workflow unit
Reproducible workflows. Every layer of biomedical data.
STaiMIC’s workflow engineering and training arm. Our training uses Nextflow, the open-source workflow manager, and community pipelines from nf-core. Reproducibility, portability and scale apply across every data layer in health research, from plain text files to multi-omics.
01 · tracks
From first run to auditable AI.
Foundations
HealthSeq-NF Foundations by Oscar Echeverri-Muñoz. Build a reusable workflow step by step in GitHub Codespaces, anchored in a published case of a multidrug-resistant E. coli strain. Seven lessons, no coding experience required. MIT licence.
computational training only · no clinical claims
Applied
Sequencing quality control and alignment with real data: FastQC, fastp, BWA-MEM2, SAMtools and MultiQC. Builds directly on Foundations.
Genomic layer
Whole exome variant analysis with nf-core/sarek, from tumour and normal reads to annotated somatic variants.
Transcriptomic layer
RNA-seq differential expression in cancer, focused on chromosome 17 (BRCA1, TP53), as a 90-minute introduction to Nextflow.
Microbiome layer
16S microbiome analysis with nf-core/ampliseq, applied to colorectal cancer.
Reproducibility and AI audit
Glass-Box: a reusable Nextflow subworkflow for auditable, AI-assisted variant triage. Apache 2.0 licence.
02 · format
How sessions run.
03 · on site
In-person workshops.
Hands-on workshops with regional partners, planned for Q4 2026. Exact dates will be announced once confirmed with each host.
ARE · 24.4539° N · 54.3773° E
Abu Dhabi, UAE
KWT · 29.3759° N · 47.9774° E