Ep 7 Technological Advancements in public health bioinformatics

Hosted by Kevin Libuit and Andrew Page, the podcast focuses on the evolution of tech adoption in pathogen genomics. The narrative begins with the shift from traditional software packages to modern cloud-based GUIs. Early software installations were cumbersome, often taking weeks and requiring an in-depth understanding of dependencies and compilers. There was also a notable shift in programming languages from Ruby and Perl to Python. Package managers evolved from systems like Debian and Homebrew to Conda and BioConda, with Mamba offering further installation improvements. The podcast touched on the use of Make as an early workflow manager and its evolution to tools like snake make, next flow, and Galaxy. The role of GUIs in democratizing access to bioinformatics tools and the transition from on-prem servers to cloud computing was also discussed. However, there were concerns about the security implications of cloud computing in certain countries. The episode also delved into the challenges of closed-source tools and emphasized the benefits of open-source alternatives, especially those funded by public money. Finally, the potential influence of AI and machine learning on genomics was explored, acknowledging initial resistance but recognizing the inevitable integration of these technologies in the future. The podcast highlighted the tech journey in pathogen genomics, the significance of open-source tools, and the exciting prospects brought about by AI and machine learning.