HDTenEightyP/NetNews huggingface dataset:
From: lm@crihan.fr (Laurent Mouchard)
Newsgroups: bionet.software,comp.unix.aix
Subject: problem with BLAST on RS6K
Date: 30 Dec 92 10:40:46 GMT
Reply-To: Laurent.Mouchard@crihan.fr
Organization: CRIHAN, France


I am trying to install BLAST on a IBM RS/6000.

I already have succeed in installing ncbitools (using the 370 confi
guration), gish and dfa.

So, I am trying to build blast but make all generates a strange
message:

# make all
ln -s ../NCBI .
ln -s ../GISH .
ln -s ../DFA .
cd lib; make  CC="cc" CCOPT="-g" OPTIONS="  -DREFINED_STATS "
cc -g -I../include -I../NCBI/include -I../GISH/include -I../DFA
      -DREFINED_STATS  -c banner.c
"../include/blast.h", line 169.0: 1506-236 (W) Macro name NCHUNKS has 
been redefined.
"../include/shmutil.h", line 14.15: 1506-046 (S) Syntax error.
"../include/blast.h", line 349.11: 1506-046 (S) Syntax error.
"../include/blast.h", line 349.23: 1506-030 (S) Identifier mfile cannot
be redeclared.
"../include/blast.h", line 472.9: 1506-132 (S) Function fatal cannot be
redeclared.
"../include/blast.h", line 480.9: 1506-132 (S) Function TickNext cannot
be redeclared.
make: 1254-004 The error code from the last command is 1.

Make Quitting.
make: 1254-004 The error code from the last command is 2.

Make Quitting.

# cat include/shmutil.h
1  #ifndef __SHMUTIL_H__
2  #define __SHMUTIL_H__
3
4  #ifdef USE_SHM
5  typedef struct shm_dat {
6                  char    *filename;
7                  key_t   key;
8                  long    filesize;
9                  FILE    *fp;
10                 int             shmid, semid, msqid;
11                 void    *shmaddr;
12         } shm_dat;
13 #else
14 typedef char *shm_dat;      <--  What's wrong?
15 #endif                           =============
16
17
18 extern int shmexists();
19 extern shm_dat *shm_attfile PROTO((char *filename, char *mode, int 
   verbose));
20 extern void *shm_addr PROTO((shm_dat *));
21 extern shm_dat  *shm_loadfile PROTO((char *filename, int mmode, int 
   smode, int qmode, int lockfile, int verbose));
23 extern int shm_sendto PROTO((char *filename, int sig));
24 extern int shm_sendtokey PROTO((key_t key, int sig));
25
26  #endif /* !__SHMUTIL_H__ */

I don't understand what happens.

Please mail-me if you have an idea or if you already have installed
BLAST on a RS6K.

Thanx.
-- 

---------------------------------------------------------------------
Laurent Mouchard         (lm)	 | C R I H A N
				 | Centre de Ressources Informatiques
From: karuzis@wccf.mit.edu (GLENN HOLM)
Subject: RE: Pres. graph. software
News-Software: VAX/VMS VNEWS 1.41    
Organization: MIT - Whitaker College
Distribution: bionet
Date: Thu, 24 Dec 1992 03:41:00 GMT

From seeing a demo, and a review in PC magazine a few months
back, Stanford Graphics might be worth looking at for a presen-
tation package for a PC.  Strong point being its graphing 
capability.  We have Slide Write, and it too can be made to
work.  Useful if you need graphs with error bars.  Getting
output to film recorder or service bureau for your slides
can be trying. Adobe Illustrator is a good general package, and
essentially gives you PostScript output, so your slides should
look good.

------------------------------------------------------------------
|Glenn Holm                         Internet:karuzis@wccf.mit.edu|
|M.I.T Dept. of Brain + Cog. Sci.   This VAX doesn't do NeXTmail |
|Cambridge, MA 02139       "Real Neuroscientists don't do gels!" |
------------------------------------------------------------------
From: SJJ@ICBR.IFAS.UFL.EDU ("JONG, SONG-MUH J")
Newsgroups: bionet.software
Subject: VBRUN100?
Date: 21 Dec 92 22:55:00 GMT
Distribution: bionet

Hi netters,

Does anyone have the VBRUN100 file? It is the runtime library of Visual 
BASIC. The current version on most of the FTP sites is 200 while a lot
of Sharewares written for Windows 3.x required 100 version. I would 
appreciate if someone points to me the location of the VBRUN100 file or
send me a copy of it. Thank you in advance!

Song-Muh Jong
sjj@icbr.ifas.ufl.edu
From: bdyke@DARWIN.SFBR.ORG (Bennett Dyke)
Newsgroups: bionet.software
Subject: Monochome monitors
Date: 30 Dec 92 20:59:54 GMT
Distribution: bionet

Over the past couple of years we have upgraded our Sun 386i workstations
to SparcStation 2s.  One of the bizarre consequences of this trade is
that Sun Microsystems did not want us to return the monochrome monitors
(Model No. BDS-1502) that came with the original computers.  These have very
nice 13" inch screens, with (I think) 100dpi resolution.  Sun has been of no
help in providing specs, and I am at a loss to figure out what how they
might be used.  Does anybody have any ideas? 

Bennett

+----------------------------------------------------------------------------+
|   Bennett Dyke                                                             |
|   Department of Genetics               Internet:  bdyke@darwin.sfbr.org    |
|   Southwest Foundation                    Phone:  (210) 674-1410 Ext 281   |
|   P.O. Box 28147                            Fax:  (210) 670-3317           |
|   San Antonio, TX 78228, USA                                               |
+----------------------------------------------------------------------------+
From: mrl775@tigger.jvnc.net
Subject: Program to compare all members of a group of sequences
Followup-To: bionet.software
Reply-To: mrl775@tigger.jvnc.net
Organization: TheNews 
Date: Wed, 30 Dec 1992 05:12:00 GMT

 Hello

Does anyone know of a program that will take a set of sequences, and find
common local alignments (sort of like what blast and blast3 do, but with each
member of the set).  I am looking to define cofactor binding sites, and have a
list of sequences that all bind the cofactor, but have no good method of
comparing them all together (a multiple alignment doesnt work).  Any hints,
pointers, source, executables would be appreciated.

Thanks

Keith
mrl775@tigger.jvnc.net
From: WAGNERF@BRUNB.BITNET (Wagner Fontes)
Newsgroups: bionet.software
Subject: RE: Pres. graph. software
Date: 23 Dec 92 19:42:21 GMT
Distribution: bionet


.        I suggest you Corel Draw. It can import data from most
applications, has a very nice presentation graphics part, and it's
easy to use.
.        We are not using a slide printer, but I think it has
drivers for it. Besides that, it prints easily on almost any
laser printer.
.        There's only one important point: It's not cheap.


         GOOD LUCK !!!


         Wagner Fontes
         Brazilian Center of Protein Sequencing
         Biochemistry & Protein Chemistry Lab.
         University of Brasilia  -  Brazil
         WAGNERF@BRUNB


.
From: dpowers@foxmail.gfc.edu (Donald R. Powers)
Newsgroups: bionet.software
Subject: LabView hardware
Date: 3 Jan 93 00:53:23 GMT
Distribution: bionet
Organization: George Fox College, Newberg, Oregon USA

I have LabView II and would like to set it up to monitor several
instruments on my Mac IIci.  Can anyone suggest a reasonably priced A/D
device I can use for an interface?  Most of what I have involves a
simple voltage inpute.  However, it is possible I might need a
differential input at some point.  Thanks!

Don Powers
*********************************************************************
This message was created on the George Fox College Fox Mail system.
The views expressed are those of the individual author only.
*********************************************************************
From: LETTIERE_DAJ@CCSUA.CTSTATEU.EDU (CCSU Biology Club President)
Newsgroups: bionet.software
Subject: Color simulator for the mac
Date: 31 Dec 92 22:24:56 GMT
Distribution: bionet

Hello,

	I know that there are programs for the IBM that will make units with 
monochrome monitors think that they are running color, allowing the use of color
programs on that machine.  Does anyone know of any programs like this for the 
macintosh (preferably freeware or shareware at an FTP site)?

					Thanks,
		
					Dan Lettiere

********************************************************************************
Internet: lettiere_daj@ccsu.ctstateu.edu

Mail:	  Central Connecticut State University
	  Dept. of Biological Sciences
	  1615 Stanley Street, Copernicus Hall
	  New Britain, CT  06050
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
From: PARSONS_A@snd01.pcr.co.uk
Newsgroups: bionet.software
Subject: Quick Jiffy's for GCG or Ig
Date: 23 Dec 92 10:13:53 GMT
Distribution: bionet
Original-To: BIO-SOFT <BIO-SOFT@UK.AC.DARESBURY>

Greetings BIONAUTS, Internetters, NetFolk, GCG/Ig Consultants,

I have just downloaded the AIDS database produced by Gerald D. Myers and Kersti
McInnes from the NCBI data repository.  After unpacking I have now ended up
with a directory structure as below.  I want to convert these sequences to a
GCG and Ig data library.  Both these packages have the tools to handle the
GenBank and PIR formatted entries but I was wondering if anyone had written a
quick jiffy just to pick out the sequences and ignore the alignments and
supporting info (I dont want to reinvent the wheel).  Also could anyone tell me
the difference between a file with no extensiona and a .NF extension file diffs
would suggest only changes in the annotation and not the sequence. 

Many  ADVthanksANCE - and a Merry Chritmas and a Peaceful New Year!

Tony Parsons  - Pfizer Central Research (UK) <<parsons_@snd01.pcr.co.uk>>


=========================  AIDS DB subdirectory structure  ===================
[.DATABASE]---+
              |
              |--[.NUC_A]------+--[.AGM]
              |                |--[.HIV_1]---------[.HFL]
              |                |                |
              |                |                +--[.NUC_CONS]
              |                |--[.HIV_2]
              |                |--[.MND]
              |                |--[.RELATED]
              |                +--[.SIV]
              +--[.PRO_A]------+--[.AGM]
                               |--[.HIV_1]---------[.HFL]
                               |                |
                               |                +--[.PRO_CONS]
                               |--[.HIV_2]
                               |--[.MND]
                               |--[.RELATED]
                               +--[.SIV]
From: keenan@HAL.HAHNEMANN.EDU ("Paul Keenan, Library Database Administrator")
Newsgroups: bionet.software
Subject: Primer Executable for VMS?
Date: 23 Dec 92 20:04:14 GMT
Distribution: bionet

Does anyone have a copy of a VMS version of the Primer program written by Mark
Daly, Steve Licoln and Eric Lander at MIT or know of an FTP site where I can
get it?   I got a copy of the source code version but ran into problems when I
tried to compile it since it expects certain symbols to be defined, which
aren't on our system.  In addition, since I'm not a C programmer it's not clear
to me exactly the function of some of these symbols perform so I can't just
replace them or define the symbols correctly.  

I appreciate in advance any help you can give me. 

Thanks,

Paul
================================================================================

H  H U  U   |Paul Keenan, Database Administrator   |Voice: 215-762-3270
HHHH U  U   |Hahnemann University Library M.S.449  |FAX:   215-762-8180
H  H UUUU   |Broad & Vine Phila., PA 19102         |Keenan@Hal.hahnemann.edu
               
================================================================================
From: dadler@u.washington.edu (David Adler)
Newsgroups: bionet.software
Subject: Re: Sequence reading software for UNIX?
Date: 30 Dec 1992 03:30:05 GMT
Organization: University of Washington
NNTP-Posting-Host: koko.pathology.washington.edu

In article <1992Dec18.163702.25093@cc.umontreal.ca>  
little@ERE.UMontreal.CA (Littlejohn Tim) writes:
> 
> UNIX Workstation users:
> ...
> On a more difficult topic, does anyone know anything about VOICE 
> recognition as a method of sequence data input?
> 

Check out a program called SimonSays running on a NeXT. I think it could  
do that job.
David
--
David A. Adler                  Pathology SM-30
University of Washington        Seattle, WA 98195
(206) 543-0716 (phone)		(206) 543-3644 (fax)
"Science is nothing but trained and organized common sense"
T.H.Huxley
Newsgroups: bionet.software
From: mail_vieglai@uqvax.cc.uq.oz.au
Newsgroups: bionet.software
Subject: Windows Environmental Library
Date: 22 Dec 92 17:50:09 AEST
Organization: University Of Queensland

   ************
Notice for Environmental Software Library.
   ************

I have a MS Windows 3.1 DLL available for distribution which provides 
functions for calculating julian time, solar position, clear sky 
insolation (400-700nm and 290-2700nm) plus a few other goodies.

The DLL is designed to provide these functions within the MS EXCEL 
4.0 spreadsheet, but there is no reason why it cann't be used with 
other software that can link to DLL's.  It can also be called from C 
or Pascal.

A small distribution fee will be charged.

Any interested persons/ parties should contact me via Email at

  MAIL_VIEGLAI@uqvax.cc.uq.oz.au

Merry Xmas all.
Ho Ho Ho Ho Ho

Cheers, DV :-)
From: noran!ringo!sjohnson@UUNET.UU.NET (Scott Johnson)
Newsgroups: bionet.software
Subject: Re. GIF files on Indigos
Date: 29 Dec 92 23:22:17 GMT
Distribution: bionet


In article <1h70lfINN4am@s-crim1.dl.ac.uk>, mbthm@s-crim1.dl.ac.uk (T.H.L.
Murcott) writes:
> Subject: Wanted Gif file viewer for PC and Silicon Graphics
> Sender: Toby Murcott
> Organization: Daresbury Lab., Warrington, U.K.
> 
> Dear Netters,
> 
> Recently a .gif file of TGN was posted to the net.  I am a relative novice at
> this game and am asking for suggestions for good .gif file viewers for a PC
> and also Silicon Graphics Indigo and Iris workstations.  Apologies if this
> is not the right group to post to.


On an Indigo (I'm not sure about the Iris) there is a utility
called 'fromgif' that converts a file from gif format to the
SGI native RGB format.

You can then use 'imgview' to look at the image.

To view the image:
	fromgif file.gif file.rgb
	imgview file.rgb

If you want to do more with the image, the Indigo provides quite
a few image processing applications in it's standard configuration.
To find out about them type 'man -k image'.

Enjoy

-- 

		-- Scott
		sjohnson@noran.com
		(608) 836-4392
From: mj@toano.win.net (Mary Jo Warsinsky)
Newsgroups: bionet.software
Subject: (none)
Date: 1 Jan 93 10:45:05 GMT
Reply-To: mj@toano.win.net (Mary Jo Warsinsky)
Distribution: bionet

INDEX BIO-SOFT
From: q00023@TIGGER.STCLOUD.MSUS.EDU
Newsgroups: bionet.software
Subject: Software request
Date: 22 Dec 92 19:45:15 GMT
Distribution: bionet

Dear netters,

	I am looking for some sharewares that deal with molecular genetics
, or biotechnology. I have no idea what kind of programs are out there
on the net. Could anyone tell me the ways to get programs that can run on PC?

Thanks in advance,

Gabriel Cheung
From: @VM1.NoDak.EDU:MCCULLUM@basil.ucnv.edu.au
Newsgroups: bionet.software
Subject: (none)
Date: 22 Dec 92 02:49:05 GMT
Distribution: bionet

SUB BIO-SOFT@IRLEARN  Dean McCullum
From: q00023@TIGGER.STCLOUD.MSUS.EDU
Newsgroups: bionet.software
Subject: question on the prograph
Date: 1 Jan 93 06:47:56 GMT
Distribution: bionet

Dear netters,
	I need to know how to use the prograph.zip program and the main use of
the program. I already unzip the program, but I don't know how to use the
program. Could anyone tell me more of the details of the program.

THANKS IN ADVANCE,
Gabriel Cheung

Newsgroups: bionet.software
From: bfrank@aardvark.ucs.uoknor.edu (FRANK,BART)
Subject: intron/exon borders
Originator: usenet@midway.ecn.uoknor.edu
Date: Wed, 30 Dec 1992 20:43:00 GMT
News-Software: VAX/VMS VNEWS 1.41    
Organization: University of Oklahoma - University Computing Services

Can anyone recommend a good program to screen human genomic seqeunces
and predict positions of intros/exon borders?

Thanks, 
Bart Frank
Internet: BFRANK@AARDVARK.UCS.UOKNOR.EDU
From: PARSONS_A@snd01.pcr.co.uk
Newsgroups: bionet.software
Subject: Quick Jiffy's for GCG or Ig
Date: 23 Dec 92 10:13:49 GMT
Reply-To: PARSONS_A@snd01.pcr.co.uk
Distribution: bionet

Greetings BIONAUTS, Internetters, NetFolk, GCG/Ig Consultants,

I have just downloaded the AIDS database produced by Gerald D. Myers and Kersti
McInnes from the NCBI data repository.  After unpacking I have now ended up
with a directory structure as below.  I want to convert these sequences to a
GCG and Ig data library.  Both these packages have the tools to handle the
GenBank and PIR formatted entries but I was wondering if anyone had written a
quick jiffy just to pick out the sequences and ignore the alignments and
supporting info (I dont want to reinvent the wheel).  Also could anyone tell me
the difference between a file with no extensiona and a .NF extension file diffs
would suggest only changes in the annotation and not the sequence. 

Many  ADVthanksANCE - and a Merry Chritmas and a Peaceful New Year!

Tony Parsons  - Pfizer Central Research (UK) <<parsons_@snd01.pcr.co.uk>>


=========================  AIDS DB subdirectory structure  ===================
[.DATABASE]---+
              |
              |--[.NUC_A]------+--[.AGM]
              |                |--[.HIV_1]---------[.HFL]
              |                |                |
              |                |                +--[.NUC_CONS]
              |                |--[.HIV_2]
              |                |--[.MND]
              |                |--[.RELATED]
              |                +--[.SIV]
              +--[.PRO_A]------+--[.AGM]
                               |--[.HIV_1]---------[.HFL]
                               |                |
                               |                +--[.PRO_CONS]
                               |--[.HIV_2]
                               |--[.MND]
                               |--[.RELATED]
                               +--[.SIV]
From: Davison@UH.EDU (Dan Davison)
Newsgroups: bionet.software
Subject: Re: intron/exon borders
Date: 30 Dec 92 21:42:46 GMT
Distribution: bionet

FRANK,BART said:
> Can anyone recommend a good program to screen human genomic seqeunces
> and predict positions of intros/exon borders?

Try the grail and geneid servers. Send the word HELP to grail@ornl.gov
and geneid@darwin.bu.edu.

dan







-- 
dr. dan davison/dept. of biochemical and biophysical sciences/univ. of
Houston/4800 Calhoun/Houston,TX 77204-5934/davison@uh.edu/DAVISON@UHOU

-----RIP Isaac Asimov 1920-1992     I'll miss him --------------------

Disclaimer: As always, I speak only for myself, and, usually, only to
myself.
From: ashok@biochemistry.cwru.edu (Ashok Aiyar)
Newsgroups: bionet.software
Subject: Re: Re. MAC-PC connection
Date: Fri, 25 Dec 1992 20:17:17 GMT
Organization: CWRU School of Medicine
Distribution: bionet
NNTP-Posting-Host: axa12-slip.dialin.cwru.edu

In article <9212250633.AA10728@net.bio.net> 
	SJJ@ICBR.IFAS.UFL.EDU ("JONG, SONG-MUH J") writes:


>There was a discussion about the need of reading and manipulating MAC disks
>on PCs. The following information from the Jauary issue of BYTE is rather
>informative:

>For high density disks:
>     Mac-In-DOS from Pacific Microelectronics (800)628-3475; (415)948-6200
>     $199 (DOS version), $249 (Windows version)

>For double-density disks:
>     MatchMaker from MicroSolutions Computer products (815)756-3411


There are other options available.  For HD disks, try the shareware program 
Macette.exe -- available from a few FTP sites - try Archie for which ones.

For DD disks, Matchmaker requires you to already possess an external Mac 
floppy drive -- which runs about $150 - $300, in addition to buying the 
MatchMaker card -- which in trun costs about $100.

A much cheaper solution is to purchase the Copy II PC Deluxe Option Board 
from Central Point which lets most PC 720K and 1.44 meg drives read, write 
and format 800K Mac disks.  It works rather well -- I use one myself.  The 
board runs about $100, and you can use your existing 3.5 inch drive.

Ashok
----------------------------------------------------------------------
                              Ashok Aiyar 
                      Department of Biochemistry
                       CWRU School of Medicine
----------------------------------------------------------------------
Newsgroups: bionet.software
From: harper@convex.csc.FI (Rob Harper)
Subject: Re: VBRUN100?
Organization: Finnish Academic and Research Network Project - FUNET
Distribution: bionet
Date: Tue, 22 Dec 92 07:05:58 GMT

In <9212212303.AA02451@net.bio.net> SJJ@ICBR.IFAS.UFL.EDU ("JONG, SONG-MUH J") writes:

>Hi netters,

>Does anyone have the VBRUN100 file? It is the runtime library of Visual 
>BASIC. The current version on most of the FTP sites is 200 while a lot
>of Sharewares written for Windows 3.x required 100 version. I would 
>appreciate if someone points to me the location of the VBRUN100 file or
>send me a copy of it. Thank you in advance!

>Song-Muh Jong
>sjj@icbr.ifas.ufl.edu

You will find VBRUN100 in different formats on nic.funet.fi in the
following directories. One of the nice features of NIC is that once you
have an anonymous ftp connection you can give the command 

"quote find searchstring" and NIC will run through the ALL_FILES database
and tell you which directory the file can be found in.

ftp> quote find VBRUN100
212-Matching case insensitively expr `VBRUN100'
212-Starting to parse /files/ALL_FILES database:
512 Aug 28 04:44 1991 pub/archive/comp.binaries.ibm.pc/volume13/vbrun100
42086 Aug 28 04:44 1991 
pub/archive/comp.binaries.ibm.pc/volume13/vbrun100/part01.Z
41696 Aug 28 04:44 1991 
pub/archive/comp.binaries.ibm.pc/volume13/vbrun100/part02.Z
41679 Aug 28 04:44 1991 
pub/archive/comp.binaries.ibm.pc/volume13/vbrun100/part03.Z
41630 Aug 28 04:44 1991 
pub/archive/comp.binaries.ibm.pc/volume13/vbrun100/part04.Z
41115 Aug 28 04:44 1991 
pub/archive/comp.binaries.ibm.pc/volume13/vbrun100/part05.Z
169871 Nov 27 21:13 1992 pub/msdos/Mirrors/cica/util/vbrun100.zip
169044 Jun 10 04:08 1991 pub/msdos/SIMTEL20-mirror/win3programmer/vbrun100.lzh
169044 Jun 10 04:08 1991 pub/msdos/windows/programmer/vbrun100.lzh
212 End of analysis.  9 matches found.

RGDS -=ROB=-
--
 ~ Rob Harper                    ~ E-mail:          harper@convex.csc.fi    
 ~ Finnish State Computer Centre ~ Molbio/software: harper@nic.funet.fi
 ~ P.O. Box 40                   ~ Telephone:       +358 0 457 2076
 ~ SF-02101 Espoo Finland        ~ Fax:             +358 0 457 2302
From: ken@iat.holonet.net (Ken Easlon)
Subject: mRNA baud rate
Organization: HoloNet National Internet Access BBS: 510-704-1058/modem
Date: Wed, 30 Dec 1992 02:42:45 GMT




I'd like to find out the data transmission rate from the nucleus of a
typical eukaryotic cell via mRNA.   My best guess at this point is
somewhere between 300 and 1200 baud.   

If anyone has any guesses or information or references regarding the rate
of mRNA transcription (per cell), I would be very interested in hearing
from you.

--
Ken Easlon
ken@holonet.net



Newsgroups: bionet.info-theory