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Achievements

Achievement: Pair Extraordinairex3Achievement: Pull Sharkx3Achievement: YOLO

Achievements

Achievement: Pair Extraordinairex3Achievement: Pull Sharkx3Achievement: YOLO

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smaniches/README.md

Santiago Maniches

I build provenance-first scientific AI systems: MCP servers, bioinformatics agents, and reproducible ML/research tooling.

My strongest public work is in agentic research infrastructure: tools that let AI systems query scientific sources with typed APIs, provenance records, verification hooks, and explicit limitations.

Lead public work

  • uniprot-mcp — UniProt MCP server with per-response SHA-256 provenance, release pinning, verification, and offline replay.
  • semantic-scholar-mcp — Semantic Scholar MCP server with 14 typed tools for paper search, citation graphs, author profiles, and recommendations.
  • alphafold-sovereign-mcp — local-first biomedical MCP over AlphaFold DB and related public sources, with a SQLite knowledge graph and explicit clinical-use limits.

Research software

  • TopoGeoML — topology-aware ML toolkit plus a preregistered graph-classification study whose headline result is negative.
  • cohomology-wall — mathematical/reproducibility archive for a tetraquadric Calabi-Yau cohomology-jumping calculation.
  • GROUPOID — pre-alpha groupoid/sheaf/Riemannian aggregation prototype for federated learning.

AI safety / biosecurity research

  • homology-cliff — ESM-2 protein-retrieval failure-mode study with preregistered evidence, calibration analysis, and explicit curation limits.

Supporting work

  • democafa_package — CAFA-style protein-function prediction data and evaluation utilities.
  • LAFA_container_guide — containerization guide for protein-function prediction methods.
  • icbo-ai-tutorial — tutorial/codespace material for ontology-agent workflows.

Contact

LinkedIn · ORCID · Kaggle · GitHub

Pinned Loading

  1. semantic-scholar-mcp semantic-scholar-mcp Public

    Semantic Scholar MCP server: 14 typed tools for paper search, citation graphs, author profiles, recommendations, PyPI/Docker.

    Python 11

  2. uniprot-mcp uniprot-mcp Public

    Auditable UniProt MCP server with per-response SHA-256 provenance, release pinning, verification, and offline replay.

    Python 3

  3. alphafold-sovereign-mcp alphafold-sovereign-mcp Public

    Local-first biomedical MCP over AlphaFold DB + 8 public sources, with SQLite knowledge graph, offline mode, and explicit clinical-use limits.

    Python 3 2

  4. TopoGeoML TopoGeoML Public

    Topology-aware ML toolkit plus preregistered graph-classification study; honest negative result, statistical harness, reproducible evidence.

    Python 1

  5. GROUPOID GROUPOID Public

    Pre-alpha groupoid/sheaf/Riemannian aggregation prototype for federated learning; tested math components, not production FL.

    Python 1

  6. cohomology-wall cohomology-wall Public

    Toeplitz determinantal formula for tetraquadric Calabi-Yau cohomology jumping with reproducible finite-field checks.

    Python 1