Double Digester Version 1.1beta2

Double Digester ("DD") 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 alpha release in August 1992 and a first beta release in early 1993. 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 (up to SunOS 4.1.3), HP workstations (older Motorola machines running HP-UX 7.0) and Macintosh computers (MacOS System 6 or 7.0/7.1).

The most current release of Double Digester is maintained for anonymous ftp access on ftp.cs.yale.edu (128.36.0.36). It is also available at other sites, which we will attempt to update when known to us.

This release changes the distribution format: the data files and program files are separated, and no separate directory is created for them both to reside in. Also, the HP-UX version has been added, and named so as not to cause problems on systems with 14-character limits on filenames. The distribution directory now contains:

   README                   (this file)

   data.sea.hqx             Mac data folder (binhexed self-extracting archive)
   data.tar                 Sun & HP data directory (tar file)

   double-digester.sea.hqx  Mac program (binhexed self-extracting archive)
   double-digester.Z        Sun program (compressed executable file)
   dd-hpux70.Z              HP program (compressed executable file)

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

Use binary mode transfer for data.tar, manual.dvi and files whose names end in ".Z"; use ascii mode for the other files.

The 28-page draft manual is written in TeX, and is provided in postscript, dvi and text formats. The text form of the manual is also part of the program itself (via a "Help" button). Note that the manual has not yet been revised to reflect the slight change in distribution format.

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@yale.edu
Senior Research Programmer                 larry_wright@qm.ycc.yale.edu
Medical Informatics Center       BITNET:   wright-lawrence@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: 1.1beta to 1.1beta2

This is a minor, maintenance release, covering three problems:

SunOS 4.1.3 changed filename handling in ways that made DD's "Digests" menu mistake files for directories; this is fixed. The previous version works fine up to SunOS 4.1.2. A Solaris version will be released once I have the necessary OS and Lisp software to create it (date unknown).
Linear map drawings, once calculated and drawn, would wrongly rescale if gel data was later revised; they now retain the scaling for the fragments they map.
The Macintosh version had occasional problems with one or more menus on the Mac menubar becoming inactive, in one instance causing a system crash on a Mac PowerBook. This appears to be a bug in the Mac CLIM implementation; the current DD does not manage to stop the deactivation, but restores all menus at the point they are selected.

The HP-UX version was also added.

Changes: 1.0alpha to 1.1beta

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 files need 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 create "Double Digester" and 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. The current release has been run briefly under System 6.0.7, but has only been tested extensively under System 7. If you have problems with normal running of DD, try running it without any desk accessories active.

Sun Specifics

The program file needs to be uncompressed, probably using the command:

        uncompress double-digester.Z

The data directory and files need to be extracted from the tar file:

        tar xvf data.tar

If you already have versions you don't want overwritten, be sure to do this in a separate directory.

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, both running SunOS 4.1.2, as well as (very briefly) on a Sparc10 running SunOS 4.1.3. 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 note on X and Suns: many Suns aren't configured to be able to display on their own screen under X. You can type "xhost +" at your shell prompt to remove all restrictions, but at some risk to your computer's security. For greater security, you should set your DISPLAY environment variable (e.g.

        for csh: setenv DISPLAY `hostname`:0.0
        for sh:  DISPLAY=`hostname`:0.0
                 export DISPLAY

) and then type:

                 xhost `hostname`

(all of which amounts to saying "I want to display on my own screen, and it's alright."). If you are running DD from a remote computer, you should set the remote shell's DISPLAY for the machine you want to view it on, and invoke xhost from a shell on your local machine giving the name of the remote computer (type "man xhost" for more information).

HP-UX Specifics

The 1.1beta2 release adds an HP-UX version, named dd-hpux70. It has been compiled and run on an HP9000/370 with 16MB of memory running HP-UX 7.0, using Lucid Common Lisp and CLIM under X11R4 with Motif. Creating and testing this version is at the limits of our aging hardware's abilities, but for the moment was the simplest way of testing System V behaviors increasingly appearing in SunOS.

Note that this is a Motorola 68030 machine running an old version of HP-UX -- this version of DD may well not work under newer releases of HP-UX or HP's new RISC architecture, and it may not be maintained in future releases of DD, but will perhaps be of use to some users.

Apart from being slightly smaller, the instructions and description for the Sun version should apply.