John Lees
PhD Student at Wellcome Trust Sanger Institute
Cambridge, England, United Kingdom
Summary
🤩
Rockstar🎓
Top SchoolJohn Lees is a PhD student at the Wellcome Trust Sanger Institute with 12 years of experience at the intersection of software engineering and statistical genomics. He leads research-grade software efforts at EMBL-EBI, building tools for bacterial genomic epidemiology, modelling and population genetics. A seasoned DevOps/back-end contributor to the prominent bioconda-recipes repository, he has packaged and maintained builds for key bioinformatics tools like raxml-ng and seqan3, improving reproducibility across the field. Trained as a physicist at Oxford and now doing a PhD in biology at Cambridge, he combines rigorous quantitative thinking with practical production engineering. Early roles in L3 support and systems administration give him a pragmatic troubleshooting mindset that complements his research focus. Colleagues rely on him for reliable pipelines and clever engineering solutions that bridge research and deployment.
12 years of coding experience
MPhys, Physics, MPhys, Physics at University of OxfordDoctor of Philosophy (Ph.D.), Biology, Doctor of Philosophy (Ph.D.), Biology at University of Cambridge
Stackoverflow
23reputation
516reached
1answer
2questions
Github Skills (18)
package-management10
conda10
bash10
bioinformatics10
cmake9
build-automation9
c-language7
openmp7
cprogramming-language7
dlib6
generics6
bit-vector6
rust6
probability-density6
python6
Programming languages (14)
Github contributions (5)
bioconda/bioconda-recipes
Sep 2018 - Nov 2022
Conda recipes for the bioconda channel.
Role in this project:
Back-end Developer & DevOps Engineer
Back-end Developer & DevOps EngineerContributions:35 reviews, 43 commits, 103 PRs in 4 years 2 months
Contributions summary:John primarily contributed to the development and maintenance of conda recipes for bioinformatics tools. Their work included adding recipes for various tools like rapidnj, fsm-lite, seer, ska, SpydrPick, Mantis, unitig-counter, squeakr, raxml-ng, and seqan3. They also addressed build issues, dependency management, and testing, demonstrating skills in DevOps practices. Their contributions also include updates to existing recipes and general maintenance of the bioconda-recipes repository.
recipescondabiocondabioinformaticspackage-management
bacpop/ska.rust
Nov 2022 - Feb 2023
Split k-mer analysis – version 2
Contributions:1 release, 23 reviews, 184 commits in 3 months
sequencesplitrustalignmentmer
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