[The GelBuddy Project]

Reference Images and Markup files

We've provided a few reference images and markup files to demonstrate the capabilities and limitations of GelBuddy. Each example includes two .JPG files (IRDye 700 and IRDye 800 images) and one or more markup (.XML) files containing calibration and other markup information. To view any of these examples under GelBuddy, download the .XML and corresponding image files to a common directory, and use the menu command File/Open Gel Markup to load the markup file. The image files will be loaded automatically.
Example 1: Sample Markup

  • example1.xml
  • example1.7.jpg
  • example1.8.jpg

    This is the image and markup used to generate Figure 3 in the GelBuddy paper (Zerr and Henikoff 2005). This image contains two strong cleavage fragment signals (in lanes 26 and 31), two weak cleavage fragment signals (in lanes 58 and 63), and spurious fragments appearing at the same location in both channels (in lanes 3, 23, 66, and 94). Alternately viewing the 700 and 800 images (by clicking on the 700/800 on the toolbar or the right mouse button) allows you to readily distinguish cleavage fragments from artifacts. Also, by using the menu command Report/View Concise Report in Log Window you can determine that:
  • in all four cases fragment lengths add up to about 1520 bp.
  • lanes 31 and 63 contain co-migrating bands.

    Example 2: Calibration Test Case

  • example2.xml
  • example2.7.jpg
  • example2.8.jpg

    This image illustrates the maximum amount of "smiling" for which GelBuddy's calibration algorithm can compensate. Note that the included markup files specifies de-smiling lines only at the 200 and 700 bp calibration points, and that the calibration ladder deviates significantly from the actual image data near the top of the image. You can correct this problem by selecting the menu commands Options/Use 800 Channel Image Data for Calibration and Options/Calibrate Full Length Product Using Image Data and dragging the red "100%" marker at the left margin of the image to the position of the full length product (about 1300 bp in this case).

    More examples coming soon!