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A Biologist's Guide to Internet Resources (3 of 6)

( Part1 - Part2 - Part3 - Part4 - Part5 - Part6 )
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Archive-name: biology/guide/part3
Last-modified: 10 November 1993

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-*- 3. Biological Information Archives

    Many archives are mentioned throughout this section and elsewhere in this
    document.  The access methods available for each archive are presented in
    section 3.5, List of 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 and Mike Cherry's collection on in the United States, Rob Harper's "Finnish EMBnet
    BioBox" on in Finland, and Reinhard Doelz's "Information
    servers in biology (gopher based)" on in

    Yanoff (1993) is an excellent list of unusual and useful Internet
    services, a few of which are mentioned in this guide.  Services listed
    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.

||  Reinhard Doelz's Biocomputing Survival Guide (Doelz 1993) covers basic
||  Unix and VMS commands and the GCG software.

-*- 3.1. Bibliographies

    Many Internet archives have searchable bibliographic databases, complete
    with abstracts.  Only a few are mentioned here. 

    A bibliography of 52,000 Drosophila research publications, dating from 
    1684 through this year, is offered on

    The US Department of Energy (DOE) Climate Data bibliography and the NASA
    Global Change Data Directory are archived on  The
    North American Benthological Society (NABS) offers a bibliography of
    recent literature in benthic biology on  The Long-Term
    Ecological Research (LTER) program has put a bibliographic database and
    catalog of data sets on  (The actual data is not available
    on-line.)  Check for bibliographies of sequence
    analysis and human genome research papers. 

    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 details, send the
    e-mail message "send guide" to  To receive notices
    of new RRDB titles, send the message "subscribe usda.rrdb".

    The U.S. Environmental Protection Agency (EPA) National Library on-line
    database can be accessed for bibliographic searches via anonymous telnet
    to  A collection of GIS-related bibliographies is
    available on

    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:

	Anatomy and Embryology
	Applied Microbiology and Biotechnology
	Applied and Environmental Microbiology
	Cell and Tissue Research
	Current Genetics
	EMBO Journal
	Environmental Physiology
	European Journal of Biochemistry
	European Journal of Physiology
	Experimental Brain Research
	Human Genetics
	IEEE Engineering in Medicine and Biology
	Journal of Bacteriology
	Journal of Biological Chemistry
	Journal of Comparative Physiology B: Biochemical, Systemic, and
	The Journal of Membrane Biology
	Journal of Molecular Evolution
	Journal of Virology
	MGG - Molecular and General Genetics
	Mammalian Genome
	Microbial Releases
	Molecular Microbiology
	Molecular and Cellular Biology
	Nucleic Acids Research
	Plant Cell Reports
	Protein Science
	Roux's Archives of Developmental Biology
	Theoretical and Applied Genetics

    The CONSLINK listserver mailing list keeps a large bibliography of
    conservation biology research papers on its archive (see section 2.4.2,
    Archives, for instructions on accessing listserver archives).

    The American Physiological Society offers TOCs for the following 
    journals via gopher on (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

    Other publishers supporting Internet access to information about their
    publications include

        Publisher			Address			Access
	Addison-Wesley		ftp
	O'Reilly & Associates		gopher
	Kluwer Academic Publishers		ftp

-*- 3.2. Directories 

    Searchable directories of scientists and research projects currently
    funded by the U.S. National Institutes of Health (NIH), National Science
    Foundation (NSF), Department of Agriculture (USDA), and genome researchers
    funded by several other departments, together with several topical 
||  directories, are available via gopher on  Searches on
    researcher name, location, and field of interest are supported.

    A directory of 2000+ people who read the bionet.* newsgroups is available
    via gopher and anonymous FTP from;  you can add yourself to
    the directory via gopher or e-mail (see instructions on the archive).  
    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,

    Several directories of ecologists and plant biologists are kept on, which is accessible via gopher and anonymous FTP.
    A directory of tropical biologists is kept in the Ecology and Evolution
    section of the gopher/anonymous FTP archive on
    Richard Thorington keeps a list of mammalogists who use e-mail.  To get
    yourself on the list (required to receive copies of it), send e-mail to
    mnhvz049@SIVM (via Bitnet) or

-*- 3.3. Software

    Several archives specializing in software for biologists are accessible
    via gopher and anonymous FTP.  Some of these are listed in section 3.5,
    List of Archives.  The first such archive in South America is the 
    Brazilian Medical Informatics archive,  The IUBio
    archive on probably has the best collection in the
    United States.  Botanists will appreciate the TAXACOM archive on

    Also, 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  Many of the latest add-on tools for the popular
    LaTeX text formatting system are archived on,
    while has a huge archive of Macintosh software,
    and keeps the important Internet RFC (Request for Comments)

    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 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, Tennant et al.
    1993), and are part of the common knowledge of many Usenet newsgroups. 

-*- 3.4. Data

    The wealth of data available on the Internet is staggering, but it is also
    widely dispersed and often difficult to track down.  Rather than compile a
    list of data sets and pointers to their locations, this guide gives a list
    of locations with only a name or phrase to suggest what data may be found
    there (see section 3.5, List of Archives).  Many Usenet FAQs (see section
    4, Useful and Important FAQs) and other Internet documents mentioned in
    this guide attempt to list available databases, but many more are known
    only by word-of-mouth.  The Usenet newsgroup sci.answers (also a mailing
    list;  see section 2.4.3, Gateways to Usenet) carries many lists that are
    updated frequently.

-*- 3.4.1. Repositories

    Various genome and other cooperative projects are now well established on
    the Internet, with large, highly organized databases that support ever more
    powerful and complex interactive or batch search queries.  Most now support
    WAIS and gopher search access, and are listed in section 3.5, List of
    Archives.  The future utility of these repositories depends on the donation
    of data by individual researchers.  Questions, as well as data submissions
    and corrections, can be sent to the relevant administrators via e-mail
    (after Garavelli 1992):

    Database				Address of administrator
    --------				------------------------
    AAtDB (Arabidopsis thaliana)
    ACEDB (Caenorhabditis elegans) and
    DDBJ enquiries
         data submissions
         updates, publication notices
    EDEX and JARS (Forest Ecology)
    EMBL problems, feedback
	 software submissions, queries
         Data Library enquiries
         Data Library submissions
    FlyBase (Drosophila)
    Inst. of Forest Genetics DB (IFGDB)
||  GDB
    GenBank enquiries
||	data submissions
	updates, publication notices
||	Entrez questions
||	BLAST Email server
||	RETRIEVE Email server
||	EST reports Email server
    Microbial Strains Data Net. (MSDN) and

    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  For information only, send "limb-info".  LiMB
    is available in hardcopy or on floppy disk:  contact 

-*- 3.4.2. Search Engines

 |  Help files can be obtained from any of the GenBank e-mail servers listed
 |  in the previous section by sending the word "help" in the Subject line
 |  or body of an e-mail message to the server in question.

    The European Molecular Biology Laboratory (EMBL) supports various types
    of searches via e-mail.  For more information, send the text "help" in
    e-mail to any one of these servers:

	EMBL File Server		NetServ@EMBL-Heidelberg.DE
        FASTA				FASTA@EMBL-Heidelberg.DE
	Quicksearch 			Quick@EMBL-Heidelberg.DE
        Swiss-Prot MPsrch		Blitz@EMBL-Heidelberg.DE

    The BLOCKS database can be searched via e-mail.  For a help file, send
    a blank e-mail message to, with the word "help"
    in the Subject line.

 |  The GenMark e-mail sequence search engine was updated in the summer of
 |  1993.  For instructions and new feature descriptions, send e-mail to
 | with the word "instructions" in the Subject line
 |  or body of the letter.  Or contact M. Borodovsky <>
 |  or J. McIninch <>.

 |  See also Henikoff (1993).

    The Sequence Retrival System (SRS) program for VAX VMS computer systems
    is available via anonymous FTP on the EMBnet node (Norway)
    or (USA).

    Three U.S. herbaria now provide e-mail search support of:

	Type specimens of the mint family from the Harvard Herbaria,
	comprising 1100 records.

	The complete herbarium catalog of Michigan State University,
	Kellog Biological Station Herbarium, an NSF LTER site, consisting
	of 6000 specimen records.

	The Flora of Mt. Kinabalu;  16,300 specimen records of all vascular
	plant collections from the mountain.

    E-mail addresses for sending queries are:

          Harvard Mint Types:
          Kellogg Herbarium:
          Flora of Mt. Kinabalu:

    Send the message "help" to receive a usage guide, and if you think
    there might be difficulties with your return address, send that as
    well by adding a line with the text "replyaddress=" followed by your
    prefered e-mail address.

    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, port 3000 (no
    username needed) and type "help" for instructions.

-*- 3.5. List of Archives

    Computer sites supporting some sort of public access, and of some
    interest to biologists are listed here, together with means of access.

    e - e-mail file requests (see notes this section for e-mail addresses). 
    E - e-mail search requests (see notes this section).
    f - anonymous FTP (see section 3.6.3, Anonymous FTP by E-mail, if you
	cannot use 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

    Internet node name			Topic/Agency		Access method
    ------------------------------------------------------------------------- (IN USA)	IUBIO Genbank, FlyBase	 fG (MD USA)		NCBI			 f (Germany)	EMBL Data Library	Efg (France)	EMBLnet			  G (TX USA)		Genbank, PIR 		 fG (MD USA)		Genbank, PDB, PIR etc.	  G	(MD USA)		Biol. Information Theory f (Finland)		Prosite, Rebase-Enzyme	  G (NY USA)		Protein Data Bank	  G			Inst. for Genomic Rsch.	 f (MA USA)					 f		Molecular evolution	  G (Finland) (Finland) (Switzerland)		EMBnet			 fG W	[10]			Ribosomal DB Project	 f			A major entry-point	 fG (NC USA)		Many subjects 		EfGt	[4]			Earth Sciences		  G
    locus.nalusda.go (USA)		Nat. Agri. Library	  G (USA)		Forest Genetics		  G (Norway)		Genome data		   T (Switzer.) (Switzerland)	Genome data		  G
|| (MD USA)		GDB Genome Data Bank	  G (MA USA)	Arabidopsis, C. elegans	  G (IA USA)	Soy genome		  G (NY USA)	Triticeae genome	  G	(USA)	Maize genome		  G (NC USA)		Chlamydomonas		  G	[2] (CO USA)				 f (WA USA)	Populus genetics	 f (USA)			USDA Extension Service	  G		CIESIN Global Change	  G (MO USA)			Missouri Bot. Garden	 f (Australia)		Bioinformatics		 fG (CA USA)			EcoNet			 f (CT USA)	 	Ecol. Data EXchange	  g (WA USA)		LTERnet			  G (Australia)	Entomology		 f (port 3300)      Physiology		  G (DE USA)	Environment		  GT	[6] (VA USA)	Ecosystems		  GT (GA USA)	Ecology, Coweeta LTER	  G (USA)		Paleoclimatology	 f	[1] (MA USA)		Harvard Univ. Herbaria	 fG (DC USA)		Smithsonian Inst.	 f	[3] (CA USA)		Vertebrate museum	  G (Brazil)		Biodiversity		 fG (France)	Molecular evolution	  G (MD USA)		Mathematical Biology	 f			Radiocarbon Abstracts	 fG W (DE USA)	Entomology		  G (MN USA)	Forestry		  G (CA USA)		Biology			  G	Evolution		 f (TX USA)	Evolution		 f (MI USA)	Geographic Name Server	   t	[7]	(Austria)	Geography		  G (CA USA)	Geology			  G (VA USA)		US Geological Survey	 f			CERI Earthquake Center	  G			CDIAC			 f (MN USA)	Geology			  G (HA USA)	Generic Mapping Tools	 f			U.S. Naval Observatory	   t	[8]		NSSDC On-Line Service	   t	[9] (IL USA) 	Physics Resources	  G (NM USA)		LANL Nonlinear Science 	  G (NM USA)		LANL Physics 		  G (IL USA)		Argonne National Lab.	 f (DC USA)		Nat. Science Foundation	 fG (MA USA)		Usenet FAQ repository	ef	[5] (NC USA)		Journal of Stat. Educ.   fG (NC USA)                SAS-related information  f (IN USA)	Supercomputing		 f			Young Scientists Net.	 f			Directory of lists	 f		LaTeX tools		 f


    4:, telnet username "swais" for WAIS seaches,
	telnet username "gopher" for plain gopher access;
    5:	see section 3.6.2, Anonymous FTP, and section 3.6.3, Anonymous FTP
	by E-mail;
    6:	Telnet username "gopher", password "envirolink";
    7:	Use port 3000, no username, "help" gets instructions;
    8:	Telnet username "ads".
    9:	Telnet username "nodis".
    10:	Anonymous FTP from within Switzerland only.

-*- 3.6. Access Tools

    All Internet tools share the quirk that they are actually three things: 
    a "server" or "daemon" program that runs all the time on a host computer
    and accepts requests to connect over the Internet, a "client" program that
    people use to connect to or access these servers, and a standard protocol
    that allows many different versions of clients and servers to talk to one
    another without difficulty. 

    Most of the recently published books about the Internet describe these
    tools in detail.  Kehoe (1992), the first to appear, was offered first
    in a free electronic version over the Internet;  it is still available
    from many anonymous FTP archives around the world, in a directory named
    something like pub/zen/.  Krol (1992) has received excellent reviews. 
    See the bibliography for other books. 

    A new item:  the EARN Association has published a Guide to Network 
    Resource Tools (May 3, 1993), which is available via e-mail from 
    listserv@EARNCC.bitnet, by sending the message "get nettools ps" for
    a PostScript version or "get nettools memo" for a plain text version.
    The guide covers almost every tool mentioned here, including example.

    A few host computers mentioned in this guide allow the public to telnet
    to the host, and then use the host computer to access servers via gopher,
    WAIS or the Web.  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.  Although licensing has been
    discussed for some of these tools (namely, certain versions of gopher),
    at present they are all free, and several are explicitly in the public
    domain or carry free GNU licenses.

-*- 3.6.1. Telnet

    Telnet allows someone using a computer with full Internet access to 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.  Several of these
    are listed in section 3.5, List of Archives, and in Yanoff (1993).

-*- 3.6.2. Anonymous FTP

    FTP stands for file transfer protocol, and is the name of a program used
    for file transfers between computers with full Internet access, assuming
    you have privileges on both the local and remote computers.  Anonymous FTP
    is a common practice whereby anyone on the Internet may transfer files from
    (and sometimes to) a 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 sites restrict when transfers may
    be made from their archives, and most prefer that large transfers be made
    only during off-hours (relative to that site).

    To receive a short guide to using anonymous FTP, send e-mail with the
    text "help" to

-*- 3.6.3. Anonymous FTP by E-mail

    Bitnet does not support telnet or FTP sessions, but many Bitnet nodes are
    also full Internet sites, and so do support telnet and FTP.  For those
    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".  There is an identical server in
    Germany:  Bitftp@DEARN from within Bitnet/EARN or from
    the Internet.  This server should be used only for FTP requests involving
    transfers within Europe.  If you have neither full Internet access nor an
    account on a Bitnet node, you can still get files from anonymous FTP
    archives by e-mail courtesy of, which will send
    instructions in response to the word "help" followed by "quit" on separate
    lines of an e-mail message.

    Also, you can retrieve formal Usenet FAQs via e-mail from the Usenet FAQ
    repository,  to get a help file, a list of all the FAQs
    stored there, and the latest version of this guide, send e-mail to with the text

        send usenet/news.answers/biology/guide

-*- 3.6.4. 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  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,,
    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 in the file pub/usenet/news.answers/gopher-faq.
    There is an entire chapter on gopher in Krol (1992).

-*- 3.6.5. Archie

    Archie helps people locate items (documents, software, etc.) in thousands
    of anonymous FTP archives around the world.  Archie clients for many types
    of computer, and documentation, can be retrieved via anonymous FTP from
    any archie server (see below) in the /pub/archie/doc/ directory, or by
    e-mail from

    Archie can be used via e-mail, by sending e-mail with a list of commands
    to  For details, send the command "help".  Due to the very
    high demand for this service, requests should be made via e-mail or clients
    rather than telnet-ing to an archie server.  Please try to use archie only
    outside of working hours, make your query as specific as possible, and use
    the archie server nearest you: in Australia; in
    Finland; in Germany; in Great
    Britain; in Israel; and in Japan; in Korea; in
    New Zealand; in Sweden; in Taiwan;,, and
    in the United States.

-*- 3.6.6. Veronica

    Veronica is a very easy rodent-oriented net-wide index to computerized
    archives.  Veronica's name is a 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.

    There is a veronica database specifically for biology resources in the
||  gopher server on, under menu item "Search Databases
    at Hopkins...".  Its name is BOING, or Bio Oriented INternet Gophers.

    At present, there are no veronica clients;  veronica is a gopher tool.
    An informal veronica FAQ is posted regularly in comp.infosystems.gopher
    and archived on as veronica/veronica-faq.

-*- 3.6.7. Wide Area Information Servers (WAIS)

    The idea behind WAIS is to make anonymous FTP archives more accessible
    by indexing their contents for easy searching and browsing.  The client's
    user interface is simple, but the concept is so powerful that nearly
    everyone with an anonymous FTP archive has spent part of 1992 and 1993
    building WAIS indices of all available material (software, data, documents
    and other information).  In the course of all this effort an enormous
    amount of information that has been available for years or even decades
    has suddenly become publicly available for the first time all in the past
    year.  WAIS servers are often used as back-end engines for gopher servers.
    Gopher archives are built by hand, but WAIS bundles and organizes related
    items automatically, and thus greatly extends the functionality of gopher.

    Good WAIS client programs for the Mac (WAIStation) and PC (PCWAIS) are
    available on the anonymous FTP archive at  If your computer
    has full Internet access, you can try out WAIS on a Unix system, courtesy
    of Thinking Machines Corp., by telnetting to  Use the
    username "wais" and give your e-mail address as the password.  See the
    newsgroup comp.infosystems.wais for more details, or see the WAIS FAQ
    (section 4, Useful and Important FAQs).

-*- 3.6.8. World-Wide Web (WWW)

    WWW is yet another tool for gathering useful information from the Internet.
    It was invented at the European Particle Physics Laboratory (CERN),
    Switzerland.  WWW looks like a document that users can open and read, but
    selecting certain words via mouse or keyboard causes other documents to be
    retrieved and opened for inspection.  The most powerful aspect of WWW at
    present is the ease with which seamless, attractive on-line documentation
    can be created, that is easy to find and browse, no matter where on the
    Internet the actual documents are.  You can try WWW, courtesy of CERN: 
    telnet to (no username needed). 

	Una Smith

Yale University, Department of Biology, Osborn Memorial Laboratories,
PO Box 6666, New Haven, Connecticut  06511-8155

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