GDE Resources

GDE is a graphic interface for launching programs for nucleic acid and protein sequence data, and even for molecular marker data. It was written by Steven Smith [Smith et al. (1994) Comp. Appl. in Biosciences 10:671-675], and has been recently updated by Eric Linton of Michigan State University. The strength of GDE is the ease with which new programs can be added to menus. GDE hides the details of running each program, such as conversion of files from one format to another, greatly simplifing the use of programs in a unified graphic interface. GDE is  used as the key component of the BIRCH bioinformatics platform.

BIRCH - GDE Tutorials

go to tutorials

Binaries, Source and Documentation

• macgde1.8.5.tar.gz - This version fixes some of the more serious problems with the old GDE. The Linux version now correctly reads in circular sequences from GenBank files. As well, bugs that caused GDE to crash when cutting long regions of sequence have been fixed. Also, the original GDE binaries, compiled in 1993, crashed under Solaris 10. This problem was corrected simply by recompiling on a modern Solaris system. The gzipped tar archive contains the full source code for macgde1.8.5, slightly modified by Brian Fristensky to compile on Solaris and Linux. It also contains the compiled binaries for each platform.  (May14, 2005).
  
• makemenus - Python script for automated creation of .GDEmenus files
  (Brian Fristensky, University of Manitoba) makemenus.tar.gz
• GDE Bugs and Workarounds

• GDE 2.2 Manual (PDF)
• GDE 2.2 Source Code - gde2.2.src.tar.Z
  
• gde2.3 - GDE 2.3 Binaries (Solaris-Sparc) - This version was distributed in 1994 as a binary fo r Solaris. Source code was never distributed.

Other GDE Sites

• BioAfrica - GDE for Linux Tulio de Oliveria, Univ. of Natal
• GDE2.2 for Linux, compiled by Dr. Ernst Molitor, Univ. of Bonn
  
• MacGDE - GDE for Macintosh OSX (Eric Linton, Michigan State Univ.)