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Building open-source scientific data governance tools
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Building open-source scientific data governance tools
26 followers · 169 following

Achievements

Achievement: YOLOAchievement: Pull Sharkx2

Achievements

Achievement: YOLOAchievement: Pull Sharkx2

Highlights

  • Pro

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@PGP-UK

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ronfinn/README.md
Ron Finn — scientific data strategy, computational biology, software engineering and data governance

Data Swamp Biosystems  ·  Cell Painting AnnData Validator  ·  Bio Run Crate

Building trustworthy scientific data systems

I work across scientific research, data strategy and software engineering. My focus is making complex research data discoverable, reproducible, traceable and ready for responsible AI/ML use.

Scientific data strategy

Target operating models, platform architecture, data products, metadata strategy, stewardship and governance-as-code.

Computational biology

Genomics, single-cell and spatial omics, bioimaging, phenotypic profiling and translational research data.

Software and data engineering

Typed Python, validation tooling, Nextflow, containers, cloud platforms, CI/CD and reproducible scientific workflows.

Programme delivery

Technical roadmaps, architecture decisions, cross-functional delivery, platform evaluation and measurable governance outcomes.

Capability map covering scientific computing, engineering, data platforms and governance

Flagship open-source systems

Data Swamp Biosystems

A deterministic synthetic biotech data estate for benchmarking catalogues, lineage systems, governance controls and AI agents.

synthetic-data data-governance AI agents

Cell Painting AnnData Validator

Semantic, provenance and AI-readiness validation for Cell Painting datasets represented as AnnData.

anndata phenotypic-profiling validation

Bio Run Crate

Validation of biological analysis-run metadata and packaging of traceable outputs as RO-Crate research objects.

RO-Crate FAIR reproducibility

Current design direction

Connecting metadata contracts, scientific workflow execution, quality controls, provenance and governed reuse into coherent research data products.

metadata-contracts lineage data-products

Open-source portfolio pulse

Automatically generated GitHub portfolio metrics Automatically generated twelve-month GitHub contribution activity The two panels above are generated as local SVG files by GitHub Actions. The profile does not depend on a public badge or statistics-image service.

Engineering principles

  • Contracts before convenience: make schemas, interfaces and expectations explicit.
  • Reproducibility by default: deterministic execution, versioned configuration and traceable outputs.
  • Governance in the workflow: validation, lineage, ownership and quality controls belong in the delivery path.
  • Build for scientific users: technically rigorous systems must remain understandable and usable by research teams.

Technical landscape

Scientific computing
Python · R · AnnData · Scanpy · Squidpy · Cell Painting · single-cell omics · spatial transcriptomics · bioimaging

Engineering
Nextflow · Docker · Kubernetes · GitHub Actions · pytest · Ruff · mypy · Pydantic · uv

Data platforms
AWS · Google Cloud · S3 · DataHub · OpenMetadata · OpenLineage · Benchling · Seqera

Strategy and governance
FAIR · ALCOA++ · metadata management · data quality · data lineage · data products · stewardship · governance as code

Scientific data should be understandable, reproducible and trustworthy by design.
London, United Kingdom

Pinned Loading

  1. dataswamp-biosystems dataswamp-biosystems Public

    Deterministic synthetic biotech data platform for generating governed organisations, metadata, scientific datasets, lineage and defects for testing data catalogues, governance platforms, AI agents …

    Python

  2. cell-painting-anndata-validator cell-painting-anndata-validator Public

    Validate the semantic correctness, metadata completeness, provenance and AI readiness of Cell Painting datasets represented in AnnData.

    Python

  3. bio-run-crate bio-run-crate Public

    Validate and package reproducible computational biology analysis runs using RO-Crate.

    Python