Associated Colleges of the South
Bioinformatics Workshop with MAGIC Tool

A. Malcolm Campbell

June 11-14, 2004

Pre-Workshop Reading + Study Guide + Excel Practice File

 

Travel Friday 11 June

Friday evening meal and discuss goals, plans, hopes, experiences, classes taught, etc.

Hand out printed materials and CDs

Movie for fun.

Saturday, 12 June

All day workshop

Start at 8:30 am

1) Introduction to DNA Microarrays (8:30 – 9 am)

2) Survey of Useful Resources (9 – 9:30)

3) Introduction to MAGIC Tool (9:30 – 9:45)

4) Raw data format + Creating Projects (9:45- 10:15)

• Create Two Projects (One_Grid and Four_Grid)

BREAK

5) Gene Lists and Addressing (11:15 – 11:45)

• Look at Excel file and .txt file
• Know the layout of your microarrays
• Load gene list into MAGIC Tool
• Begin with 1 grid file address it

6) Gridding (11:45-12:15)

• Generate Grid for 1 grid pair of tiff files
• Produce and save .grid file under One_Grid project

7) Recap and Questions (12:15– 12:30)

LUNCH

8) Generate a grid file for the 4 grid pair of tiff files in the Four_Grid project (2 – 3)

9) Segmentation and Generating Ratios (3 – 5)

• Close Four_Grid and Open One_Grid project
• Load tiff files and open saved grid file
• Discuss the 3 ways to segment features
• Discuss 4 ways to produce ratios
• Generate 12 ratios for One_Grid project
  • Append files each time
• Generate 2 ratios for Four_Grid project
  • Save as separate files

DINNER

Sat. evening movie or individual practice.

Sunday, 13 June

All day workshop

Start at 9:00 am

10) Quality Control for DNA Microarrays (9 – 9:30)

11) Case Studies with DNA Microarrays (9:30 - 10)

12) Transformation of Data (10 – 10:30)

• Transform your last appended One_Grid .exp file
• Transform your two Four_Grid .exp files
• Download and transform 4_grid Hypothetical Data (see MAGIC Tool Page)
• Add 4_grid Hypothetical Data to your Four_Grid Project

BREAK

13) Explore Ratio Data (11 – 12:30)

• Add GeneInfo.info file to your Four_Grid Project
• Attach GeneInfo.info to your Hypothetical 4 grid .exp file

LUNCH

14) Managing Data (2 – 2:45)

• Average Replicates
• Merge Files
• Limit Data (columns)
• Filter Genes (rows)

15) Clustering Data (2:45- 3:30)

• Disucss Correlation Coefficients
  • Refer to Instructor's Guide and Math Help for Details
• Work with Excel File from Laurie Heyer
• Calculate Dissimilarities
• Cluster By Heiarchical and QT Methods (4_grid Hypothetical Data)

16)Visualizing Clustered Data (3:30 – 5)

DINNER

Sunday evening movie, or individual practice, or small group curriculum brainstorming

Monday, 14 June

Half day workshop
Wrap up, assessment of workshop, plans to create curriculum

Start at 9:00 am

17) Recap and Questions (9 – 9:30)

18) Generating Tiff files for teaching purposes (9:30 – 10:30)

BREAK

19) Curriculum discussions and workshop assessment + Group Photo (11 – noon)

20) Depart with box lunch to help travelers