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Achievement: Starstruck

Achievements

Achievement: Starstruck

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@CNAG-Biomedical-Informatics

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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 grew up in the era of BASIC home computers. My first computer was an MSX, and I’ve been building software ever since. My scientific career has taken me from molecular modeling and genomics to biomedical informatics, where I develop open-source infrastructure for interoperable biomedical data, reproducible research, and AI-assisted science.

🧬 Research software

Most of my collaborative and production research software is developed within the CNAG Biomedical Informatics initiative:

➡️ https://github.com/CNAG-Biomedical-Informatics

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.

🚀 Personal projects

Outside research, I still enjoy building software simply because I find it interesting.

  • 🎛️ Pad-Lattice — Turn a Novation Launchpad into a control surface for supervising autonomous coding agents.
  • 📚 ShelfSchool — A self-hosted library management system for small schools.

🔬 Research interests

  • Bioinformatics
  • Biomedical informatics
  • Scientific software
  • Data interoperability
  • Genomics
  • AI-assisted science
  • Open source

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 Projects that are no longer maintained are archived rather than removed.

Pinned Loading

  1. CNAG-Biomedical-Informatics/convert-pheno CNAG-Biomedical-Informatics/convert-pheno Public

    A software toolkit for the interconversion of standard data models for phenotypic data

    Perl 16 1

  2. CNAG-Biomedical-Informatics/beacon2-cbi-tools CNAG-Biomedical-Informatics/beacon2-cbi-tools Public

    Beacon v2 - CNAG Biomedical Informatics - Tools (Data ingestion tools)

    Perl 3

  3. 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

  4. 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

  5. pad-lattice pad-lattice Public

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

    Python 1

  6. shelf-school shelf-school Public

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

    Python