HDTenEightyP/NetNews huggingface dataset:
From: gardner@zinc.med.yale.edu (Kevin Gardner)
Subject: Re: Secondary structure assignment
Followup-To: bionet.software
Summary: How about Ramachandran plots? 
Keywords: protein secondary structure/Ramachandran plot
Organization: Dept of Mol. Biophysics & Biochemistry, Yale University
Date: Thu, 13 Aug 1992 16:06:37 GMT

	A quick and dirty approach: Ramachandran plot...I have Fortran
code available for taking .pdb files and generating said plots from
these coordinates.  It might not be as sophisticated as you're looking
for, but it would at least allow some classification.
-- 
*************************************************************************
Kevin Gardner
Yale University Dept. of Molecular Biophysics and Biochemistry
Internet: gardner@zinc.med.yale.edu      Bitnet: gardner@yalemed
From: pgil@TEMIN.LANL.GOV (Paul Gilna)
Newsgroups: bionet.software
Subject: Re: Genbank services?
Date: 18 Aug 92 15:09:45 GMT
Distribution: bionet


From BIOSCI-REQUEST@genbank.bio.net Tue Aug 18 08:57:05 1992
Subject:      Genbank services?
To: Bio-soft@genbank.bio.net
Content-Length: 829
X-Lines: 15

(stuff about retrieval/search services deleted)

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


The group at LANL, currently responsible for all data entry of sequence
data under the present GenBank contract will continue to be responsible
for sequence data submission under a formal agreement with NCBI. Our
role will be exclusively in the solicitation and acquisition of
submitted data (not necessarily geographically limited to north
america), which today represents over 95% of our workload.

We will pass all data to NCBI for distribution.


--paul
From: cptully@med.unc.edu (Christopher P. Tully)
Newsgroups: bionet.software
Subject: Re: Screen Capture
Date: 17 Aug 92 20:20:03 GMT
Distribution: bionet
Organization: UNC-CH School of Medicine

In article <01GNKP7T67ZO8WWAXW@beloit.edu> JONESBB@BELOIT.EDU writes:
>
>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
>

 
I don't know what version of mac system you're using, but I have done COLOR 
screen captures in a Mac IIsi amd Mac IIci running system7 with no trouble at
all.  I believe the key sequence is Command-Shift-3.  As for capturing the 
whole screen, so waht?  Just load the image into a good paint editor and cut
out the section that you want.

Chris Tully
cptully@med.unc.edu
Newsgroups: bionet.software
From: RODRIGOL@BIOMED.UIO.NO (Rodrigo Lopez)
Subject: RE: sequence analysis software
Organization: The Norwegian EMBnet Node
Date: Fri, 21 Aug 1992 15:30:53 GMT
X-News-Reader: VMS NEWS 1.22

In <9208211457.AA00109@genbank.bio.net> WAGNERF@BRUNB.BITNET writes:

> 
> 
>        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

The above information is correct though some pointer to the actual
place could be usefull.

*The netserver at embl:

netserv@embl-heidelberg.de 

this is mail server, send a message containing the world help and 
you will get a message with an introduction to the system.

*The Finish EMBnet node ftp server:

nic.funet.fi

Try this one from Archie!

*The Swiss EMBnet node ftp server:

ftp.unibas.ch

*The Univeristy of Indiana ftp server:

bioftp.indiana.edu

*The Norwegian EMBnet node ftp server:

pcpub.uio.no

Just to mention a few.

R:-)
From: b44340@ACHILLES.CTD.ANL.GOV (A. Milosavljevic)
Newsgroups: bionet.software
Subject: server for identification of human repetitive DNA
Date: 20 Aug 92 18:58:53 GMT
Distribution: bionet



Identification of Human Repetitive DNA Elements via Electronic Mail

                    Aleksandar Milosavljevic
            Biological and Medical Research Division
                   Argonne National Laboratory
                  Argonne, Illinois 60439-4833

                           Jerzy Jurka
         Linus Pauling Institute of Science and Medicine
                       440 Page Mill Road
                   Palo Alto California 94306

  An electronic mail server at pythia@anl.gov has been installed that
performs two kinds of tasks:

(1) Identifies occurrences of around 50 known repetitive elements in human
genomic DNA sequences.

    The regions that are identified as occurrences of repetitive elements
  in the incomming DNA sequence are aligned against the repetitive
  element. The alignments are then mailed back to the sender.

(2) Identifies subfamily membership of Alu sequences

    The incoming sequence is first aligned against the Alu consensus
  sequence and then it is identified as belonging to one of the
  subfamilies of Alu sequences based on the bases in a set of diagnostic
  positions.

  To obtain more detailed information on the current availability of
the services and on examples of its use, send a message with a word
"help" in the "Subject"-line to the internet address pythia@anl.gov.

  The server is still in the testing phase, so please report any
problems.  We would also appreciate your comments on possible
improvements of the server. Send your comments to pythia-admin@anl.gov.

  Work supported by the Grant DE-F603-91ER61152 from the U. S.
Department of Energy, Human Genome Program, and in part by the U.S.
Department of Energy, Office of Health and Environmental Research,
under Contract No. W-31-109-ENG-38.

  The U. S. Government retains a nonexclusive, royalty-free license to
publish or reproduce the published form of this contribution, or allow
others to do so, for U. S. Government purposes.


Newsgroups: bionet.software
From: gilbertd@fly.bio.indiana.edu (Don Gilbert)
Subject: IUBio archive update
Organization: Biology, Indiana University - Bloomington
Date: Thu, 13 Aug 1992 23:29:26 GMT


This is an update notice of new information available at IUBio archive,
either thru anonymous ftp or using Internet Gopher to ftp.bio.indiana.edu. 

Additions to IUBio Gopher hole include ........................
New ways to search the IUBio information 
  IUBio-Software+Data/
     Search all IUBio archive ReadMes, Docs & Help files <?>
  Network-News/
     Search all Bionet News at IUBio archive <?>

Gopher links to various biology FTP archives:
   Other-Bio-Gophers-Etc/FTP-Archives/
      National Center for Biotechnology Information FTP server/
      Genbank at Intelligenetics FTP server/
      Protein Data Bank FTP server/
      PHYLIP phylogeny package FTP server/
      Ribosomal Database Project FTP server/
      GDB Human Genome Data FTP server/


New archive files include.........................................
...size...date.....path/name................
  126795 Jul 29 ./biology/ibmpc/fastmap.zip   -- popgen. lod scores
  240186 Aug  5 ./biology/ibmpc/pedraw14.zip  -- pedigree drawing
   62739 Aug  7 ./biology/mac/bio_ess.hqx 

   62180 Aug  2 ./biology/quantgen/quercus/qg3.p   -- quantitative genetics
   69723 Aug  2 ./biology/quantgen/quercus/qg6.p 
   14895 Aug  2 ./biology/quantgen/quercus/qg3.6.doc 
    1161 Aug  2 ./biology/quantgen/quercus/Quercus.readme 

  268640 Jul 21 ./fly/flylist.txt                 -- drosophila data
   92759 Aug 13 ./fly/P_list.txt 
    3469 Jul 23 ./fly/new_stocks.txt 
  114815 Jul 20 ./fly/drosophila-phylogeny.hqx 

   85978 Jul 16 ./molbio/ibmpc/ramha1.exe         -- random cDNA mutagenisis
  298583 Jul  7 ./molbio/mac/aligner.hqx          -- sequence aligner
  802811 Jul  7 ./molbio/mac/dnastack.hqx         -- sequence editor+
   50615 Jul 20 ./molbio/mac/hyperpcr.hqx         -- pcr calculator
  258532 Aug 13 ./molbio/mac/gbsearch-ncbi.hqx    -- genbank search by mail
  513583 Aug  4 ./molbio/loopdloop/loopdloop.hqx  -- rna fold drawing

   26105 Jul 14 ./util/mac/sdsc_imagetyper.hqx 
  138409 Aug 13 ./util/wais/wais-sources.tar.Z 
  373094 Jul  9 ./util/gopher/gopherapp/gopherapp.hqx 
    3902 Aug  7 ./util/gopher/good.summary 
-- 
Don Gilbert                                     gilbert@bio.indiana.edu
biocomputing office, biology dept., indiana univ., bloomington, in 47405
Newsgroups: bionet.software
From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert)
Subject: Mac Hypercard stack for Genbank search at NCBI
Organization: Biology, Indiana University - Bloomington
Date: Thu, 13 Aug 1992 15:12:57 GMT


Version 3 of Genbank Search stack for Macintoshes is 
now available.  This version sends requests to
the BLAST search server at ncbi.nlm.nih.gov.

The GenBank Search is a Macintosh Hypercard stack for 
interacting with the computer services from Genbank
at NCBI.  These free search and fetch services thru 
electronic mail include:

* Searching of the current GenBank, or several other databanks,
  for similarities with a query nucleic acid or protein sequence 
  of yours, and

* Retreival of a sequence in the current GenBank by keywords,
  locus name or accession number.  Several other databanks are 
  also available for retreival.  

To use this GenBank Search stack, you must have:
--  a Macintosh with Hypercard version 2, and Mac System 6.0.5
    or later,
--  that Mac needs to be connected to the national Internet 
    network, thru an Appletalk or Ethernet cable,
--  that Mac must have the MacTCP communications software, 
    and Hypercard version 1.2 or later, from Apple Computer,
--  you must have a valid Internet return mail address. 

This stack includes a simple sequence editor, so you can 
enter your sequence directly here, and it includes features 
to read from disk a variety of sequence formats. 

GenBank Search stack is available via anonymous FTP or
Internet Gopher to ftp.bio.indiana.edu, in folder
/molbio/mac as gbsearch-ncbi.hqx.

-- Don

-- 
Don Gilbert                                     gilbert@bio.indiana.edu
biocomputing office, biology dept., indiana univ., bloomington, in 47405
From: wmelchior@NTBTOX.NCTR.FDA.GOV ("Bill Melchior, NCTR/FDA")
Newsgroups: bionet.software
Subject: Object oriented programming
Date: 19 Aug 92 18:36:59 GMT
Reply-To: wmelchior@NTDOC.NCTR.FDA.GOV
Distribution: bionet

Last week there was a thread on OOP -- object oriented programming.

I like to try to keep up with what's going on even though I'm not a
programmer.  For folks like me, could someone who knows something
about the field make a stab at a brief, simple definition of 
"object oriented programming"?  I'd like to know what it is, not
what language (C++, ?) is used; or maybe it's defined by what it is NOT?
  
Thanks.
________________________________________________________________________________
The opinions stated are mine, not those of NCTR or its sponsoring organizations.
  
Bill Melchior                                ||   "You have lawyers the way
National Center for Toxicological Research   ||    other people have mice."
Jefferson, AR  72079                         ||
(501) 543-7206                               ||   -Kenneth Duncan, English
                                             ||    Health & Safety Executive,
WMELCHIOR@NTDOC.NCTR.FDA.GOV                 ||    to US regulators
From: lpcasson@phoenix.Princeton.EDU (Lawrence P. Casson)
Subject: Re: gcg
Originator: news@nimaster
Organization: Princeton University
Distribution: bionet
Date: Thu, 13 Aug 1992 23:15:29 GMT

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


Newsgroups: bionet.software
From: mathog@seqvax.caltech.edu (David Mathog)
Subject: Sequencing survey
News-Software: VAX/VMS VNEWS 1.41    
Organization: Division of Biolgy, CALTECH
Date: Fri, 14 Aug 1992 01:18:00 GMT

We're thinking about setting up a sequencing facility for the division and
are now in the process of collecting feedback from people who have
experience in this area.  If the shoe fits, please take a few minutes to fill
out this questionnaire, if not, no need to reply.

Thanks in advance for your time,

David Mathog
mathog@seqvax.caltech.edu
manager, sequence analysis facility, biology division, Caltech




Background:

We currently have a central facility for analyzing sequence, but no
equivalent facility for generating it.  We would like to provide a
sequencing service that works something like this: 

 LAB ->  $$$ + DNA  -> Facility (shortest time possible) -> Sequence -+
  ^                                                                   |
  |                                                                   |
  +-------------------------------------------------------------------+

Each lab would do its own DNA preps, but all of the actual sequencing
reactions and reading of the sequences would be done by the central 
facility.  The final sequences would be deposited directly into the
end users' directories on our sequence analysis facility's computer.

A survey of the division indicated that roughly 2500 sequencing
(radioactive) gels are run each year. 



Questions:

1.  What has been your experience (positive and negative) with the 
various commercially available fluorescent sequencers?

2.  Which of the various types of fluorescent sequencing reactions 
have you tried and how well have they worked?

3a.  Assuming that the incoming DNA just needs to be pipetted into the
sequencing reactions how much manpower are we going to need to handle the
expected workload? 

3b.  How many machines will it require?

3c.  We'd like to turn around the average job in a day or less, is
this a reasonable goal?  What sort of schedule do you run?  How much 
do you charge/sequencing reaction (if you charge)?

4.  What software do you use to analyze the traces, how well does 
it work, and what does it cost?

5. If you've got the numbers - what does it REALLY cost you to
convert a single DNA sample to sequence?  If possible, break it down
reagents/overhead/labor/machinery/etc.  Also, if you've got the
numbers, what did it used to cost you to sequence with 35-S/32-P?  (We
will need at least an estimate of these numbers to justify the expense
of setting up the facility). 

6. If you ever used one of the commercial sequencing services how much
did it cost, what was their turn around time, and were you pleased
with the results? 

7.  If _you_ were going to set up a facility like this, how would you do 
it?

8.  Any other comments or suggestions?

Thank you for filling out the form!
From: bashford@scripps.edu (Don &)
Newsgroups: bionet.software
Subject: Re: Object oriented programming
Date: 19 Aug 92 23:48:59 GMT
Distribution: bionet
Organization: The Scripps Research Institute, La Jolla, CA, USA

>>>>> In article <0095F555.4A4EEF00.243@NTBTOX.NCTR.FDA.GOV>, wmelchior@NTBTOX.NCTR.FDA.GOV ("Bill Melchior, NCTR/FDA") writes:


Bill> For folks like me, could someone who knows something
Bill> about the field make a stab at a brief, simple definition of 
Bill> "object oriented programming"?  I'd like to know what it is, not
Bill> what language (C++, ?) is used; or maybe it's defined by what it is NOT?

Here are some paraphrases and quotes stolen from Chapter 1 of Bjarne Stroustrup's
"The C++ Programming Language" (2nd ed.).

The original programming paradigm is Procedural Programming:

   Decide which procedures you want; use the best algorithms you can find.

Languages like C and Fortran provide functions or subroutines as
the basic building block.  But as programs became larger people began
to shift their focus towards the orginization of data.  *Modules* were
built which contained related procedures with the data they operate on.
Thus we have the Modular Programming Paradigm:

   Decide which modules you want; partition the program so that data
   is hidden in modules.

This kind of programming is possible in C and supported directly in
Modula-2.  For example, if you want a stack you can put static pointers
to it in a stack.c file along with functions for pushing, popping, etc.
But what if you want to have more than one stack?  Do you need to
write stack_a.c and stack_b.c defining functions like pop_a, pop_b, etc.?
Yuk!  What you really need is the ability to craft a "stack" data
type and then declare the existence of as many stacks is you like.
This leads to the Data Abstraction Paradigm:

   Decide which types you want; provide a full set of operations for
   each type.

This can be done in C++.  But you may find that you have alot of data
types that are similar but not the same and you are duplicating alot
of effort in providing the "full set of operations for each type".
You would like to be able to define a base type that has the features common
to the similar types, then impliment the particular types by
declaring that they inherit the features of the base type and then adding
the details of that particular type.  This is the Object Oriented Paradigm:

   Decide which classes (types) you want: provide a full set of operations
   for each class; make commonalities explicity by using inheretence.

This is supported in C++.
From: LEARN@UCRVMS.BITNET
Newsgroups: bionet.software
Subject: RE: NCBI retrieve
Date: 20 Aug 92 00:38:00 GMT
Distribution: bionet

In <9208191834.AA17577@genbank.bio.net>  mathog@seqvax.bio.caltech.edu
(David Mathog) writes:

>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.

I played with the retrieve service last week and I agree with David heartily.
Perhaps I am spoiled by the GenBank IRX server, and I would always prefer an
interactive search, but it seemed like a real pain in the neck to use.  David's
suggestions for separate search and retrieve services is an excellent start to
improve the NCBI server.  The "# of lines" information is crucial.  Also the
SEPARATE option for the retrieve service is an important addition.

Jerry Learn
From: oberste@fcs260c.ncifcrf.gov (Oberste)
Newsgroups: bionet.software
Subject: Re: EPS from Unix to Mac (Was Re:gcg)
Date: 20 Aug 92 17:02:19 GMT
Distribution: bionet
Organization: Frederick Cancer Research and Development Center

In article <9208142333.AA19863@genbank.bio.net> mangalam@SALK-SC2.SDSC.EDU writes:

<much stuff deleted>

>   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.

Get HP2PICT from ftp.bio.indiana.edu. It will convert an HPGL file to PICT
format which can then be edited in your draw program (we use SuperPaint with
good results). Each object in the original HPGL file is rendered as an 
individual object in the PICT file, allowing editing of individual elements.


-- 
Steve Oberste                            Internet: oberste@ncifcrf.gov
LCMS, PRI, NCI-FCRDC
PO Box B                        "Never put off until tomorrow that which
Frederick, MD 21702-1201            you can do the day after tomorrow"
From: ness@aecom.yu.edu (Seth Ness)
Newsgroups: bionet.software
Subject: (none)
Date: 20 Aug 92 14:41:23 GMT
Distribution: bionet

signoff seth ness

-- 
 Seth L. Ness                        Ness Gadol Hayah Sham          
 Ness@aecom.yu.edu
From: THOMPSON@JAGUAR.CSC.WSU.EDU (Steve Thompson: VADMS genetics)
Newsgroups: bionet.software
Subject: ProfileScan questions
Date: 12 Aug 92 20:00:28 GMT
Distribution: bionet

Hi Netlanders and Profile users--

I apologize for not posting regarding my profiles for a while.   I've been
involved getting ready to teach this Fall, taking a few vacations, and have
spent the last two weeks at the Woods Hole MBL Molecular Evolution workshop.

Several people have asked how to update the .fil file that GCG's ProfileScan
uses to include other profiles in its search strategy.  Unfortunately I do NOT
know how Dr. Gribskov generated the cutoff values in this file.  I'm sure a
very careful reading of his references would cull out such knowledge but I have
not read them with this purpose in mind.  If Michael or some of the GCG
development people read this, maybe they will be courteous enough to tell us
all an easier method than trying to figure it out for ourselves.  Regardless, I
will summarize the responses that I collect regarding this question and repost
in a couple of weeks.

I also expect to continue the development work on still more profiles, however, 
I do have a teaching load this coming fall, so they will not be quick in
coming.  Thanks for all the encouraging words that I have gotten in this
project and some day I may even get the annotation of the existing profiles in
our library finished.

							Steve Thompson

			presently (for two more days) thompson@evol5.mbl.edu

but usually at:

                              Steven M. Thompson
            Consultant in Molecular Genetics and Sequence Analysis
VADMS (Visualization, Analysis & Design in the Molecular Sciences) Laboratory
           Washington State University, Pullman, WA 99164-1224, USA
          AT&Tnet:  (509) 335-0533 or 335-3179  FAX:  (509) 335-0540
                  BITnet:  THOMPSON@WSUVMS1 or STEVET@WSUVM1
                   INTERnet:  THOMPSON@wsuvms1.csc.wsu.edu
Newsgroups: bionet.software