This FAQ may be freely distributed, provided that it is not edited in any way, beyond removal of the headers. It may be freely adapted, provided that the adapted document is neither represented as being this FAQ, nor as being written by me. Please cite this FAQ as the original document. This FAQ may not be sold for profit, nor included in any document that is sold for profit, in either the original or an adapted form, without permission from the author. However, its use is explicitly permitted in paper-based journals or newsletters that are provided to subscribers at or below the cost of printing and mailing. If you make significant use of any document, data or software provided via the Internet, the authors would be grateful if you would cite them or otherwise acknowledge their efforts. Virtually every service or resource mentioned in this FAQ (and this FAQ itself) is the un-paid, personal effort of scientists and graduate students. This FAQ may be cited as: Smith, Una R. (1993) "A Biologist's Guide to the Internet." Usenet news.answers. Available via anonymous ftp from rtfm.mit.edu in pub/usenet/news.answers/biology/guide. ~20 pages. The most current version of this FAQ is posted monthly in the Usenet newsgroups sci.bio, bionet.general and news.answers, and archived as "pub/usenet/news.answers/biology/guide" in the anonymous ftp archive on rtfm.mit.edu. -*- 2. Networking The Internet has become an excellent place in which to look for academic and professional position announcements, conference announcements and calls for papers, and important notices about recent events in many fields of biology, especially molecular biology. Generally, notices of all forms appear on the Internet well in advance of traditional journals and newsletters. Increasingly, scientific interest groups, both formal and informal ones, maintain electronic discussion groups, directories, digests and newsletters. These resources are distributed in three principal ways: via Usenet newsgroups, (automated) listserver mailing lists, and mailing lists administered by real people. Increasingly, the two forms of mailing list have "gateways" into Usenet newsgroups. -*- 2.1. Some Mind-Boggling Statistics Recently, approximately 300 thousand articles per week were distributed worldwide through Usenet (Anonymous 1993). This traffic constituted roughly 40 megabytes per day of announcements, questions and answers, advice and bits of program code, references, heated debates, and data in various formats. There are now nearly a million registered computers on the Internet, and thus tens of millions of people; an estimated 7 million people have accounts on 65 thousand computers carrying Usenet, and nearly 2 million people read Usenet news at least occasionally (Reid 1993b). There are several thousand world-wide Usenet newsgroups, several thousand listserver mailing lists, and several thousand other, generally small, mailing lists. It appears that there are on the order of 10 thousand people who read biology-related Usenet newsgroups (Reid 1993a), and there may be that many using mailing lists for topics in biology. All together, there are a hundred or so newsgroups and mailing lists (via listservers or others) that may be of particular interest to biologists. Most are named below. -*- 2.2. Netiquette The professionally-oriented newsgroups and mailing lists follow certain conventions of etiquette. These are none other than those used by most people at public events such as academic conferences. In fact, most of the science-related newsgroups (and mailing lists) are very much like mid-sized meetings of any professional society, except that they never end. The participants come and go as they please, but the discussions and exchange of ideas and information continue as though they had a life of their own. Submitted articles tend to be of the following types: * Discussions on topics of general interest. Discussions on specific topics, techniques, or organisms are also frequent. * Announcements of upcoming conferences or other events, or grant deadlines. In Usenet, announcments can be set to expire (and thus disappear from the list of current articles), and may be limited in their distribution so that they are seen only by readers in the appropriate organization or geographical area. * Academic and professional job announcements, including many graduate fellowships. These are generally posted in newsgroups/mailing lists reserved for such notices, often in advance of publication elsewhere. * Reports or comments on new books, papers, methods or software. Full citation of sources is always appropriate and appreciated. Requests for references or comments are also welcome and, when posed as specific questions of general interest, often lead to interesting discussions. Unacceptable articles include: * commercial advertisements, political lobbying messages, and anything not pertaining directly to the topic or purview of the newsgroup or mailing list. Discussions about some commercial products, especially books and software, are generally allowed as long as they do not constitute advertisements. * Requests by students for explicit answers to homework and exam or essay questions are generally not welcome. Requests for help understanding problems in biology are welcome, but the requester should demonstrate at least a basic understanding of the question. Some helpful suggestions: * Always include your full name and e-mail address Put these at the end of your message, with your usual signature. You might want to use a .signature file (standard on most Unix systems, also implemented for Usenet and e-mail readers under VM/CMS) to make this automatic. This is necessary because strange things often happen to headers in e-mail or Usenet articles sent from one network to another. * Send private replies whenever appropriate Answers to very esoteric questions are often best sent directly to the person who asked for help, rather than to the newsgroup; the choice of whether to post a (public) reply or send (private) e-mail is a personal decision. If you send a reply by e-mail, and would prefer that it be kept private, you should say so in your note, because otherwise the other person may share your comments with others. If the original poster promises to post a summary at the outset, then all replies should be sent by e-mail, unless they constitute an important re-direction of the original question. * Summarize the replies to your article Whenever a question or request for information results in many replies, it is expected that the person who posted the original article will compile and post a summary of the responses. * Use care when writing summaries - The "best" answers should come first. - All answers should be separated clearly, and nicely formatted. - Redundant, irrelevant or verbose comments, and errors of fact or spelling should be edited out. It is appropriate to use square brackets and dots to indicate editing [...]. - Exercise discretion and tact, to ensure a fair and accurate summary. - The contributors of each answer (individually or as a group) should be named, unless they asked that their names be withheld. * Avoid starting "flame wars", a.k.a. nasty arguments If something you read angers you, save it for a few hours while you do something else (don't reply on an empty stomach). Go back to it when you are calm and relaxed (and you've have thought of a good rebuttal). * Be generous when interpreting the arguments of others. * Avoid jargon, write as though addressing an educated lay audience. * Remember, the exercise will be good for you. If you simply must say something highly critical, consider sending it via personal e-mail, rather than posting or mailing to the group. -*- 2.3. Usenet Definition: Usenet is a convention, in every sense of the word. Usenet is a system of organized newsgroups sharing many features with traditional newsletters, mailing lists and focused scientific societies. Usenet is Internet-based (although before the Internet existed it was distributed via UUCP), and strongly developed so that end users need know only how to interact with the particular Usenet "reader" program on their computers. Features of Usenet that make it far superior to the two types of mailing lists include the threading of all articles on a related topic, the ability to control the distribution of posted articles to hierarchical levels (e.g., the author's university, state, country, or continent), the ability to cancel an article even after it has been distributed, and automatic expiration of dated articles. Usenet is "free", but not cheap; because it requires a lot of computer disk space, and a certain amount of installation and regular maintenance work by a system administrator, not all computer systems carry Usenet. If Usenet is carried locally, it may still be necessary to prod the local Usenet administrator to add the bionet and bit.listserv newsgroups to the local "feed". See Spafford (1993) for the definitive history of Usenet and a list of software for virtually every type of computer. -*- 2.3.1. Newsgroups of Special Interest An F after the newsgroup name indicates a FAQ is available. An M indicates that the newsgroup is moderated. A G indicates that the newsgroup has a gateway to a parallel mailing list. See notes below for details. alt.bbs.internet F Announcements of new Internet services alt.cyb-sys Cybernetics and Systems alt.info-theory Information theory a la Shannon alt.internet.access.wanted F Help getting full Internet access alt.internet.services F Announcements of new Internet resources alt.lang.sas SAS discussion alt.native Indigenous peoples alt.sci.* [6 groups] alt.sustainable.agriculture bionet.agroforestry G Agroforestry research bionet.announce FGM Announcements bionet.biology.computational GM Comp. and math. applications in biology bionet.biology.n2-fixation G Biological nitrogen fixation bionet.biology.tropical G Tropical biology and ecology bionet.general FG General discussion bionet.genome.chrom22 G Chromosome 22 of humans bionet.genome.arabidopsis G Arabidopsis thaliana genome project bionet.immunology G Research in immunology bionet.info-theory FG Information theory applied to biology bionet.jobs G Job opportunities in biology bionet.journals.contents GM Biological journal TOCs bionet.journals.note G Publication issues in biology bionet.molbio.ageing G Cellular and organismal ageing bionet.molbio.bio-matrix G Computer searches of biological databases bionet.molbio.embldatabank G Info about the EMBL Nucleic acid database bionet.molbio.evolution G Evolution, especially molecular bionet.molbio.gdb G The GDB database bionet.molbio.genbank G The GenBank nucleic acid database bionet.molbio.genbank.updates GM Sequence data for local updates bionet.molbio.gene-linkage G Genetic linkage analysis. bionet.molbio.genome-program G Human Genome Program issues bionet.molbio.methds-reagnts G Tips on lab techniques and materials bionet.molbio.hiv G The molecular biology of HIV bionet.molbio.proteins G Proteins and protein database searches bionet.molbio.rapd G Randomly Amplified Polymorphic DNA bionet.neuroscience G Research issues in the neurosciences bionet.plants G Plant biology, inc. genetics and ecology bionet.population-bio G Population biology, especially theory bionet.sci-resources GM Information about funding agencies, etc. bionet.software G Software for biology, esp. free/shareware bionet.software.sources GM Software source codes bionet.users.addresses G Help locating biologists who use e-mail bionet.virology G Research in virology bionet.women-in-bio G Discussion by and about women in biology bionet.xtallography G Protein crystallography bit.listserv.biosph-l G Biosphere, ecology, Discussion List bit.listserv.devel-l G Tech. Transfer in Internat. Development bit.listserv.ecolog-l G Ecological Society of America bit.listserv.ethology G Ethology List bit.listserv.info-gcg G GCG Genetics Software Discussion bit.listserv.sas-l G SAS Discussion bit.listserv.scifraud G Discussion of Fraud in Science bit.listserv.stat-l G Statistical consulting bit.listserv.uigis-l G User Interface for GIS bit.listserv.vpiej-l G Electronic Publishing Discussion List comp.infosystems.gis G Geograpical Information Systems comp.infosystems.gopher F The Internet gopher access tool comp.infosystems.wais F The Internet WAIS access tool comp.text.tex F TeX, LaTeX and related text format systems comp.theory.cell-automata G Cellular automata research comp.theory.dynamic-sys G Ergodic theory and dynamic systems comp.theory.self-org-sys G Topics related to self-organization info.grass.programmer GM GRASS GIS programmer issues info.grass.user GM GRASS GIS user issues news.announce.important FM news.announce.newusers F news.answers FM All FAQ documents news.lists FM sci.answers FM FAQ documents pertaining to science sci.anthropology sci.archaeology sci.bio F sci.bio.technology G Any topic relating to biotechnology sci.environment sci.geo.* [3 groups] sci.* [approx. 60 other newsgroups] Note 1: The bionet.* groups are also mailing lists. To subscribe, send e-mail to biosci@daresbury.ac.uk if you live in Europe, or to biosci@net.bio.net otherwise. Charters (brief descriptions) of some of these groups are given in the BIOSCI FAQ (posted in bionet.announce and available via anonymous ftp from net.bio.net in the directory pub/BIOSCI/ or by e-mail on request from biosci@net.bio.net). Note 2: The bit.listserv.* groups are also Bitnet "listserver" mailing lists. Appendix A includes 100 or so listserver mailing lists, and charters for each of these groups can be obtained from the listserver (see section 2.4) that administers them. Note 3: The comp.theory.* groups are also Internet "inet" mailing lists. Send e-mail to Erik Fair , or see the list of Internet mailing lists posted regularly in news.answers for details. Note 4: The info.* groups are mailing lists with gateways into Usenet at the University of Illinois. See section 2.5 for e-mail subscription information, or ask your local Usenet administrator to get these groups. Note 5: Sci.bio.technology is also a listserv mailing list. -*- 2.3.2. The Bionet and Bit.listserv Domains Unlike most Usenet newsgroups, the newsgroups in these two domains all have gateways into mailing lists. The cross-posting of articles to more than one newsgroup is discouraged, since at this time the e-mail subscribers will get multiple copies of any cross-posted articles. As their names imply, the bit.listserv newsgroups started out as (and remain) listserver mailing lists. A few "main-stream" Usenet newsgroups, comp.infosystems.gis for instance, are also listserver mailing lists. Neither the bionet nor the bit.listserv domains are main-stream Usenet domains, meaning that they do not conform to all Usenet conventions, and consequently are carried by no more than 30-50% of Usenet sites. This is not necessarily a bad thing, since virtually no readers at most sites are biologists, and e-mail subscriptions are available. If your site carries Usenet, but not either of these domains, a simple request to your Usenet administrator might be all that's needed to get them too. The mailing lists associated with the bionet newsgroups are administered by David Kristofferson's BIOSCI service, which is funded by the US National Science Foundation for the express purpose of supporting computer networking among biologists. By providing personal e-mail subscriptions to the bionet newsgroups, BIOSCI has effectively formed a bridge between biologists with e-mail and those with Usenet (once familiar with Usenet, few people have the patience for e-mail subscriptions). David Kristofferson is responsible for proposing the creation of the bionet domain of Usenet and starting many of the bionet newsgroups. Requests for e-mail subscriptions to bionet newsgroups are handled by biosci@net.bio.net (for requests from the Americas) and biosci@daresbury.ac.uk (for all others). A FAQ describing administrative details of the bionet newsgroups is available from biosci@net.bio.net or biosci@daresbury.ac.uk, and appears regularly in the bionet.announce newsgroup. Note: rules for forming new bionet newsgroups differ somewhat from those used elsewhere in Usenet. Various other FAQs dealing with the interests of specific newsgroups are posted in those newsgroups. Tom Schneider's FAQ for bionet.info-theory is available by anonymous ftp from ncifcrf.gov: look for the file bionet.info-theory.faq in the pub/delila/ directory. -*- 2.3.3. Other Biology Domains The European Molecular Biology Network (EMBnet) runs a group of Usenet- style newsgroups (domain name embnet.*) that are available in Europe. E-mail subscriptions are also available, and these newsgroups can be read and searched via gopher and WAIS on bioftp.unibas.ch. The Long Term Ecological Research Network (LTERnet) has a similar setup (domain name lter.*). Ask helper@lternet.edu about e-mail subscriptions, or check the gopher on lternet.edu. -*- 2.3.4. Sources of Information Usenet FAQs, including this one, are archived on a number of publicly accessible archives, and can be retrieved via anonymous ftp or e-mail. The main FAQ archive is on rtfm.mit.edu. To retrieve the latest version of this FAQ from rtfm.mit.edu, connect there using ftp, give the username "anonymous" and your e-mail address as the password. Change to the pub/usenet/news.answers/biology directory and use the "get" command to copy the file named "guide" to your own computer. If you have only e-mail access to the Internet, you can send an e-mail message to mail-server@rtfm.mit.edu, containing the message help index to receive instructions on how to search the archive and receive files from it by e-mail. You are strongly encouraged to read the following introductory and etiquette FAQs before posting any messages to any newsgroup. They are what might be considered the "mandatory course" for new users. Also listed are other FAQs of general use or interest to biologists. The files below are stored in pub/usenet/news.answers/ in the anonymous ftp archive on rtfm.mit.edu, and are posted frequently to the Usenet newsgroups news.answers, comp.answers and sci.answers, as appropriate. Title Archive filename -------------------------------------------------------------------- Introductory information What is Usenet? what-is-usenet/part1 Answers to Frequently Asked Questions usenet-faq/part1 about Usenet Introduction to news.announce news-announce-intro/part1 Etiquette issues A Primer on How to Work With the usenet-primer/part1 Usenet Community Emily Postnews Answers Your Questions emily-postnews/part1 on Netiquette Hints on writing style for Usenet usenet-writing-style/part1 Rules for posting to Usenet posting-rules/part1 Technical issues How to Create a New Usenet Newsgroup creating-newsgroups/part1 USENET Software: History and Sources usenet-software/part1 How to become a USENET site site-setup NetNews/Listserv Gateway Policy bit/policy UNIX BBS Software FAQ with Answers unix-faq/bbs-software Introduction to the news.answers news-answers/introduction newsgroup Instructions for posting to news.answers news-answers/guidelines Anonymous FTP List - FAQ ftp-list/faq Mail Archive Server (MAS) software list mas-software General resources Gopher [FAQ] gopher-faq FAQ: How to find people's E-mail addresses finding-addresses FAQ: College Email Addresses college-email/part[1-3] Top-level international country top-level-domains domain names How to Get Information about Networks network-info/part1 Public Dialup Internet Access List pdial Updated Internet Services List internet-services Mailing Lists Available in Usenet bit/gatelist How to find sources finding-sources Anonymous FTP List - Sites ftp-list/sites[1-3] Scientific resources A Biologist's Guide to the Internet biology/guide Biological Information Theory biology/info-theory and Chowder Society Sources of Meteorological Data FAQ weather-data Computer Graphics Resource Listing graphics/resources-list/ part[1-3] Space FAQ space/* [15 parts] Amos Bairoch has assembled a very useful list of Molecular Biology Archives and Mailservers which is available on many ftp sites. Paul Hengen has written a FAQ for the bionet.molbio.methds-reagnts newsgroup. It is available via anonymous ftp on ncifcrf.gov in pub/methods/FAQlist and on net.bio.net. -*- 2.4. Listserver Mailing Lists Appendix A at the end of this FAQ includes most listserver mailing lists of particular interest or use to biologists. Internet addresses are given whenever possible, and all addresses are in standard Internet format, with the exception that portions of the Internet node names that reflect original Bitnet node names are given in uppercase. Listservers were developed many years ago on Bitnet, when certain computer programs named "listserv" were created and allowed to act like regular computer users: receiving and sending out e-mail, and keeping files. These listservers were given the task of maintaining electronic mailing lists, handling all membership requests (subscriptions and cancellation of subscriptions, and so on). Many list owners collect monthly logs of all messages sent to the list, and some also provide files of other information. The listserver will send "back issue" logs and other files on request. -*- 2.4.1. Commands Being computer programs, with nothing else to do, listservers just sit and wait for e-mail to arrive, read it, and perform the appropriate task immediately. They respond only to a small set of commands. A summary (Thomas 1992) of these commands can be retrieved by sending the message "send listserv refcard" to any listserver. The main listserver is listserv@BITNIC.educom.edu, but there are many listservers around the world. Specificially, there is one on each computer for which a mailing list is mentioned in appendix A. Most listservers maintain more than one mailing list. To subscribe to any of these mailing lists, people send e-mail to the listserver at the same address. For example, subscriptions to the Smithsonian Institution's biological conservation list, CONSLINK, may be obtained by sending the message subscribe conslink to listserv@SIVM.si.edu. Send subscription and other administrative requests to the listserver, not the list; e-mail messages sent directly to the mailing list will (generally) be sent to all the list subscribers. Only the listserver can process subscription requests, and the listserver only knows about requests that it receives directly. -*- 2.4.2. Archives In addition to handling the membership requests for particular mailing lists, most listservers also archive all messages sent to each list in monthly log files. These files, along with other items contributed by list subscribers, are archived by the listserver and can be retrieved by e-mail. The listserver at SIVM.si.edu keeps an especially good archive of various directories of conservation organizations and field stations, several newsletters, and a large collection of bibliographic references relating to biological conservation. The listserver at UMDD.umd.edu keeps an archive of job and conference announcements submitted to the Ecological Society of America. Commands for retrieving files from listserver archives are described in the listserver command reference guide (Thomas 1992), and include: review index send filelist send listserv refcard help -*- 2.4.3. Gateways into Usenet Some of the listserver mailing lists in appendix A below are also Usenet newsgroups: biosph-l@UBVM.cc.buffalo.edu is bit.listserv.biosph-l biotech@UMDD.umd.edu is sci.bio.technology ecolog-l@UMDD.umd.edu is bit.listserv.ecolog-l devel-l@AUVM.american.edu is bit.listserv.devel-l ethology@FINHUTC.hut.fi is bit.listserv.ethology gis-l@UBVM.cc.buffalo.edu is comp.infosystems.gis info-gcg@UTORONTO.bitnet is bit.listserv.info-gcg info-tex@ is comp.text.tex (gate is list-->group only) sas-l@UGA.cc.uga.edu is bit.listserv.sas-l stat-l@vm1.mcgill.ca is bit.listserv.stat-l uigis-l@UBVM.cc.buffalo.edu is bit.listserv.uigis-l vpiej-l@VTVM1.cc.vt.edu is bit.listserv.vpiej-l American University has established itself as the clearing house and semi-official keeper of automated gateways between listserver mailing lists and Usenet newsgroups. Questions about the procedure for establishing a gateway for any listserver mailing list may be posted to the Usenet newsgroup bit.admin or sent to news-admin@AUVM.american.edu. A FAQ on this topic appears regularly in the bit.admin newsgroup. -*- 2.5. Other Mailing Lists Besides Usenet and the listserver mailing lists, there are several thousand special-interest mailing lists available over the Internet, including: List name Subscriptions address, topic, etc. ----------------------------------------------------------------------- aatdb-info@weeds.mgh.harvard.edu curator@weeds.mgh.harvard.edu Arabidopsis thaliana alife@cognet.ucla.edu alife-request@cognet.ucla.edu Artificial life digest avifauna@rcp.pe phillips@cipa.ec (Roberto Phillips) Neotropical birds b-e-group@forager.unl.edu b-e-requests@forager.unl.edu Behavioral ecology digest biogopher@comp.bioz.unibas.ch doelz@urz.unibas.ch (Reinhard Doelz) Biology information systems biologia@athena.mit.edu biologia-request@athena.mit.edu Tropical biology, in Spanish bryonet@uni-duisburg.de hh216fr@uni-duisburg.de (Jan-Peter Frahm) Bulletin for bryologists ecologia@athena.mit.edu ecologia-request@athena.mit.edu Tropical ecology, in Spanish ent-list@um.cc.umich.edu hcfb@um.cc.umich.edu (Mark O'Brien) Entomology env-link@andrew.cmu.edu env-link+forms@andrew.cmu.edu (Josh Knaur) Environmentalists digest forest@lists.funet.fi forest-request@lists.funet.fi Forestry orchids@SCUacc.scu.edu mailserv@SCUacc.scu.edu "subscribe orchids " plant-taxonomy@mailbase.ac.uk mailbase@mailbase.ac.uk "join plant-taxonomy " primate-talk@primate.wisc.edu primate-talk-request@primate.wisc.edu "subscribe " wildnet@access.usask.ca wildnet-request@access.usask.ca Conservation issues digest [unknown] kelley@flowcyt.cyto.purdue.edu (Steve K.) Cytometry [unknown] info@s27w007.pswfs.gov Dendrome forest genetics digest There is a 4-part FAQ in news.answers (da Silva 1993) that includes brief descriptions of the charter of each mailing list. This FAQ is stored in FAQ archives in the directory /mailing-lists/. Some Usenet newsgroups have non-listserver gated mailing lists. These include the following. Usenet newsgroup Mailing list Subscriptions address ------------------------------------------------------------------------ sci.space space@isu.isunet.edu space-request@isu.isunet.edu Subscription requests should be of the form "subscribe Your Name". -*- 2.6. Newsletters Many of the mailing lists mentioned in above section are actually digests, where readers' queries and comments are condensed into a single large document that is distributed periodically. Yet another variation on this theme is electronic newsletters. Those not listed elsewhere in this guide include: * Boissiera. Editor ? * Candollea. Editor ? * Flora Online: Journal of Collections-Oriented Botanical Research, published by the Buffalo Museum of Science, USA. Editor ? visbms@UBVMS.bitnet. Available via gopher and anonymous ftp from huh.harvard.edu. * Bean Bag: Leguminosae Research Newsletter, edited by Charles R. Gunn and Joseph H. Kirkbride, Jr. . Available via gopher and anonymous ftp from huh.harvard.edu. * Botanical Electronic News (BEN), edited by Adolf Ceska, Canada. Available via gopher and anonymous ftp from huh.harvard.edu, and the wildnet mailing list. * Environmental Resources Information Network (ERIN) Newsletter, Australia Available via gopher and anonymous ftp from huh.harvard.edu. * LTER Data Management Bulletin (DATABITS). Available via gopher on lternet.edu. * Climate/Ecosystem Dynamics (CED). E-mail subscriptions are available from Daniel Pommert , gopher access available via lternet.edu. * The Chlamydomonas Newsletter. E-mail subscriptions are available from Mike Adams , gopher access available via chlamy.botany.duke.edu. The paper journal The Scientist is available in an online version via anonymous ftp on nnsc.nsf.net, courtesy of the Institute for Scientific Information and the NSF Network Service Center. -*- 2.7. Directories A database of 86,000 records covering scientists and research projects currently funded by the U.S. National Institutes of Health (NIH) is available via gopher on merlot.welch.jhu.edu. Searches on researcher name, location, and field of interest are supported. A directory of researchers using Artificial Intelligence in Molecular Biology (AIMB) is maintained at the National Library of Medicine. To be included, send e-mail to Larry Hunter . -*- 3. Information Archives A number of people have begun to organize the many free biological information archives, databases and services on the Internet into well-organized menus using gopher servers. These include Don Gilbert's IUBIO service on ftp.bio.indiana.edu in the United States, Rob Harper's "Bionaut software and data paradise" on gopher.csc.fi in Finland, and Reinhard Doelz's "Information servers in biology (Gopher based)" on gopher.embnet.unibas.ch in Switzerland. All of these services are accessible via gopher "clients". Yanoff (1993) is an excellent list of unusual and useful Internet services, a few of which are mentioned in this guide. Anyone who does a lot of field work will appreciate the Geographic Name Server, which can provide the latitude and longitude, and the elevation of most places in the United States: all cities and counties are covered, as well as some national parks and some geographical features (mountains, rivers, lakes, etc.). Telnet to martini.eecs.umich.edu, port 3000 (no username needed) and type "help" for instructions. Other services include: an on-line dictionary, weather maps, a general weather report service, an archive of statistical programs and data sets, and various computers allowing public telnet sessions so that people who have Internet access but not Usenet can read and post Usenet articles. Stern (1993) offers an extensive list of anonymous ftp archives offering meteorological data. -*- 3.1. Bibliographies Every week now there are more archives coming online as WAIS servers. Many contain bibliographic databases, complete with abstracts. An example is the US Department of Energy (DOE) Climate Data database, and the NASA Global Change Data Directory, archived on ridgisd.er.usgs.gov. The results of online WAIS searches can be saved as files or sent to you as e-mail. The Long-Term Ecological Research (LTER) program has put a bibliographic database and catalog of data set descriptions on a gopher server at lternet.edu. The actual data is not available online. The U.S. Department of Agriculture (USDA) Extension Service offers the Research Results Database (RRDB), containing brief summaries of recent research from the USDA's Agricultural Research Service (ARS) and Economic Research Service (ERS), by e-mail. For information, send the e-mail message "send guide" to almanac@esusda.gov. To receive notices of new RRDB titles, send the message "subscribe usda.rrdb". Bibliographies on specialized topics are available on many servers: Check the gopher server on gopher.genethon.fr for bibliographies of sequence analysis and human genome research papers. Various Usenet newsgroups and mailing lists provide the tables of contents (TOCs) for current issues of a few journals of interest to biologists. Tom Schneider distributes Unix AWK scripts for converting many of these TOCs into BibTeX-style bibliography records: these scripts are posted in the Usenet newsgroup bionet.journals.note. The journal TOCs available in bionet.journals.contents include: 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 The American Physiological Society offers TOCs for the following journals via gopher on gopher.uth.tmc.edu (port 3300): Advances in Physiology Education American Journal of Physiology (6 consolidated journals) Journal of Applied Physiology Journal of Neurophysiology News in Physiological Sciences Physiological Reviews The Physiologist The PHOTOSYN listserver mailing list distributes TOCs for Photosynthesis Research, but these are not archived on the listserver. -*- 3.2. List of Archives Computer sites supporting some sort of public access, and of some interest to biologists: Internet node name Topic/Title Access method ------------------------------------------------------------------------- sunsite.unc.edu (NC USA) Many subjects E f G t [4] pinus.slu.se Agriculture G locus.nalusda.go (USA) Nat. Agri. Library G ncbi.nlm.nih.gov (MD USA) NCBI f ftp.embl-heidelberg.de (Germany) EMBL Data Library E f g coli.polytechnique.fr (France) EMBLnet G fly.bio.indiana.edu (IN USA) Genbank G ftp.bchs.uh.edu (TX USA) Genbank, PIR f G helix.nih.gov (MD USA) Genbank, PDB, PIR etc. G ncifcrf.gov (MD USA) Biol. Information Theory f finsun.csc.fi (Finland) Prosite, Rebase-Enzyme G pdb.pdb.bnl.gov (NY USA) Protein Data Bank G ftp.tigr.org Inst. for Genomic Rsch. f golgi.harvard.edu (MA USA) f s27w007.pswfs.gov (USA) Forest Genetics G biomed.uio.no (Norway) Genome T biox.embnet.unibas.ch (Switzerland) Genome G merlot.welch.jhu.edu (MD USA) Genome G weeds.mgh.harvard.edu (MA USA) Arabidopsis, C. elegans G [5] mendel.agron.iastate.edu (IA USA) Soy genome G greengenes.cit.cornell.edu (NY USA) Triticeae genome G teosinte.agron.missouri.edu (USA) Maize genome G chlamy.botany.duke.edu (NC USA) Chlamydomonas stocks G [2] picea.cfnr.colostate.edu (CO USA) f life.anu.edu.au (Australia) Bioinformatics f G igc.org (CA USA) EcoNet f gopher.yale.edu (CT USA) LTERnet, EDEX, JARS g lternet.edu (WA USA) LTERnet G spider.ento.csiro.au (Australia) Entomology f gopher.uth.tmc.edu (port 3300) Physiology G envirolink.hss.cmu.edu (DE USA) Environment G T ecosys.drdr.virginia.edu (VA USA) Ecosystems G T ngdc1.ngdc.noaa.gov (USA) Paleoclimatology f [1] huh.harvard.edu (MA USA) Harvard Univ. Herbaria f G simsc.si.edu (DC USA) Smithsonian Inst. f [3] ucmp1.berkeley.edu (CA USA) Vertebrate museum G bdt.ftpt.br (Brazil) Biodiversity f G dogwood.botany.uga.edu (GA USA) Botany G zookeeper.zoo.uga.edu (GA USA) Zoology G sparc.ecology.uga.edu (GA USA) Ecology G wigeo.wu-wien.ac.at (Austria) Geography G geogopher.ucdavis.edu (CA USA) Geology G isdres.er.usgs.gov (VA USA) US Geological Survey f pippin.memst.edu CERI Earthquake Center G cdiac.esd.ornl.gov CDIAC f granta.uchicago.edu (IL USA) Physics Resources G xyz.lanl.gov (NM USA) LANL Nonlinear Science G mentor.lanl.gov (NM USA) LANL Physics G stis.nsf.gov (DC USA) Nat. Science Foundation f rtfm.mit.edu (MA USA) FAQ repository e f [] e - e-mail file requests (see notes this section). E - e-mail search requests (see notes this section). f - anonymous ftp (see section 3.4.2 if you have e-mail but not ftp) g - gopher server G - gopher server plus WAIS index searches t - public telnet access T - public telnet access plus e-mail returns of search results W - WAIS server plus WAIS index searches These database access methods fall into two categories, depending on whether or not keyword or other searches are supported (uppercase codes). This list is very incomplete, and I offer it on a trial basis to see if it is worth expanding (and keeping up to date :-). Notes: 1: info@mail.ngdc.noaa.gov; 2: chlamy@acpub.duke.edu; 3: david@simsc.si.edu; 4: info@sunsite.unc.edu, telnet username "swais" for WAIS seaches, telnet username "gopher" for plain gopher access; 5: Richard Durbin , Jean Thierry-Mieg -*- 3.2.1. Online Help Various genome projects are now well established on the Internet, with large, highly organized databases that support increasingly powerful and complex interactive or batch search queries. Most of them now support WAIS and gopher search access. The biologists who use and contribute to these databases in their research receive a lot of their technical support through discussions and announcements in the bionet.* domain of Usenet: Genomic or other database Relevant Usenet newsgroup ------------------------- ------------------------- AAtDB and ACEDB bionet.genome.arabidopsis PIR (and SWISS-PROT) bionet.molbio.proteins The Brookhaven Protein Data Bank bionet.xtallography GenBank (NCBI and Los Alamos) bionet.molbio.genbank The EMBL Databank bionet.molbio.embldatabank Human Genome Database (GDB) bionet.molbio.gdb Museums and Herbaria on Internet bionet.plants Posting about these databases to the corresponding newsgroups will usually get the attention of someone on the appropriate database staff immediately, with responses following within hours. Questions, as well as data submissions and corrections, can generally be sent directly to the relevant administrators (after Garavelli 1992): Database Address of administrator -------- ------------------------ AAtDB (Arabidopsis thaliana) curator@weeds.mgh.harvard.edu ACeDB (Caenorhabditis elegans) Brookhaven pdb@chm.chm.bnl.gov DDBJ ddbjsubs@flat.nig.ac.jp EDEX and JARS (Forest Ecology) goforest@gopher.yale.edu EMBL problems, feedback nethelp@embl-heidelberg.de software submissions, queries software@embl-heidelberg.de Data Library enquiries datalib@embl-heidelberg.de Data Library submissions datasubs@embl-heidelberg.de FlyBase (Drosophila) flybase@nucleus.harvard.edu Inst. of Forest Genetics DB (IFGDB) ifgdb@s27w007.pswfs.gov GDB help@welch.jhu.edu GenBank gb-sub@life.lanl.gov Harvard University Herbaria beach@huh.harvard.edu LTER helper@lternet.edu NCBI repository@ncbi.nlm.nih.gov PIR fileserv@nbrf.georgetown.edu SWISS-PROT bairoch@cmu.unige.ch LiMB, the Listing of Molecular Biology databases (Keen et al. 1992) describes most of these databases, and many more, including the names, regular mail addresses and telephone numbers of their keepers. To get the current version of LiMB by e-mail, send the text "limb-data" to bioserve@life.lanl.gov. For information only, send "limb-info". LiMB is available in hardcopy or on floppy disk: contact limb@life.lanl.gov. -*- 3.2.2. Search Engines The European Molecular Biology Laboratory (EMBL) supports various types of searches via e-mail: EMBL File Server NetServ@EMBL-Heidelberg.DE FASTA FASTA@EMBL-Heidelberg.DE Quicksearch Quick@EMBL-Heidelberg.DE The Swiss-Prot database can be searched via e-mail using the MPsrch program on the Blitz server. MPsrch is a program for carrying out similarity searches of protein sequence databases using the best local similarity algorithm of Smith and Waterman. For more information, send the text "help" in e-mail to blitz@embl-heidelberg.de The Sequence Retrival System (SRS) program for VAX VMS computer systems is available via anonymous ftp on the Norwegian EMBnet node biomed.uio.no or genetics.upenn.edu (USA). -*- 3.3. Software Archives Several anonymous ftp archives specializing in software for biologists are accessible via gopher. One that is currently available only via anonymous ftp is the Brazilian Medical Informatics archive on ccsun.unicamp.br. The IUBio archive on ftp.bio.indiana.edu probably has the best collection in the US. The archive on huh.harvard.edu has software of interest to botanists. Other biology archives include ftp.bchs.uh.edu, ncbi.nlm.nih.gov in the United States and in Europe ftp.embl-heidelberg.de (Germany), gopher.embnet.unibas.ch (Switzerland), nic.funet.fi and gopher.csc.fi (Finland). The gopher server on merlot.welch.jhu.edu has a nice view of gopher land, including a strong collection of other gophers offering biomedical, biological and earth sciences images and image analysis tools. Also, wuarchive.wustl.edu has an excellent collection of educational software, especially for teaching mathematics at the college and university levels. The National Center for Supercomputing Applications has developed a collection of outstanding software tools for electronic communications and image analysis, and makes it publicly available on zaphod.ncsa.uiuc.edu. Many of the latest add-on tools for the popular LaTeX text formatting system are archived on sun.soe.clarkson.edu, while sumex-aim.stanford.edu has a huge archive of Macintosh software, and nic.ddn.mil keeps the important Internet RFC (Request for Comments) documents. Jan-Peter Frahm has made available via e-mail "A Guide to Botanical Software for MS-DOS Computers". The software is shareware or in the public domain. For a copy, write him at hh216fr@duc220.uni-duisburg.de. Bionet.software is a good place to look for information about specific software programs with applications to biology. There are many Usenet groups devoted to discussion of software, particularly freeware and shareware. The well-known, huge anonymous ftp repositories of software are all mentioned in various published guides to the Internet (Kehoe 1992, Krol 1992, Lane and Summerhill 1992, LaQuey and Ryer 1992, Malamud 1992, Tennant et al. 1993), and are part of the common knowledge of many Usenet newsgroups. -*- 3.4. Access Tools Most of the recently published books about the Internet describe these tools in detail. Kehoe (1992), the first book to appear, was offered first in a free electronic version over the Internet. The first edition, January 1992, is still available online from many anonymous ftp archives around the world, in a directory named something like pub/zen/; read files stored there for help producing a printed document. Krol (1992) has received excellent reviews. See appendix B for others. All the tools mentioned in this section share the quirk that they are actually two things: a "server" or "daemon" program that runs all the time on a host computer and accepts requests to connect over the Internet, and a "client" program that people use to connect to or access these servers. A few host computers in this FAQ allow the public to telnet to the host, and then use the host computer to access servers via either gopher or WAIS. These arrangements are offered as a courtesy to those people who do not have the necessary client software on their own computers, and want to try these tools before going to the trouble of installing the client software themselves. -*- 3.4.1. Telnet Telnet is a protocol whereby someone who is logged onto an account on a computer with full Internet access can access another computer over the Internet and login there, assuming he or she has login privileges on that computer as well. Anonymous telnet sessions are generally not permitted, but occasionally usernames are created with restricted privileges, for use by the Internet public. -*- 3.4.2. Anonymous Ftp Ftp is a protocol for file transfers between computers with full Internet access. Ftp allows people to transfer files to and from a remote computer on the Internet, assuming they have privileges on both the local and remote computers. "Anonymous ftp" indicates that people may login to the remote system with the userid "anonymous" and an arbitrary password. By convention, anonymous ftp users provide their e-mail addresses when asked for a password. This is useful to those archive managers who must justify to their bosses the time spent providing this free (but not cheap) service. Some computers set restrictions on when transfers may be made from their archives, and most prefer that large transfers be made only during off- hours. Bitnet does not support telnet or ftp sessions, but many Bitnet nodes are also Internet nodes, and so do support telnet and ftp. For those people who only have access to computers on Bitnet, Princeton University offers a file transfer service by e-mail. Bitftp@PUCC.bitnet will send a help file in response to the message "help". Those people who have no access to a computer on either the Internet or Bitnet can retrieve files from anonymous ftp archives by e-mail courtesy of ftpmail@decwrl.dec.com, which will send instructions in response to the words "help" and "quit" on separate lines of an e-mail message. Here is an example of how to send for a document on the archive at rtfm.mit.edu. This example will return a list of all the FAQs stored in the directory pub/usenet/news.answers/. Send the message send usenet/news.answers/index by e-mail to mail-server@rtfm.mit.edu. -*- 3.4.3. Gopher Gopher is a user-interface program that makes ftp and other types of connections for computer users when they select an item in a menu. It is an easy way to get stuff off the Internet without having to know where the stuff lives. Gopher is free, and there are nice versions for most types of computers, especially Unix workstations and Macs. It was invented at the University of Minnesota; current versions can be retrieved via anonymous ftp from boombox.micro.umn.edu. The name is a clever pun on the "go-for" person who runs errands for people, and on the burrowing rodent, which pops down a "hole" in the Internet and comes back up who-knows-where. Bionet.general, bionet.software, and bionet.users.addresses are good places to learn more about biology- related gopher services. Comp.infosystems.gopher is the newsgroup for gopher-related issues in general. The FAQ for this group is stored on rtfm.mit.edu in the file pub/usenet/news.answers/gopher-faq. There is an entire chapter on gopher in Krol (1992). -*- 3.4.4. Archie Archie is a program that helps people locate software in any of the thousands of anonymous ftp archives around the world. A copy of the software can be retrieved via anonymous ftp from any archie server, including ftp.cs.widener.edu, in the /archie/clients/ directory. There are versions of archie for all sorts of Unix systems, as well as VMS and PCs running a variety of network software. Good places to look for help installing archie on any computer are from archie-admin@ans.net or bionet.users.addresses. Documentation is available via anonymous ftp on ftp.ans.net in the /pub/archie/doc/ directory, or by e-mail from archie-admin@ans.net. Archie can be used via e-mail, by sending e-mail with a list of commands to archie@ans.net. For details, send the command "help". Due to the high demand for this service, the archie administrators on ans.net prefer that requests be made via e-mail. -*- 3.4.5. Veronica Veronica is the Very Easy Rodent-Oriented Net-wide Index to Computerized Archives. The reason Veronica's name is so long is so that it can play on the concepts of both gopher and archie. (Remember the comic book couple Archie and Veronica? Veronica does for gopher what archie does for anonymous ftp.) Veronica searches through hundreds of gopher holes looking for anything that matches a keyword supplied by the user, and assembles a list of gopher servers that contain items of interest. Note: Veronica checks *titles* of gopher items only, not their contents. Veronica was only invented in late 1992, but already seems very promising. -*- 3.4.6. WAIS WAIS stands for Wide Area Information Servers. The idea is to make anonymous ftp archives more accessible by indexing their contents and making those indexes searchable with software distributed to anyone on the Internet. The user interface is simple so far, but the concept is so powerful that every person with an anonymous ftp archive has spent part of this past year building WAIS indices of all available material (software, data, documents and other information). In the course of all this effort a great deal of information has suddenly become publicly available all in the past year, only a few of which are mentioned in the section of this FAQ on Internet archives. Good WAIS client programs for the Mac (WAIStation) and PC (PCWAIS) are available on the anonymous ftp archive at think.com. If your computer has full Internet access, you can try out WAIS on a Unix system, courtesy of Thinking Machines Corp., by telnetting to quake.think.com. Use the username "wais" and give your e-mail address as the password. See the newsgroup comp.infosystems.wais for more details. The FAQ for this group is stored on rtfm.mit.edu in the file pub/usenet/news.answers/wais-faq/getting-started. -*- 3.4.7. The World-Wide Web (WWW) The World-Wide Web is yet another tool for gathering useful information from the Internet. It was invented at the European Particle Physics Laboratory (CERN), Switzerland. The Web looks like a document that users can open and read, but clicking on certain words causes other documents to be retrieved and opened for inspection. The most powerful aspect of the Web at present is the ease with which seamless, attractive online documentation can be created, that is easy to find and browse, no matter where on the Internet the actual documents are. You can try the Web, courtesy of CERN: telnet to info.cern.ch (no username needed). -*- 4. Commercial Services The three most common types of commercial services are (1) restricted-use computer accounts allowing Internet access (e-mail or full access) via modem from personal computers, (2) on-line bibliographic databases that can be searched via modem or over the Internet, and (3) access via modem or the Internet to private Usenet-style special-interest networks, but only e-mail access to the rest of the Internet. The best sources of information about these services are the books on the Internet listed in appendix B, the advertizing sections of scientific journals, and reference books such as the "Directory of Online Databases" published quarterly by Cuadra/Elsevier, which runs to about 1000 pages, and the companion guide "Online Database Selection: A User's Guide to the Directory of Online Databases" from Elsevier. For the benefit of people without full Internet access (telnet and ftp in addition to e-mail), Peter Kaminski maintains a list of commercial access providers (Kaminski 1993). E-mail requests for this list can be sent to info-deli-server@netcom.com: use "send PDIAL" as the subject. -*- 5. Useful and Important FAQs Title Archive Filename -------------------------------------------------------------------- Updated Internet Services List internet-services How to find sources (READ THIS BEFORE POSTING) finding-sources You will learn a great deal about the Internet and what it has to offer if you track down some of the items mentioned in this FAQ. If you still want to know more, browse around in Usenet. Also, a number of commercial books have been published recently which give a very thorough guide to the Internet; see appendix B and check your local academic bookstore or university library. -*- 5.1. What's a FAQ and where can I get one? There are now hundreds of Internet documents, including this one, written expressly to answer frequently asked questions. They are often refered to in the Usenet community as "FAQs" (sounds like "fax"). You will find them in the Usenet newsgroup news.answers (and subsets in sci.answers and news.answers.newusers). There is an anonymous ftp archive for FAQs, on rtfm.mit.edu (RTFM stands for Read The F------ Manual), in the directory pub/usenet/news.answers/. See section 3.4.2 for help retrieving FAQs from this archive. -*- 5.2. Does anyone have an e-mail address for X? Please, don't ask this in a newsgroup or mailing list. It's rude! The quickest, most efficient way to answer this is to call or write to X directly. If anyone can help you with this, it's X. To date, most biologists don't have e-mail addresses, or if they do, they don't read their e-mail very often, so you really are better off contacting them directly. If you must try to find this information via the computer networks, please start by reading Kamens (1993a) or Lamb (1993) or the relevant section of one of the books listed in appendix B. Also, you can check for the latest strategy in the newsgroup bionet.users.addresses (which is graciously watched-over by Robert Harper). But wait, there's more: many gopher servers listed in this FAQ have searchable directories of biologists, and phonebooks of various sorts from around the world. -*- 5.3. How to find a good graduate program? Go talk to the undergraduate or graduate advisor in your department, if you're a college student. Start browsing through the scientific journals, and the new book stack in the library. Ask your favorite professors for advice. Sadly, the Internet can not be all things to all people, and questions about how to pick graduate programs generally do not get satisfactory replies. -*- 5.4. Where can I get old newsgroup/mailing list articles? All the biology-related Usenet newsgroups (since 1991) are archived for searching via gopher, WAIS, and anonymous ftp on ftp.bio.indiana.edu, in the directory /usenet/bionet/. The bionet newsgroups (some dating back to 1987) are archived for WAIS and anonymous ftp on net.bio.net. Browse through gopher land for additional Usenet newsgroup archives. Most listserver mailing lists are archived on the computer where they are administered. To subscribe and get an index of log files on the istserver archive for the ECOLOG-L mailing list, for example, send e-mail to listserv@UMDD.umd.edu with the text: subscribe ECOLOG-L Your Name index ECOLOG-L -*- 5.5. Where can I find biology-related job announcements? The bionet.jobs newsgroup is a good place to start, but you might also want to check the ECOLOG-L listserver mailing list, which is run by the Ecological Society of America and carries many job announcements. Most other newsgroups and mailing lists carry occasional job notices. The American Physiological Society offers announcements appearing in The Physiologist via gopher on gopher.uth.tmc.edu (port 3300). Usenet has several newsgroups devoted to jobs, including misc.jobs.offered. -*- A. Assorted Listserver Mailing Lists Note, an "M" before the descriptive title indicates a moderated list. All submissions should be sent to the moderator, not the list. The listserver for such groups can provide the name and e-mail address of the moderator. A "G" indicates a gateway into a Usenet newsgroup, an "A" indicates that the listserver maintains some files for this group. Agriculture and Animal Husbandry ag-econ@ERS.bitnet Agricultural Economics and ERS Test List ag-exp-l@vm1.nodak.edu Agricultural Expert Systems ageng-l@ibm.gwdg.de Agricultural Engineering and Intel. Control agric-l@UGA.cc.uga.edu Agriculture Discussion aqua-l@vm.UOGUELPH.ca Aquaculture Discussion List camel-l@SAKFU00.bitnet Discussion Forum on Camel Research dairy-l@UMDD.umd.edu Dairy Discussion List hort-l@VTVM1.cc.vt.edu Va Tech Horticulture Dept. Announcements hortpgm@VTVM1.cc.vt.edu Va Tech Horticulture Dept. Program mgarden@WSUVM1.csc.wsu.edu Master Gardeners newcrops@vm.cc.purdue.edu Discussion list for New Crops spud@WSUVM1.csc.wsu.edu Potato Research vetmed-l@UGA.cc.uga.edu Veterinary Medicine Anthropology and Archaeology anct-ne@vm.byu.edu Ancient Near Eastern Studies anthro-l@UBVM.cc.buffalo.edu General Anthropology Bulletin Board arch-l@TAMVM1.tamu.edu Archaeology List humevo@GWUVM.gwu.edu M Human Evolutionary Research Discussion native-l@TAMVM1.tamu.edu Issues Pertaining to Aboriginal Peoples pacarc-l@WSUVM1.csc.wsu.edu Pacific Rim Archaeology Interest List Biology bee-l@albany.edu Discussion of Bee Biology bio-dost@ege.edu.tr Biologists in Turkey biomch-l@nic.surfnet.nl Biomechanics and Movement Science bnfnet-l@FINHUTC.hut.fi Biological Nitrogen Fixation Forum entomo-l@vm.UOGUELPH.ca Entomology Discussion List ethology@FINHUTC.hut.fi Ethology herm@ege.edu.tr Medicinal and Aromatic Plants Discussion iapwild@vm1.nodak.edu International Arctic Project Wildlife l-etho@UQAM.bitnet EthØÃ1Xref: wariat.org sci.bio:3043 bionet.general:1155 sci.answers:127 news.answers:7160 Path: wariat.org!malgudi.oar.net!zaphod.mps.ohio-state.edu!darwin.sura.net!emory!nigel.msen.com!yale.edu!not-for-mail From: Una Smith Newsgroups: sci.bio,bionet.general,sci.answers,news.answers Subject: A Biologist's Guide to Internet Resources (FAQ) Followup-To: poster Date: 17 Apr 1993 18:17:34 -0400 Organization: Department of Biology, Yale University Lines: 1628 Sender: una@yale.edu Approved: news-answers-request@MIT.Edu Expires: 1 January 1994 Message-ID: <1qpvluINN9di@MINERVA.CIS.YALE.EDU> Reply-To: Una Smith NNTP-Posting-Host: minerva.cis.yale.edu Summary: Networking, free data and software sources, and much, much more. Supercedes: <1p5899INNinh@MINERVAsystem theory and modelingã glosas-l@acadvm1.UOTTAWA.ca GLObal Systems Analysis and Simulation Listã inns-l@UMDD.umd.edu International Neural Network Societyã ndrg-l@WVNVM.wvnet.edu Nonlinear Dynamics Research Groupã neural-n@ANDESCOL.uniandes.edu.co Artificial Neural Networks Discussionãã Conservation and Environmental Studiesãã apaspan@GWUVM.gwu.edu APA Scientific Grassroots Networkã aquifer@IBACSATA.bitnet Pollution and grondwater rechargeã aseh-l@TTUVM1.bitnet American Soc. of Environmental Historiansã comdev@vm.ecs.rpi.edu Communication & international developmentã consbio@UWAVM.u.washington.edu Conservation Biology Listã conslink@SIVM.si.edu Discussion on Biological Conservationã devel-l@AUVM.american.edu Technology Transfer in Int. Developmentã econet@MIAMIU.bitnet Ecological and Environmental Discussionã envst-l@BROWNVM.brown.edu Environmental Studies Discussion Listã itrdbfor@asuvm.inre.asu.edu Dendrochronology Forumã laspau-l@HARVARDA.harvard.edu Latin America Scholarship Programã meh2o-l@TAUNIVM.tau.ac.il Middle East waterã natura-l@UCHCECVM.bitnet Ecology and Envir. Protection in Chileã odp-l@TAMVM1.tamu.edu Ocean Drilling Program Open Discussionãã Ecologyãã biosph-l@UBVM.cc.buffalo.edu Biosphere, ecology, Discussion Listã biodiv-l@bdt.ftpt.ansp.br Biodiversity networksã bird_rba@ARIZVM1.ccit.arizona.edu National Birding Hotline Cooperativeã birdband@ARIZVM1.ccit.arizona.edu Bird Bander's Forumã birdchat@ARIZVM1.ccit.arizona.edu National Birding Hotline (Chat Line)ã birdcntr@ARIZVM1.ccit.arizona.edu National Birding Hotline (Central)ã birdeast@ARIZVM1.ccit.arizona.edu National Birding Hotline (East)ã birdwest@ARIZVM1.ccit.arizona.edu National Birding Hotline (West)ã birdtrip@ARIZVM1.ccit.arizona.edu Special BIRDCHAT LOGO Projectã ecolog-l@UMDD.umd.edu Ecological Society of Americaã ots-l@YALEVM.cis.yale.edu Organization for Tropical Studiesãã Geology and Geography (including GIS)ãã acdgis-l@AWIIMC12.imc.univie.ac.at Geographic Information Systemsã climlist@OHSTVMA.acs.ohio-state.edu Climatology Distribution Listã coastgis@IRLEARN.ucd.ie Coastal GIS Distribution Listã cpgis-l@UBVM.cc.buffalo.edu Chinese Professionals GIS Use Listã geograph@FINHUTC.hut.fi Geographyã geology@PTEARN.fc.ul.pt Geology Discussion Listã geonet-l@IUBVM.ucs.indiana.edu Geoscience Librarians & Informationã gis-l@UBVM.cc.buffalo.edu Geographic Information Systemsã idrisi-l@toe.towson.edu Idrisi Discussion Listã maps-l@UGA.cc.uga.edu Maps and Air Photo Systems Forum ã quake-l@vm.nodak.edu QUAKE-L Discussion Listã seism-l@BINGVMB.cc.binghamton.edu Seismological Data Distributionã seismd-l@BINGVMB.cc.binghamton.edu Seismological Discussionã stat-geo@UFRJ.bitnet Forum of Quantitative Methods in Geosciencesã tgis-l@UBVM.cc.buffalo.edu Temporal Topics on GIS Listã ucgis-l@UBVM.cc.buffalo.edu Univ Consort for Geo Info & Analysis Listã uigis-l@UBVM.cc.buffalo.edu User Interfaces for Geographic Info. Sys.ã vigis-l@UWAVM.u.washington.edu Virtual Reality and GISãã Marine biologyãã brine-l@UGA.cc.uga.edu Brine Shrimp Discussion Listã diatom-l@IUBVM.ucs.indiana.edu Research on the diatom algaeã hypbar-l@TECHNION.technion.ac.il HyperBaric & Diving Medicine Listã marine-l@vm.UOGUELPH.ca Marine Studies/Shipboard Educationãã Molecular biologyãã biotech@UMDD.umd.edu Biotechnology Discussion List ã confocal@UBVM.cc.buffalo.edu Confocal Microscopy Listã cyan-tox@GREARN.csi.forth.gr The Cyanobacterial Toxins Discussion Listã dis-l@IUBVM.ucs.indiana.edu Drosophila workers to receive DIS Newsletterã ebcbbul@HDETUD1.tudelft.nl Computers in Biotechnology, Rsch. and Edu.ã ebcbcat@HDETUD1.tudelft.nl Catalogue of 'Biotechnological' softwareã embinfo@IBACSATA.bitnet EMBNet (European Molecular Biology Network)ã emflds-l@UBVM.cc.buffalo.edu Electromagnetics in Med., Sci. & Com.ã forumbio@scf.fundp.ac.be Forum on molecular biologyã genetics@INDYCMS.iupui.edu Clinical human geneticsã info-gcg@UTORONTO.bitnet GCG Genetics Software Discussionã lpn-l@BROWNVM.brown.edu Laboratory Primate Newsletter Listã nibnews@ccsun.unicamp.br NIBNews (Biology and Medical Informatics)ã rbmi@FRORS13.bitnet Molecular Biology Research Groupãã Neurobiologyãã cogsci-l@vm1.yorku.ca Cognitive Science Discussion Groupã dasp-l@earn.cvut.cs Digital Acoustic Signal Processingã neuchile@CUNYVM.cuny.edu Chilean Neurosciences Discussion Listã neuro1-l@UICVM.uic.edu Neuroscience Information Forumã neus582@UICVM.uic.edu Methods in Modern Neuroscienceã sbnc-l@BRUSPVM.bitnet Brazilian Society of Neurosciences & Comp.ãã Taxonomy and Systematicsãã class-l@ccvm.sunysb.edu Classification and phylogeny estimationã muse-l@HARVARDA.harvard.edu Muse Software Discussion Listã museum-l@UNMVMA.unm.edu Museum discussion listã rapd-l@vm.byu.edu RAPD sequencing discussion listã roots-l@vm1.nodak.edu Genealogy listã taxacom@HARVARDA.harvard.edu Taxonomic and systematic collections listãã Teaching and Researchãã biocis-l@SIVM.si.edu Biology Curriculum Innovation Studyã conslt-l@IUBVM.ucs.indiana.edu Research and practice in mentoringã grants-l@JHUVM.hcf.jhu.edu NSF Grants & Contracts ã hpsst-l@QUCDN.queensu.ca History and Philosophy of Scienceã iopi@life.anu.edu.au M Int. Organization for Plant Informationã iubs@life.anu.edu.au M Int. Union of Biological Societies ã job-list@FRORS12.bitnet Job offers from EARN Institute membersã methods@vm.ecs.rpi.edu Research methodologyã navigate@UBVM.cc.buffalo.edu Navigating The Internet Workshop Listã newedu-l@vm.usc.edu New Paradigms in Education Listã nihggc-l@UBVM.cc.buffalo.edu NIH Grants and Contracts Distribution Listã scifraud@uacsc2.albany.edu Discussion of Fraud in Scienceã vpiej-l@VTVM1.cc.vt.edu Electronic journal discussionsã wisenet@UICVM.uic.edu Women In Science and Engineering NETworkããã-*- B. Bibliographyãã Anonymous (1993) "Total traffic through uunet for the last 2 weeks". ã Usenet news.lists, 8 February. Posted by newsstats@uunet.uu.net.ãã Barr, D. and M. Horton (1993) "Rules for posting to Usenet". Usenetã news.announce.newusers. FAQ archive filename posting-rules/part1.ãã Brader, M. and J. Schwarz (1993) "Answers to Frequently Asked Questionsã about Usenet". Usenet news.announce.newusers. FAQ archive filenameã usenet-faq/part1.ãã Crepin-Leblond, O.M.J. (1993) " Top-level international country domainã names". Usenet comp.mail.misc. FAQ archive: top-level-domains.ãã Granrose, J., M. Jones and T. Czarnik (1993a) "Anonymous FTP List - FAQ".ã Usenet comp.misc. FAQ archive: ftp-list/faq.ãã Granrose, J., M. Jones and T. Czarnik (1993b) "Anonymous FTP List - Sites".ã Usenet comp.misc. FAQ archive: ftp-list/sites[1-3].ãã Fotis, N.C. (1993) "Computer Graphics Resource Listing". Usenetã comp.graphics. FAQ archive filename graphics/resources-list/part[1-3].ãã Garavelli, J. (1992) "Announcements of the Protein Informationã Repository". Usenet bionet.molbio.proteins, December.ãã Goldmann, N. (1992) "Online Information Hunting". Windcrest, Blue Ridgeã Summit, PA.ãã Kahin, B. (1992) "Building Information Infrastructure: Issues inã the Development of the National Research and Education Network".ã McGraw Hill, New York. 432 pages.ãã Kamens, J.I. (1993a) "FAQ: How to find people's E-mail addresses". Usenetã comp.mail.misc. FAQ archive filename finding-addresses.ãã Kamens, J.I. (1993b) "How to find sources (READ THIS BEFORE POSTING)". ã Usenet comp.mail.misc. FAQ archive filename finding-sources.ãã Kamens, J.I. (1993c) "How to become a USENET site". Usenetã news.admin.misc. FAQ archive filename site-setup.ãã Kamens, J.I. (1993d) "Introduction to the news.answers newsgroup". ã Usenet news.answers. FAQ archive filename news-answers/introduction.ãã Kamens, J.I. (1993e) "Mail Archive Server (MAS) software list". ã Usenet comp.mail.misc. FAQ archive filename mas-software.ãã Kaminski, P. (1993) "Public Dialup Internet Access List (PDIAL)". Usenetã alt.internet.access.wanted FAQ archive filename pdial. ãã Keen, G., G. Redgrave, J. Lawton, M. Cinkosky, S. Mishra, J. Fickett,ã and C. Burks (1992) "Access to molecular biology databases". ã Mathematical Comput. Modelling 16:93-101.ãã Kehoe, B.P. (1992) "Zen and the Art of the Internet: A Beginner'sã Guide to the Internet", 2nd Edition (July). Prentice Hall,ã Englewood Cliffs, NJ. 112 pages. The 1st Edition, (February)ã is available in Postscript format via anonymous ftp fromã ftp.cs.widener.edu and many other Internet archives.ãã Krol, E. (1992) "The Whole Internet: Catalog & User's Guide".ã O'Reilly & Associates, Inc., Sebastopol, CA. 376 pages.ãã Lamb, D. (1993) "FAQ: College Email Addresses". Usenet soc.college.ã FAQ archive filename college-email/part[1-3].ãã Lane, E.S. and C.A. Summerhill (1992) "An Internet Primer forã Information Professionals: A Basic Guide to Networking Technology".ã Meckler Corporation, Westport, CT. ~200 pages. In press.ãã LaQuey, T. and J.C. Ryer (1992) "The Internet Companion: A Beginner'sã Guide to Global Networking". Addison-Wesley Publishing Co.,ã Reading, MA. 208 pages.ãã Lawrence, D.C., G. Woods and G. Spafford (1993) "How to Create a Newã Usenet Newsgroup". Usenet news.announce.newusers. FAQ archive: ã creating-newsgroups/part1.ãã Leech, J. (1993) "Space FAQ". Usenet sci.astro. FAQ archive space/*.ã ã Malamud, C. (1992) "Exploring the Internet: A Technical Travelogue".ã Prentice Hall, Englewood Cliffs, NJ. 376 pages.ãã Marine, A. (1992) "Inter: Getting Started". SRI International,ã Menlo Park, CA. 380 pages.ãã McIntosh, J. (1993a) "NetNews/Listserv Gateway Policy." Usenet bit.admin.ã FAQ archive: bit/policy.ãã McIntosh, J. (1993b) "Mailing Lists Available in Usenet." Usenetã bit.admin. FAQ archive: bit/gatelist.ãã Quarterman, J.S. and S. Wilhelm (1992) "UNIX, POSIX, and Open Systems:ã The Open Standards Puzzle". Addison-Wesley Publishing Co.,ã Reading, MA. 448 pages.ãã Reid, B. (1993a) "Usenet Readership Report for January 1993". Usenetã news.lists.ãã Reid, B. (1993b) "Usenet Readership Summary Report for January 1993". ã Usenet news.lists.ãã Schneider, T. (1993) "Biological Information Theory and Chowder Society".ã Usenet bionet.info-theory. FAQ archive: biology/info-theory.ãã da Silva, S. and C. Von Rospach and G. Spafford (1993) "Publiclyã Accessible Mailing Lists". Usenet news.lists. FAQ archive: ã news.lists[1-4].ãã Smith, Una R. (1993) "A Biologist's Guide to the Internet."ã Usenet sci.bio. FAQ archive: biology/guide.ãã Spafford, G. (1993) "USENET Software: History and Sources". Usenetã news.admin.misc. FAQ archive filename usenet-software/part1.ãã Spafford, G. and R. Atkinson (1992) "How to Get Information aboutã Networks". Usenet news.admin.misc. FAQ archive: network-info/part1.ãã Spafford, G. and M. Horton (1992) "Introduction to news.announce". ã Usenet news.announce.newusers. FAQ archive filenameã news-announce-intro/part1.ãã Spafford, G. and A.J. Offutt VI (1992) "Hints on writing style forã Usenet". Usenet news.announce.newusers. FAQ archive filenameã usenet-writing-style/part1.ãã Spafford, G. and C. Salzenberg (1992) "What is Usenet?". Usenetã news.announce.newusers. FAQ archive filename what-is-usenet/part1.ãã Spafford, G. and C. Von Rospach (1992) "A Primer on How to Work With theã Usenet Community". Usenet news.announce.newusers. FAQ archiveã filename usenet-primer/part1.ãã SRI (1992) "Internet: Mailing Lists". SRI International, Menlo Park, CA.ãã Stern, I. (1993) "Sources of Meteorological Data FAQ". Usenetã sci.geo.meteorology. FAQ archive filename weather-data.ãã Templeton, B. (1991) "Emily Postnews Answers Your Questions onã Netiquette". Usenet news.announce.newusers. FAQ archive filenameã emily-postnews/part1.ãã Tennant, R., J. Ober and A.G. Lipow (1993) "Crossing the Internetã Threshold: an Instructional Handbook", 1st Edition. Libraryã Solution Press, San Carlos, CA. 134 pages.ãã Thomas, E. (1992) "Revised LISTSERV System Reference Library".ã Listserv@BITNIC.educom.edu, release 1.7c. Retrievable from anyã listserver using the mail message "send listserv refcard".ãã UofMN Gopher Team (1993) "Gopher Frequently Asked Questions (FAQ)".ã Usenet comp.infosystems.gopher. FAQ archive: gopher-faq.ãã Wohler, B. (1993) "NN Frequently Asked Questions (FAQ) with Answers".ã Usenet news.software.nn. FAQ archive: nn-faq.ãã Woodbury, G.W. (1993) "UNIX BBS Software FAQ with Answers". Usenetã comp.bbs.misc. FAQ archive: unix-faq/bbs-software.ãã Yanoff, S. (1993) "Updated Internet Services List". Usenetã alt.internet.services. Available from rtfm.mit.edu FAQã archive as filename internet-services.ãã-*- C. Contributorsãã Many, many thanks toãã James Beach, Harvey Chinn, Dan Davison, Reinhard Doelz,ã John Garavelli, Don Gilbert, Rob Harper, Dan Jacobson,ã David Kristofferson, Francis Ouellette, Renato Sabatini,ã and Tom Schneider,ãã who have provided substantial ideas and material for this FAQ and/orã advice on related issues. Harvey Chinn has served as my editor, andã many improvements of organization were suggested by him.ãã Additional material and suggestions were contributed by: ãã David Bridge, Steve Clark, Josh Hayes, Tom Jacobs, Andy Johnston,ã Jonathan Kamens, Jim McIntosh, Ross Smith, Roy Smith, andã Christophe Wolfhugel.ãã There exists a (mostly anonymous) cast of thousands who have madeã significant, even enormous individual contributions to the resourcesã mentioned in this FAQ, and who are largely responsible for the thingã we call the Internet in its broadest sense. They must all be veryã proud of what they have helped to create. ãã-- ãã Una Smith Biology Department smith-una@yale.eduã Yale Universityã New Haven, CT 06511ã