Michael Hall
Research Fellow at The University of Queensland
Queensland, Australia
Summary
🤩
Rockstar🎓
Top SchoolMichael Hall is a Research Fellow and computational genomics specialist with nine years' experience building genome-graph and pangenome tools to improve antimicrobial resistance surveillance and bacterial evolution studies. He blends academic rigor—from a PhD at Cambridge and postdoctoral work at EMBL-EBI and the Doherty Institute—with practical software engineering in Rust and Python to deliver fast, reproducible bioinformatics for public health labs. Michael has a strong track record in open-source contributions to widely used projects like Snakemake and Bioconda, where he’s improved workflow scripting, wrappers, and build automation. He focuses on long-read sequencing, Nanopore applications, and scalable, species-agnostic frameworks that make genomic data actionable for decision-makers. Colleagues value him for translating complex methods into production-ready tools and for mentoring early-career researchers across international collaborations.
10 years of coding experience
Bachelor’s Degree, Cell and Molecular Biotechnology, Bachelor’s Degree, Cell and Molecular Biotechnology at QUT (Queensland University of Technology)Master’s Degree, Bioinformatics (Research Extensive), Master’s Degree, Bioinformatics (Research Extensive) at The University of QueenslandDoctor of Philosophy - PhD, Bioinformatics, Doctor of Philosophy - PhD, Bioinformatics at University of Cambridge
English
Stackoverflow
3,033reputation
1.2mreached
40answers
20questions
seaborn
top-5%
gzip
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python
top-5%
Github Skills (39)
conda-forge10
snakemake10
python10
package-management10
scripting10
conda10
build-system10
bash10
cicd10
automation10
bioinformatics10
sh10
workflow-management10
automations10
shell10
Programming languages (25)
Github contributions (5)
snakemake/snakemake-wrappers
Apr 2019 - Sep 2021
This is the development home of the Snakemake wrapper repository, see
Role in this project:
Backend Developer & DevOps Engineer
Backend Developer & DevOps EngineerContributions:4 reviews, 19 commits, 9 PRs in 2 years 5 months
Contributions summary:Michael primarily contributed to the development of Snakemake wrappers for various bioinformatics tools, including Clustal Omega, NanoSim-H, SNP-Mutator, and others. Their work involved writing wrapper scripts, integrating tools, and creating test cases to ensure functionality. Additionally, the user demonstrated DevOps skills by updating the existing wrappers and improving documentation.
snakemake
snakemake/snakemake
Jul 2019 - Oct 2022
This is the development home of the workflow management system Snakemake. For general information, see
Role in this project:Back-end Developer
Back-end DeveloperContributions:11 reviews, 11 commits, 17 PRs in 3 years 3 months
Contributions summary:Michael primarily contributed to the Snakemake workflow management system by adding and refining features related to scripting and configuration. Their work includes implementing support for Bash scripts, allowing the script directive to accept pathlib.Path objects, and refactoring f-strings to enhance code maintainability and compatibility. They also modified and extended existing functionality by adding keywords to vim syntax files and adding a short option for restart times.
snakemakereproducibilityworkflow-management
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