Welcome to Klea
===============

Knowledge vaLidated Expert AI Assistant for Neuroscience.

Klea is a suite of AI tools for Neuroscience.  It provides a general
purpose agent with coding capabilities, a generic RAG pipeline, and
MCP servers for modelling and analysis.

Architecture
------------

The project is organised as a monorepo with four installable packages:

.. list-table::
   :header-rows: 1

   * - Directory
     - Package
     - CLI
     - Purpose
   * - ``utils_pkg``
     - ``klea_utils``
     - ``klea-stores-create``
     - Shared utilities, vector store management, base graph classes
   * - ``rag_pkg``
     - ``klea_rag``
     - ``klea-rag``, ``klea-rag-serve``
     - Generic RAG pipeline with multi-domain support
   * - ``agent_pkg``
     - ``klea_agent``
     - ``klea``, ``klea-serve``
     - General purpose agent with coding capabilities
   * - ``mcp_pkg``
     - ``neuroml_mcp``
     - ``nml-mcp``
     - MCP server for NeuroML tooling

Each package is built on a shared foundation in ``klea_utils``, which
provides configurable LLM setup (with runtime model switching), vector
store abstraction (Chroma / PGVector / Qdrant), and the
:class:`~klea_utils.graph.base.BaseLangGraph` orchestrator framework.
Web interfaces are available via NiceGUI (primary) and Streamlit.

``klea_agent`` is the main application: a general purpose agent that can
also code.  ``klea_rag`` is an additional component, primarily consumed by
``klea_agent`` as a retrieval/RAG service.

Prototype Deployments
---------------------

These prototype Klea RAG deployments are available on HuggingFace that use the web interface.

- `NeuroML RAG <https://huggingface.co/spaces/NeuroML/NeuroKLEA>`__
- `OpenWorm RAG <https://huggingface.co/spaces/sanjayankur31/OpenWormLLM>`__

Please note that there are limited resources/credits available for these
prototypes, and so they may fall over if there is too much activity.
They are not production deployments.

Funding
-------

Klea is funded by the `BioFAIR <https://biofair.uk/>`_ Pathfinder
Projects grant `"Creating AI-enabled analysis pipelines for FAIR
neuroscience data"
<https://biofair.uk/updates/2026/biofair-pathfinder-projects-launch-with-800k-to-transform-uk-fair-practices/>`_,
awarded to `Padraig Gleeson
<https://profiles.ucl.ac.uk/11654-padraig-gleeson>`_ and `Ankur Sinha
<https://profiles.ucl.ac.uk/77575-ankur-sinha>`_ at `University College
London <https://openneuroai.org/>`_.

.. image:: _static/biofair-logo.png
   :alt: BioFAIR logo
   :class: biofair-logo
   :width: 30%
   :align: center

.. toctree::
   :caption: Usage
   :hidden:

   install
   concepts/index
   glossary
   tutorials/index
   cookbook/index
   cli/index

.. toctree::
   :caption: Develop
   :hidden:

   contributing
   api/index

.. toctree::
   :caption: Project
   :hidden:

   getting-help
   code-of-conduct