SYEH@BIONET-20.BIO.NET (Spencer Yeh) (03/28/89)
Dear Biologists,
BIONET is introducing a new mechanism, called "anonymous FTP," by
which to distribute its collection of public domain software and
databases for molecular biology. FTP is the standard Internet file
transfer protocol. Anonymous FTP can be used from any Internet
computer site to transfer files at no cost to the user from the BIONET
NET.BIO.NET Sun computer. Bitnet sites cannot use this service unless
they are Internet sites also. A special account has been set up with
the username "anonymous." All files in the "anonymous" directory
(also known as the "ftp" directory) can be copied by anyone on the
Internet without needing a computer account on our machine.
To access the BIONET public domain archives by anonymous FTP, run the
FTP program on your local computer to open a connection to the
net.bio.net computer:
$ftp net.bio.net
You will be asked to log on to our computer. To do so, use a username
of "anonymous" ("ftp" will also work), and ANY password. Once you are
logged in to the net.bio.net computer you can run commands to see the
contents of a directory, switch directories, and transfer files.
To make things easy, each directory in the BIONET archives has a file
called "readme.doc" which gives information about that directory. The
top level directory's readme.doc file shows a sample session of using
FTP. The other readme.doc files describe the contents of a particular
directory. Transfer these files to your local computer so that you
can read them.
BIONET users can access a help topic about anonymous FTP by typing
HELP ANONYMOUS-FTP at the BIONET @ prompt.
Currently the following programs and databases are available through
this service:
"db" anonymous FTP directory: (databases)
alu Jurek Jurka's Alu sequence and alignment database.
seqanalref Amos Bairoch's listing of sequence analysis literature references.
"dos" anonymous FTP directory: (MS-DOS software)
dearchive Dearchiving programs
mskermit Kermit terminal emulator/ communications
program for IBM PC's.
util Other utility programs (currently empty).
alx3 Osamu Gotoh's ALN3 and ALP3:
Triple alignment programs for nucl. acids or proteins.
gel J.R. Thompson's GEL:
Calculates fragment from standard curve.
molecule J.R. Thompson's MOLECULE:
Graphic depiction of output from PCFOLD.
oligo Kevin Beadles' OligoMutantMaker:
Assists with site-directed mutagenesis expt. design.
pcfold Michael Zuker's PCFOLD:
RNA folding by energy minimization.
plasmid Joe Lipsick's PLASMID PAINT:
Draws and prints circular plasmids on CGA monitor.
seqaid Don Roufa's SEQAID II:
Multi-functional DNA/ Protein analysis package.
tdalign Dan Davison's TDALIGN:
Fast global alignment of two sequences.
"mac" anonymous FTP directory: (Macintosh software)
dearchive Dearchiving programs
mackermit MacKermit terminal emulation/ communications program.
antiviral Various anti-viral programs for Macintosh.
util Other miscellaneous utility programs.
gelfragsizer Don Gilbert's Gel Frag Sizer:
A Hypercard stack to calculate fragments from standards
We hope the molecular biology community will find this service to be
of use to their research. Please feel free to make suggestions for
improvements to this service, especially suggestions for incorporation
of any high-quality public domain software or databases that would be
of broad interest to our community.
Sincerely,
Spencer Yeh Internet: syeh@bionet-20.bio.net
Applications Analyst
BIONET
(415) 962-7338
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