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Model Context Protocol

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📚 Useful Resources

MCP (Model Context Protocol)

• MCP Official Docs — Spec, tutorials, and guides
• MCP-UI — Official standard for interactive UI in MCP
• MCP Auth Guide (Auth0) — Deep dive into MCP auth spec updates

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AGENTS.md

Subagent definitions for automating ngrok setup on Linux/WSL2. The MCP server needs ngrok to expose localhost:8000 publicly for Claude Desktop and remote clients.

ngrok-detect

Checks whether ngrok is installed and reports its path and version. Read-only — no side effects.

Instructions

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import os
import requests
import asyncio
import nest_asyncio
from typing import Annotated, Literal
from typing_extensions import TypedDict
from dotenv import load_dotenv

# LangChain & LangGraph Imports
from langchain_openai import ChatOpenAI

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{
	"folders": [
		{
			"name": "🏗️ architecture",
			"path": "biosciences-architecture"
		},
		{
			"name": "🤖 deepagents",
			"path": "biosciences-deepagents"
		},

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Agent Team Definition

Nine specialized agents coordinate across the Open Biosciences platform. Each agent owns specific repos and has clear responsibilities.

Agent Roster

1. Program Director

Field	Value

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# # Advanced Retrieval with LangChain

# Standard Library Imports
import getpass
import os
from operator import itemgetter
from uuid import uuid4

# Third-Party Imports
from dotenv import load_dotenv

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❯ /lifesciences-graph-builder What known genes or pathways are implicated in minimizing Doxorubicin toxicity
while preserving its anti-tumor efficacy?

● I'll execute the Fuzzy-to-Fact protocol to answer this question about Doxorubicin toxicity mitigation. Let me start by loading the necessary MCP tools and beginning Phase 1 ANCHOR.

● Now let me load additional tools I'll need for the full protocol.

● Tools loaded. Starting the Fuzzy-to-Fact protocol now.

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Fine-tuning Embeddings for RAG: A Hands-on Walkthrough (2025 Edition)

Introduction

Welcome to this walkthrough on fine-tuning embedding models to enhance Retrieval-Augmented Generation (RAG) systems. This guide will walk you through the steps to fine-tune an embedding model on domain-specific data, evaluate its performance, and implement it into a RAG pipeline.

The core idea behind fine-tuning embeddings is simple:

Move the embeddings for questions relating to a document closer together with that document

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Deep Agents Cloud Deployment Guide

This guide documents how to deploy Deep Agents to LangSmith cloud with a focus on workspace/file lifecycle - a critical topic for production deployments.

Overview

Deep Agents CAN be deployed to LangSmith cloud. From the official LangChain documentation:

"Deep agents applications can be deployed via LangSmith Deployment and monitored with LangSmith Observability."

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Agent Memory - All demos

based on running test script from https://github.com/donbr/agent-memory

uv run python -m agent_memory

Agent Memory - All Demos