HDTenEightyP/NetNews huggingface dataset:
From: pathology@mscf.med.upenn.edu
Newsgroups: bionet.software
Subject: Re: Genbank services?
Date: 19 Aug 92 15:28:55 GMT
Distribution: bionet,world
Organization: Univ of Penn - Med School Computer Facility

In article <Aug.18.13.17.22.1992.9650@genbank.bio.net>, kristoff@genbank.bio.net (David Kristofferson) writes:
> 
> The free dial-up IRX account is the only thing that will disappear.
> NCBI allows IRX-style queries by e-mail, and IG is going to charge for
> interactive IRX access on its timesharing service.
> 

The IRX account is extremely valuable for searching for sequences for which one 
does not have exact accession information.  Does the NCBI plan on starting any 
interactive searching of sequence data?  I would very much like continuation of 
the IRX-type account without having to pay for the IG account (research funds 
are very limited, you know).

Gregg Wells
Department of Pathology
University of Pennsylvania
Philadelphia, PA
USA
e-mail:  pathology@a1.mscf.upenn.edu
Newsgroups: bionet.software
From: dsc@xray.hmc.psu.edu (David S. Channin)
Subject: Postscript Versions of NIH grant applications: FAQ ?
Reply-To: dsc@xray.hmc.psu.edu
Organization: Dept. of Radiology, Hershey Medical Center, Hershey PA
Distribution: na
Date: Sun, 16 Aug 92 18:34:37 GMT



I heard recently that there are postscript (or other format) versions of
form PHS 398 (or others) available. I would appreciate any pointers.

Thanks.

dsc


Newsgroups: bionet.software
From: pcj1@cunixf.cc.columbia.edu (Pierre Jelenc)
Subject: SigmaPlot help
Organization: Columbia University
Date: Wed, 19 Aug 1992 18:31:16 GMT


I am trying to figure out how to use SigmaPlot (Mac version), and I have
been unable to determine how to produce error bars when one column
contains the x values (days in this case), and several columns contain
y values (weights from growth curves from several animals).

As far as I can determine, SigmaPlot will calculate error bars for columns,
not rows, which is what I need.

Pierre

Pierre Jelenc                        pcj1@cunixf.cc.columbia.edu 
                                    Columbia University, New York
From: WAGNERF@BRUNB.BITNET (Wagner Fontes)
Newsgroups: bionet.software
Subject: MS Word Windows Crash
Date: 22 Aug 92 20:21:43 GMT
Distribution: bionet



Hi Netters !


I just wonder if there is anyone working with Microsoft Word for Windows,
using many font types and sizes, and the ... system crashes all the time!?!
From: varner@UMD5.UMD.EDU (Mark Varner)
Newsgroups: bionet.software
Subject: Re: NCBI internet access inquiry
Date: 17 Aug 92 13:41:16 GMT
Distribution: bionet


The IP address of ncbi.nlm.nih.gov is 130.14.20.1 

Sorry if this came twice.  Our mailer picked up the wrong address when
replying, and I wasn't sure if the cc: got sent when the To: was
bounced back.

Mark
From: inna@vms.huji.ac.il
Newsgroups: bionet.software
Subject: Thanks: Secondary structure assignment
Date: 16 Aug 92 16:41:18 GMT
Distribution: world
Organization: The Hebrew University of Jerusalem

  Thanks to everyone who answered my question.
As it turned out, the program which does secondary structure assignment
based on the atomic co-ordinates is called DSSP and to obtain it one should
contact Sander@EMBL-Heidelberg.de

	Inna
From: ucbhpom@uk.ac.ucl (Andrew Pomiankowski)
Newsgroups: bionet.software
Subject: unsubscribe
Date: 19 Aug 92 14:13:13 GMT
Distribution: bionet
Original-To: bio-software@uk.ac.daresbury
Pp-Warning: Illegal Received field on preceding line

please unsubscribe me. ucbhpom@ucl.ac.uk
From: kristoff@genbank.bio.net (David Kristofferson)
Newsgroups: bionet.software
Subject: Re: Genbank bulletin boards
Date: 18 Aug 92 20:21:14 GMT
Distribution: bionet
Organization: GenBank Online Service

SBAIRD@ACADVM1.UOTTAWA.CA (Stephen Baird) writes:

 >I almost forgot....what about the bionet bulletin boards who will be
 >responsible for them?

 As I mentioned in my last message (but am repeating again so that no
 one will miss this), the BIOSCI/bionet newsgroups will continue to be
 run by the current staff (Kenton Hoover and I) at IntelliGenetics in
 the U.S. and at SERC Daresbury Lab in the U.K.  (Alan Bleasby, Paul
 Griffiths, Steve Marshall et al.)

				Sincerely,

				Dave Kristofferson
				GenBank Manager

				kristoff@genbank.bio.net
From: inna@vms.huji.ac.il
Newsgroups: bionet.software
Subject: Secondary structure assignment
Date: 13 Aug 92 11:05:13 GMT
Organization: The Hebrew University of Jerusalem


 Can anyone help me to find the program which does secondary structure
assignments based on the atomic co-ordinates.
The reference is Kabsch, W. & Sander, C. (1983). Biopolymers, 22, 2577-2637.

  Thank you for your time.

----------------------------------------------------------------------
 Inna Perlov 			   Phone      972-2-584848
 Hebrew University 		   E-Mail    Inna@hujivms.bitnet
 Computation center			     Inna@vms.huji.ac.il
 Givat-Ram 91904 Jerusalem	   FAX	      972-2-527349
 Israel
----------------------------------------------------------------------
From: GREG@EDU.CLAREMONT.POMONA (Tigger)
Newsgroups: bionet.software
Subject: signoff help, please
Date: 14 Aug 92 16:19:39 GMT
Distribution: bionet
X-Vms-Cc: GREG
Original-To: bio-software@uk.ac.daresbury
Content-Transfer-Encoding: 7BIT
Mime-Version: 1.0
X-Vms-To: in%"bio-software@daresbury.ac.uk"

A user at this site recently graduated without signing off of this list.
Typical student.  Could someone tell me how to get him signed off?  I'm
sorry to have to send this to the list, but I have already sent three or
four messages to the problems/queries address listed in the headers, to
no avail.

Any help or suggestions on how to get him signed off this list would be
greatly appreciated.

Greg Orman                                     greg@pomona.claremont.edu
Systems Manager                                greg@pomona.bitnet
Seaver Academic Computing Services
Pomona College                                 Standard disclaimer-type stuff
Newsgroups: bionet.software
From: berti@cyclops.bri.nrc.ca (Paul Berti)
Subject: Scoring in PIMA
Organization: Institut de recherche en biotechnologie, Montreal
Date: Thu, 20 Aug 92 19:27:36 GMT

Some time ago someone asked a question about PIMA (pattern induced multiple
alignment).  I've lost the original message, but here's my response
anyways.



>Also... doesn't PIMA work with coding sequences when aligning proteins, or
>something like that?  Anyone know?

No, not quite.  PIMA's scoring scheme is shown below (from the manual):


                       Amino Acid Classes                     Match score

                                                                  -2
                _______________ X __________________               0
               /          /           \             \
            _ f _        /       ______r _______     \             1
          /  /    \     /       /   /     \     \     \
         /  c      \   e       /   m       p     \   _ j __        2
        /  /  \     \ / \     /   / \     / \     \ /   \  \
       /  a    b     d   \   /   l   k   o   n     i     h  \      3
      /  / \  / \   /|\   \ /   / \ / \ / \  /\   / \   / \  \
     C   I V  L M  F W Y   H   N   D   E  Q  K R  S T   A G   P    5

     Note: During clustering,  matches  between  unrelated  amino
     acids,  i.e.  connected  only  through  the  'X' (wild-card)
     class, score -2


This means that all amino acids score 5 when aligned against themselves.  
Other a.a.'s are scored according to the above diagram: e.g. consider
Asn (N).  It scores 5 aligned against itself, 3 against D, 2 against E, 
1 against H, Q, K, R, S, & T and 0 against everything else.  

I hope this helps.

 

b.t.w. - I've been using PIMA for a few weeks now (in fact it's running 
in another window right now); it's the best multiple alignment program
I've seen, bar none. 


Paul
berti@bri.nrc.ca
From: WAGNERF@BRUNB.BITNET (Wagner Fontes)
Newsgroups: bionet.software
Subject: RE: sequence analysis software
Date: 21 Aug 92 15:51:57 GMT
Distribution: bionet



       The best source for the kind of software you are looking for
 is EMBL   -->  EMBL-DB AT GENBANK.BIO.NET


                 Dr. Wagner Fontes
                 Brasilian Center of Protein Sequencing
                 Biochemistry - Protein Chemistry Laboratory
                 University of Brasilia
                 Brazil
Newsgroups: bionet.software
From: Bo Servenius <biogen10@gemini.ldc.lu.se>
Subject: Screen capture for Mac
Organization: Lund University, SWEDEN
X-Useragent: Nuntius v1.1
Date: Fri, 14 Aug 1992 09:23:42 GMT

Dear Netters:

Doing some work with the ABI373A dna sequencer I have got
the need to do screen captures. Anyone knows about a good
program that could be found over internet for this purpose.

Many thanks in advance for any tip

BOSSE
Newsgroups: bionet.software
From: rs54@cunixf.cc.columbia.edu (Richard Sucgang)
Subject: Re: gcg
Reply-To: rs54@cunixf.cc.columbia.edu (Richard Sucgang)
Organization: Columbia University
Distribution: bionet
Date: Fri, 14 Aug 1992 11:24:22 GMT

In article <1992Aug13.231529.26113@Princeton.EDU> lpcasson@phoenix.Princeton.EDU (Lawrence P. Casson) writes:
>In article <1992Aug2.181655.18486@news.columbia.edu> rs54@cunixf.cc.columbia.edu (Richard Sucgang) writes:
>>
>>I have found that a lot of gcg programs can output PostScript. If

>write EPS files.  It writes them okay, producing files with filled data
>and resource forks.  However, EPS files generated on our UNIX system and
>FTP'd to the Mac have empty resource forks (SURPRISE, SURPRISE!!).  I
>assume that this acounts for the inability of MacDraw Pro to display
>them.  Does anybody know if it's possible to convert these to files that
>can be used with MacDraw?
>

I take it you want the Previewing pict, which is located in the resource
fork, and hence is absent. Unfortunately, I don't know of an easy way to
generate a pict resource outside of using resedit, and a PostScript
previewer that can output Pict (I think TScript can do it).

Good luck!

-rich
Richard Sucgang  : Dept. of Anatomy and Cell Biology Columbia University
(sucgang@cuhhca.hhmi.columbia.edu | rs54@cunixf.cc.columbia.edu)
"...Dr. Jekyll and Mr. Hyde, individually, collectively or otherwise."
From: smith@mcclb0.med.nyu.edu
Newsgroups: bionet.software
Subject: Re: X-Windows on the Mac
Date: 22 Aug 92 15:08:16 GMT
Distribution: bionet,world
Organization: NYU Medical Center, New York, NY 10016, USA

In article <9208211916.AA18797@darwin.sfbr.org>, bdyke@DARWIN.SFBR.ORG (Bennett Dyke) writes:
> Does anybody know of software that will enable the Macintosh to
> emulate an X-terminal?

We have just tried eXodus from White Pine.  By and large it is very good.  
Also, it works nicely in color! (I was not able to get MacX working in color, 
but that is not saying much necessarily...).  I particularly like the Motif-
style rootless windows.  It really needs a Mac with lots of memory (they
recommend 4mb to run DECwindows, and I agree, but you can get by with 3mb: 
dedicated to eXodus, that is, if you only want 1-2 windows on the screen. 
Finally you need a big screen: the 13" one is just too little space to get 
more than one window on and have rrom for anything more...  WE intend to run 
on ci's with 20mb memory and 20" screens.  It should be great: on a Quadra it 
should be spectacular!

+----------------------------------------------------------------------------+
|Ross Smith,  Research Computing Resource, Department of Cell Biology, NYU-MC|
|550 First Ave., NYC, 10016-6402.  Phone: (212) 263-5356: FAX: (212) 263-8139|
|E-Mail:  SMITH@NYUMED.BITNET (BITNET),   SMITH@MCCLB0.MED.NYU.EDU (Internet)|
+----------------------------------------------------------------------------+
From: JONESBB@BELOIT.EDU
Newsgroups: bionet.software
Subject: Screen Capture
Date: 14 Aug 92 19:18:00 GMT
Distribution: bionet


The built-in screen capture for the mac has limitations.  It must capture the
whole screen, it will only work in black and white mode (no shades of gray)
and ti cannot capture pulled-down menus.

There are other screen capture programs.  Try Black Box, which you can get by
anonymous ftp from sumex.stanford.edu.  It is more than a screen capture
utility, but that is one of its functions.

Ben Jones,  BioQUEST

Newsgroups: bionet.software
From: chh9@quads.uchicago.edu (Conrad Halton Halling)
Subject: I need descriptions of formats for GenBank and EMBL
Reply-To: chh9@midway.uchicago.edu
Organization: University of Chicago Computing Organizations
Date: Wed, 19 Aug 1992 19:44:42 GMT

I am writing a program that must parse the CDS fields of GenBank and EMBL
entries.  Are official descriptions of the GenBank and EMBL formats
available?

For example, I need to know what the format is when complement() and
join() are used.  Is the order "complement(join(1..10,20..40))" or
"join(complement(1..10),complement(20..40))"?

(I guess I'm slow, but I just discovered that the format of EMBL entries
has changed completely.  This probably broke everyone's software -- I
know it will break some of my programs.)

-- 
Conrad Halling
c-halling@uchicago.edu
From: ES@UK.AC.AFRC.JII
Newsgroups: bionet.software
Subject: NCBI internet access inquiry
Date: 17 Aug 92 12:25:00 GMT
Distribution: bionet
Original-To: BIO-SOFTWARE@UK.AC.DARESBURY

Hello there,

Could anyone provide us with the internet access number of NCBI?
The address NCBI.NLM.NIH.GOV being unknown of our computer address 
database, we can't currently use ftp to that site.

Many thanks

Eric Schoonejans

es @ jii.afrc.ac.uk
From: mws%molly@SDSC.EDU (Michael W. Smith)
Newsgroups: bionet.software
Subject: NCBI searching and retrieval
Date: 19 Aug 92 21:13:25 GMT
Distribution: bionet

Hi Netlanders,

I managed to delete the recent mail messages concerning the new NCBI
email services (saved a lot of disk space I bet).  Could someone send me a
copy of the email information that NCBI recently released.

mike

  *********************** Michael W. Smith **************************
  *             Salk Institute for Biological Studies               *
  * Molecular Genetics Laboratory     phone: (619)453-4100, ext 376 *
  * P. O. Box  85800                  fax:   (619)558-9513          *
  * San Diego, CA   92138             E-mail: mws@molly.sdsc.edu    *
  *******************************************************************
From: rbm8p@Virginia.EDU (Rick MacDonald)
Newsgroups: bionet.software
Subject: Ramachandran map?
Keywords: ramachandran
Date: 22 Aug 92 00:37:36 GMT
Organization: University of Virginia

Where can I find a numerical representation of the Ramachandran map
of protein conformation space?

Rick 
rbm8p@virginia.edu
From: wjb1@ellis.uchicago.edu (William J. Buikema)
Newsgroups: bionet.software
Subject: software to draw membrane spans
Date: 12 Aug 92 16:51:43 GMT
Reply-To: wjb1@midway.uchicago.edu
Organization: University of Chicago Computing Organizations

I'm trying to find any kind of software that will take an amino acid 
sequence and generate a picture showing membrane spanning regions and
inner and outer membrane connections.  Basically anything that will chain
together the letters and enclose them in circles will do, provided the
resultant file can be edited.  Has anyone seen such a program?


William J. Buikema              internet: wjb1@midway.uchicago.edu
University of Chicago               or    w-buikema@uchicago.edu
Dept. of Molecular Genetics &       or    hetman@uchicago.edu 
    Cell Biology, CLSC 313
920 E. 58th St.
Chicago, IL  60637
From: bdyke@DARWIN.SFBR.ORG (Bennett Dyke)
Newsgroups: bionet.software
Subject: X-Windows on the Mac
Date: 21 Aug 92 19:16:58 GMT
Distribution: bionet

Does anybody know of software that will enable the Macintosh to
emulate an X-terminal?

Thanx in advance.

Bennett


-- 
+----------------------------------------------------------------------------+
|   Bennett Dyke                                                             |
|   Department of Genetics               Internet:  bdyke@darwin.sfbr.org    |
|   Southwest Foundation                    Phone:  (512) 674-1410 Ext 281   |
|   P.O. Box 28147                            Fax:  (512) 674-2126           |
|   San Antonio, TX 78228, USA                                               |
+----------------------------------------------------------------------------+
From: mangalam@SALK-SC2.SDSC.EDU
Newsgroups: bionet.software
Subject: Re: Images
Date: 14 Aug 92 02:44:27 GMT
Distribution: bionet

Bart Man (pun?) or Brent, depending on which part of the message you
believe writes:

>I am looking for an anonymous FTP site that may have color or b&W scanned
>images of MRI, PET or CAT, (or anything remotely similar).  Does anyone
>know of a site?  I heard that NIH had such a site.
>
>please e-mail:  bkronenb@sdcc13.ucsd.edu
  
   The directories associated with NIH Image, now in its 1.45 incarnation,
have at least one series of MRI data (25 slices, I think).  It can be found
at alw.nih.gov in /pub/image/images(?) or something close.  If you need
others, I can probably dig up at least a few other series.  
   And while the fingers are still pliable, here's a LOUD PLUG for NIH
Image, one of the best image analysis programs available (FOR FREE, WITH
SOURCE CODE, WITH A MACRO LANGUAGE, WITH AN ON-LINE AUTHOR, WITH A READABLE
MANUAL).   GNUdos to Wayne Rasband for his work.


Cheers,

Harry



Harry Mangalam                                   Vox:(619) 453-4100, x250
Dept of Biocomputing                                   Fax:(619) 552-1546
The Salk Institute                             mangalam@salk-sc2.sdsc.edu
10010 N Torrey Pines Rd                        mangalam@salk-sgi.sdsc.edu
La Jolla CA 92037                                    mangalam@salk.bitnet

Newsgroups: bionet.software
From: mathog@seqvax.caltech.edu (David Mathog)
Subject: NCBI retrieve - it works, but...
News-Software: VAX/VMS VNEWS 1.41    
Organization: Division of Biolgy, CALTECH
Date: Wed, 19 Aug 1992 19:05:00 GMT

I've just spent some time messing with NCBI retrieve.  The turnaround time
for a request varied from 2 hours (17:00 PST) to 5 minutes (9:30 PST),
which is fast enough. 

However, the service is a bit schizophrenic - it tries to be both a search
service and a retrieval service, and so is not really very good at either. 

First of all, it's completely nuts that you cannot retrieve an entry by its
accession number or name without also getting hit with spurious cross
references from other entries.

Similarly, the search function is compromised by insisting that it send the
entire database entry on a hit.  Here's a fun one, try "brown AND
drosophila" against Genbank.  There are 18 hits, most of them are for
somebody named Brown and a Drosophila entry.  However, you also get Yeast
Chromosome III (somebody named Brown, and a homology to Drosophila). When
it tries to mail this entry it exceeds the maximum number of lines/entry
and truncates the list at entry 6 - you don't even get to look at the last
12!.  This problem is only going to get worse with time as other huge
genomic stretches are entered into the databases. All we need back from a
search statement like this is enough information to determine if the hits
are the ones we want.  I'd also REALLY like to be able to restrict the
search either by fields, or at least by proximity, but we'll leave that
discussion for another time.

Anyway, for a quick fix, what about breaking this up into two services?

NCBI SEARCH:    Command words: DATALIB, MAXHITS, BEGIN
  Same search lines as now, but return =
  Accession number (or entry name) + # of lines in entry + description line 
  (Needed for the MAXLINES parameter ^^^^^^^^^^^^^^^^^^^ in retrieve)

NCBI RETRIEVE:    Command words: DATALIB, MAXDOCS, MAXLINES, SEPARATE, BEGIN
  Standard keyed retrieval by accession numbers or names.
  (SEPARATE = "mail each entry separately")

Comments anybody?

David Mathog
mathog@seqvax.caltech.edu
manager, sequence analysis facility, biology division, Caltech
From: kristoff@genbank.bio.net (David Kristofferson)
Newsgroups: bionet.software
Subject: Re: Genbank services?
Date: 18 Aug 92 20:17:22 GMT
Distribution: bionet
Organization: GenBank Online Service

SBAIRD@ACADVM1.UOTTAWA.CA (Stephen Baird) writes:

>Dear David Kristofferson,
>	I am a little unclear as to what services Genbank will be
>offering to the public after the end of September. I gather the
>FASTA, BLAST, BLAZE and RETRIEVE e-mail servers will no longer be
>available.  Instead of these servers, researchers will be able to
>use the NCBI BLAST and RETRIEVE e-mail server as well as the
>various FASTA e-mail servers from the University of Houston's
>gene-server, EMBL, and PIR. I don't think BLAZE will be available
>to anyone for free anymore.

You are correct in all of the above, although I am still not certain
when IG/MASPAR will stop free BLAZE access.  At this point one should
assume September 29th unless you hear otherwise.  I should add that
FASTA is also available by e-mail from EMBL.

>	What about data submission?  Will Genbank still be the main
>North American public repository?

Paul Gilna already answered the above regarding LANL's role.  I add
that IntelliGenetics will continue to distribute and support the
Authorin data submission program through March 1993.

> What about the FTP server and
>the Genbank database updates, will this be NCBI's responsibility?

Yes.  You can FTP to ncbi.nlm.nih.gov now.

>Are there other public services that Genbank offers that will no
>longer be available?

The free dial-up IRX account is the only thing that will disappear.
NCBI allows IRX-style queries by e-mail, and IG is going to charge for
interactive IRX access on its timesharing service.

I hasten to add that the BIOSCI/bionet newsgroups will continue at
IntelliGenetics and SERC Daresbury without interruption.

				Sincerely,

				Dave Kristofferson
				GenBank Manager

				kristoff@genbank.bio.net