1818181818 1818181818 1818181818 1818181818 1818 1818 1818 1818181818 1818 1818 1818 181818181818 18181818 1818181818 18181818 181818181818 18181818 1818 1818 1818 18181818 1818 1818 1818 1818 1818 1818 1818 1818 1818 1818 1818 1818181818 1818 1818181818 1818181818 1818 1818 1818181818 1818 1818181818 1818181818 1818 1818 No 18 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% BIO-NAUT NEWSLETTER << EDITED BY ROBERT HARPER >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Quite recently on the INFO-GCG LIST at the University of Toronto there was some discussion as how to recover old messages from the notebooks. Well I wrote about two different ways that you can retreive old messages. Many people found the instructions helpful and it has been suggested that I clump the whole thing together and make BioBit #18 out of it... so here goes. Way back in BioBit #12 I explained how to use LDBASE to retreive individual messages from LISTSERV. Unfortunately LDBASE can only be used by folks on BITNET who have the capability to do "interactive" messaging... so this rules out ALL of the people in the UK and people who are ONLY on Internet sites. However there are a couple of ways to get the job done simply by relying on mail. I will cover the two methods in this edition of BioBit. ***** Method #1 By far the easiest way to recover past information is to ask for the old notebooks that are stored on LISTSERV. The LISTS at IRLEARN store all the messages entered into them in a monthly notebook (archive) which contains all the messages distributed by the list during one month. For the BioSci LISTS at IRLEARN you would just send an E-mail message to LISTSERV@IRLEARN.BITNET You should leave the Subj: line blank and in the main body of the mail message put you commands, one per line. The info you request will be delivered (in about 24 hrs) to you via e-mail. Here are some useful LISTSERV commands: REVIEW +BIONEWS gets you the names and e-mail addresses of the current members in the Bionews list. INDEX +BIONEWS gets you an index of the notebooks available in the Bionews list. They take the form LOGYYMM where YY is the year and MM is the month. GET +BIONEWS gets you that month's notebook e.g. GET +BIONEWS LOG9008 will get you the notebook for the month of August 1990 Here is an example of a mail batch file which you could send to LISTSERV@IRLEARN.BITNET -------------8< cut here 8<----------------- REVIEW BIO+NAUT INDEX BIO+JRNL GET BIO+JRNL LOG9008 -------------8< cut here 8<----------------- In the immortal words of Bo Diddley "Don't write a cheque your tail can't cash" If you are getting LOGS of BIO+JRNL then they will be BIG so you should have enough disk space to receive them. As a reminder here is a list of the names of the lists you can query at LISTSERV@IRLEARN.BITNET +AGEING +BIONEWS BIO+JRNL +BIOMATR BIO+SOFT EMBL+DB +BIOJOBS +GENBANK GENE+ORG GNOME+PR +METHODS BIO+NAUT SCI+RES AG+FORST MOL+EVOL +PROTEIN *********************** IMPORTANT REMINDER *********************** Listserv commands for the BIOSCI lists should be addressed only to LISTSERV@IRLEARN.BITNET and *NOT* to *ANY OTHER E-MAIL ADDRESS* ****************************************************************** Well that gets the simple method out of the way. Now lets look at how we can be more selective. I will use the examples that I gave in INFO-GCG so I do not have to go though all the same proceedures again to generate examples. The only thing to remember is that if you want to query the BIOSCI lists then you should address you queries to LISTSERV@IRLEARN.BITNET instead of LISTSERV@UTORONTO.BITNET **** METHOD #2 These instructions were originally sent to the INFO-GCG list. So they are specific for the LISTSERV@UTORONTO.BITNET. If you use your common sense you should be able to make the neccessary substitutions and make batch mail files work with the BIOSCI lists at LISTSERV@IRLEARN.BITNET ... put on your thinking cap now. << Batch to the Past... Part 1 >> You can reterive old messages from INFO-GCG by getting the LOG of the notebooks, but what if you want to be more selective? And what if you don't have LDBASE to carry on an interactive session with LISTSERV. Well Tom Easton recently pointed out that you can still make queries by mail using a small BATCH job. Here is a rundown on the technique. The process is twofold: 1) You run a batch job to find the information you want from INFO-GCG 2) You run a second batch job to recover the specific items that you found out about in the first batch job. It goes like this: All that you need to do is send a batch job to LISTSERV@UTORONTO.BITNET and the output of your job will be returned to you as DATABASE.OUTPUT. So what would be some interesting topics to look for? SEARCH CLARK AND ALIGN IN INFO-GCG ! clark cos he writes well... alignment ! cos it a hot topic. SEARCH PROSITE IN INFO-GCG ! cos Amos likes to read the answers ! before he reads the questions. SEARCH TUTORIAL IN INFO-GCG ! everyone has a vested interest somewhere Here is a simple batch job for you to try... modify it by putting in your own KEYWORDS and send it off to LISTSERV@UTORONTO.BITNET --------8< cut here 8<---------- //Infogcg JOB Echo=YES,Reply-via=MAIL Database search DD=Mine //Mine DD * Search clark and align in info-gcg index search prosite in info-gcg index search tutorial in info-gcg index /* -------8< cut here 8<------------- You should get the replies within and hour or so if the net is running smoothly. The next message will show the results of the above BATCH job. ..... we now wait for the results to arrive... << Batch to the Past... Part II >> This is the result of the batch job sent by mail to LISTSERV@UTORONTO The turn around time was about 30 minutes from Finland to Canada. The information is given in the form of a table. ITEM # The specific number of a message in the database Date When the message was entered Time The time it was entered Recs The number of lines in the message (approx) Subject The subject of the message (Good subjects are essential) For example Item 000076 was written by Clark or mentions the name Clark, and it had the string "align" in it but the subject gives no clue as to what the message was about. So use good subjects in your mail messages cos it will certainly help people who want to do searches on the datadase. > Search clark and align in info-gcg --> Database INFO-GCG, 16 hits. > index Item # Date Time Recs Subject ------ ---- ---- ---- ------- 000075 90/01/26 16:12 123 Wish list for version 7 000076 90/01/29 10:25 71 000077 90/01/30 11:33 36 Re: Wish list for version 7 000083 90/02/02 16:19 49 RE: 000093 90/02/05 11:13 40 profiles and additions for version 7 (or before?) 000097 90/02/05 12:41 54 flame 000117 90/02/07 23:00 151 How much HELP do we need ? 000118 90/02/08 00:47 92 RE: How much HELP do we need ? 000180 90/03/05 18:45 22 RE: statistical significance 000200 90/03/16 10:36 89 RE: Sequence Analysis Primer 000267 90/05/25 17:26 34 Version 7: Prosite and more 000325 90/07/17 17:39 426 DCL script for EMBL's FastA mail service 000436 90/11/12 10:11 64 RE: multiple sequence alignment 000438 90/11/13 11:14 67 multiple sequence alignment 000439 90/11/13 22:30 96 Volunteers sought 000443 90/11/15 09:25 45 Multiple sequence alignment > search prosite in info-gcg --> Database INFO-GCG, 27 hits. > index Item # Date Time Recs Subject ------ ---- ---- ---- ------- 000040 89/11/03 22:28 540 Data banks corss-referencing. 000049 89/11/20 20:11 276 PROSITE Newsletter Issue Nb. 1 000091 90/02/05 10:13 36 RE: Database for Consensus-Sequences? 000093 90/02/05 11:13 40 profiles and additions for version 7 (or before?) 000101 90/02/06 12:29 70 ProSite database for consensus sequences 000106 90/02/06 22:58 98 PROSITE 000109 90/02/06 23:04 109 RE: Prosite 000127 90/02/09 21:59 49 PROSITE in machine readable form 000165 90/02/24 16:03 109 Pattern Search in GCG 000189 90/03/09 17:52 37 Intro, Prosite, and Skiing 000193 90/03/13 13:31 76 RE: SWISS-PROT and GenPept 000203 90/03/25 22:50 72 RE: genpept/swissprot 000260 90/05/09 21:54 76 Databases announcements 000263 90/05/16 14:45 26 PROSITE to FIND conversion program available 000267 90/05/25 17:26 34 Version 7: Prosite and more 000272 90/06/04 23:36 56 Prosite Index 000273 90/06/05 10:46 29 Re: Version 7: Prosite and more 000279 90/06/06 09:27 17 Version 7: Prosite 000282 90/06/06 10:04 31 RE: Version 7: Prosite 000284 90/06/07 14:26 37 improved PROSITE conversion program 000285 90/06/08 16:49 18 Prosite Database 000286 90/06/09 11:33 50 RE: Prosite Database 000287 90/06/10 23:57 22 Prosite Database 000340 90/08/01 12:36 17 new database 000422 90/11/05 11:20 33 LDBASE search on "Magic" 000437 90/11/12 22:09 28 RE: LDBASE search on "Magic" 000442 90/11/12 16:24 42 Programs to search Prosite > search tutorial in info-gcg --> Database INFO-GCG, 14 hits. > index Item # Date Time Recs Subject ------ ---- ---- ---- ------- 000113 90/02/07 10:35 36 RE: The lost users 000117 90/02/07 23:00 151 How much HELP do we need ? 000130 90/02/12 15:14 68 Re: User Interface 000229 90/04/05 14:06 34 GCG tutorials-is anyone happy with theirs? 000303 90/07/08 20:39 39 GCG tutorial. 000349 90/08/08 12:36 39 Tutorial for GCG (Joint writing working group) 000355 90/08/21 18:06 131 How to teach GCG 000362 90/08/22 18:09 274 Biocomputing Tutorial by Reinhard Doelz 000363 90/08/23 13:17 35 FTP preview of BIOLOGICAL TUTORIAL. 000364 90/08/23 14:26 58 Biocomputing Manual Preview 000367 90/08/23 18:34 31 BIOCOMPUTING TUTORIAL. 000389 90/09/23 05:38 27 BIOCOMPUTING TUTORIAL 000390 90/09/24 09:24 21 problems with zoo'ing manuals 000418 90/10/30 17:50 47 Biocomputing tutorial. Once you have got the indexes that you are interested in you now have to ran another batch job to to recover them. I will deal with that next. > From the first mail batch job we got an index and ITEM # 000076 written on the 29/01/90 did not have any subject, and ITEM # 000083 was a reply to this message with no name... so as part of the exercise let's recover mystery message ITEM # 000083.... to see what it was, and anyways its shorter:-) ****** EXTRACT FROM FIRST BATCH JOB ******* > index Item # Date Time Recs Subject ------ ---- ---- ---- ------- 000076 90/01/29 10:25 71 000083 90/02/02 16:19 49 RE: We now repeat the process. We send a mail batch file to LISTSERV@UTORONTO.BITNET See how I keep repeating the LISTSERV address get that right... always send to LISTSERV and not to the LIST... (no matter how many times this is repeated someone always gets it wrong). Leave the Subj: line blank and in the main body of the text put the following batch job. ------------8< cut here 8<-------------- //Infogcg JOB Echo=YES,Reply-via=MAIL Database search DD=Mine //Mine DD * Search clark and align in info-gcg index print 000083 /* -----------8< cut here 8<--------------- And in the fullness of time listserv sends back the DATABASE.OUTPUT and we can discover the secrets of the mystery message with no name. DATABASE.OUTPUT > Search clark and align in info-gcg ! SEARCH PART of BATCH JOB --> Database INFO-GCG, 18 hits. > index ! INDEX PART of BATCH JOB Item # Date Time Recs Subject ------ ---- ---- ---- ------- *** Rest of the list deleted ! 448 and 449 have clark and align ! in the body of the message so ! so they are now added to the ! index bringing the total to 18 000448 90/11/16 09:14 52 << Batch to the past... Part I >> 000449 90/11/16 09:37 106 << Batch to the Past... Part II >> > print 000083 ! PRINT PART of BATCH JOB >>> Item number 83, dated 90/02/02 16:19:10 -- ALL Lisa Caballero (Genetics@Salk) writes: / Regarding Stephen Clarks message, I have a few comments: / ^^^^^ *** HERE IS KEYWORD CLARK **** / [stuff deleted] /for a contig of lenth 40, its much too stringent when aligning ^^^^^ *** HERE IS KEYWORD ALIGN **** ****** Epilogue Well that is about it. Back to the Future only had three parts, and Batch to the Past only has three parts. So I hope this opens up a new avenue to explore the backlogs on the BIOSCI lists at LISTSERV@IRLEARN.BITNET Happy experimentation. -=ROB=-