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@CNAG-Biomedical-Informatics

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mrueda/README.md

mrueda - computational biology, high-performance computing, and open-source scientific software

Manuel Rueda 👋

I am a computational biologist based in Barcelona. I build open-source scientific software for biomedical data interoperability, reproducible genomics, and AI-assisted research.

I lead the CNAG Biomedical Informatics subteam, where we develop open-source infrastructure for biomedical data and reproducible analysis. I also develop independent software for healthcare, education, and human-computer interaction.

🧬 Research software at CNAG

My research spans structural computational biology, genomics, and biomedical informatics. Selected collaborative projects include:

  • 🧩 Convert-Pheno (Biomedical data) - A toolkit for converting phenotypic data between standard data models.
  • 🧬 CBIcall (Genomics) - A configuration-driven framework for reproducible variant calling in large sequencing cohorts.

Further collaborative projects are available through CNAG Biomedical Informatics.

🚀 Independent open-source projects

Area Project Description
🧬 Research Digital Genome Workstation (DGW) Interactive and non-destructive editing of genome variants.
🎛️ AI interfaces Pad-Lattice Physical and virtual interfaces for monitoring and controlling AI agents.
💊 Healthcare & pharmacy RecallRx Country-aware medicine recall search using official regulatory sources.
💊 Healthcare & pharmacy Nomenclator Delta Search and compare monthly changes in Spain's official pharmaceutical Nomenclátor.
💊 Healthcare & pharmacy DataMatrix2Codes Decode and process GS1 DataMatrix barcodes used on pharmaceutical packaging.
📚 Education Shelf-School A self-hosted library management system for small schools.
📚 Education Montessori Virtual Room Explore Montessori materials and activities in an interactive virtual classroom.

🧪 Experiments

  • 🎵 Music Key Detector (Audio analysis) - A compact experiment for estimating likely major or minor keys, with confidence and ambiguity reporting.

💾 Background

I began programming in BASIC on an MSX and have continued building software throughout my scientific career. My background as a musician informed Pad-Lattice's use of MIDI grid controllers as interfaces for AI agents.

Pinned Loading

  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

    Human-in-the-loop control surfaces for monitoring and directing AI agents across Novation Launchpads, browsers, phones, and tablets.

    Python 3

  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