|
Archive-name: biology/guide/part3
Last-modified: 10 November 1993 See reader questions & answers on this topic! - Help others by sharing your knowledge
-*- 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 ftp.bio.indiana.edu and Mike Cherry's collection on
weeds.mgh.harvard.edu in the United States, Rob Harper's "Finnish EMBnet
BioBox" on gopher.csc.fi in Finland, and Reinhard Doelz's "Information
servers in biology (gopher based)" on gopher.embnet.unibas.ch in
Switzerland.
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 ftp.bio.indiana.edu.
The US Department of Energy (DOE) Climate Data bibliography and the NASA
Global Change Data Directory are archived on ridgisd.er.usgs.gov. The
North American Benthological Society (NABS) offers a bibliography of
recent literature in benthic biology on gopher.nd.edu. The Long-Term
Ecological Research (LTER) program has put a bibliographic database and
catalog of data sets on lternet.edu. (The actual data is not available
on-line.) Check gopher.genethon.fr 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 almanac@esusda.gov. 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 epaibm.rtpnc.epa.gov. A collection of GIS-related bibliographies is
available on bastet.sbs.ohio-state.edu.
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
Binary
Biotechniques
CABIOS
Cell and Tissue Research
Chromosoma
Current Genetics
EMBO Journal
Environmental Physiology
European Journal of Biochemistry
European Journal of Physiology
Experimental Brain Research
Histochemistry
Human Genetics
IEEE Engineering in Medicine and Biology
Immunogenetics
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
Photosynthetica
Plant Cell Reports
Planta
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 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
Other publishers supporting Internet access to information about their
publications include
Publisher Address Access
--------------------------------------------------------------
Addison-Wesley world.std.com ftp
O'Reilly & Associates gopher.ora.com gopher
Kluwer Academic Publishers world.std.com 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 gopher.gdb.org. 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 net.bio.net; 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, hunter@work.nlm.nih.gov.
Several directories of ecologists and plant biologists are kept on
huh.harvard.edu, 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 sunsite.unc.edu.
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 mnhvz049@SIVM.si.edu.
-*- 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, ccsun.unicamp.br. The IUBio
archive on ftp.bio.indiana.edu probably has the best collection in the
United States. Botanists will appreciate the TAXACOM archive on
huh.harvard.edu.
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, 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) curator@weeds.mgh.harvard.edu
ACEDB (Caenorhabditis elegans) rd@mrc-lmba.cam.ac.uk and
mieg@kaa.cnrs-mop.fr
Brookhaven pdb@chm.chm.bnl.gov
DDBJ enquiries ddbj@ddbj.nig.ac.jp
data submissions ddbjsub@ddbj.nig.ac.jp
updates, publication notices ddbjupdt@ddbj.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@morgan.harvard.edu
Inst. of Forest Genetics DB (IFGDB) ifgdb@s27w007.pswfs.gov
|| GDB help@gdb.org
GenBank enquiries info@ncbi.nlm.nih.gov
|| data submissions gb-sub@ncbi.nlm.nih.gov
updates, publication notices update@ncbi.nlm.nih.gov
|| Entrez questions entrez@ncbi.nlm.nih.gov
|| BLAST Email server blast@ncbi.nlm.nih.gov
|| RETRIEVE Email server retrieve@ncbi.nlm.nih.gov
|| EST reports Email server est_report@ncbi.nlm.nih.gov
Microbial Strains Data Net. (MSDN) msdn@bdt.ftpt.br and msdn@phx.cam.ac.uk
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.
-*- 3.4.2. 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 blocks@howard.fhcrc.org, 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
| genmark@ford.gatech.edu with the word "instructions" in the Subject line
| or body of the letter. Or contact M. Borodovsky <mb56@prism.gatech.edu>
| or J. McIninch <gt1619a@prism.gatech.edu>.
| See also Henikoff (1993).
The Sequence Retrival System (SRS) program for VAX VMS computer systems
is available via anonymous FTP on the EMBnet node biomed.uio.no (Norway)
or genetics.upenn.edu (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: herbdata@huh.harvard.edu
Kellogg Herbarium: herbdata%kbs.decnet@clvax1.cl.msu.edu
Flora of Mt. Kinabalu: herbdata@herbarium.bpp.msu.edu
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 martini.eecs.umich.edu, 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
-------------------------------------------------------------------------
ftp.bio.indiana.edu (IN USA) IUBIO Genbank, FlyBase fG
ncbi.nlm.nih.gov (MD USA) NCBI f
ftp.embl-heidelberg.de (Germany) EMBL Data Library Efg
coli.polytechnique.fr (France) EMBLnet G
ftp.bchs.uh.edu (TX USA) Genbank, PIR fG
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
megasun.bch.umontreal.ca Molecular evolution G
nic.funet.fi (Finland)
gopher.csc.fi (Finland)
nic.switch.ch (Switzerland) EMBnet fG W [10]
rdp.life.uiuc.edu Ribosomal DB Project f
world.std.com A major entry-point fG
sunsite.unc.edu (NC USA) Many subjects EfGt [4]
gopher.ciesin.org Earth Sciences G
locus.nalusda.go (USA) Nat. Agri. Library G
s27w007.pswfs.gov (USA) Forest Genetics G
biomed.uio.no (Norway) Genome data T
gopher.embnet.unibas.ch (Switzer.)
biox.embnet.unibas.ch (Switzerland) Genome data G
|| gopher.gdb.org (MD USA) GDB Genome Data Bank G
weeds.mgh.harvard.edu (MA USA) Arabidopsis, C. elegans G
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
gopher.duke.edu (NC USA) Chlamydomonas G [2]
picea.cfnr.colostate.edu (CO USA) f
poplar1.cfr.washington.edu (WA USA) Populus genetics f
esusda.gov (USA) USDA Extension Service G
infoserver.ciesin.org CIESIN Global Change G
mobot.org (MO USA) Missouri Bot. Garden f
life.anu.edu.au (Australia) Bioinformatics fG
igc.org (CA USA) EcoNet f
gopher.yale.edu (CT USA) Ecol. Data EXchange 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 GT [6]
ecosys.drdr.virginia.edu (VA USA) Ecosystems GT
sparc.ecology.uga.edu (GA USA) Ecology, Coweeta LTER G
ngdc1.ngdc.noaa.gov (USA) Paleoclimatology f [1]
huh.harvard.edu (MA USA) Harvard Univ. Herbaria fG
simsc.si.edu (DC USA) Smithsonian Inst. f [3]
ucmp1.berkeley.edu (CA USA) Vertebrate museum G
bdt.ftpt.br (Brazil) Biodiversity fG
coli.polytechnique.fr (France) Molecular evolution G
fconvx.ncifcrf.gov (MD USA) Mathematical Biology f
cheops.anu.edu.au Radiocarbon Abstracts fG W
bluehen.ags.udel.edu (DE USA) Entomology G
minerva.forestry.umn.edu (MN USA) Forestry G
ucsbuxa.ucsb.edu (CA USA) Biology G
evolution.genetics.washington.edu Evolution f
evolution.bchs.uh.edu (TX USA) Evolution f
martini.eecs.umich.edu (MI USA) Geographic Name Server t [7]
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
saturn.soils.umn.edu (MN USA) Geology G
kiawe.soest.hawaii.edu (HA USA) Generic Mapping Tools f
tycho.usno.navy.mil U.S. Naval Observatory t [8]
nssdca.gsfc.nasa.gov NSSDC On-Line Service t [9]
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
info.mcs.anl.gov (IL USA) Argonne National Lab. f
stis.nsf.gov (DC USA) Nat. Science Foundation fG
rtfm.mit.edu (MA USA) Usenet FAQ repository ef [5]
jse.stat.ncsu.edu (NC USA) Journal of Stat. Educ. fG
ftp.sas.com (NC USA) SAS-related information f
zaphod.ncsa.uiuc.edu (IN USA) Supercomputing f
lupulus.ssc.gov Young Scientists Net. f
ksuvxa.kent.edu Directory of lists f
sun.soe.clarkson.edu LaTeX tools f
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: 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 info@sunsite.unc.edu.
-*- 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 bitftp@vm.gmd.de 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 ftpmail@decwrl.dec.com, 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, rtfm.mit.edu: to get a help file, a list of all the FAQs
stored there, and the latest version of this guide, send e-mail to
mail-server@rtfm.mit.edu with the text
help
index
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 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).
-*- 3.6.5. 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-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 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: archie.au in Australia; archie.funet.fi in
Finland; archie.th-darmstadt.de in Germany; archie.doc.ic.ac.uk in Great
Britain; archie.cs.huji.ac.il in Israel; archie.kuis.kyoto-u.ac.jp and
archie.wide.ad.jp in Japan; archie.sogang.ac.kr in Korea; archie.nz in
New Zealand; archie.luth.se in Sweden; archie.ncu.edu.tw in Taiwan;
archie.ans.net, archie.rutgers.edu, archie.sura.net and archie.unl.net
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 gopher.gdb.org, 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 veronica.scs.unr.edu 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 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, 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 info.cern.ch (no username needed).
--
Una Smith
Yale University, Department of Biology, Osborn Memorial Laboratories,
PO Box 6666, New Haven, Connecticut 06511-8155 smith-una@yale.edu
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