HDTenEightyP/NetNews huggingface dataset:
From: MCCAINKW@DUVM.BITNET (Kate)
Newsgroups: bionet.software
Subject: non-commercial OCR software
Date: 10 Apr 92 11:51:28 GMT
Distribution: bionet

Does anyone out there who is more familiar with internet resources or
clever people know of some non-commercial (e.g. freeware, shareware)
optical character recognition software that will run on a Mac under
System 7? I have access to a scanner and a primitive (no superdrive)
Mac II but the only OCR software I know about is $$$.  I want to run
some tests on text entry and manipulation for a project in quantitative
history of genetics in the post-war period. I have compiled data for a
"map" of about 16 major geneticists (research relationships of scholarly
works) but the data entry is massive.

Thanks for any help.

Kate McCain                       "Die Gedankenexperimente sind Frei!!"
College of Information Studies
Drexel University
From: dweeks@WATSON.HGEN.PITT.EDU (Daniel E. Weeks)
Newsgroups: bionet.software
Subject: Unix shell for Macintosh??
Date: 15 Apr 92 14:14:28 GMT
Distribution: bionet

RE: Unix-like shell program for the Macintosh

Hello,

I am looking for public-domain or inexpensive software
for the Macintosh which would allow me to run "batch
jobs" or csh shell programs.  Specifically, I would
like to be able to use a csh-like script on the Mac
to call programs that I have written.  I would like
these programs to run in the background under Multifinder
so that I can continue to use my Macintosh while they
are running.  I almost figured out how to do this with MPW,
except that the programs couldn't run in the background.

More specific questions:
 1) Does anyone have experience with MINIX on the Macintosh?
 Will that allow me to do this?

 2) I haven't tried System 7 yet.  Is there something in
 there that would allow me to run "batch jobs"?

Thank you for your help and advice.

Sincerely,
  -- Dan Weeks --

********************************
| Daniel E. Weeks              | 
| Department of Human Genetics |  Internet: 
| University of Pittsburgh     |    dweeks@watson.hgen.pitt.edu
| Crabtree Hall, Room A310     |
| 130 DeSoto Street            |  Bitnet:
| Pittsburgh, PA 15261         |    weeks@pittvms.bitnet
|                              |
| (412) 624-3066               |
| FAX: (412) 624-3020          |
********************************
From: nigel@codon3.berkeley.edu ()
Newsgroups: bionet.software
Subject: HyperBlast....does it exist?
Date: 7 Apr 1992 16:23:55 GMT
Organization: University of California, Berkeley
Distribution: bionet
Reply-To: nigel@codon3.berkeley.edu ()
NNTP-Posting-Host: codon3.berkeley.edu
Keywords: Blast for the Mac (HyperBlast)

HI folks,

I'm looking for a "Blast" package for the Mac, and someone mentioned HyperBlast.
I assume this is a hypercard stack that acts as a front end....sounds like
just the thing I'm after.  Only problem is, I can't find it anywhere.  Archie
turns up blank, as do my own  attemps at rummaging through the archives.  I
would appreciate any pointers to a source for this stack

thanx

-nigel

Newsgroups: bionet.software
From: txt15@po.CWRU.Edu (Tao Tao)
Subject: E. coli promoter prediction program?
Organization: Case Western Reserve University, Cleveland, Ohio, (USA)
Date: Wed, 8 Apr 92 17:19:12 GMT


In a paper in Journal of Biological Chemistry (264:5531-4; M.C. O'Neil and 
F. Chiafari), a computer protocol has been discribed that would search the
sequence for potential promoters.  I would like to know from the fellow netters
the answers for the following question about this program:

1. Where could I get this program?
2. Which system will it run under?
3. Are there anyone who has ever tried it? And what is the impression?

Thanks in advance!

Tao
From: Chris_Upton@darwin.biochem.ualberta.ca
Newsgroups: bionet.software
Subject: Re: Molecular Biology Software for Windows
Date: 15 Apr 92 22:37:25 GMT
Organization: University of Alberta

In article <sg0enINNilt@matt.ksu.ksu.edu> dje@matt.ksu.ksu.edu (Daniel Jay
Enebo) writes:
> 
>We are looking for info and opinions on molecular biology software packages fo
>r PC clones.  We have a 33/386 and use Windows 3.1.  What is available out the
>re?  Anything like MacVector??  What about GeneWorks?? We need all the standar
>d features: plasmid construction, RNA folding, protein analysis (ie. hydrophob
>icity etc.), PCR primers, seq. alignment, sequence project management, etc.
>Any help will be greatly appreciated.
> 
>P.S.  We only have a few days to select a package.          
> 
>Thanks,
>Dan
> 
>-- 
>|  Daniel Enebo             |  dje@matt.ksu.edu       |
>|  Division of Biology      | ----------------------- |
>|  Kansas State University  |  Cell Cycle Regulation  |
>
 
PC GENE from Intelligenetics would be one commercial package to check out.
I don't think it NEEDS Windows. It's sort of the PC version of GeneWorks.

Chris Upton
Biochem
U of Alberta
Newsgroups: bionet.software
Subject: Re: 3D image reconstruction from 2D projections?
From: brownt1@lincoln.ac.nz
Date: 16 Apr 92 12:49:57 +1200

In article <1992Apr15.220142.19529@cco.caltech.edu>, sasha@cco.caltech.edu (Alexander Zeyliger) writes:
> I was just given a project on 3D image reconstruction from 2D projections.
> However, I am having problems locating an efficient algorithm that does that.
> If you know anything about it and don't mind, please send me email or post
> a note to this newsgroup.


I'm in the middle of something along those lines.  I have digitised plan 
and elevations of tree root systems, and i want to re-create the three 
dimensional structure.  As I have plan and elevation, all the information 
is there, it's just a matter of matching the bits.  This is a major task 
though, the 'images' are very large collections of strings of line 
segments (Terracad export format i think).  If there's anything out there 
on getting three dimensional data from slightly mis-matched plan and 
elevation data, I'd be very interested.

I'm not sure if your problem is exactly the same, are you dealing with 
structured data or bitmaps (images).  Anyway, if your request doesn't
bring forth anything here, comp.graphics would probably be the place to
try. 

Cheers -tb
----------------------------------------------------------------------
     Terry Brown, INTERNET brownt1@lincoln.ac.nz, 
                  UUCP     tb@tbnode.equinox.gen.nz,
From: Davison@UH.EDU (Dan Davison)
Newsgroups: bionet.software
Subject: Re: Molecular Biology Software for Windows
Date: 15 Apr 92 02:11:49 GMT
Distribution: bionet

Daniel Jay Enebo said:
> We are looking for info and opinions on molecular biology software
> packages for PC clones.  We have a 33/386 and use Windows 3.1.  What
> is available out there? 


Not that I've heard of. There are packages that will run in a DOS box,
but not windows-specific.  I've not noticed anything advertised,
either. I know of *one* app - Macaw. Please post a summary of whatever
you discover!


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: William_D_WARREN@UMAIL.UMD.EDU (ww40)
Newsgroups: bionet.software
Subject: Compiling Primer 0.5 on a VAX
Date: 9 Apr 92 23:28:00 GMT
Distribution: bionet

Gidday all,

I was wondering if anyone has compiled the PCR Primer designing program
PRIMER0.5 on a VAX running VAX/VMS V5.4 and is willing to uuencode it and
send it to me ?  PLEASE DON'T JUST SEND IT ....I DON'T WANT 20 !! Just
one will do :-)  ...  OFFERS ONLY AT THIS STAGE
Thanks
BILL
From: smiyazaw@smlab.eg.gunma-u.ac.jp (Sanzo Miyazawa)
Newsgroups: bionet.software
Subject: Re: Japanese server available? ...address?
Date: 6 Apr 92 11:28:46 GMT
Distribution: bionet
Organization: Gunma University, Faculty of Technology, in Japan

In article <9203311620.AA00908@fermat.Mayo.EDU>, peters@MAYO.EDU writes:
> I would like to know if the Japanese Server is still available
> and if so what the current address is.  I tried to use the last address
> which was posted during the last half of 1991, but "host is unknown"...
> 
> The last address I have is:
> 	flat-netserv@smlab.eg.gunma-u.ac.jp
> 
> What is the current address and is it still available?
> 
> Thanks much,
> Ken Peters
> peters@mayo.edu
> 
> Please reply to my mail address indicated above, as well as any posting to
> the list, as we have intermittent network problems and I sometimes do not
> receive the biosci messages.

	It is still available, however, unfortunately smlab.eg.gunma-u.ac.jp is
	not directly IP-reachable from sites outside of Japan; it is connected
	to the Internet but IP-reachable only from sites within Japan.
	(You could not directly login or ftp my system directly from your site,
	if your site is located outside of Japan.)
	
	Of course, e-mail can reach my site without any problem.

	So e-mail server at my site is still working.
	
	Please send a empty mail to flat-netserv@smlab.eg.gunma-u.ac.jp 
	and then you will get a brief manual of how to use this server.


P.S.
	Anonymous-ftp service at my site is therefore unavailable now.
	I hope my site will soon become IP reachable from outside of Japan.
From: weemba@libra.wistar.upenn.edu (Matthew P Wiener)
Newsgroups: bionet.software
Subject: Looking for MAPMAKER
Date: 6 Apr 92 18:22:01 GMT
Reply-To: weemba@libra.wistar.upenn.edu (Matthew P Wiener)
Organization: The Wistar Institute of Anatomy and Biology

Somebody here is looking for MAPMAKER [1], a program to construct primary
genetic linkage maps.  The reference says it is available for the asking.
FTP, e-mail, whatever--the VMS version is preferred to the Unix version.

[1] Eric Lander, Philip Green, Jeff Abrahmason, Aaron Barlow, Mark J Daly,
Stephen E Lincoln, Lee Newburg, "MAPMAKER: An Interactive Computer Package
for Constructing Primary Genetic Linkage Maps of Experimental and Natual
Populations", GENOMICS 1, pp174-181 (1987).
-- 
-Matthew P Wiener (weemba@libra.wistar.upenn.edu)
Newsgroups: bionet.software
From: djt2@po.CWRU.Edu (Dennis J. Templeton)
Subject: Are vector sequences available through genbank.bio.net?
Reply-To: djt2@po.CWRU.Edu (Dennis J. Templeton)
Organization: Case Western Reserve University, Cleveland, OH (USA)
Date: Tue, 7 Apr 92 16:22:17 GMT


Are vector sequences available through genbank.bio.net?   I have seen
references to such a "synthetic DNA" database, but I don't see it on the DB
list in the on-line genbank access.  Am I looking in the wrong place? or
just SOL?

Specifically, I'm looking for seq's of the Hieter yeast vectors pRS303-306
and pRS 313-316 (Genetics 122:19-27).

thanks for any input---

dennis
From: toms@fcs260c2.ncifcrf.gov (Tom Schneider)
Newsgroups: bionet.info-theory
Subject: Re: Weak signal detection in the N-cap of protein helices
Keywords: N-cap proteins helices info theory statictics small data sets
Date: 9 Apr 92 20:21:36 GMT
Organization: NCI Supercomputer Facility, Frederick, MD

In article <1992Apr9.133126.26623@ncsu.edu> samodena@csemail.cropsci.ncsu.edu
(S. A. Modena@) writes:

>... Morris
>is doing a straight Schneider-style calculation from a probability matrix
>with small dataset correction strategies being applied to adjusting the
>values in the matrix....one purpose being to avoid any "zero values" by
>substituting the general background frequency of a non-appearing amino acid
>for it's zero value in the matrix.

Keeping in mind Steve's disclaimer, this doesn't sound like a good idea.  For
one thing, the uncertainty measure, $H = -\sum P_i log_2 P_i$ [I'm using TeX
notation], works perfectly fine when $P_i = 0$ since the limit of p log p as p
-> 0 is 0.  Adjusting the values of the matrix to be the general background
frequency has to be wrong.  Consider the situation where I have 20,000
sequences, so when I get a zero, it's pretty sure that is right.  If I forced
that position to be the general frequency, I'd be messing up the matrix.  So
this solution is bad since it does not converge to the correct result with
large numbers of sequences.  On the other hand, we should still be looking for
better ways to do the small sample corrections.  Of course, the authors can
tell us if this is what they really were doing or not...

  Tom Schneider
  National Cancer Institute
  Laboratory of Mathematical Biology
  Frederick, Maryland  21702-1201
  toms@ncifcrf.gov
From: samodena@csemail.cropsci.ncsu.edu (S. A. Modena)
Newsgroups: bionet.info-theory
Subject: Scientific American article
Date: 16 Apr 92 23:13:05 GMT
Organization: Dept. of Crop Science, NCSU, Raleigh, NC.
Originator: samodena@csemail.cropsci.ncsu.edu

An overview article on the machinations and politics of computing 
and the Human Genome Project: 

        Trends in Genetics: Hacking the Genome
        Deborah Erickson
        Scientific American: 266(4):128-137 1992

Lead in: "The masses of information written in human DNA are 
being translated into the precise ones and zeros of computer 
code.  The choices made now will determine whether the genome 
project is a font for future discovery or a binary junkyard." 

---
+------------------------------------------------------------------+
|     In person:  Steve Modena     AB4EL                           |
|     On phone:   (919) 515-5328                                   |
|     At e-mail:  nmodena@unity.ncsu.edu                           | 
|                 samodena@csemail.cropsci.ncsu.edu                |
|                 [ either email address is read each day ]        |
|     By snail:   Crop Sci Dept, Box 7620, NCSU, Raleigh, NC 27695 |
+------------------------------------------------------------------+
         Lighten UP!  It's just a computer doing that to you.
OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
         
Newsgroups: bionet.info-theory
From: bchtantw@nuscc.nus.sg (Dr Tan Tin Wee)
Subject: Hypertext & DNA sequence annotation
Organization: National University of Singapore
Date: Mon, 13 Apr 1992 04:03:06 GMT

Being a newcomer to the field of hypertext, I would
appreciate very much if anyone could clue me in on references/
books on the annotation of DNA sequences using hypertext.
Are there DNA sequence databases that use hypertext, or
are relational databases hypertextual?

Thank you.

Tin Wee Tan
bchtantw
bchtantw@nuscc.nus.sg

-- 
    Tin-Wee TAN                        /  INTERNET: bchtantw@nuscc.nus.sg
    Dept of Biochemistry               /  BITNET:   BCHTANTW@NUSVM
    National University of Singapore   /  Tel:      (65)-772-3678
    Singapore 0511                     /  Fax:      (65)-779-1453
From: gapdrr@gsusgi2.gsu.edu (Daniel R T Rothman)
Newsgroups: bionet.info-theory
Subject: dspace question and relatedly, D
Date: 14 Apr 92 21:44:24 GMT
Organization: Georgia State University

tom schneider was gracious enough to forward several of his papers to me
recently. while perusing them, i had some questions, and some general thoughts.
most of what I comment on is taken from tom's paper "Theory of Molecular
Machines I. Channel Capacity of Molecular Machines" from J. theor. biol. 148.

BTW tom: this is going to be slightly different from what i sent you. i've
   invested a bit more thought in it since i wrote you.

first: tom states that dspace represents the degrees of freedom available
    to the components of a three-D system, where the coordinate origin is
    established at the systems center of gravity (cg). 
	normally, the degrees of freedom for this system would be calculated
    as 6n (where n is the number of components), representing the 3 spatial
    dimensions, and the 3 directions of orientation. these would then be
    appropriately constrained for the structure of the system.
	the paper states that the orientations of the components are not
    germaine, and thus may be ignored, yielding, by my calculations (6-3)n
    degrees of freedom. tom uses the formula 3n-6 for dspace.
	this formula appears to break down for small n ie 1 or 2. 3n-6 degrees
    of freedom in a 1 component system suggests that -3 coordinates are
    necesary to describe the system. i will yield that this result may be
    interpreted as saying that there is no information requisite to describe
    a system with one component, when a natural coordinate system is used.
        this dspace formula apppears to break down further with 2 system 
    components.  with 2 system components it yields 0 coordinates reqquired to 
    describe the system. it would appear to me that even with a natural 
    coordinate system, at least one coordinate is necesary. assuming the origin
    is cooincident with one component, andan axis is aligned with the other, 
    a displacement along that axis is still required.

second: it occured to me that the vectorization that is done to the
    informational degrees of freedom was very similar to the vectorization done
    in non-linear diff-eq's. i haven't done enough work with large non-linear
    systems to be authoritative about this, but was wondering if someone could
    offer more insights into this.
Newsgroups: bionet.info-theory
From: huh@wccf.mit.edu (GENE SIMON HUH)
Subject: Repeats and significance
News-Software: VAX/VMS VNEWS 1.41    
Keywords: statistics, repeat, significance 
Organization: MIT - Whitaker College
Date: Thu, 16 Apr 1992 23:34:00 GMT

Dear Netters,

     I have a question which seemed appropriate to ask in this newsgroup.  I 
have been studying a 1.5 kilobase sequence and have found no less than nine 
occurrences of a five-base repeat.  These repeats are more or less randomly 
distributed throughout the 1.5 kb sequence, although some clustering appears 
to be evident.  No other short sequences are repeated to this extent in this 
or any other randomized sequence (of similar length and base composition) that 
I have generated.  It seems to me that, given no other information, that this 
repeat is popping up much more frequently than expected by chance alone.

     So, my question is:  Is there a generalized formula for calculating the 
probability, given a sequence of length N, that *any* sequence of length X 
will exist Y times?  I wish to make the probability calculation without 
prebiasing myself with respect to the sequence of either the N-mer or the 
X-mer.  The calculation seemed simple at first to me; however, when 
considering factors such as the number of possible ways in which Y X-mers 
could be distributed throughout the N sequence, I get bogged down and end up 
with values of P which are either suspiciously high or -- *GASP* -- greater 
than unity, depending upon how I screw up the calculation ... ;-(

     I therefore appeal to you mathematical types out there: Is my intuitive 
grasp of statistical significance in sequence analysis way off?  Am I 
thinking too hard?  Too soft?  Am I a victim of "math anxiety"?  Am I a 
DOOFUS?  I would appreciate answers by e-mail (or posted here) to all but the 
most latter of these inquiries.  My apologies to everybody if a similar 
question has been debated recently here.

     But seriously, folks, I'm interested in knowing a rigorous formula.

Thanking you in advance,

Gene Huh
(huh@wccf.mit.edu)

Newsgroups: bionet.info-theory
From: gapdrr@gsusgi2.gsu.edu (Daniel R T Rothman)
Subject: seeking: crossover/mutation rates
Organization: Georgia State University
Date: Tue, 14 Apr 1992 17:49:10 GMT

i am seeking rates for some genetic operators (in occurences/copy/kilo 
base pair if possible). Specifically:
	mutation
	crossover
	insertion
	deletion
	inversion
	fragmentation (formation of new DNA strand)
	replication (formation of a new DNA strand)
and any others that are appropriate.

thanks
From: toms@fcs260c2.ncifcrf.gov (Tom Schneider)
Newsgroups: bionet.info-theory
Subject: Re: promoters for M. capricolum (was: Hyperplane separability)
Keywords: information theory, molecular machines, promoters, homosequences
Date: 5 Apr 92 18:25:25 GMT
Organization: NCI Supercomputer Facility, Frederick, MD

In article <brenner.702379747@husc10> brenner@husc10.harvard.edu (Steven Brenner)
writes:

|If cruciform structures are bad (a completely unfounded assumption at
|this point), then having aaaaaa or ttttt would be good.

Now I follow!

|I'm suggesting that the total "uncertainty loss" -- or information --
|for these promoters includes both that for (a) binding properly and
|(b) initating transcription.  The reasons I gave for why strings of
|t's and a's might be useful affect mostly the latter ra[th]er than the
|former. 

Indeed this may be the case.  Then there are two possibilities (at least):  1.
The two share information so that Rs/Rf is roughly 1.  2.  They don't share
information, so Rs/Rf is > 1.  If you had a way to figure out the number of
sites in the genome you could distinguish between these.  Unfortunately, this
is not easy - estimates for the number of promoters in E. coli don't even
exist.  (The estimate CANNOT be made from the patterns at the sites if the
whole idea is to compare it with Rs!)  It's not clear, for example, that there
aren't two (or even more) promoters for every gene in E. coli.

|I do have 50 bases after the position and the background is very near
|zero.

Interesting for a supposedly skewed organism.

| Unfortunately, I only have information from a decent number of
|sequences (based on where people started sequencing) for 5 bp upstream
|of the TTG.  The information content in that area appears possibly
|significant, but small.  (The heights are about 0.4 bits/site, but
|that's using Rsequence rather than Rsequence* [for skewed genomes].)

0.4 may not be significant if you don't have many sequences.

|>So: how did you pick these out?  
|
|These promoters were *all* of those listed in GenBank for this
|organism.  The way all but two they got in there is that original authors
|used the "hmmm, it looks like there's a promoter here based
|upon what I think a promoter looks like, and because its
|just a little ways upstream of the first gene I found."  In fact, the
|group which found something like 80% of those I listed gave no method
|at all by which they picked putative promoters.  Further, they didn't
|pick some others which seemed just as good to me (based on E. coli
|data) but weren't where the group expected them to be.

So it's really a big guess, and I wouldn't trust the results very much!

|This is my first attempt at trying to apply information-theory to
|sequences.  Thanks for the help in determining what's a reasonable
|deduction and what isn't!

see above :-)  The question is whether you are willing/able/interested in doing
some experiments to pin down a bunch of these promoters.  It's a lot of work,
and unfortunately I don't see an easy way to estimate Rf.

  Tom Schneider
  National Cancer Institute
  Laboratory of Mathematical Biology
  Frederick, Maryland  21702-1201
  toms@ncifcrf.gov