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@NIAID-BRC-Codeathons NIAID BRC Codeathons

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    13 repositories

    • NIAID-BRC-Codeathons.github.io

      Public
      Astro
      •3•1•0•0•Updated Feb 13, 2026Feb 13, 2026

    • viral-phylogenetics

      Public
      Optimizing protein language model to predict viral protein structures at scale
      Python
      •1•1•0•0•Updated Jan 16, 2026Jan 16, 2026

    • workflow-generation-mcp

      Public
      Automating bioinformatics workflow design, refinement, and execution using generative AI models guided through the Model Context Protocol (MCP)
      0•0•0•0•Updated Jan 16, 2026Jan 16, 2026

    • gene-function-prediction

      Public
      Leveraging machine learning and AI to predict functions of characterized and uncharacterized genes using K-mers, ensemble methods, and LLM embeddings
      Perl
      •0•0•0•0•Updated Jan 14, 2026Jan 14, 2026

    • hiperrag-literature-extraction

      Public
      Leveraging high-performance retrieval-augmented generation to extract and curate structured biological data for CEPI priority pathogens from scientific literatu…
      2•1•0•0•Updated Jan 8, 2026Jan 8, 2026

    • RDF-knowledge-graph-construction

      Public
      Transforming Pathogen Data Network Resources to RDF using Large Language Models
      HTML
      •
      Apache License 2.0
      •0•0•0•0•Updated Nov 20, 2025Nov 20, 2025

    • storyseq-sequence-narrative

      Public
      Automating sequence identification and contextualization using BLAST, database queries, and LLM narrative synthesis to accelerate pathogen and AMR gene discover…
      Python
      •3•0•1•0•Updated Nov 16, 2025Nov 16, 2025

    • pubmed-miner

      Public
      Automated extraction of viral sequence features, mutations, and epitopes from PubMed literature using LLMs to accelerate outbreak response and genomic analysis
      Python
      •5•1•0•1•Updated Nov 14, 2025Nov 14, 2025

    • workflow-training-data-extraction

      Public
      Creating structured question-answer training datasets from BRC resources and publications to train LLMs for bioinformatics workflow generation
      Python
      •1•1•0•0•Updated Nov 14, 2025Nov 14, 2025

    • ai-dataset-and-analysis-discovery

      Public
      Enabling bench scientists to start with analysis goals and receive both relevant datasets and executable workflows—a complete path from question to execution.
      0•0•0•0•Updated Nov 13, 2025Nov 13, 2025

    • ai-co-scientist-protein-function

      Public
      Extending the Co-Scientist framework to build reasoning agents for protein function prediction using CEPI and BV-BRC datasets for priority pathogens
      1•0•0•1•Updated Oct 31, 2025Oct 31, 2025

    • rhea-workflow-automation

      Public
      Extending the Rhea platform with MCP+RAG to enable automated workflow generation leveraging Galaxy and BV-BRC for infectious disease analysis
      1•0•0•1•Updated Oct 31, 2025Oct 31, 2025

    • outbreak-surveillance-monitoring

      Public
      AI-powered outbreak surveillance aggregating web data sources including social media, news, case reports, and public health databases
      0•1•0•0•Updated Oct 31, 2025Oct 31, 2025
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