From: IN%"POSTMASTER@EMBL.BITNET" "General PostMaster" 7-FEB-1990 17:26:16.32 To: HARPER@cc.Helsinki.FI CC: Subj: Automatic response to : GET SOFTWARE:BIOBIT.11 Received: from jnet-daemon by cc.Helsinki.FI; Wed, 7 Feb 90 17:25 EET DST Received: From EMBL(NETSERV) by FINUHB with Jnet id 4770 for HARPER@FINUH; Wed, 7 Feb 90 17:25 O Date: Wed, 07 Feb 90 16:07:21 From: EMBL Network File Server Subject: Automatic response to : GET SOFTWARE:BIOBIT.11 To: HARPER@cc.Helsinki.FI Reply-to: General PostMaster Organisation: European Molecular Biology Laboratory Postal-address: Meyerhofstrasse 1, 6900 Heidelberg, W. Germany 1111111111 1111111111 1111111111 1111111111 111 111 111 111 111111111 111 1111111111 111111111 111 111111111 111111111 1111111111 111111111 111 111 111 111 111 111 111 111 111 111 1111111111 111 1111111111 1111111111 111 111 1111111111 111 1111111111 1111111111 111 111 No 11 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% INDEPENDANT NEWSLETTER PRODUCED AT HELSINKI UNIVERSITY, FINLAND << EDITED BY ROBERT HARPER >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Well at long last a software server has opened up in Europe, and you can access it with plain old common or garden mail. The server is situated at EMBL (European Molecular Biology Laboratory) and it is managed by Rainer Fuchs. So far it caters for different operating systems (MS-DOS, MAC, VAXVMS), and in the future it is hoped that anyone who has an interesting programme which is related to the biological sciences can have it made available for distribution on the EMBL server. This editon of BIOBIT will be a "show and tell" session with the server so that if anybody in Europe wants to try it out then they will have some notes to which they can make reference. I will use the DOS_SOFTWARE directories as an example. All requests to the server should be sent to: NETSERV@EMBL For example you can make up a batch mail file to get all of the neccessary documentation at one go. The server looks at every line of your mail file and processes it as a command so if you put the following seven lines in your mail message you should get all the information you would need to get started. ---------------8< cut here 8<---------------- HELP HELP DOS_SOFTWARE HELP VAX_SOFTWARE HELP MAC_SOFTWARE DIR DOS_SOFTWARE DIR VAX_SOFTWARE DIR MAC_SOFTWARE --------------8< cut here 8<---------------- The server will then send you seven seperate mail messages for each command in your batch file. Lets look at the results from the DIR DOS_SOFTWARE command. DIR DOS_SOFTWARE Directory of MS DOS Molecular Biology Software on EMBL File Server ------------------------------------------------------------------ To receive files from this directory use the command: GET DOS_SOFTWARE:filename.ext (a) Molecular Biology Software filename CMOLECUL.UUE version May 87 size 70 k compressed PAK ASCII conversion UUE author Thompson J. R. (Cedergren R.) description graphics output of PCFOLD result files (CGA card req.) literatur Nucl. Acids Res. 10 (1982), 8351-8356 source code available as MOLECSRC.UUE filename EMOLECUL.UUE version May 87 size 70 k compressed PAK ASCII conversion UUE author Thompson J. R. (Cedergren R.) description graphics output of PCFOLD result files (EGA card req.) literatur Nucl. Acids Res. 10 (1982), 8351-8356 source code available as MOLECSRC.UUE filename HMOLECUL.UUE version May 87 size 70 k compressed PAK ASCII conversion UUE author Thompson J. R. (Cedergren R.) description graphics output of PCFOLD result files (Hercules card req.) literatur Nucl. Acids Res. 10 (1982), 8351-8356 source code available as MOLECSRC.UUE filename MOLECSRC.UUE version May 87 size 70 k compressed PAK ASCII conversion UUE author Thompson J. R. (Cedergren R.) description Source code for MOLECULE literatur Nucl. Acids Res. 10 (1982), 8351-8356 source code Pascal filename EZ-FIT$.UUE version 1.1 size 170 k compressed PAK ASCII conversion UUE author Perella F. W. description Calculation of enzyme and receptor kinetics literatur Anal Biochem. 174 (1989), 437-447 source code none filename GEL$.UUE version 17.2.89 size 50 k compressed PAK ASCII conversion UUE author Thompson J. R. description Calculation of DNA restriction fragment sizes literatur Anal. Biochem. 115 (81), 113-122 source code Pascal filename MOTIF$.UUE version unknown size 45 k compressed PAK ASCII conversion UUE author Giles I. description Motif searching program literatur CABIOS 5 (1989), 227-232 source code C filename OLIGO.UUE version 1.0 size 105 k compressed PAK ASCII conversion UUE author Beadles K. description Oligo-directed single amino acid substitution literatur none source code none filename PATTERN$.UUE version unknown size 55 k compressed PAK ASCII conversion UUE author Giles I. description Pattern searching program literatur CABIOS 5 (1989), 227-232 source code C filename PCFOLD$.UUE version 4.0 size 160 k compressed PAK ASCII conversion UUE author Zuker M. description RNA folding literatur Meth. Enzymology 180 (1989), 262-288 source code Fortran, Asm filename PLASMID.UUE version 1.1 size 75 k compressed PAK ASCII conversion UUE author Lipsick J. description Plasmid drawing program (CGA card req.) literatur none source code Basic filename SEQAIDFD.UAA version 3.5 size 185 k compressed PAK ASCII conversion UUE (split) author Roufa D. description DNA and protein sequence analysis package (Part 1 of 2) literatur none source code none filename SEQAIDFD.UAB version 3.5 size 185 k compressed PAK ASCII conversion UUE (split) author Roufa D. description DNA and protein sequence analysis package (Part 2 of 2) literatur none source code none filename TDALIGN$.UUE version 1.61 size 120 k compressed PAK ASCII conversion UUE author Davison D. (Thompson K.) description Sequence alignment literatur none source code none (b) Archiving/Decoding Software filename UUEMBL.UUE version unknown size 35 k compressed PAK ASCII conversion UUE author Fuchs R. (Dumas M.) description UUEncoded form of UUD uudecoder and UUE uuencoder literatur none source code C filename UUD.C version unknown size 20 k compressed no ASCII conversion no author Dumas M. description Source code for recommended uudecoder literatur none source code C filename UUDECODE.PAS version unknown size 6 k compressed no ASCII conversion no author unknown description Source code for bootstrap uudecoder literatur none source code Pascal filename UUD19.BAS version unknown size 5 k compressed no ASCII conversion no author unknown description Source code for bootstrap uudecoder literatur none source code Basic Files with the extension ".uue", ".uaa" etc. must be decoded with UUD. See HELP DOS_SOFTWARE for details. STEP ONE: Now all the files are in UUE format so the very first step you have to make is to get a UUDECODER for yourself. I recommend that you get UUD19.BAS... which is a bootstrap decoder. Once the files arrive on your mainframe by mail you should edit out the mail headers so that you only have the BAS code and the UUE code. You will then have to download them to your micro via KERMIT. Get someone at your computer centre to do this for you if you have never heard of KERMIT before... (somethings I refuse to explain) 1) GET DOS_SOFTWARE:UU19.BAS and compile it with either BASICA or GWBASIC, and it will give a very small UUDECODER... under 1K in size and very fast. 2) GET DOS_SOFTWARE:UUEMBL.UUE The UUEMBL.UUE package which is the *RECOMMENDED* ENcoder/DEcoder for all of the EMBL software. It is able to handle split files (UAA, UAB etc)... and since all of the EMBL files begin with a DUMAS TABLE there should be no problems with the tilde/caret conversions that can happen when mail goes through the gateways... into the UK for example. 3) Use UUD19 to decode the UUEMBL.UUE package. At the DOS prompt type UUD19 UUEMBL.UUE and after you have blinked your eyes a couple of times it will have been decoded to produce a self-extracting EXE file which will automatically unpack itself to give you the *OFFICIALY RECOMMENDED* set of EN/DEcoders to be used with *ALL* the software available from EMBL. The programmes from this package can automatically take care of files which have been split for posting over the network... so *ONLY* use them with any software you get from the server. STEP TWO: Send a mail message to the server to GET the files you want... usually I would leave the subject line blank and put the commands straight into the body of the message. GET DOS_SOFTWARE:GEL$.UUE Would get the programme for the calculation of restriction enzyme fragments. When I did this the server delivered the UUE file to me here in Finland in under an hour... some people have all the luck:-) When in MAIL on VAX VMS you can EXTRACT/NOHEADER to a file... lets say GEL.UUE. Use KERMIT once again to download GEL.UUE to you micro and decode it using UUD.EXE (The one you got from the self-extracting package) Once the file is on the micro it is DECODED with UUD For example.... ***Oh No Not Again!!*** F:\HARPER\RAIN>uud gel.uue This gives a file called GEL$.EXE which is a self-extracting file. This is very convenient since you do not need to worry any more about how to unpack archives with ARC PKARC etc... The file will unpack to give two files GEL.DOC and GEL.EXE For example.... ***Oh No Not Again!!*** F:\HARPER\RAIN>gel$ Expanding GEL.DOC Finished. Expanding GEL.EXE Finished. Now comes the crunch will the GEL.EXE programme work? Lets cross our fingers... boot it up and see? ***Oh No Not Again!!*** F:\HARPER\RAIN>gel ####### Program GEL : Version 2/18/89 JRT ###### # # # Select Function By First Letter # # # # Documentation Screen # # Input standard fragments and mobilities # # Get standards from a disk file # # Quit the Program and Exit to DOS # # # # ? # # # ################################################## And there it is... a perfectly working file brought from the EMBL server to the mainframe at Helsinki University and downloaded onto your Uncle Robert's "Oh No Not Again!!" micro. If it works for me, then I hope it will work for you. *#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#* -=ROB=- ** Robert Harper ** HARPER@FINUHA ** HARPER@CC.HELSINKI.FI ** *#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*#*