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mrueda/README.md

Hi, I'm Manuel Rueda 👋

I'm a computational biologist based in Barcelona with a passion for building software. I develop open-source infrastructure for interoperable biomedical data, reproducible genomics, and trustworthy AI-assisted research.

Current focus: sustainable scientific software, biomedical data standards, reproducible analysis workflows, and practical applications of AI in research.

🧬 Research software

Most of my collaborative and production research software is developed within the CNAG Biomedical Informatics laboratory.

Our work focuses on biomedical data interoperability, sustainable scientific software, and trustworthy AI for biomedical research.

Many projects on this account begin as personal ideas, prototypes, or independent tools before evolving into collaborative research software.

🚀 Open-source projects

I enjoy building software that solves real-world problems, whether for research, healthcare, education, or developer productivity.

Some examples include:

  • 📚 Shelf-School (Education) — A self-hosted library management system for small schools.

  • 💊 DataMatrix2Codes (Healthcare) — Decode and process GS1 DataMatrix barcodes used in pharmaceutical packaging in Spain.

  • 🧠 RecallRx (Healthcare) — A static, open-source search app for medicine recalls from official regulatory sources, with structured country-aware data for healthcare professionals, pharmacies, developers, and researchers.

  • 🎛️ Pad-Lattice (Developer Tools) — Repurpose MIDI grid controllers as extensible physical interfaces for monitoring and controlling AI agents.

  • 🎵 Music Key Detector (Music) — Estimate the likely major or minor key of an audio file, with confidence scores, ambiguity detection, and ranked alternatives.

💾 From BASIC to biomedical informatics

I grew up in the era of BASIC home computers. My first computer was an MSX, and I’ve been interested in computers ever since. My scientific career has taken me from structural computational biology to genomics and biomedical informatics.

Older repositories are preserved as part of my professional journey. Projects that are no longer maintained are archived rather than removed.

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  1. CNAG-Biomedical-Informatics/clarid-tools CNAG-Biomedical-Informatics/clarid-tools Public

    ClarID: A Human-Readable and Compact Identifier Specification for Biomedical Metadata Integration

    Perl 2

  2. CNAG-Biomedical-Informatics/cbicall CNAG-Biomedical-Informatics/cbicall Public

    CBIcall is a configuration-driven framework for reproducible variant calling in large sequencing cohorts, enabling standardized pipelines from FASTQ to analysis-ready VCFs across heterogeneous comp…

    Python 2

  3. pad-lattice pad-lattice Public

    Novation Launchpad Pro Mk1 control surface for supervising autonomous coding agents.

    Python 1

  4. shelf-school shelf-school Public

    Open-source library management for small schools: catalog books, track copies, and handle checkouts with QR/barcode photos.

    Python 1

  5. recallrx recallrx Public

    Country-aware medicine recall search from official regulatory sources.

    Python 1

  6. datamatrix2codes datamatrix2codes Public

    Parser for GS1 DataMatrix scanner strings from Spanish medicine boxes, with Excel support for pharmacy workflows

    Python 2