========= DNA / GUI ========= ***************************************************************************** Copyright 1989, 1990, 1991, 1992, 1993 Washington University. Permission to use, copy, modify, and distribute the DNA Graphical User Interface software and related documentation solely for noncommercial applications is hereby granted by Washington University free of charge, provided that the copyright notice "Copyright 1989, 1990, 1991, 1992, 1993 Washington University" appears on all copies of the software and that this permission notice appears in all supporting documentation. The name of Washington University or of any of its employees may not be used in advertising or publicity pertaining to the software without obtaining prior written permission from Washington University. WASHINGTON UNIVERSITY MAKES NO REPRESENTATION ABOUT THE SUITABILITY OF THIS SOFTWARE FOR ANY PURPOSE. IT IS PROVIDED "AS IS" WITHOUT ANY EXPRESS OR IMPLIED WARRANTY. ***************************************************************************** ---------- Background ---------- The DNA Graphical User Interface (DNA/GUI) is a software program for assisting in the quantitative analysis of 1D-electrophoretic-gel images. The software is written in C for UNIX workstations using the X Window System. This software does NOT include an image acquisition phase. Rather, the software begins with a digital image acquired from any one of a number of sources. An image might be acquired directly from a gel that has been stained with ethidium bromide and transilluminated with ultraviolet light or from an autoradiogram that has been illuminated with visible light. In a typical scenario, an image will be captured by a CCD camera and saved on a small computer attached to the camera; from there, the image would be sent over a local network to a graphics workstation for analysis and review by DNA/GUI. Results may be printed and forwarded to an electronic database. The digital image and quantitative results may be archived for later recall, perhaps to compare with other images. The DNA/GUI software features lane detection and delineation, band detection, and an image-normalization feature to remove or minimize image frowning. Results include lane-by-lane band mobilities and base-pairs. While much of the analysis is fairly automatic, a user is given ample opportunity to edit results so as to make saved information as accurate as possible. The editing is minimized in images of gels which are free of artifacts and for which reasonable attention was given to the gel-formation and electrophoresis experiment. Images of poorly-prepared gels require more editing. This version of the software also has some difficulty resolving very closely-spaced bands. The DNA/GUI system is described in a 1992 issue of BioTechniques: H.A. Drury, K.W. Clark, R.E. Hermes, J.M. Feser, L.J. Thomas, Jr., and H. Donis-Keller. "A Graphical User Interface for Quantitative Imaging and Analysis of Electrophoretic Gels and Autoradiograms", BioTechniques, vol. 12, No. 6 (June, 1992), pp. 892-901. A more detailed description may be found in the DNA/GUI User's Guide. This is found as a Postscript file with this software release. The DNA/GUI project began in 1989; at least four people contributed source code, but only one person remains. Source modules written by several people do not adhere to a uniform standard. Hopefully, this will eventually be improved. ------- Support ------- We will report bugs and enhancements in the "/pub/DNAGUI/news" file at the ftp site (wubcl.wustl.edu 128.252.122.2). We welcome suggestions for changes but cannot promise they will be implemented; rather, you are encouraged to tailor DNA/GUI for your needs. -------------------------------- Hardware / Software Requirements -------------------------------- DNA/GUI can be built to run on SUN SPARCstations and DEC DECstations running UNIX and the X Window System, including the X library, the Xt library, and the Xaw, Xmu toolkits. ------------------------------- Background for Building DNA/GUI ------------------------------- An executable "dui" will be built with "dui.sh" which references the following files and directories: Imakefile for creating a Makefile Dui.c an initializing/executive module Browsers a subdirectory of .c modules + Imakefile Callbacks < ditto > Colorbar < ditto > Display < ditto > Features < ditto > Files < ditto > Graph < ditto > Image < ditto > Normalize < ditto > ScreenSetup < ditto > Sizing < ditto > includes a directory of .h files dui.sh a script for building "dui" The following directories are not relevant to the build but are needed later (none of these directories need be located in the directory where dui is built): app-defaults a directory containing a file "DnaGui" which is an X11 resources file. HELP a directory of text files of helpful information which can be read from the program. PALETTE a directory of files containing color-mapping instructions; the program accesses these when there is a request to change the installed color table. GEL-FORMAT a directory of files accessed from the program. TEMPLATE-DEF'N a directory of files accessed from the program. The following files and directories are not relevant to the build but may be referenced later (they need not be located in the directory where dui is built): IMAGES a directory of images and image descriptors. man a directory of manual pages. copyright.h a copyright notice. USERS_GUIDE a directory containing a Postscript file of a User's Guide. See the file "release.notes" before building. ----------------------------- Directions for Building "dui" ----------------------------- (1) "sh dui.sh" This does the build and creates the executable "dui". (2) "vi app-defaults/DnaGui" OR "vi {pathname}/app-defaults/DnaGui" There are 4 lines near the front of the file for which absolute path names need be supplied to indicate the location of certain directories: HELP, PALETTE, GEL-FORMAT, TEMPLATE-DEFINITION . Edit these lines to supply an absolute path name. (3) "setenv XAPPLRESDIR app-defaults/" OR "setenv XAPPLRESDIR {pathname}/app-defaults/" This tells the X11 server where to look for the file which contains the X resources. (4) "dui" This runs the program. See the User's Guide for details. Consult the file "release_notes" for build problems. ------------- Image Formats ------------- DNA/GUI works best with images in the "import" format or with headerless (raw) files. The "import" format is described in the User's Guide or can be inferred from the .imp files in the IMAGES directory. A manual page for "import" is in the man directory. It will also accept images with 160- or 512-byte headers obtained from a Photometrics CCD camera. Images may be up to 1024 byte or short pixels in either direction. Images greater than 512 in either dimension are downsampled to fit in the 512x512 image-display space. If the program does not recognize the image size or format, it will prompt with an "odd-image" popup and ask a few leading questions; it may or may not be able to handle the image. If a non-import image can be used, an import version of the image is created; and subsequent processing deals with the import version. ------------ User's Guide ------------ A DNA/GUI User's Guide is available as a Postscript file (guide.ps) in the USERS_GUIDE directory. The Guide is about 40 pages. If you are unable to print Postscript files, a printed version of the User's Guide can be mailed to you; please send a check for $10.00 (to cover the costs of reproduction and mailing) payable to "Washington University", include your name and address, and mail to: Washington University Medical School Biomedical Computer Lab 700 S. Euclid Ave. St. Louis MO 63110 Phone: 314-362-2135 Fax: 314-362-0234 email: kwc@wubcl.wustl.edu Several of the figures are not included in the guide.ps file because some are quite large and take a long time to print. They are included as .eps files in the USERS_GUIDE/FIGURES directory. Paper copies of the figures can be mailed to those who have trouble printing the .eps files. --------------- Acknowledgments --------------- DNA/GUI was supported in part by the National Center for Human Genome Research under grants HG00331 (formerly National Institutes of General Medical Sciences Grant GM42972), HG00304, and HG00201; by the National Center for Research Resources Grant RR01380; and by the James S. McDonnell Foundation Grant 8724 to the Center for Genetics in Medicine at Washington University. Many of the ideas for adjusting the installed color table were taken from Michael VanHilst of the Smithsonian Astronomical Observatory's SAOIMAGE program project. Some ideas and code for a graph widget were adapted from the X11 Graph Widget Package by Upinder S. Bhalla and John Uhley of the California Institute of Technology. A full copy of their copyright notice may be found in the file "Graph.doc" in the Graph subdirectory.