The State Public Health Bioinformatics Group (StaPH-B) is a consortium of public health scientists interested in addressing the common barriers impeding bioinformatics implementation in state public health laboratories. Our efforts are focused in the following areas:

• Building and sustaining an appropriate bioinformatics infrastructure within regional state PHLs
• Training public health scientists on the fundamentals of bioinformatics
• Development of bioinformatics applications, tools and pipelines
• Facilitation of CLIA approval for Bioinformatics applications, tools and pipelines
• Partner with the CDC and APHL to ensure compatibility and utility of our efforts.

StaPH-B members possess a wide range bioinformatics experience, from molecular biologists gaining familiarity with NGS and web-based applications, to experienced practitioners with advanced degrees in the field capable of scripting custom tools. This diversity of experience allows StaPH-B to approach problems from a multitude of perspectives and develop high-efficacy solutions that are both technically sound, and practical to public health investigations.

1. Building templates for various solutions regarding state informatics infrastructure

   • e.g. security documents for Linux OS, University Affiliations, etc.

2. Cloud computing

   • StaPH-B Google/AWS VM with preloaded bioinformatics applications

3. Defining communication standards between Bioinformatics specialists and Epidemiologists

4. Development and validation of bioinformatics tools for various applications:

   • NGS quality assessment
   • In silico ​ taxonomic identification, serotyping, virulence determination, and antimicrobial resistance from NGS data
   • Reference-based cluster analysis (hqSNP)
   • Reference-free cluster analysis (pan genome based clustering)