Articles

Name	Topic
Clinical Trial Site Issue Triage Assistant
Mental Models (wtih 🤖) for Making Reproducible Interactive Data Prototypes with Snakemake, Docker, CI, and PyShiny
Reproducibility with GitHub Actions for running Snakemake pipelines	reproducibility, workflow manager, ci/cd
Remains of the Day - SQL	SQL
Part I: Reproducible analyses in R with Docker	R, Docker, reproduciblility
Part II: Reproducible analyses in R with Docker	R, Docker, reproducibility, volume-mounting
Part III: Reproducible analyses in R with Docker	Docker, R, reproducibility, privacy
Docker for Reproducible Analyses in R	Docker, R, reproducibility, analysis, GitHub, renv
Creating reproducible analyses… when you’re not the author of the code	DevOps, Scientific Computing, Reproducibility, ML
Using Pyenv and Virtualenv for managing multiple Python versions and environments	Pyenv, Virtualenv, Python
Docker Diaries: Docker → Singularity	Docker, Singularity, HPC
Creating a new Docker Image from a Running Container	Docker Image
Run a Docker container - identify transdiagnostic latent factors	Reproducibility
hello-world.nf on the research cluster	Nextflow, Bioinformatics
hello-world.nf meets GitHub Actions	Nextflow, Bioinformatics
Articles that I revisit over years	Musings
Who are research software engineers? Part I
Why I decided to pursue Carpentries Instructor Certification	Reproducibility, Community
RNA-Seq Notes	Bioinformatics
Factor Levels or Binary Variables? A Case-Study in Statistical Modelling of Bipolar Disorder and the Aging Brain	Statistics
Whoʼs the culprit for bias in aging clocks?	Statistics
Automated RSS-to-weekly research digest pipeline	ResearchOps, DevOps, Tool Development
Replication of Arcadia Notebook Pub: Applying method used for extracting gene feature contributions from UMAP to another dataset	ResearchOps, Replication, Community, Publishing Plaforms
(Semi) spec-driven development
AI-Native Development	AI coding assistants, agents, tests
Build and Ship a Full-Stack App with AI Coding Assistants	AI coding assistants, agents, tests
Deployment	AI coding assistants, agents, tests, CI/CD, deployment
Observability stack for order-tracker