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Double Digester restriction mapping program announcement

Lawrence Wright wright-lawrence at cs.yale.edu
Mon Feb 15 11:47:58 EST 1993


Double Digester (DD), an interactive, graphical computer program to help 
build restriction maps from double digest data, is now available via 
anonymous ftp.

DD attempts to provide full and realistic representation of experimental 
uncertainties and map ambiguities, with interactive user control over 
all values used and hypotheses to be tested.  Data can be entered via
mouse, keyboard or text files.  Raw data are critiqued for discrepancies
in lane molecular weights and fragment counts, with suggestions as to
possible problems.  DD normally completes its initial calculations in a
few seconds, or at most minutes, either making available all possible 
maps in graphical format ranked by the goodness of fit between fragments,
or reporting that map interpretations are either impossible or too numerous
and ambiguous to be worth calculating without additional constraints.

The current version runs on both Macintosh and Sun computers, and has 
been tested in several labs at various sites.  We have found it to be
reliable in its results, and reasonably robust, but this should
nevertheless be considered a beta release.  DD also requires substantial
amounts of memory and disk space (see below).

DD is available from ftp.cs.yale.edu (128.36.0.36), with username 
"anonymous" and your email address as password.  To get to the DD 
directory, enter "cd /pub/double_digester".  Be sure to follow the
instructions below concerning which files need to be transfered using
binary mode, and which using ascii.

Below is a copy of the "README" file available there, which gives details
about the DD distribution files and system requirements.

-----------------------------------------------------------------------

                      Double Digester v1.1beta
                      ========================
                          15 February 1993

Double Digester is a program designed to help researchers in molecular
biology assemble restriction maps of DNA using data from double digest
experiments.  This is a second, beta version, following the limited 
release in August 1992.  It has been used in several laboratories, 
and should give helpful and reliable results, but is still being tested
and refined, and has a few rough edges.  Feedback and suggestions would 
be most welcome.

This is an interactive, graphics-based program.  It is written in
Common Lisp using the Common Lisp Interface Manager (CLIM), and is
currently available for Sun Sparcstations and Macintosh computers.
The 30-page manual is written in TeX, and is provided in postscript,
dvi and text formats -- you will probably only want one of these.
The text form of the manual is also part of the program itself, 
via a "Help" button.

The other files in this directory are:

   double-digester.sea.hqx  Mac version (binhexed self-extracting archive)
   double-digester.tar.Z    Sun version (compressed tar file)

   manual.dvi               DD Manual (dvi format)
   manual.ps                DD Manual (postscript format)
   manual.txt               DD Manual (ascii text format)

IMPORTANT NOTE: Use binary mode transfer for double-digester.tar.Z and 
manual.dvi, and ascii mode for the other files.

Additional details on changes, size, machine requirements, etc., are
provided below, as well as in the manual.  Please send questions, 
comments and suggestions to:

Larry Wright                   INTERNET: wright-lawrence at yale.edu
Senior Research Programmer               larry_wright at quickmail.yale.edu
Medical Informatics Center     BITNET:   wright-lawrence at yalecs.bitnet
3 TMP - Anesthesiology         UUCP:     yale!wright-lawrence
Yale School of Medicine        FAX:   (203) 737 2243, 785 6664
New Haven, CT 06510-3333       Phone: (203) 785 7453, 785 2802


Changes Since the August 1992 Version
-------------------------------------

Double Digester ("DD") has been made much more robust and simpler to use,
while also being extended in various ways.  Changes of particular interest
are:
     * DD has a simplified, 1-window layout, better integrated with 
       native X and Macintosh window managers.

     * Graphical data entry with a mouse makes it easy to enter data 
       working directly from a gel photo.

     * All digests are automatically critiqued for possible issues
       concerning fragment counts and total material per lane.

     * Input data is much more carefully screened, querying the user
       to resolve ambiguities and reporting on things DD can't interpret.

     * Common errors (such as attempting to write to a file without 
       having write permission) are generally caught and reported, and
       serious errors (such as deciding to continue on a large problem
       and running out of memory) are normally recovered from.

     * File names, default directories, etc. are all handled more flexibly
       and robustly.

     * An entirely new manual has been written by John Reinitz, and is
       accessible online using a detailed table-of-contents menu (or
       simply browsing).


Macintosh Specifics
-------------------

The distribution file needs to be "unbinhexed", using one of the programs 
(such as CompactPro and Stuffit) which do this.  The result will be a file 
ending in ".sea", short for self extracting archive.  Click on this to 
install DD, including a folder called "data" which contains files with 
sample double digest and gel standard data.

The DD application occupies about 2.8 MB of disk space, and requires
about 5 MB of memory to run.  If you give DD more memory (using
"Get Info" from the "File" menu to change the "Current size"
setting before you run DD), it will be able to deal with more and/or
harder digests before it runs out of memory.  If this requires running
in virtual memory, however, DD will run very much slower than if it
can run entirely in built-in memory (select "About This Macintosh"
from the Apple Menu to find out about your machine).

The current version of DD has been tested on the following types of
Macintosh: MacIIx, MacIIfx, Quadra and PowerBook.  It has run on
monochrome, grayscale and 8-bit color displays.  It should work
under System 6, but have only tested recent revisions under System 7.
If you have problems with normal running of DD, try running it without
any desk accessories active.


Sun Specifics
-------------

The distribution file needs to be uncompressed and untarred.  The 
simplest way to do this is:

        zcat double-digester.tar.Z | tar xvf -

which will create a directory called "dd-1.1beta", containing the 
application "double-digester" and a "data" directory with sample 
double digest and gel standard data.

The DD application occupies about 12MB of disk space, and uses about
24 MB of memory (physical or swap) to run.  You will probably need at
least 40 MB of swap space, preferably 50 MB or more, to allow for
windowing and other software on your system.  If you need more swap
space, you or your system administrator might want to consider using
swap files as an alternative to reconfiguring disks (cf. man pages on
mkfile and swapon).

The current version of DD has been tested on a Sun SparcstationII
running OpenWindows 3.0 with 32 MB of memory, and on a Sparcstation ELC
with 24 MB of memory running OpenWindows 2.0.  Remote display on a
HP9000/370 workstation using the Motif window manager, and on a Macintosh
running a MacX server, has also been tested.  A previous version was
also built and run on an HP9000/370 with 16MB of memory, using Lucid
Common Lisp and CLIM under X11R4 with Motif.




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