Edmund Miller
Texas, United States
Summary
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RockstarEdmund Miller is a bioinformatics engineer with nine years of experience bridging computational pipelines and reproducible science, currently contributing to Seqera and the nf-core core team from Texas. He has deep hands-on expertise modernizing and automating RNA‑seq and other genomics workflows—refactoring nf-core/rnaseq subworkflows and building pytest-driven test frameworks for nf-core/modules to raise pipeline robustness. Trained to PhD level in molecular and cell biology, he pairs wet‑lab insight with DevOps-style engineering, shipping integrations for tools like STAR, HISAT2, SAMtools and Picard. Past work spans industry roles at Element Biosciences and an earlier pivot from blockchain engineering, showing an unusual mix of domain biology, production bioinformatics, and systems-level software craftsmanship.
9 years of coding experience
Github Skills (33)
javascript10
website-development10
dsl10
testing10
workflow-engine10
astar10
nextflow10
emacs-lisp10
fstar10
php10
rna-seq10
bioinformatics10
dstar10
staruml10
nf-core10
Programming languages (33)
Github contributions (5)
nf-core/modules
Nov 2020 - Jan 2023
Repository to host tool-specific module files for the Nextflow DSL2 community!
Role in this project:
QA Engineer / Test Automation Engineer
QA Engineer / Test Automation EngineerContributions:418 reviews, 199 commits, 308 PRs in 2 years 2 months
Contributions summary:Edmund primarily contributed to the testing framework of the nf-core/modules repository, focusing on the integration of pytest-workflow. Their commits demonstrate a refactoring of existing tests for various bioinformatics tools (e.g., FastQC, BWA, Picard, Samtools, TrimGalore) to utilize the pytest-workflow framework, which suggests an effort to modernize and standardize the testing procedures. The user also added and corrected several tests, specifically for different tools and data types, as well as removing input symlinks and fixing typos within the tests.
nf-corehostnextflow-dsl2nextflowdsl2
nf-core/rnaseq
Oct 2022 - Nov 2022
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
Role in this project:DevOps Engineer
DevOps EngineerContributions:9 reviews, 56 commits, 13 PRs in 28 days
Contributions summary:Edmund primarily focused on refactoring and installing nf-core subworkflows, integrating them into the main RNAseq pipeline. Their work involved incorporating and managing modules related to various bioinformatics tools like HISAT2, STAR, SAMtools, Picard, and RSeQC. These changes included adding workflows for processing BAM files, handling duplicate reads, and generating quality control metrics, demonstrating a focus on automating and streamlining the pipeline's execution.
countsbioinformaticsrsemrnaquality-control
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