HARPER@HYLKA.HELSINKI.FI (ROBERT HARPER FINLAND) (04/19/89)
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No 5
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<< EDITED BY ROBERT HARPER >>
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GETTING BIONET PROGRAMMES VIA FTP
Recently BIONET announced that they would distribute software for
molecular biology via FTP. Sounds great! but can ordinary users on
EARN/BITNET take advantage of it?
Recently I did a small survey on BIOBIT to discover just how many
people knew what FTP meant or if they had ever used it, and it
would appear that in Europe at least not many people know very
much about the techniques involved. So lets begin by defining
terms and getting a few facts straight. FTP stands for File
Transfer Protocol. It allows you to transfer files between two
host systems that are on InterNet.
So basically your host system should have the FTP programme and be
connected to InterNet. If you can fulfill those two requirements
then you could for example access the archives at Simtel20. There
is alot of software just waiting to be picked up.
The following FTP session was logged on a VAX and the connection
was between Finland and the United States. As you will see the
basic FTP commands are very simple, and very reminicent of MSDOS
commands (DIR= Directory, CD= Change Directory etc). After you
have opened the connection you are asked for a USERNAME and since
this is ANONYMOUS FTP you simply give the USERNAME anonymous. You
are then asked for a PASSWORD to which you can reply GUEST, though
you can give your REAL identity if you want to.
This session is very rudimentary since my own experiance with FTP
is only at the novice level. I usually find that I learn by
following examples, so this edition of BIOBIT is simple in order
that you can follow the example and learn from it.
Let me say that I was pleasantly surprized by the fact that the
FTP process was both simple to use and incredibly fast. If your
computer center does not have FTP then you should consider going
to the barricades to get it.
Getting the files is one thing making them work on your micro is
another story... and that will be the theme of BIOBIT No 6...
namely we will look at the mystries of UUDECODE are ARC
-=ROB=-
%%%%%%%%%%%%%%%%% FTP SESSION WITH COMMENTS %%%%%%%%%%%%%%%%%%%%%%%%%%%
The Finnish Ministry of Education has the possibility to FTP files
from the USA. After setting up the FTP programme apparently you
should be able to give the name NET.BIO.NET and get through to the
BIONET host computer... lets try it?
ftp> open net.bio.net
220 NET.BIO.NET FTP server (Version 4.180 Wed Dec 14 14:16:08 PST 1988)
ready.
Remote User Name:anonymous */ the convention is to use ANONYMOUS/*
Remote Password:guest */ and the password is GUEST/*
Well I want to see what the other machine is saying so I will put
FTP into VERBOSE mode... perhaps later when I am accustomed to
working with FTP I won't need to bother with it.
ftp> verbose
Show FTP server's responses.
Now lets see what goodies BIONET has for us with the DIR command.
ftp> dir
200 PORT command successful.
150 Opening ASCII mode data connection for /bin/ls (0 bytes).
total 17
drwxrwsr)x 8 172 101 1024 Mar 5 19:36 Public
drwxrwsr)x 2 3 101 512 Aug 12 1988 bin
drwxrwsr)x 2 3 101 512 Dec 18 01:51 dev
drwxr)xr )x 2 0 10 512 Feb 28 23:24 domain
lrwxrwxrwx 1 0 10 6 Mar 1 18:18 pub )> Public
lrwxrwxrwx 10 1 Jan 23 21:40 public )> Public
)rw)rw) r)) 1 172 10 8330 Mar 6 21:44 readme.doc
drwxrwxrwx 2 3 101 512 Mar 7 11:03 receive
drwxrwsr)x 3 3 101 512 Aug 12 1988 usr
226 Transfer complete.
I suppose the PUBLIC directory is where they keep the stuff. Lets
go there with CD (Change Directory) command.
ftp> cd public
250 CWD command successful.
Now that we are down in the Public directories I wonder what they
have... have to do a DIR again.
ftp> dir
200 PORT command successful.
150 Opening ASCII mode data connection for /bin/ls (0 bytes).
total 7
drwxr)sr)x 2 0 101 512 Mar 5 19:36 barrnet
drwxrwsr)x 3 172 101 512 Mar 1 00:30 db
drwxrwsr)x 12 172 101 512 Mar 1 00:27 dos
drwxrwsr)x 6 172 101 512 Mar 1 00:29 mac
)rw)rw)r)) 1 172 101 217 Feb 28 23:49 readme.doc
drwxrwsr)x 3 172 101 512 Jan 23 21:58 sri)nic
drwxrwsr)x 2 172 101 512 Feb 28 23:24 unix)hacks
226 Transfer complete.
Looks like they have it well organised... since I do most of my
work on and IBM clone... I will head for the DOS directory. Looks
like they might have stuff for the MAC as well.
ftp> cd dos
250 CWD command successful.
How many directories have I come down through... Oh well never
mind let's worry about that later. Now for a look at the goodies.
ftp> dir
200 PORT command successful.
150 Opening ASCII mode data connection for /bin/ls (0 bytes).
total 11
drwxrwxr)x 2 172 10 512 Mar 1 00:15 dearchive
drwxrwxr)x 2 172 10 512 Feb 23 18:07 gel
drwxrwxr)x 2 172 10 512 Mar 1 00:15 molecule
drwxrwxr)x 2 172 10 512 Mar 1 00:15 mskermit
drwxrwxr)x 2 172 10 512 Feb 25 00:56 oligo
drwxrwxr)x 2 172 10 512 Jan 24 20:35 pcfold
drwxrwxr)x 2 172 10 512 Feb 23 19:37 plasmid
)rw)rw)r)) 1 172 101 753 Mar 1 00:27 readme.doc
drwxrwxr)x 2 172 10 512 Mar 1 18:14 seqaid
drwxrwxr)x 2 172 10 512 Feb 24 22:34 tdalign
drwxrwxr)x 2 172 10 512 Jan 24 20:36 util
226 Transfer complete.
I suppose I should have a look at that README.DOC. It will most
likely tell me about the programmes avaiable. Lets get it with the
GET command. But first of all lets put on HASH so I can see that
the the line does not go down during the transfer.
ftp> hash
Display # for each 1K bytes transfer.
ftp> get readme.doc
200 PORT command successful.
150 Opening ASCII mode data connection for readme.doc (753 bytes).
#
775 bytes transmitted in 3 seconds (258 bytes/s)
226 Transfer complete.
Three seconds to come from California to Finland... can't complain
Uncle Dave. I think I will slip out to DCL and have a look at that
document. An exclamation mark takes you out of FTP and puts you at
VAX command level. Then you can use the TYPE command to have a
look at the readme.doc
ftp> !
$ type readme.doc
"dos" anonymous FTP directory:
dearchive Dearchiving programs
mskermit Kermit terminal emulator/ communications
program for IBM PC's.
util Other utility programs (currently empty).
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.
Interesting... I have always had my eye on that PLASMID PAINT ever
since I read about it on the BIONET Bboards. I think I will get
it. Lets pop out of this sub process and back to FTP> with the LOG
command.
$ log
Process HARPER_1 logged out at 7)MAR)1989 16:25:39.71
Down into the PLASMID directory first of all with CD.
ftp> cd plasmid
250 CWD command successful.
...and have a look inside and what the contents are.
ftp> dir
200 PORT command successful.
150 Opening ASCII mode data connection for /bin/ls (0 bytes).
total 83
)rw)rw)r)) 1 172 10 73099 Feb 23 19:37 plasmidc.uue
)rw)rw)r)) 1 172 10 6743 Feb 23 19:37 plasmsrc.uue
)rw)rw)r)) 1 172 10 3528 Feb 23 19:32 readme.doc
226 Transfer complete.
Hhhhhmmm... they have got the files UUENCODED so it is coming
across as ASCII so I do not need to change the settings to BINARY.
Quite big file 73099 Kbytes... wonder how long it will take to
transfer?
ftp> get plasmidc.uue
200 PORT command successful.
150 Opening ASCII mode data connection for plasmidc.uue (73099 bytes).
########################################
#################################
73099 bytes transmitted in 61 seconds (1217 bytes/s)
226 Transfer complete.
Only a minute... I must have a lucky streak today. The network is
working like a dream. Well I had better not press my luck any
further... best to log off now and have a look at that PLASMID
PAINT
ftp> bye
221 Goodbye.
Rob "simplicity is often rewarding" Harper