Daniel Mcdonald
Scientific Director at American Gut Project / The Microsetta Initiative
California, United States
Summary
🤩
Rockstar🎓
Top SchoolDaniel Mcdonald is a Scientific Director and PhD-trained computer scientist with 18 years of experience building scalable microbiome projects and the analysis software that powers them. He leads the American Gut Project / Microsetta Initiative, bridging academia and industry to turn complex biological samples—literally poop—into reusable data and reproducible insights. Technically hands-on, he contributes to prominent open-source bioinformatics tooling such as scikit-bio and QIIME, improving core back-end functionality and data-processing pipelines. Based in California, he combines interdisciplinary quantitative biology with software engineering to ensure analyses scale for global cohorts. Colleagues rely on him for cross-disciplinary collaboration, long-term platform design, and pragmatic decisions that keep research both rigorous and production-ready.
18 years of coding experience
4 years of employment as a software developer
Doctor of Philosophy (PhD), Computer Science, Doctor of Philosophy (PhD), Computer Science at University of Colorado at Boulder
Github Skills (10)
unit-testing10
bioinformatics10
biom10
refactoring10
python10
data-processing10
data-structure9
algorithm9
data-structures9
algorithms9
Programming languages (15)
Github contributions (5)
scikit-bio/scikit-bio
Dec 2013 - Mar 2022
scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.
Role in this project:
Back-end Developer
Back-end DeveloperContributions:2 releases, 143 reviews, 483 commits in 8 years 5 months
Contributions summary:Daniel's commits focused on implementing and refining core functionality within the scikit-bio library, a bioinformatics tool. The commits involve adding, modifying, and maintaining code related to various classes and methods within the library. The developer appears to be working on new features and improvements to the core framework and functionality.
scikitlicensedpythondata-sciencealgorithms-and-data-structures
biocore/qiime
Feb 2010 - Jan 2015
Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.
Role in this project:Back-end Developer
Back-end DeveloperContributions:1 review, 214 commits, 6 PRs in 4 years 11 months
Contributions summary:Daniel primarily focused on refactoring and improving existing methods within the QIIME software repository. They moved and refactored code related to parsing and processing data related to OTU tables. Additionally, the user made changes to the core functionalities like the generate_lane_mask method, showing a solid understanding of the codebase, and contributing to the overall performance and efficiency. These commits demonstrate a solid understanding of the project's core functionalities and the underlying data structures.
qiimeanalysismicrobiomeqiime2
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