Considerations when using and deploying open source software

Kelsey Florek, PhD, MPH
Senior Genomics and Data Scientist
Wisconsin State Laboratory of Hygiene
May 17, 2022

Key Factors to Open Source Software

User Community

Developer Community


Security Assessments

Open Source Software provided by Apache Software Foundation

record events, errors, and routine system operations communicating diagnostic messages to system administrators and users

"the single biggest, most critical vulnerability of the last decade" - Tenable


GitHub Default: the owner retains all rights to the source code and no one is permitted to reproduce, distribute, or create derivative works


nextstrain / augur

StaPH-B / docker-builds

StaPH-B / staphb_toolkit

ncbi / sra-human-scrubber

Open Source Guidelines