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Via:      UK.AC.DL.DLVH; 21 JAN 93 21:49:07 GMT
Newsgroups: bit.listserv.info-gcg
Date:         Thu, 21 Jan 1993 21:40:00 GMT
Reply-To:     AJB@DLVH.DARESBURY.AC.UK
              <INFO-GCG@UTORONTO.BITNET>
From:         AJB@DLVH.DARESBURY.AC.UK
Subject:      Ooops (was Re: Strange STRINGSEARCH behaviour)

Apologies all,

The solution is simple... I need to invest in a pair of glasses :-(
Its been pointed out to me that the EMBL entry contains a spelling
mistake i.e.   borellia != borrelia

Alan Bleasby
SERC Daresbury Laboratory
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Newsgroups: bit.listserv.info-gcg
Date:         Sat, 23 Jan 1993 11:08:57 -0600
Reply-To:     hogan@GCG.COM
              <INFO-GCG@UTORONTO.BITNET>
From:         hogan@GCG.COM
Subject:      fix for findpatterns
Comments: To: info-gcg@utoronto.bitnet@gcg.com

I just wanted to expand on Rodrigo Serrano's fix to FINDPATTERNS.  He may not
have realized that the file enzdata.inc is included in a number of our applib
routines which are then linked to a number other pattern matching programs
(including FINDPATTERNS).

If you want to change the GCG code to accommodate a larger pattern file
(specifically tfsites.dat) the complete VMS fix for enlarging MAXENZCOUNT
follows:

$ gcg

$ gcgsupport

$ copy geninclude:enzdata.inc []

edit enzdata.inc and increase MAXENZCOUNT (I've gone as high as 3000 without
raising virtual memory requirements above the 25,000 pages we recommend)

The line

         Parameter MAXENZCOUNT     = 2000,   ! size of enzdata buffer

should be changed to read

         Parameter MAXENZCOUNT     = 2500,   ! size of enzdata buffer

$ copy enzdata.inc geninclude:enzdata.inc

$ remakelib applib

$ make/compile findpatterns

$ make/compile map

$ make/compile mapplot

$ make/compile mapsort

MOTIFS, REFORMAT and PEPTIDESORT also use these applib routines, but  these
programs are not used with tfsites.dat and so do not have to be remade with the
higher parameter.

The procedure for making the change on a UNIX system is similar.

% gcg

% gcgsupport

% getsrc include enzdata.inc

edit enzdata.inc and increase MAXENZCOUNT (I've gone as high as 3000 without
raising virtual memory requirements above the 25,000 pages we recommend)

The line

         Parameter MAXENZCOUNT     = 2000,   ! size of enzdata buffer

should be changed to read

         Parameter MAXENZCOUNT     = 2500,   ! size of enzdata buffer

% putsrc include enzdata.inc

% buildlib

% buildfapp findpatterns map mapplot mapsort

The buildlib command will build all of the libraries that need to be updated.
How extensive this build is will depend on the status of the library files at
your site.
For example, if you recently installed the entire package from CD and did not
run build, this command will compile all of the GCG libraries (this will take
some time).
If the programs being built are running when you start the buildfapp command,
the build will fail with an error message about  "text file busy".

------------------------------------------------------
Michael Hogan, PhD              phone:  (608) 231-5200
Genetics Computer Group, Inc.     fax:  (608) 231-5202
575 Science Dr., Suite B        e-mail: help@gcg.com
Madison, WI  53711              e-mail: hogan@gcg.com
------------------------------------------------------
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Newsgroups: bit.listserv.info-gcg
Date:         Tue, 26 Jan 1993 13:41:28 -0800
Reply-To:     Harry Mangalam <mangalam@SALK-SC2.SDSC.EDU>
              <INFO-GCG@UTORONTO.BITNET>
From:         Harry Mangalam <mangalam@SALK-SC2.SDSC.EDU>
Subject:      Re: Prokaryotic TFD?
Comments: To: GAGUTMAN@UCI.EDU, INFO-GCG@UTORONTO.BITNET

>Is there a prokaryotic equivalent of the Transcription Factor Database,
>to identify potential protein-binding motifs in E. coli DNA
>in particular?


Hi George,

Just happened to checking the list and saw your post.  In fact, the TFD
includes prokaryotic motifs, as well as the euk ones.  The latest version
can be got at ncbi.nlm.nih.gov in /pub/repository/tfd (or ..TFD ?).  It may
not be as detailed as you want, but it's free and it's easily available.
   You might also want to check out Doug Prestridge's program Signalscan to
use as a way of searching your DNA for the motifs.  I'm not sure the GCG
programs can perform a similar function (corrections, please?), but you
could probably build a little script that could take a sequence, do a
"findpatterns" with it, then go to the next.

Cheers
Harry

Harry Mangalam                                   Vox:(619) 453-4100, x250
Dept of Biocomputing                                   Fax:(619) 552-1546
The Salk Institute                        1'   mangalam@salk-sc2.sdsc.edu
10010 N Torrey Pines Rd                   2'        hjm@salk-sgi.sdsc.edu
La Jolla CA 92037                         3'         mangalam@salk.bitnet
From: liz@molbiol.ox.ac.uk
Newsgroups: bit.listserv.info-gcg
Subject: Re:      RE: VMS GCG 7.2 Image problems
Date: 22 Jan 93 09:17:10 GMT
Organization: Oxford University Molecular Biology Data Centre
Nntp-Posting-User: liz

In article <1993Jan20.131824.24442@ulrik.uio.no>, rodrigol@biotek25.uio.no (Rodrigo Lopez) writes:
> 
> Mention to the TFSites.Dat file problem (it being too big for
> FindPatterns) is also there. In this context I would
> recommend the following alternative:
> 
> $ copy geninclude:enzdata.inc []
> 
> change:
> 
>  Parameter MAXENZCOUNT     = 2000,   ! size of enzdata buffer
> 
> to:
> 
>  Parameter MAXENZCOUNT     = 2500,   ! size of enzdata buffer
> 
> $ copy enzdata.inc geninclude:enzdata.inc
> $ make/compile findpatterns
> 
> 
> -- 
> ***************************************************************************
> * RODRIGO LOPEZ SERRANO              Biotechnology Centre of Oslo         *
> * Tel: XX-47-2-958756                Gaustadalleen 21                     *
> * Fax: XX-47-2-694130                P.B. 1125 Blindern                   *
> *                                    0316 Oslo 3 Norway                   *
> * rodrigol@biomed.uio.no                                                  *
> * rodrigol@ulrik.uio.no                                                   *
> ***************************************************************************

I don't think it's as simple as this - I think you will have to recompile all
the of subroutines that include enzdata.inc (and the routines that use include
files that include enzdata.inc!) and then remake the object libraries before 
running the make/compile findpatterns step.


Liz

________________________________________________________________________________
Elizabeth Cowe			Oxford University Molecular Biology Data Centre
liz@molbiol.ox.ac.uk			   Sir William Dunn School of Pathology
						   South Parks Road, Oxford, UK
________________________________________________________________________________
 
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Newsgroups: bit.listserv.info-gcg
From: rodrigol@biotek25.uio.no (Rodrigo Lopez)
Subject: Re:      Re: Remaking GCG Images
Organization: The Norwegian EMBnet node
Date: Sat, 23 Jan 1993 16:28:33 GMT

In article <01GTUALDKHMO00074F@hmivax.humgen.upenn.edu>,         Charles Bailey <BAILEY@HMIVAX.HUMGEN.UPENN.EDU> writes:
|> Elizabeth Cowe (liz@molbiol.ox.ac.uk) writes on 22-Jan-1993"
|> |In article <1993Jan20.131824.24442@ulrik.uio.no>, rodrigol@biotek25.uio.no
|> |(Rodrigo Lopez) writes:
|> |>
|> | [change MAXENXCOUNT parameter assignment]
|> |>
|> |> $ copy enzdata.inc geninclude:enzdata.inc
|> |> $ make/compile findpatterns
|> |
|> |I don't think it's as simple as this - I think you will have to recompile all
|> |the of subroutines that include enzdata.inc (and the routines that use include
|> |files that include enzdata.inc!) and then remake the object libraries before
|> |running the make/compile findpatterns step.
|> 
|> This is correct in principle, but the MaxEnzCount parameter isn't used in any
|> of the library subroutines, so you can get away in this case with simply
|> recompiling the affected applications.  Along these lines, Motifs also uses
|> EnzData, so you might want to remake it with the higher max.  The same could be
|> said of Map* and PeptideSort, though one might argue that it's unlikely you'll
|> need to run them with >2K enzymes.  In general, however, I'd advocate remaking
|> binaries whenever the source is changed; when debugging, it's nice to know that
|> the source you're reading is actually what's running (or not).
|> 
|> I hope this helps.  Good luck to all.
|> 
|>                                         Regards,
|>                                         Charles Bailey
|> 
|> !-------------------------------------------------------------------------------
|> !             Dept. of Genetics / Howard Hughes Medical Institute
|> ! University of Pennsylvania School of Medicine  Rm. 430 Clinical Research Bldg.
|> !     422 Curie Blvd.  Philadelphia, PA 19104 USA      Tel. (215) 898-1699
|> !          Internet: bailey@genetics.upenn.edu  (IN 128.91.200.37)
|> !-------------------------------------------------------------------------------

My original posting was meant as a specifical fix for the Find-
Patterns program. Liz & Charles correctly point out that all 
PROGRAMS making use of EnzData.Inc should be rebuild, but ONLY,
as pointed by Charles, IF one requires more than 2K of enzymes
with Map, MapPlot, MapSort, PeptideSort, Motifs, etc...

-- 
***************************************************************************
* RODRIGO LOPEZ SERRANO              Biotechnology Centre of Oslo         *
* Tel: XX-47-2-958756                Gaustadalleen 21                     *
* Fax: XX-47-2-694130                P.B. 1125 Blindern                   *
*                                    0316 Oslo 3 Norway                   *
* rodrigol@biomed.uio.no                                                  *
* rodrigol@ulrik.uio.no                                                   *
***************************************************************************
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Newsgroups: bit.listserv.info-gcg
Date:         Sat, 23 Jan 1993 01:58:00 EST
Reply-To:     Charles Bailey <BAILEY@HMIVAX.HUMGEN.UPENN.EDU>
              <INFO-GCG@UTORONTO.BITNET>
From:         Charles Bailey <BAILEY@HMIVAX.HUMGEN.UPENN.EDU>
Subject:      Re: Remaking GCG Images
Comments: To: Info-GCG@UToronto.BitNet

Elizabeth Cowe (liz@molbiol.ox.ac.uk) writes on 22-Jan-1993"
|In article <1993Jan20.131824.24442@ulrik.uio.no>, rodrigol@biotek25.uio.no
|(Rodrigo Lopez) writes:
|>
| [change MAXENXCOUNT parameter assignment]
|>
|> $ copy enzdata.inc geninclude:enzdata.inc
|> $ make/compile findpatterns
|
|I don't think it's as simple as this - I think you will have to recompile all
|the of subroutines that include enzdata.inc (and the routines that use include
|files that include enzdata.inc!) and then remake the object libraries before
|running the make/compile findpatterns step.

This is correct in principle, but the MaxEnzCount parameter isn't used in any
of the library subroutines, so you can get away in this case with simply
recompiling the affected applications.  Along these lines, Motifs also uses
EnzData, so you might want to remake it with the higher max.  The same could be
said of Map* and PeptideSort, though one might argue that it's unlikely you'll
need to run them with >2K enzymes.  In general, however, I'd advocate remaking
binaries whenever the source is changed; when debugging, it's nice to know that
the source you're reading is actually what's running (or not).

I hope this helps.  Good luck to all.

                                        Regards,
                                        Charles Bailey

!-------------------------------------------------------------------------------
!             Dept. of Genetics / Howard Hughes Medical Institute
! University of Pennsylvania School of Medicine  Rm. 430 Clinical Research Bldg.
!     422 Curie Blvd.  Philadelphia, PA 19104 USA      Tel. (215) 898-1699
!          Internet: bailey@genetics.upenn.edu  (IN 128.91.200.37)
!-------------------------------------------------------------------------------
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X-VMS-To: IN%"info-gcg@utoronto"
Newsgroups: bit.listserv.info-gcg
Date:         Tue, 26 Jan 1993 12:38:00 PST
Reply-To:     GGUTMAN@UCIVMSC.BITNET
              <INFO-GCG@UTORONTO.BITNET>
From:         GGUTMAN@UCIVMSC.BITNET
Subject:      Prokaryotic TFD?

Is there a prokaryotic equivalent of the Transcription Factor Database,
to identify potential protein-binding motifs in E. coli DNA
in particular?

     George

*****************************************************************
* George A. Gutman                                              *
* Department of Microbiology            Tel:(714)856-6593       *
*          and Molecular Genetics       FAX:(714)856-8598       *
* University of California             BITNET: GAGUTMAN@UCI     *
* Irvine CA 92717                    INTERNET: GAGUTMAN@UCI.EDU *
*****************************************************************
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Date:         Thu, 21 Jan 1993 08:12:35 -0500
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Newsgroups: bit.listserv.info-gcg
Date:         Thu, 21 Jan 1993 13:39:28 -0600
Reply-To:     Maggie <smith@GCG.COM>
              <INFO-GCG@UTORONTO.BITNET>
From:         Maggie <smith@GCG.COM>
Subject:      GCG and Solaris
Comments: To: info-gcg@utoronto.bitnet@gcg.com

>Would GCG like to describe their timescale for converting the GCG
>package from SUNOS (BSD Unix) to Solaris (System V Unix).

>I have heard a rumour that this might be in version 8.0.
>Is this correct?
>When is version 8.0 planned to be released?

>--
>GARY WILLIAMS,  Computing Services Section,  Janet:       G.Williams@UK.AC.CRC
>MRC-CRC & Human Genome Mapping Centre,       Internet:    G.Williams@CRC.AC.UK
>Watford Rd, HARROW, Middx, HA1 3UJ, UK
>Tel 081-869 3294   Fax 081-423 1275

Gary,

Our plan is to support Solaris 2.x under GCG Version 8.0-Unix.  We hope
to have it ready by the end of 1993.

If we find that it is possible to support it sooner we will post a notice
to INFO-GCG.

Regards,

Maggie Smith
Genetics Computer Group

smith@gcg.com
608-231-5200
       -5202 (fax)
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Newsgroups: bit.listserv.cics-l
Date:         Fri, 22 Jan 1993 16:57:08 PST
From:         Lenny Spohrer <HBO7@UCSFHC.BITNET>
Subject:      writing to master console

in a CICS 211 MVS/XA environment
when trying to write to the master console message appears only the
first time a message is sent
the console is defined as  a console in the TCT
have tried attaching a task and writing directly  works first time only
routing via BMS works first time only

any help on what we are doing wrong or how to do it will be appreciated

thanks
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Newsgroups: bit.listserv.cics-l
Date:         Tue, 26 Jan 1993 09:00:00 -06
From:         Jim Laney <LANEYJW@AUDUCADM.DUC.AUBURN.EDU>
Subject:      Reply to Close VSAM files fro
Comments: To: CICS-L@uga.cc.uga.edu

*** Original Author: CICS-L @ UGA - ** Remote User **; 01/25/93 22:33

>Received: from uga.cc.uga.edu by AUDUCADM.DUC.AUBURN.EDU (IBM MVS SMTP V2R1)
>   with TCP; Mon, 25 Jan 93 22:33:02 CST
>Received: from UGA.CC.UGA.EDU by uga.cc.uga.edu (IBM VM SMTP V2R2)
>   with BSMTP id 5778; Mon, 25 Jan 93 23:30:44 EST
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>Date:         Mon, 25 Jan 1993 14:07:25 CST
>Reply-To:     CICS List <CICS-L@uga.cc.uga.edu>
>Sender:       CICS List <CICS-L@uga.cc.uga.edu>
>From:         Helen Havener <HHHM10%SDNET.BITNET@uga.cc.uga.edu>
>Subject:      Close VSAM files from batch
>To:           Multiple recipients of list CICS-L <CICS-L@uga.cc.uga.edu>
>
We have an application program using VSAM files running under CICS 2.1.2.
At night batch processing against these VSAM files requires our operators
to close and reopen these files.  Our users would like to be able to open
and close these files in their batch jobs.  What products are available
that will accomplish this?  Is there a way to do it using CICS command level
programming?  Thank you for your help.

*** Comments from LANEYJW - Laney, Jim; 01/26/93 08:48am:
We use NETEC's CAFC product to open/close files in batch.  This
product utilizes LU62 (and optionally LU0) to communicate the
request to CICS.  It will also update it's control file status
when CICS is down.  You can ship other requests (transactions)
to CICS (such as CEMT) utilizing their batch interface.  We run
CICS 2.1.2 under MVS/ESA.  NETEC's number is:  (214) 343-9744.

***********************************************************************
*  Jim Laney                                                          *
*  Division of University Computing                                   *
*  Auburn University, Al. 36849                                       *
*  INTERNET: LANEYJW@MAIL.AUBURN.EDU                                  *
*  BITNET  : LANEYJW%MAIL.AUBURN.EDU@AUDUCVAX                         *
***********************************************************************
From: ds008@OASIS.CALPOLY.EDU
Newsgroups: bit.listserv.cics-l
Subject: Re: Close VSAM files from batch
Date: 26 Jan 93 16:06:56 GMT
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              26 Jan 1993 00:47:11 EST from Fran Hensler <FJH@SRU.BITNET>

From: Richard Walls
      Systems Programming
      Information Systems

   We have used teh MacKinney product here at Cal Poly and other MVS shops
I've worked in. Had no problems with it on CICS's from 1.6.1 to 2.1.2


Rich
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Newsgroups: bit.listserv.cics-l
Date:         Thu, 21 Jan 1993 15:52:39 CST
Comments:     Converted from PROFS to RFC822 format by PUMP V2.2X
From:         Chuck Nelson <NELSON@TWSUVM.BITNET>
Subject:      spool output from CICS to VM

I have written program for our applications people to use so they can
send notes from within a program to a user on VM (PROFS). We are runnning
VSE/ESA under VM/ESA 1.1 with CICS 2.1.

My problem is that the files need to have 80 char. record length so they
will be read as notes and not print files. I have LINELENGTH(80) set on the
SPOOLOPEN command but when the files get to VM they have a record length
of 132.

Has anyone tried to do this before and succeeded that I may benefit from
your wisdom? Is there something I am missing in a definition someplace
which will help me?

Please reply directly to me as I am not a member of this list.

Thanks,

Chuck Nelson
Tech. Support Analyst
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Organization: Slippery Rock University - Computer Center
Newsgroups: bit.listserv.cics-l
Date:         Tue, 26 Jan 1993 00:47:11 EST
From:         Fran Hensler <FJH@SRU.BITNET>
Subject:      Re: Close VSAM files from batch

CICS/CEMT from MacKinney Systems will open/close CICS files from batch JCL.
We've been using it for years.  We are VSE -- I don't know about MVS.

Francis J. Hensler, CDP                     BITNET: FJH@SRU
Software Support Specialist                 Phone: (412) 738-2033
Slippery Rock University Computer Center    PANET:     8-654-2033
Slippery Rock, PA  16057-1326  USA   "Yes, Virginia, there is a Slippery Rock"
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Newsgroups: bit.listserv.cics-l
Date:         Thu, 21 Jan 1993 10:28:37 EST
From:         Barry Brooks <BARRY@NERVM.BITNET>
Subject:      CODE-1 Plus

I am interested in speaking with anyone who is using the CODE-1 PLUS
product from Group 1 Software.  Specifically, I would like to talk to
those who are coding their own CICS applications to call CODE-1 PLUS
address matching and/or database lookup functions.  If you send me a
personal note with your phone number, I will call you.
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Newsgroups: bit.listserv.cics-l
Date:         Mon, 25 Jan 1993 09:14:00 CST
From:         "Larry Ludwig 753-1875 (NIU 815)" <A01LRL2@NIU.BITNET>
Subject:      cICS to AS400 via TCPIP

I am trying to access CICS from an AS400 via TCPIP.  If I include
the CICS QUERY feature in my terminal definition I do not receive
my logon screen and therefore cannot establish a connection
between CICS and terminals on the AS400.  If I remove the QUERY
feature, the connection is made.  The QUERY feature is used
successfully by all other terminals accessing CICS via TCPIP.
My CICS level is 2.1.2.  I don't know the level of either TCPIP
but if it's important I'll ask.  Has anyone else had this problem?
Suggestions?

Larry Ludwig
CICS System Programmer
Northern Illinois University

A01LRL2@NIU
From: D1SAR@AKRONVM.BITNET (Steve Rimar)
Newsgroups: bit.listserv.cics-l
Subject: Re: Close VSAM files from batch
Date: 26 Jan 93 17:16:26 GMT
Comments: Gated by NETNEWS@AUVM.AMERICAN.EDU
Return-Path: <@VM1.CC.UAKRON.EDU:D1SAR@AKRONVM>

We use the same product that someone else has told you about.
IPCP from SDS.  Software Diversified Services.
I like the online functions.

* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
*                                                                       *
*  STEVE RIMAR                       INTERNET: D1SAR@VM1.CC.UAKRON.EDU  *
*  INFORMATION SERVICES              BITNET:   D1SAR@AKRONVM            *
*  THE UNIVERSITY OF AKRON                                              *
*  AKRON, OHIO  44325           "THE SPEED OF THE LEADER DETERMINES THE *
*                                THE RATE OF THE PACK"  W.L.            *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
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