From: IN%"POSTMASTER@EMBL.BITNET" "General PostMaster" 7-FEB-1990 17:23:05.29 To: HARPER@cc.Helsinki.FI CC: Subj: Automatic response to : GET SOFTWARE:BIOBIT.5 Received: from jnet-daemon by cc.Helsinki.FI; Wed, 7 Feb 90 17:22 EET DST Received: From EMBL(NETSERV) by FINUHB with Jnet id 6586 for HARPER@FINUH; Wed, 7 Feb 90 17:22 O Date: Wed, 07 Feb 90 16:05:26 From: EMBL Network File Server Subject: Automatic response to : GET SOFTWARE:BIOBIT.5 To: HARPER@cc.Helsinki.FI Reply-to: General PostMaster Organisation: European Molecular Biology Laboratory Postal-address: Meyerhofstrasse 1, 6900 Heidelberg, W. Germany 5555555555 555 5555555555 5555555555 555 5555555555555 5555555555 5555555555 5555555555 555 555 555 555 555 555 555 555 555 555 555555555 555 555 555 555555555 555 555 555555555 555 555 555 555555555 555 555 555 555 555 555 555 555 555 555 555 5555555555 555 5555555555 5555555555 555 555 5555555555 555 5555555555 5555555555 555 555 No 5 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% << EDITED BY ROBERT HARPER >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 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