IUBIO ARCHIVE FOR BIOLOGY
Welcome to the IUBio Archive of biology software and data. This is
an anonymous ftp archive that you will find on the computer with
the Internet name of ftp.bio.indiana.edu.
Molecular biology is the area of concentration, and it is also a
home for Drosophila research data. It will include
software for Macintosh, VAX-VMS, Unix, MS-DOS and any other
important computer operating systems. Access to the archive is via
anonymous FTP (file transfer protocol) programs that connect to
computers on the Internet.
ACCESS TO IUBIO ARCHIVE
-----------------------
This IuBio Archive is on the Internet network of computers with the
name
FTP.Bio.Indiana.Edu
The actual host computer and Internet number for this archive may
change. The Internet address of the current Iubio archive computer
is 129.79.224.25.
If your computer system is linked to the Internet, it probably has
an FTP 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
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.
CURRENT CONTENTS OF THE ARCHIVE
-------------------------------
An abbreviated directory of the archive
Archive.doc About this archive (this document)
Files Full list of archive files
Files.new Most recent archive files
biology/ General biology
chemistry/ Chemistry
fly/ Drosophila stocks and data
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
mac/ Macintosh software
rnafold/ RNA secondary structure
search/ Databank searching
The folders bin/, dev/, etc/, private/ and usr/ are for
archive housekeeping; please ignore them.
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.
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.
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 via
anonymous ftp from ftp.bio.indiana.edu.%
* If no date is given explicitly, use the file dates.
% Substitute the name of the archive you obtained it from.
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
via anonymous ftp to ftp.bio.indiana.edu.
-------------- Don Gilbert
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 .ARC 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
-----------------
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. The
archiver previously common to all of the above operating systems
is the ARC format popularized by System Enhancement Assoc. for MS-DOS
machines. Many of the programs, especially those useful only on
one operating system, are in the "native" archive format, whatever
is most popular on that OS.
Over the past several years, the ARC format has lost favor. There
is now a multi-platform archive format called ZIP (first popular
on MS-DOS). I am evaluating this, and may change to ZIP as a
standard for this archive. Right now, there is quite a range
of formats. 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 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.
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.
Some Macintosh programs may be stored in "MacBinary" format, which
is binary and adds file system information at the start of the
files. Your transfer software needs to know about macbinary for
you to use these (NCSA Telnet, VersaTerm Pro, Red Ryder and most
mac communications software does support MacBinary).
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
Here is an example session with the IUBio archive (Unix host) from
a Unix computer (^^^^^ indicates lines that you complete).
MyHost% ftp ftp.bio.indiana.edu
^^^^^^^^^^^^^^^^^^^^^^^
Connected to fly.bio.indiana.edu.
220 fly FTP server (Version 6.9 Wed Oct 30 12:13:34 EST 1991) ready.
Name (ftp.bio.indiana.edu:gilbertd): anonymous
^^^^^^^^^
331 Guest login ok, send e-mail address as password.
Password: joe
^^^
230-Next time please use your e-mail address as your password
230- for example: joe@sunflower.bio.indiana.edu
230-Please read the file Readme
230- it was last modified on Wed Jun 5 20:00:12 1991 - 148 days ago
230 Guest login ok, access restrictions apply.
ftp> dir
^^^
200 PORT command successful.
150 Opening ASCII mode data connection for /bin/ls.
total 70
-rw-r--r-- 1 gilbert archive 13425 Jun 6 01:00 Archive.doc
-rw-r--r-- 1 gilbert archive 36939 Sep 29 17:41 Files
-rw-r--r-- 1 gilbert archive 3397 Sep 29 18:14 Files.new
drwxrwxrwx 3 ftp archive 512 Oct 31 13:32 Incoming
lrwxrwxrwx 1 root daemon 11 Oct 30 17:46 Readme -> Archive.doc
dr-x-----x 2 root wheel 512 Oct 30 17:23 bin
drwxr-xr-x 4 gilbert archive 512 Oct 29 23:07 biology
drwxr-xr-x 6 gilbert archive 512 Aug 16 18:41 chemistry
dr-xr-xr-x 2 root wheel 512 Oct 29 22:30 dev
dr-xr-xr-x 2 root wheel 512 Oct 30 17:27 etc
drwxrwxr-x 4 matthewk archive 1024 Oct 24 21:02 fly
drwxr-xr-x 7 gilbert archive 1536 Sep 29 16:49 help
drwxr-xr-x 19 gilbert archive 512 Aug 15 23:06 molbio
drwx------ 2 gilbert archive 512 Oct 22 15:18 private
drwxr-xr-x 5 gilbert archive 512 Aug 17 00:51 science
dr-xr-xr-x 3 root wheel 512 Oct 29 22:29 usr
drwxr-xr-x 6 gilbert archive 512 Aug 15 23:05 util
226 Transfer complete.
1075 bytes received in 0.013 seconds (78 Kbytes/s)
ftp> get Readme iubio-archive.readme
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
200 PORT command successful.
150 Opening ASCII mode data connection for Readme (13425 bytes).
226 Transfer complete.
local: iubio-archive.readme remote: Readme
13804 bytes received in 0.068 seconds (2e+02 Kbytes/s)
ftp> cd molbio
^^^^^^^^^
250 CWD command successful.
ftp> dir
^^^
200 PORT command successful.
150 Opening ASCII mode data connection for /bin/ls.
total 19
drwxr-xr-x 2 gilbert archive 512 Sep 29 16:52 align
drwxr-xr-x 2 gilbert archive 512 Sep 29 17:03 atarist
drwxr-xr-x 2 gilbert archive 1024 Aug 1 14:33 codon
drwxr-xr-x 2 gilbert archive 1024 Sep 29 16:47 data
drwxr-xr-x 4 gilbert archive 512 Aug 15 22:46 evolve
drwxr-xr-x 2 gilbert archive 512 Jun 4 21:27 gcg
drwxr-xr-x 2 gilbert archive 512 May 14 15:30 genbank
drwxr-xr-x 3 gilbert archive 1024 Aug 15 23:48 ibmpc
drwxr-xr-x 5 gilbert archive 2560 Sep 29 17:00 mac
drwxr-xr-x 2 gilbert archive 512 May 14 16:01 ncbi
drwxr-xr-x 2 gilbert archive 512 Aug 7 22:42 primer
drwxr-xr-x 4 gilbert archive 512 Oct 21 22:23 readseq
drwxr-xr-x 2 gilbert archive 512 May 14 16:18 renzyme
drwxr-xr-x 2 gilbert archive 512 May 14 16:18 rnafold
drwxr-xr-x 3 gilbert archive 512 Sep 29 17:05 search
drwxr-xr-x 3 gilbert archive 512 Oct 21 21:56 unix
drwxr-xr-x 3 gilbert archive 512 Sep 29 17:02 vax
226 Transfer complete.
1051 bytes received in 0.11 seconds (9.5 Kbytes/s)
ftp> cd readseq
^^^^^^^^^^
250 CWD command successful.
ftp> dir
^^^
200 PORT command successful.
150 Opening ASCII mode data connection for /bin/ls.
total 206
-rw-r--r-- 1 gilbert archive 56832 May 14 16:16 readseq.arc
-rw-r--r-- 1 gilbert archive 11381 Oct 21 22:22 readseq.c
-rw-r--r-- 1 gilbert archive 2595 May 14 16:16 readseq.doc
-rw-r--r-- 1 gilbert archive 5061 May 14 16:16 readseq.p
-rw-r--r-- 1 gilbert archive 63559 May 14 16:16 readseq_sun.uue
drwxr-xr-x 2 gilbert archive 512 Oct 21 22:23 sparc-bin
-rw-r--r-- 1 gilbert archive 42507 Oct 21 22:22 ureadseq.c
-rw-r--r-- 1 gilbert archive 1365 May 14 16:17 ureadseq.h
-rw-r--r-- 1 gilbert archive 21010 May 14 16:17 ureadseq.p
drwxr-xr-x 2 gilbert archive 512 Oct 21 22:25 vms-vax-bin
226 Transfer complete.
676 bytes received in 0.13 seconds (5.2 Kbytes/s)
ftp> get readseq.doc
^^^^^^^^^^^^^^^
200 PORT command successful.
150 Opening ASCII mode data connection for readseq.doc (2595 bytes).
226 Transfer complete.
local: readseq.doc remote: readseq.doc
2670 bytes received in 0.015 seconds (1.7e+02 Kbytes/s)
ftp> binary
^^^^^^
200 Type set to I.
ftp> get readseq.arc
^^^^^^^^^^^^^^^
200 PORT command successful.
150 Opening BINARY mode data connection for readseq.arc (56832 bytes).
226 Transfer complete.
local: readseq.arc remote: readseq.arc
56832 bytes received in 0.096 seconds (5.8e+02 Kbytes/s)
ftp> bye
^^^
221 Goodbye.