 
                      IUBIO ARCHIVE FOR BIOLOGY


IUBio Archive is an archive of biology data and software.  The
archive includes items to browse, search and fetch public
software, molecular data, biology news and documents. It is a
public archive that you will find at the Internet address
iubio.bio.indiana.edu.  This archive, maintained at Indiana
University Biology department since 1989, has moved recently from
one computer to another.

Access to the archive is via HTTP (world wide web), Internet Gopher, 
anonymous FTP (file transfer) and e-mail programs that connect to 
computers on the Internet. 

      ftp:, gopher:, http://iubio.bio.indiana.edu/
	  mailto: archive@iubio.bio.indiana.edu
	  
Molecular biology is the area of concentration, and it is also a
home for Drosophila research data.  The archive maintains
software for all computer systems important to biology. 

Public software categories served here include
  biology, chemistry, science, utilities, 
  molecular biology sections including 
    alignment, codon, autoseq, browsing, consensus, evolve, 
    pattern, primer, restrict-enzymes, rna-fold, search, 
    ibmpc, mac, mswin, unix, vax

See also IUBio Bio-Mirror archive of large data sets at
  ftp to iubio.bio.indiana.edu, cd /biomirror
This includes GenBank, EMBL and DDBJ and other biosequence data.

Search services include
  GenBank nucleic databank (WAIS query of full release and weekly updates)
  Swiss-Prot and PIR protein databanks
  Bionet news (full, searchable archive since Dec 1990)
  SRS (Sequence Retrieval System) - including Genbank, protein and others
     for both simple and sophisticated text/annotation queries of databanks
  SRS-FastA - for sequence similarity searches against any user-defined
    subset of Genbank & protein data, including subsets for popular species
      Arabidopsis, Caenorhabditis, Drosophila, Oryza, Poaeceae, Rattus,
      Murinae, and Saccharomyces 
  
This is a user- and developer- supported archive.  Authors of software
are invited to send their work to the Incoming folder by FTP.
  
E-mail access -- for most IUBio services, including software, Genbank,
Swiss-protein, FlyBase and other databank searches, Bionet news
searches, and software archives, send a mail message to
    archive@iubio.bio.indiana.edu

FlyBase, a Drosophila Genome Database service is accessible now
separately at

    ftp:,  http://flybase.bio.indiana.edu/
	  mailto: flybase-server@flybase.bio.indiana.edu

These IP addresses and computer names can and do change, but
the service name (iubio or flybase) will be maintained.
 



ACCESS TO IUBio ARCHIVE
-----------------------

This IUBio Archive is on the Internet network of computers with the
name
         IUBio.bio.indiana.edu

The actual host computer and Internet number for this archive may
change.  An alternate Internet name that has been in use for several years,
and will continue to work, is FTP.Bio.Indiana.Edu. 

The best way to use the resources of this archive now is thru either
Internet Gopher or thru World Wide Web.  
Among these several advantages over FTP are:  
  Gopher and WWW are easier to use than FTP; 
  Gopher and WWW allow a richer set of information services, including
    searching thru indexed data, and retrieving "typed" files,
    such as pictures and formatted documents;
  Gopher and WWW cause less network traffic and load on the archive
    computer.

From a gopher program, connect to iubio.bio.indiana.edu as the
gopher server.  From a WWW program, connect to this URL:
   http://iubio.bio.indiana.edu/

If your computer system is linked to the Internet, it probably
has an FTP program even if it doesn't have an Internet Gopher
program.  Each FTP program has it's own peculiarities, but most
follow a general syntax:
   ftp  ftp.bio.indiana.edu     -- connect to archive computer
   user: anonymous              -- log on to archive computer
   password: your e-mail address
   ? or help             -- general help for ftp

   cd  subdirectory      -- change to subdirectory
   cd  ..                -- change to superdirectory

   binary                -- use full binary transfer
   ascii                 -- use text transfer
   get  any.file         -- fetch a file from the archive
   put  my.file          -- put a file to the archive
                            (only for Incoming/ directory)
   bye                   -- close the connection

This archive uses Unix conventions and software.  *PLEASE NOTE*, all
FTP commands and file names are CASE-Sensitive.  Mostly these are all
lowercase.  You will need to use your shift key some places, like
"Incoming" and "Readme".   See below for a detailed example session.



For all IUBio services, including Genbank, Swiss-protein, FlyBase
and other databank searches, Bionet news searches, and software archives,
send a mail message to
   gopher@iubio.bio.indiana.edu

For only FlyBase Drosophila information, send the mail message to
   gopher@flybase.bio.indiana.edu

In both cases, you start by sending mail with any or no subject, and
any or no message body. GopherMail will reply by sending you it's main
gopher menu.

The return mail provides you a menu of selections, then you mark
your choices, and return that mail.  Repeat this process to select
many items.  Use the "Subject:" of your mail mesage for queries to
search items like Genbank or FlyBase Genes.

Send the word "help" in the subject line to get help on this service.
GopherMail software was written by Fred Bremmer.



CURRENT CONTENTS OF THE ARCHIVE
-------------------------------

An abbreviated directory of the archive

Archive.doc     About this archive (this document)
ls-lR.Z         Full list of archive files, in unix compressed format
                (used for mirroring, use 'get ls-lR' for readable list)

biology/        General biology
chemistry/      Chemistry
flybase/        Drosophila genome data, stocks, people and documents
help/           Help documents
molbio/         Molecular biology
science/        General sciences
usenet/         Archive of biology news from Usenet
util/           Computer and archive utilities

Incoming/       Contributions go here

./molbio:
align/          Sequence alignment
codon/          Codon tables
data/           Molecular data
evolve/         Evolution and phylogeny
ibmpc/          MSDOS software
journals/	Table of contents of journals
mac/            Macintosh software
primer/		PCR and primer calculation software
restrict-enz/	Restriction enzyme software and data
rnafold/        RNA secondary structure
search/         Databank searching
unix/		Unix specific software
vax/ 		VMS-Vax specific software

The folders bin/, dev/, etc/, and usr/ are for
archive housekeeping; please ignore them.

Thru Internet Gopher, there are several additional items of
general interest to biologists, including GenBank, the databank
of all gene sequences,  BIOSCI Network News, Prosite database,
the Genome of Drosophila book, and other biology data are
indexed for key word searching.  You can also find links to
all other BioGophers in this archive, with easy access to even 
more biology data, software and other information.

Much of the software includes a short abstract or "readme" file
describing it and its requirements.  This is normally named the
same as the software file, but with the suffix ".readme".  These
readme files, and other help and information files in the
archive can be searched via Gopher to let you find software
based on key words you may know (e.g., find software for signal
sequence prediction).

Most of the software is as received from the authors or contributor.
In the case of software source, it may or may not be ready to compile
and run on a given operating system.  Even those programs that do
run may require adjustments to read the data formats that you use.
I have edited and recompiled many of the programs in source form
for different platforms to one extent or another, and can say that
most will run but may require the talents of a programmer to
install them.

The archive of Bionet newsgroups, Sci.Bio and Info-GCG from the
Usenet electronic news media was added starting with news from
about 1 Dec 91.  See the /usenet/Readme file for details.  This
news archive can be searched for specific items via Gopher.

If you have suggestions, questions or comments, please let me know.
Addresses are listed below.



HISTORY
-------

This archive was first started in October 1989 on the computer
called IUBio.Bio.Indiana.Edu.  At that time, the archive was my
personal reference collection of public molecular biology
software and data. I made the archive available to others
because the only similar archive available at the time, at
BioNet, closed it's public software operation.  It seemed little
extra effort for me to make my collection available to others
(my mistake...).

During the summer of 1991, the archive moved to Cricket.Bio.
Indiana.Edu, my desktop Macintosh running Apple Unix. This
computer has served well, handling the traffic of 300 callers/week
and 1000 files/week transferred to people around the world.

Somewhere around this time, the California Education and Research
Federation Network selected this archive as it's 1991
Biological Sciences winner for its CERFnet award for excellence
in networked applications.

As of Nov 1991, the archive moved to a computer called
Fly.Bio.Indiana.Edu.  Through the Bloomington Drosophila stock
center, NSF's Division of Instrumentation and Resources has provided
the funds for the purchase of a Sun Sparcstation 2 to function as
the fly community's database server, and also to host the public
IUBio archive.

By 1992, the archive through FTP and Gopher had been serving out
data to the biology scientific community at high rates.  In 1992, roughly
10,000 files per month were FTP'ed from the archive, and roughly
20,00 gopher transactions per month were recorded.  By 1993 - 1994.
this had grown to over 100,000 gopher transactions per month,
and around 18,000 FTP transfers per month.



ACKNOWLEDGEMENTS
----------------

I would like to thank all of the hard working and often
under-acknowledged authors who have contributed their software
and data collections to this and other public archives.  It is
they who deserve credit for what this and other public archives
mean to you and your ability to do your work.

Please keep in mind that frequently the authors of these works
receive little or no credit from their peers, the authors
represented in this archive for the most part receive no money
for their efforts, which are commonly done on weekends,
evenings, vacations.  If you would, please remember to mention
the authors who make their software and databases available to
you as it aids your work.

Any program or database that is available publicly is published.
If the author does not have a paper publication that you can
cite, I recommend this form:

    Doe, John, 1991*.  (Insert title of software or database).
    Published electronically on the Internet, available at
    ftp://iubio.bio.indiana.edu/ .%

* If no date is given explicitly, use the file dates.
% Substitute the universal resource locator (URL) for the given package.

You need not cite this archive for files you obtain here,
however you may consider it equivalent to a paper journal
or book in some ways.  It is certainly an information
resource.  The proper citation for this public archive is:

  Gilbert, D.G., 1989.  IUBio archive of molecular and general
  biology software and data.  An Internet resource available
  at ftp,gopher,http://iubio.bio.indiana.edu.


I am very pleased to acknowledge the many people and organizations
that have helped support IUBio archive.  Much of the current hardware
is made available by co-operation with FlyBase,  supported
by a grant from the US National Institutes of Health.   Current
and past equipment support has come from Indiana University,
National Science Foundation, and many of you who use the archive.
(see http://iubio.bio.indiana.edu/contributors ).


In early 1993, this archive faced a space-crunch.  Its only 
1-gigabyte disk was full.  I was faced with throwing out
valuable software & data, and spending a long time searching
for government grant funds.   When the community of users
learned of this predicament, many of them quickly and cheerfully
sent money to expand the disk space of this archive.
Through the contributions of these many fine people, companies 
and institutions, we were able to triple the storage space of
for this archive.  The archive now has a home of its own, provided
by several of you who use and benefit from it, and no longer has
to rely exclusively on extra resources from other projects.

See the "Contributors" document for a list of the many who have 
helped keep this archive a growing resource for you.
 


CONTRIBUTING TO THE ARCHIVE
---------------------------

Contributions of broad interest in any area of biology, and related
areas of chemistry and other sciences, are welcome.  These may be
software or data.  Contributions of interest over several computer
platforms should either be plain text files or .ZIP or .TAR.Z archives.
You may put your contribution in the "Incoming" directory,
using your FTP put command.  You may also send e-mail compatible
files (usually .UUE or .HQX encoded files or plain text) to

  Archive@Bio.Indiana.Edu               (preferred Internet address)

  Don Gilbert, BioComputing Office      (land mail)
  Biology Department, Indiana University
  Bloomington, IN  47405   USA

Any general mail about the archive should be addressed here also.




USING THE ARCHIVE VIA FTP
-------------------------

Using Internet Gopher is generally very simple, either a
point'n'click operation on computers with graphic user
interfaces, or simple menu operations on character terminals.

FTP is still primarily a command-line service.  You need to know
and remember the commands to use it.  Here is a brief primer.

To change from the main directory to a subdiretory, use the
command:
         ftp> cd subname
To move up one level,
         ftp>  cd ..
To move over to another subdirectory at the same level,
         ftp>  cd ../anothersub
Some examples,
         ftp> cd molbio/align
         ftp> cd /molbio/evolve

Some of the programs are in source form, or include data or
documentation that is useful on many platforms.  Since most of the
programs require many files and to save space and transmission
time, we store many of these programs in some archived format.  

In general there are different prefered archive formats for each
computer platform.  The ZIP archive format is perhaps most widely
used, but it still is mainly found on MS-DOS computers (Unix and VMS
ZIP utilities are available, but up-to-date ZIP for Macintosh
is lacking at this time).  The TAR.Z format is common on Unix
computers, and utilities for using TAR.Z are available on MS-DOS,
Macintosh and VMS.   The Stuffit-BINHEX format is mainly Macintosh,
but utilities exist on Unix and MS-DOS for using this format.

Right now, there is quite a range of formats at this archive. 
You pretty much need to refer to the list of file suffixes below
to determine which is which.  Look in the /util subdirectory for
programs which will decode these archived files.

In some cases, the archive files and programs are stored here only
as BINARY files.  This means for FTP you must set your transmission
software to transfer a full 8-bit byte, with the ftp command
"Binary".   See below list of file suffixes to tell which are in
binary format.  Internet Gopher users can ignore this, as the Gopher
software handles text versus binary by itself.

Most or all Macintosh files have been converted to .HQX format, or
BinHex.  This is an ascii (text) encoded form that you can fetch
with the normal FTP setting of text (or ascii) transfer. You need
Stuffit, BinHex 4.0 or other programs to decode this format.

Many of the archives and any of the .DOC, .TXT or .README files are
in Ascii (plain text) format, suitable for transfer with a default
Ascii method, or via e-mail programs.  The encoded programs (.HQX
or .UUE suffixes) require that you have a decoder on your computer.
These are for
  Macintosh  .HQX  [Archive.Util.Mac]BinHex.*
  MSDOS  .UUE  [Archive.Util.IBMPC]UUDecode.Bas, *.C
  VMS    .UUE  [Archive.Util.VMS.UUEncode]*.*
  Unix   .UUE  use MS-DOS or VMS source code


File name suffixes
------------------

TEXT (ascii) File formats
----
.DOC     Plain text documentation
.TXT     Plain text documentation
.README  Plain text documentation

.HQX     Macintosh BinHex encoded file
.UUE     MS-DOS, VMS, Unix UUEncode encoded file

.C       C source text
.F       ForTran source text
.FOR     ForTran source text
.P       Pascal source text
.PAS     Pascal source text
.COM     VMS command text
.MAKE    Unix command text

.DAT     general data file (usually text)
.SEQ     sequence data, usually nucleic acids (text)
.PEP     amino acid sequence data (text)
.AA      amino acid sequence data (text)

BINARY File formats (requires ftp binary command before transfer)
------
.ARC    Archived files (MS-Dos, Macintosh, Unix, VMS)
.ZIP    Archived (MS_Dos, Unix, VMS, others)
.ZOO    Archived files (MS_Dos, Unix, VMS, others)
.TAR    Unix archived files
.Z      Unix compressed file
.TAR.Z  Unix archived + compressed file
.BCK    VMS Backup archive
.SIT    Macintosh archive
.EXE    VMS or MSDOS program


.
