HDTenEightyP/NetNews huggingface dataset:
From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert)
Subject: Re: Object oriented programming
Organization: Biology, Indiana University - Bloomington
Distribution: bionet
Date: Wed, 19 Aug 1992 20:57:57 GMT

This is a very off-the-cuff description of object oriented programming --
I hope someone else may provide a better one.

OOP is a bit like Darwin's theory of evolution applied to programming:
In the beginning, there was one simple object type, which doesn't know
much more than how to create and destroy itself.  New object types 
evolve from that ancestor object, by acquiring new methods (new ways
of interacting with other objects).  These decendent object retain 
all the methods of their ancestors, and can always use their
inherited methods with little effort.  That is one big advantage of
OOP over procedural programming -- inheritance of methods.

If an ancestor object is changed, all of its decendant objects change
also -- new features can be added very simply.  This is one of NeXT's
bragging points -- they added ability to use Kanji text to all existing
NeXT apps simply by teaching an ancestral text object about Kanji.

The power of OOP is most evident when you have a large object library
to build applications from -- you can more easily build new applications,
add new features, and add those features to many applications at once
if they rely on object libraries.  The programming I've been doing with
MacApp (Apple's OOP library for Macintoshes) shows that well to me.
I have three well-used programs, SeqApp, GopherApp and LoopDLoop, which
share many of the same underlying objects (where appropriate), and if
I enhance an object for one, it is fairly easy to get that enhancement
into another of the apps. 

I believe that in the coming several years, we are all going to be working
with object oriented operating systems, o-o applications, probably o-o
databases, etc.  The concept of ancestor-descendent objects, that carry
around their own methods for dealing with data, and that are extensible
thru subclassing, is a concept that saves programming time and makes for 
more robust and adaptable software.  It isn't the holy grail for 
programming, but OOP helps a lot in many ways.  If you are a programmer,
there is no good reason not to start working with OOP now -- you can get
good, inexpensive C++ compilers on all common platforms, and C++ lets you 
continue using procedural C mixed with object C as desired.  SmallTalk,
Object Pascal, and various other OOP languages are available, but C++ is
the most common and with the most OOP library support.

-- Don

-- 
Don Gilbert                                     gilbert@bio.indiana.edu
biocomputing office, biology dept., indiana univ., bloomington, in 47405
From: georgen@sickkids.on.ca (George Ng)
Newsgroups: bionet.software
Subject: Re: PC Internet Connection & Gopher
Date: 15 Aug 92 16:00:09 GMT
Distribution: bionet
Organization: The Hospital for Sick Children

In article <9208112123.AA07150@genbank.bio.net> JMILLER%BIOVX1.SPAN@STAR.STANFORD.EDU writes:
> 1. A connection to internet requires that your computer be directly connected,
>not through a modem. Either you will need an ethernet card installed in

Not true.  It is possible to get an Internet connection over phone lines using
modems by running programs like SLIP (serial line internet protocol?) or
ppp (point-to-point protocol).  Granted, you'll be limited by the speed of your
modem (usually 9600-38.4kbps) in comparison to Ethernet cable (peak rate of
10mbps) but at least you have an Internet connection.

gn


-- 
georgen@resunix.ri.sickkids.on.ca	(NeXTMail ok)
molecular genetics, hospital for sick children
From: IW01@LIVERPOOL.AC.UK
Newsgroups: bionet.software
Subject: Enzyme Kinetics Programs, anyone?
Date: 20 Aug 92 11:22:10 GMT
Organization: University of Liverpool

Anyone out there have recommendations for enzyme kinetic analysis programs to
run on a PC?  At the moment our Department has a very crude program running
on Apple IIs, and since we now have mostly PCs a new program is required.

Minimum features required: Calculation of Km, Vmax, and Ki parameters
(preferably derived from more than one type of plot).  If the program could
also output plots of the data in a presentation-quality format this would be
a bonus, but is not essential (as an aside, has anyone found a satisfactory
method for producing Dixon and Lineweaver-Burk plots on any presentation
graphics package?).

Thanks in advance for all assistance.  Please mail or post; I will summarise
if I receive sufficient responses.

 Ian.

/============================================\/=========================\
| Ian Webber,                                ||  VOICE: (051) 794 5565  |
| Department of Pharmacology & Therapeutics, ||  FAX:   (051) 794 5540  |
| University of Liverpool,                   ||=========================|
| P.O.Box 147, Liverpool, L69 3BX, U.K.      ||  JANET: IW01@UK.AC.LIV  |
\============================================/\=========================/
From: SBAIRD@ACADVM1.UOTTAWA.CA (Stephen Baird)
Newsgroups: bionet.software
Subject: Genbank services?
Date: 18 Aug 92 14:37:38 GMT
Distribution: bionet

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.
	What about data submission?  Will Genbank still be the main
North American public repository?  What about the FTP server and
the Genbank database updates, will this be NCBI's responsibility?
Are there other public services that Genbank offers that will no
longer be available?
	Thank you for any clarification of these questions,
From: mangalam@SALK-SC2.SDSC.EDU
Newsgroups: bionet.software
Subject: Re:EPS from Unix to Mac (Was Re:gcg)
Date: 14 Aug 92 23:33:31 GMT
Distribution: bionet

>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
>>you type PostScript, and configure printer output to an EPS file,
>>you can then download that file directly to a PostScript printer, and
>>get your file! I know, 'coz i've had it work! Of course, you can take the
>>same eps file, and manipulate it into other programs, like FreeHand or
>>Illustrator.
>>
>
>My lab is using MacDraw Pro which is supposed to be able to read and
>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?
>
>Larry Casson
>lpcasson@phoenix.princeton.edu

To stamp your files with the correct resource fork, you can use SDSC
Imagetyper (ftp.bio.indiana.edu or sdsc.edu) or use a related program
called BunchTyper (sumex-aim.stanford.edu) which can stamp a 'bunch' of
files at a time.
   I don't think that you will be able to modify an EPS file, whether or
not it has a resource fork.  Certainly, you won't be able to modify it as
vector objects.  If that's your desire, you'll have to write HPGL files
from GCG, import into a program that can import this format (Corel Draw and
I believe that the newest version of Hijack (also for Windows) does) and
then export as a pict to get it to Canvas or MacDraw.

Good Luck

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
From: will@turbo.bio.net (Will Nelson)
Newsgroups: bionet.software
Subject: Re: NCBI internet access inquiry
Date: 17 Aug 92 17:20:29 GMT
Distribution: bionet
Organization: GenBank Online Service

I tried replying to you by e-mail, but the elements
of the fully qualified domain name in your "From:"
line are reversed. Anyway, NCBI.NLM.NIH.GOV has address 130.14.20.1.
-- 
Will Nelson
Systems Programmer, IntelliGenetics, Inc.
will@presto.ig.com
Newsgroups: bionet.software
From: acc@basinger.inescn.pt (Antonio Costa)
Subject: Ray-tracing scenes
Keywords: Image synthesis
Organization: CG & CAD - INESC Norte
Date: Wed, 12 Aug 92 22:38:44 GMT

Hi.

For everybody that uploaded the RTrace ray-tracer (at asterix.inescn.pt
[192.35.246.17] in directory pub/RTrace), I have put a lot of scene files
(both in SFF and SCN format) in directory pub/RTrace/scene-demos

Many have been converted from other graphic formats (NFF, T3D, OFF).
Others have been converted from chemical/molecular/medical data.

Please fell free to contact me (acc@asterix.inescn.pt or
basinger@inescn.pt)

PS: the MAC version of RTrace (for THINK C compiler) is almost ready.
Please contact Reid Judd (reid.judd@east.sun.com) to get the program.

Regards,
Antonio Costa.
.........................................................................
     O     O
    /     /                        I N E S C
   | O   |        Antonio Costa        | E-Mail   acc@asterix.inescn.pt
   | |\  |   O                         |          acc@basinger.inescn.pt
   | | \ |  /  O  Comp. Graphics & CAD | DECnet   inescn::a_costa
   | |  \| /  /                        | VAX-Mail +26802001576::a_costa
   | |  /  | |    Largo Mompilher 22   | UUCP     {mcvax,...}!...
   O | |-O | |    4100 Porto PORTUGAL  | Bell     +351+02+321006
    /   \ /   \
   O     O     O          "Let the good times roll..."
Newsgroups: bionet.software
From: tlinn@newshost.uwo.ca (t.   linn)
Subject: Re: Inquiry regarding sequence analysis (esp promoters/enhancers)
Organization: The University of Western Ontario, London, Canada.
Date: Fri, 14 Aug 1992 06:57:34 GMT

In article <1992Aug7.013257.12200@u.washington.edu> rbradbur@hardy.u.washington.edu (Robert Bradbury) writes:

>   I am interested in obtaining opinions in two areas:
>
>     1) Are there databases which contain a list of the known promoter/enhancer
>	sequences for eukaryotes and/or is there software which can use this
>	information to identify these regions in a given sequence?  I would
>	prefer packages which are designed for this specific task rather than
>	a collection of GCG commands which will always be out of date given the
>	ever increasing number of promoter/enhancer sequences.
>
>    2) Could people send me brief notes regarding their experience with PC
>       (DOS or UNIX) based software packages for sequence analysis (scanning
>       CD-ROM databases, sequence comparisons, PCR primer and probe design, etc).
>       I'm interested in stand-alone systems which do not require large computers.
>       E-mail response is fine, I will post a summary for general reference.
>
>   Thanks,
>   Robert Bradbury		uunet!sftwks!bradbury or rbradbur@u.washington.edu
>

Check out David Ghosh's extensive TFD (Transcription Factors
Database), in particular the SITES table for the sequences of all(???) known
factor-binding sites (there are some 2036 entries!).  The database is
available from the National Center for Biotechnology Information
(NCBI) by FTP to NCBI.NLM.NIH.GOV in the 'repository' directory.  Also, a
couple of new email servers were just recently made available from
NCBI that should allow you to perform searches on this database: to find
out how they work just send an email message only containing the word HELP
to blast@ncbi.nlm.nih.gov and retrieve@ncbi.nlm.nih.gov.  The
publications describing this terrific piece of work are:

Ghosh, D. (1990)  Nucleic Acids Research 18:  1749-1756.
Ghosh, D. (1991)  Trends in Biochemical Sciences 16:  455-457.
Ghosh, D. (1992)  Nucleic Acids Research 20S:  2091-2093.

Also check out the EPD (Eukaryotic Promoter Database):
EPD -  Eukaryotic Promoter Database. A collection of biologically
functional, experimentally defined RNA POL II promoters active in
higher eukaryotes. Maintained by Philipp Bucher
(Philipp.Bucher@Isrec.Arcom.ch).       Last update: Dec. 17, 1991.

This is also available by FTP'ing to ncbi.nlm.nih.gov in the
'repository' directory.  I'm not as familiar with that DB so I can't
offer specifics.

Good luck!


Keith

--
Keith L. Steward                          Voice: 519 679-2111 ext.
6618 Dept. Microbiology & Immunology        Fax: 519 661-3499
Dental Sciences Bldg.                  Internet: KLSTEWARD@UWO.CA
University of Western Ontario
London, Ontario, Canada, N6A 5C1
--
--
Keith L. Steward                          Voice: 519 679-2111 ext. 6618
Dept. Microbiology & Immunology             Fax: 519 661-3499
Dental Sciences Bldg.                  Internet: KLSTEWARD@UWO.CA
University of Western Ontario
London, Ontario, Canada, N6A 5C1
Newsgroups: bionet.software
From: Bo Servenius <biogen10@gemini.ldc.lu.se>
Subject: The new Alpha ships from Digital - anyone any experiences?
Organization: Lund University, SWEDEN
X-Useragent: Nuntius v1.1
Date: Mon, 17 Aug 1992 21:26:41 GMT

Dear Netters!

Have anyone of you any experiences of running Alpha based
computers (VMS or UNIX) for the GCG packaged or other Biocomputing
interesting programs. 

Any comments are appreciated

BOSSE
From: GBCA26@UK.AC.GLASGOW.VMS3 ("David Leader : Glasgow University Biochemistry : UK")
Newsgroups: bionet.software
Subject: Preview Pict for EPS (was gcg)
Date: 15 Aug 92 11:03:00 GMT
Distribution: bionet
Original-To: BIO-SOFT@UK.AC.DARESBURY

Dear Netters,
        Lawrence P. Cassons asks about generating Mac PICT previews for EPS
files downloaded from gcg and other non-mac machines. I too am interested
in this. There is a commercial package called Smart Art from Ansys that can
do this, but the British agent have disappeared from the phone book and I
can't trace them. I'd be interested if anyone knows the address of the US
agent, or knows of a shareware package that can do the same thing.
David Leader
Department of Biochemistry,
University of Glasgow
Glasgow G12 8QQ,
UK
GBCA26@UK.AC.GLA.VMS3
From: lapointe@THORIN.UTHSCSA.EDU (David Lapointe)
Newsgroups: bionet.software
Subject: Grant Tracking Software
Date: 12 Aug 92 21:50:09 GMT
Distribution: bionet

Net-People,

We are looking for Macintosh software to enable a department 
(say) to track the status of grants (in progress, pending, funded) 
as well as accounting/reporting capability.

Any suggestions (Commercial/PD) are appreciated.

Thanks

 .david
+-------------------------------------------------------------------+
| David S Lapointe PhD                     lapointe@uthscsa.edu     |
| Computing Resources                      lapointe@uthscsa (BitNet)|
| 7703 Floyd Curl Drive                                             |
| UTHSCSA                                  (512) 567-2200 (voice)   |
| San Antonio,TX 78284-7832                (512) 567-2204 (fax)     |
+----------*** Called or not, the Gods will be present ***----------+
Newsgroups: bionet.software
From: branham@binah.cc.brandeis.edu (Tom Branham, Biophysics Grad. Brandeis)
Subject: Re: Secondary structure assignment
Reply-To: branham@binah.cc.brandeis.edu
Organization: Brandeis University
Date: Thu, 13 Aug 1992 23:07:13 GMT

Good idea!  Could also be done fairly simply in most any spreadsheet....
                           ..........Tom Branham
From: kuznetsov@embl-heidelberg.de
Newsgroups: bionet.software
Subject: PostScript level II
Date: 14 Aug 92 15:08:59 GMT
Organization: EMBL, European Molecular Biology Laboratory

Hi, Bionetters!
I need to encode a bitmap image (created by my program as a rectangular 
array filled by color indices, actually it is an image of a protein) to 
PostScript file. I cannot do it with the standard PS (as it runs only 
monochrome-variable-scale images and colors are opaque). The only one 
solution (as I know) within the standart PS is the method of dithering,
but this way leads to loss of resolution. 
I heard about the extention to PS which gives the user possibility to
work with color bitmap images. On my best knowledge it is called 
PostScript level II. Can somebody give a pointer to a manual 
describing the new capabilities? 

Many thanks in advance,
Dmitry Kuznetsov
KUZNETSOV@EMBL-Heidelberg.DE
From: collet@scripps.edu (Thomas Collet)
Newsgroups: bionet.software
Subject: Bibliography software needed !
Date: 21 Aug 92 00:14:15 GMT
Organization: The Scripps Research Institute, La Jolla, California, USA

Newsgroups: bionet.software
Subject: Bibliography program
Summary: 
Followup-To: 
Distribution: world
Organization: The Scripps Research Institute, La Jolla, California, USA
Keywords: 

Can anyone recommend a program for the Mac that keeps
track of literature references? Ideally, it should allow
output in the proper format for publications.
Please respond by email to my account below, as I don't 
follow this group closely. If there is enough interest, 
I will post a summary.
Thanks,


Thomas
From: pathology@mscf.med.upenn.edu
Newsgroups: bionet.software
Subject: Curve fitting for electrophysiology data
Date: 13 Aug 92 02:11:04 GMT
Organization: Univ of Penn - Med School Computer Facility

Can anyone recommend a program for fitting ion current versus voltage data 
across membranes to Eyring multi-site and multi-barrier models of current flow?
Such data, for example, are generated from electrophysiology experiments with
channel proteins in membranes. 

Thanks for any help.  I will post a summary of responses to this question.

Gregg Wells
Department of Pathology
University of Pennsylvania
Philadelphia, Pennsylvania
USA
e-mail:  pathology@a1.mscf.upenn.edu
From: pc386@il.ac.tau.ccsg (BENNY SHOMER 9238)
Newsgroups: bionet.software
Subject: Re:
Date: 13 Aug 92 13:47:39 GMT
Distribution: bionet
Original-To: Oligo@il.ac.tau.ccsg, bookkeaping@il.ac.tau.ccsg, software@il.ac.tau.ccsg,
        bio-software@uk.ac.daresbury
X-Mailer: ELM [version 2.4dev PL52]

Dear Netlanders.
 A request was made yesterday:

>Have thought about putting together a Hypercard stack or an Excell
>worksheet for my oligos, or maybe even better a Hypercard stack
>linked to an Excel spreadsheet. Guess that someone already has
>created
>something like this so maybe I do not have to reinvent the wheel.
   {  rest of stuff deleted....}

I have written a hypercard stack similar to the one  you describe.
It is  a relatively simple, non  debugged stack. I have found it suitable
for my needs, as well as other people in our/neighboring labs.

I have the stack packed and ready for Email delivery as an .hqx file, which
can be binhex decoded and is a self extractable module. 
I don't know whether this is allright to post binhexed files directly to the
group (it is 52Kb large). 
Please comment on this- Is it O.K. if I post it as a message? If yes, I'll do
so in the next day or so. If not, then maybe someone who have an access to a 
server can put it there for ftp. I will send him the stack.

Sincerely, Benny.
**************************************************************
* Benny Shomer                                                 *
* Tel-Aviv University                                          *
* Sackler School of Medicine, Dept.of Embryology and Teratology*
*--------------------------------------------------------------*
* Snail:  Sheba Medical Center, Tel-Hashomer, 52625,   Israel. *
* E-mail :  PC386@CCSG.TAU.AC.IL                               *
* Tel :  972-3-640-9238     FAX :   972-3-642-2046             *
*                                   (c/o Dr. R. Ehrlich)       *
*                                                              *
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
%        So Many Computers , So Little Time ...                %
%                                                              %
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Newsgroups: bionet.software
From: branham@binah.cc.brandeis.edu (Tom Branham, Biophysics Grad. Brandeis)
Subject: Re: Secondary structure assignment
Reply-To: branham@binah.cc.brandeis.edu
Organization: Brandeis University
Date: Thu, 13 Aug 1992 13:14:33 GMT

Quanta will calculate hydrogen bonds and then analyze the secondary structure
in its Protein Design Module, but it seems like a rather large investment
if all you want to do is determine the secondary structure.........
                              ........Tom Branham
From: Davison@UH.EDU (Dan Davison)
Newsgroups: bionet.software
Subject: Re: help with consensus sequence
Date: 13 Aug 92 19:58:41 GMT
Distribution: bionet

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

Pattern Induced Multiple Alignment, by Randy Smith and Temple Smith,
indeed works on proteins. It's on the gene-server@bchs.uh.edu
(anonymous ftp from ftp.bchs.uh.edu) and should be on the other molbio
servers.


dan
gene-server manager
-- 
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: kristoff@genbank.bio.net (David Kristofferson)
Newsgroups: bionet.software
Subject: Re: noooooo mmoooorrreee
Date: 19 Aug 92 17:49:52 GMT
Distribution: bionet
Organization: GenBank Online Service

WGANNON@BOOTES.UNM.EDU writes:

>pleeze unsubscribe me too!  wgannon@unmb.unm.edu

Done.  Please send this type of request to either
biosci@genbank.bio.net or biosci@daresbury.ac.uk depending upon which
site sends you your mail.

				Sincerely,

				Dave Kristofferson
				GenBank Manager

				kristoff@genbank.bio.net
From: varner@UMD5.UMD.EDU (Mark Varner)
Newsgroups: bionet.software
Subject: Re: NCBI internet access inquiry
Date: 17 Aug 92 13:37:58 GMT
Distribution: bionet

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

I used the nslookup command available on our Unix box.
From: cherry@ochre.mgh.harvard.edu (Mike Cherry 726-5955)
Newsgroups: bionet.software
Subject: Re: gcg
Date: 16 Aug 92 23:23:00 GMT
Distribution: bionet
Organization: Molecular Biology, Massachusetts General Hospital, Boston
News-Software: VAX/VMS VNEWS 1.41

In article <1992Aug14.112422.22836@news.columbia.edu>, rs54@cunixf.cc.columbia.edu (Richard Sucgang) writes...
>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
> 
>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).

You can use GCG to create an HPGL file. Just use the HPGL command before 
running the graphics producing program. Then use the HP2PICT HyperCard 
stack available via anonymous ftp from ftp.bio.indiana.edu in the util/mac 
directory. This stack will display one page of graphics and allow you to 
then copy and paste into MacDraw.

However, the method I prefer is to use VersaTerm PRO to display the GCG 
graphics using tektronix emulation. Then copy and paste from VersaTerm PRO 
to MacDraw. There is an option for VersaTerm with the GCG TEKTRONIX 
command.

Mike Cherry