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1. MitoRAG MitoRAG Public

   Local mitochondrial research assistant: 12-agent RAG over Neo4j KG with PubMed, Semantic Scholar, Europe PMC and bioRxiv search, PDF ingestion, and 3D knowledge graph explorer.

   Python 2

2. autonomous-drug-discovery-agent autonomous-drug-discovery-agent Public

   Local research-only AI agent for evidence-grounded therapeutic target discovery with PubTator3, Open Targets, Neo4j, ChEMBL/RDKit, and FastAPI.

   Python

3. MitoAggNet MitoAggNet Public

   Research framework for testing multimodal predictors of explicitly defined protein phenotypes

   Python

4. neurofold-harbor neurofold-harbor Public

   Five Harbor-compatible RL benchmarks for controlling coarse-grained protein aggregation: Abeta42, alpha-synuclein, tau, TDP-43, HTT polyQ. Frozen simulators, three-valued validation gates, negative…

   Python

5. openhumsim-rl openhumsim-rl Public

   Mechanistic multi-organ physiology research simulator with measurement-aware observations, verification tooling and a Gymnasium-compatible RL API.

   Python

6. KneeMechBridge KneeMechBridge Public

   Traceable reduced-order Python framework for multiscale knee mechanobiology, uncertainty propagation, validation maturity, reproducible benchmarks, and a research dashboard—explicitly not a clinica…

   Python