Computational Structural Biology Workflows & Automation — Hands-on

Productionize your structural bioinformatics work. Design robust, auditable pipelines that run on laptops, HPC, or cloud with consistent results. Orchestrate multi-tool workflows (MD, docking, modeling, analysis) , track provenance and data versions, and publish report bundles automatically.

Computational Structural Biology Workflows & Automation

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Session Index

Session 1 — Workflow Design & Environments Session 2 — Orchestration: Snakemake/Nextflow/CWL Session 3 — Reproducibility, Data & Deployment Session 4 — Mini Capstone: Template → Automated Pipeline

Session 1

Fee: Rs 6300

Workflow Design & Environments

Pipelines for modeling, docking, MD & analysis: DAGs, tasks, artifacts

Theory

Environment management & portability

conda/mamba Docker Singularity/Apptainer

Parameterization & configuration patterns

YAML/JSON secrets & profiles

Session 2

Fee: Rs 8400

Orchestration: Snakemake/Nextflow/CWL

Choose a workflow engine; rules/processes, resources & checkpoints

Snakemake Nextflow CWL/WDL (overview)

Scaling: local → HPC/cloud; schedulers & executors

Slurm/SGE/PBS AWS/GCP/Azure profiles & queues

Retry, caching & checkpointing; long MD/docking tasks

job arrays resume & re-entrancy

Session 3

Fee: Rs 11200

Reproducibility, Data & Deployment

Version control & data lineage

Git/GitHub/GitLab DVC/artifact stores metadata manifests

Testing, CI/CD & packaging for pipelines

pytest/unit checks GitHub Actions/GitLab CI container registries

FAIR outputs & automated reports

Quarto/Markdown checksums/provenance release tagging

Session 4

Fee: Rs 14000

Mini Capstone: Template → Automated Pipeline

Automate a mini workflow (prep → docking/MD → analysis) with configs, containers & scheduler profile

Theory + Practical

Push-button run: CI trigger, artifact upload & Quarto report bundle

release assets manifest/checksums

Deliverables: figures, tables, README & manifest

PDF CSV/TSV HTML

PDF

Computational Structural Biology Workflows & Automation Training | Snakemake/Nextflow, Containers, HPC & CI/CD

Computational Structural Biology Workflows & Automation — Hands-on