Sequence Analysis on the Mac

B_FOLEY at uvmvax.bitnet B_FOLEY at uvmvax.bitnet
Fri Jan 5 11:15:00 EST 1990


     Indiana University provides a wealth of Macintosh software
for molecular biologists.  Don Gilbert (GILBERTD at IUBACS.BITNET)
is the coordinator of this fine effort.  There is also much
software available here for IBM and other systems.
     Below is a short description provided by Don Gilbert:

--------------------------------------------------------------------

IUBIO ARCHIVE FOR BIOLOGY

The IuBio Archive will maintain biology software and data.  Molecular
biology is the area of concentration.  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 access computers on the Internet.


ACCESS TO IUBIO ARCHIVE
-----------------------

IuBio is on the Internet network of computers with the name
   IuBio.Bio.Indiana.Edu       (IP name)
   129.79.1.101                (IP address)

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  iubio.bio.indiana.edu     -- connect to iubio
   user: anonymous
   password: guest  or  your real user name (prefered)
   ? or help             -- general help for ftp
   cd  [.subdirectory]   -- change directory
   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 [archive.receive] directory)
   bye                   -- close the connection



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

An abbreviated directory of the archive is

Directory IUBIO$DUA0:[ARCHIVE]

ARCHIVE.DOC;2       About this archive
ARCHIVE.LIS;1       Full Archive directory list
BIOLOGY.DIR;1       General biology
CHEMISTRY.DIR;1     Chemistry
HELP.DIR;1          Help documents
MOLBIO.DIR;1        Molecular biology
RECEIVE.DIR;1       Place for contributions
SCIENCE.DIR;1       General sciences
UTIL.DIR;1          Computer and archive utilities

Directory IUBIO$DUA0:[ARCHIVE.MOLBIO]

ALIGN.DIR;1     Sequence alignment, including multiple aligners
DATA.DIR;1      Molecular data
EVOLVE.DIR;1    Evolution and phylogeny
IBMPC.DIR;1     MSDOS software
MAC.DIR;1       Macintosh software
RNAFOLD.DIR;1   RNA secondary structure
SEARCH.DIR;1    Databank searching


Most of the software is as received from the authors or other.  In the case of
software source, it may or may not be ready to compile and run on a given
operating system.

I plan to be adding more software, data and documentation over the next
several months.  If you have suggestions, questions or comments, please
let me know.  Addresses are listed below.


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 .ARC archives.  You may
put your contribution in the [Archive.Receive] 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 at IUBio.Bio.Indiana.Edu         (preferred IP address)

  GilbertD at IUBACS                       (bitnet 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.

This archive of biology software and data is sponsored by the Biology
department, Unversity Computing Services, and Institute of Molecular
Biology, at Indiana University and by your hard working archivist, Don
Gilbert.


USING THE ARCHIVE
-----------------
Users not familiar with the Vax VMS operating system of this archive
will find the subdirectory syntax a bit weird.  To change from one
directory to another, as from your FTP program, you need to enclose
directory path in square brackets "[]".  To change from the main
directory to a subdirectory, use the command:
         ftp> cd [.subname]

See Archive.Doc in the archive for further details.

                        -- Don Gilbert




More information about the Bio-soft mailing list