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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 at 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 <filetype>
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 at 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 at 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 at 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 at IRLEARN.BITNET
instead of LISTSERV at UTORONTO.BITNET
**** METHOD #2
These instructions were originally sent to the INFO-GCG list. So they
are specific for the LISTSERV at 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 at 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 at 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 at 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 at 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.
<Batch to the Past... Part III >>
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 at 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 at 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 at IRLEARN.BITNET
Happy experimentation.
-=ROB=-
