MicroArray Genome Imaging & Clustering Tool

Developed at Davidson College by Laurie Heyer and her undergraduate students.

• Free software with open source
• Works on all platforms (Mac, PC, Linux, UNIX)
• From spot finding through clustering and mining

Paper: MAGIC Tool: Integrated microarray data analysis (Bioinformatics, 2005)

Supplementary Figures: Gridding, Segmentation algorithms, Segmentation browser, Selection criteria

Download MAGIC Tool software

• BUGS: Please report bugs to Laurie Heyer
• SUPPORT: MAGIC Tool software is provided without warranty or guarantee of support. However, NSF funding allows us to provide limited support via email to:
  magictool "dot" help "at" gmail "dot" com

Documentation

• User's Guide (1.9 MB PDF file)
• Herramienta MAGIC Guía del Usuario (3.3 MB PDF file)
• Instructor's Guide with additional math background for understanding data analysis (2.1 MB PDF file)
• NEW Flash Tutorials - animations illustrating how to use MAGIC Tool (More coming soon!)

Download small sample files (1 grid and 4 grid) for practice

Download BIG tiff files for advanced practice

• Whole yeast genome (Y01 Version from Stanford - provided by Laura Hoopes and Jessica Brown)
  • red Pomona097_w685.tif (12.4 MB .tif File)
  • green Pomona097_w595.tif (12.4 MB .tif File)
  • Jpeg version for orientation (300 kB .jpg File)
• Whole yeast Genome (ISB Version - provided by Laura Hoopes and Allen Kuo)
  • red Hoopes_635_nm.tif (9.8 MB .tif File)
  • green Hoopes_532_nm.tif (9.8 MB .tif File)
  • Jpeg version for orientation (1 MB .jpg File)
  • Whole yeast Genome (ISB Version - provided by Mary Lee Ledbetter)

Joe DeRisi et al. diauxic shift experiment (including tiff files, courtesy Pat Brown from Stanford University)

DeRisi et al. 1997 reprint (PDF File)

Dry-Lab Instructions to Explore DeRisi Experiment

Jpeg version for orientation (jpg File)

Compressed set of all DeRisi tiff files

Individual DeRisi tiff files:

• 1303_ch2_OD014_red.tif (2 MB .tif File)
• 1303_ch1_OD014_green.tif (2 MB .tif File)
• 1310_ch2_OD046_red.tif (2 MB .tif File)
• 1310_ch1_OD046_green.tif (2 MB .tif File)
• 1311_ch2_OD080_red.tif (2 MB .tif File)
• 1311_ch1_OD080_green.tif (2 MB .tif File)
• 1312_ch2_OD180_red.tif (2 MB .tif File)
• 1312_ch1_OD180_green.tif (2 MB .tif File)
• 1302_ch2_OD370_red.tif (2 MB .tif File)
• 1302_ch1_OD370_green.tif (2 MB .tif File)
• 1309_ch2_OD690_red.tif (2 MB .tif File)
• 1309_ch1_OD690_green.tif (2 MB .tif File)
• 1313_ch2_OD730_red.tif (2 MB .tif File)
• 1313_ch1_OD730_green.tif (2 MB .tif File)

 

Download gene lists and Information Files

• 1 grid of 12x24 spots - yeast genome (.txt File) (excel version with column headers)
• 4 grids of 12x24 spots - yeast genome (.txt File) (excel version with column headers)
• 4 horizontal girds of 23 x 24 spots - yeast genome (.txt File) (excel version with column headers)
• Pomona Y01 gene list (.txt File) (excel version with column headers)
• Hoopes ISB gene list (.txt File) (excel version with column headers)
• DeRisi gene list (.txt File) (excel version with column headers)
• Yeast Information File (.info File) (works for all yeast microarrays and MAGIC Tool)

Download expression file for practice

• 4 Grid Expression File (.exp File)
• 1 Grid Expression File (.exp File)
• DeRisi's Diauxic Shift Ratios (.exp File)

Related Resources

GCAT Home Page

Genomics Course

Bioinformatics Course: students' online tutorial for microarray data analysis

Teaching Chips