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Purpose

This bioinformatics implementation guide was written by Tiffany Hsu during her APHL-CDC Bioinformatics Fellowship in order to serve public health laboratories (PHL) in:

1. Understanding the history of bioinformatics in public health.
2. Determining whether they need a bioinformatician (or not)
3. Identifying the infrastructure needed to support a bioinformatician

For any questions, she can be contacted at tyhsu389(at)gmail(dot)com.

Table of Contents

• Chapter 1: The Growing Role of Bioinformatics
  • History of the Advanced Molecular Detection (AMD) initiative
• Chapter 2: The State of Bioinformatics in New England
• Chapter 3: Initiating a bioinformatics project
  • 4 Steps to defining a bioinformatics project
  • Step 1: Defining the project
• Chapter 4: Choosing a bioinformatician
  • Collaborate or hire?
  • Choosing a bioinformatician
  • Going Rogue: Not hiring a bioinformatician
• Chapter 5: Building bioinformatics infrastructure
  • Step 2: Setting up compute infrastructure
    • 3 approaches to obtaining compute infrastructure
• Chapter 6: Building a Bioinformatics Pipeline
  • Step 3: Piloting a bioinformatics project
  • Step 4: Creating a production level pipeline
• Chapter 7: Learning from the bioinformatics leader laboratories