Hacking Cancer Research with LLM-based Agents and the Model Context Protocol

Teaching materials and shared workspace for the hackathon at Institut Curie, Paris, 17–18 September 2026.

Dates Thursday 17 (13:00) – Friday 18 September 2026 · Location Institut Curie, 11 Pierre et Marie Curie, BDD building, Annexes, ground floor · Organisers Laurence Calzone (Institut Curie) and Eliott Jacopin (RIKEN)

Everything here is aimed at beginners with LLM-based agents and MCP. No prior experience with agents, MCP or software engineering at large is assumed.

Start here

If you want to…	Go to
get your laptop ready before the event	docs/setup.md
learn how to write an MCP server	plugins/ (each plugins/demo-*/ is a one-feature server with its own README) and the authoring skill
see what already exists before you build	inventory/
install the demo plugins into your own agent	below

What is in this repository

inventory/          what already exists: servers, skills, and the gaps
plugins/            six installable plugins: one skill, five one-feature MCP servers
tests/              structural checks that every plugin's manifests agree with each other
docs/               setup and background
scripts/            check_servers.py — launches every plugin's server over stdio
plugin.spec.json    the plugin decisions; input to the manifest generator

The repository is also a marketplace of six sibling plugins, each with its own manifests, so the demo servers and skill work in whatever agent you already use.

Install the demo plugins

Six plugins ship in this repository, all offline and instant — no API keys, no network:

Plugin	What it shows	Try this
demo-skill	the Agent Skills syntax: one skill, authoring-an-mcp-server	"Help me write an MCP server for my own analysis."
demo-tools	tools add, subtract, multiply, divide; divide by zero raises ToolError so the model gets a readable error result	"Use demo-tools to divide 10 by 4, then divide 1 by 0."
demo-progress	tool count_to (10 one-second steps by default) with ctx.report_progress each step	"Use demo-progress to count to 10."
demo-elicitation	tool greet that asks the user their name via a Resolve/Elicit resolver; accept/decline/cancel; hosts without form elicitation get an MCP error	"Use demo-elicitation to greet me."
demo-prompt	no tools, one prompt summarise_gene(gene); in Claude Code it appears as /demo-prompt:summarise_gene	run the prompt for TP53
demo-resource	no tools, resource genes://panel (JSON) and template genes://panel/{symbol}; in Claude Code it appears under @	"Read the resource genes://panel/KRAS from demo-resource."

Each plugin directory has its own README with more detail; the table above links to them.

Claude Code

claude plugin marketplace add sysbio-curie/MCP_Hackaton
claude plugin install demo-tools@sysbio-curie

or, inside a session:

/plugin marketplace add sysbio-curie/MCP_Hackaton
/plugin install demo-tools@sysbio-curie

Install several by repeating the install line, e.g. claude plugin install demo-progress@sysbio-curie. Run claude plugin list, or /mcp inside a session, to check that a server connected.

From a local clone, load one plugin without installing it:

claude --plugin-dir plugins/demo-tools

Codex

Unverified — the manifests are written to the published spec but have not been exercised with a live Codex client:

codex plugin marketplace add sysbio-curie/MCP_Hackaton
codex plugin add demo-tools@sysbio-curie

Agent Plugins 1.0 clients (Cursor, GitHub Copilot in VS Code, Kiro)

The Agent Plugins 1.0 spec defines the package — each plugins/<name>/ directory is one — but installation is each client's own. In VS Code: Command Palette → "Chat: Install Plugin from Source", which accepts either a Git URL or a local plugin directory path (e.g. the absolute path of plugins/demo-tools).

VS Code local-path install: to be confirmed by the maintainer. It relies on the root plugin.json files deliberately omitting $schema — see Plugin formats for why. After changing a plugin you must reinstall it in VS Code: it keeps its own copy under ~/Library/Application Support/Code/agentPlugins/ (macOS) and does not pick up edits to the source directory on its own.

Cursor and Kiro: unverified.

Any other MCP host

Copy the server entry out of plugins/<name>/mcp.json and replace ${PLUGIN_ROOT} with the absolute path of that plugin directory. For example, demo-tools:

{
  "mcpServers": {
    "demo-tools": {
      "command": "uv",
      "args": ["run", "--no-project", "--quiet", "--with", "mcp>=2.1,<3",
               "python", "/path/to/MCP_Hackaton/plugins/demo-tools/tools_server.py"]
    }
  }
}

uv run --with builds the environment on first launch, so there is nothing to install first, and because the server is the code in the tree — not a published package — editing it changes what the plugin does.

Plugin formats

One repository, one marketplace, six sibling plugins under plugins/, each self-contained with its own manifests for every ecosystem, because the ecosystem has not converged:

Format	Manifest	MCP config	Marketplace
Agent Plugins 1.0	plugins/<name>/plugin.json	plugins/<name>/mcp.json	.agents/plugins/marketplace.json
Claude Code	plugins/<name>/.claude-plugin/plugin.json	plugins/<name>/.claude-plugin/mcp.json	.claude-plugin/marketplace.json
Codex	plugins/<name>/plugin.json (with Codex extras under extensions["com.openai"])	plugins/<name>/mcp.json	.agents/plugins/marketplace.json

There is no .codex-plugin/ folder — Codex reads the same plugin.json and mcp.json as the open Agent Plugins format — and no root .mcp.json: Claude Code would read a root .mcp.json as project configuration and never expand the placeholder. The only real difference between the two MCP configs is the placeholder for the plugin's own directory — ${PLUGIN_ROOT} in the open format and Codex's, ${CLAUDE_PLUGIN_ROOT} in Claude Code's.

Install strings have the shape <plugin>@sysbio-curie, e.g. demo-tools@sysbio-curie.

The root plugin.json files deliberately omit the Agent Plugins $schema key. VS Code 1.138.0 / GitHub Copilot Chat 0.66.0 routes any plugin.json whose $schema starts with https://agent-plugins.org/schemas/ and ends with /plugin.schema.json to a "copilot native" loader whose placeholder-substitution tables are empty and which sets no working directory, so the server is launched as the literal string ${PLUGIN_ROOT}/tools_server.py with cwd the home directory and never starts (microsoft/vscode #303219 and #305310, both unfixed). Without a matching $schema, VS Code falls through to its Claude-format loader (.claude-plugin/plugin.json), which does substitute both ${CLAUDE_PLUGIN_ROOT} and ${PLUGIN_ROOT}, export them as environment variables, and set cwd to the plugin directory — which is why installing from a local path works there. This is the one place the tree is knowingly non-conformant with Agent Plugins 1.0: tests/test_plugin_structure.py gates the "plugin.json needs $schema" check on its AGENT_PLUGIN_SCHEMA_REQUIRED constant (currently False) for exactly this reason. Once VS Code fixes the loader, flip that constant to True and restore "$schema": "https://agent-plugins.org/schemas/1.0.0/plugin.schema.json" as the first key of each root plugins/<name>/plugin.json (the spawning-agent-plugins generator writes it back on spawn --force, or add it by hand).

Verification status: the Claude Code install path has been verified end to end on the maintainer's machine. VS Code local-path install (Agent Plugins 1.0) is to be confirmed by the maintainer now that the $schema omission above has landed. Codex is written to its published spec only and has not been exercised with a live client.

Which SDK version

All material targets the MCP Python SDK v2 (mcp>=2.1, currently 2.1.1), which implements the 2026-07-28 protocol revision. If a tutorial you find elsewhere says from mcp.server.fastmcp import FastMCP, it is written for v1 and the entry point has changed:

from mcp.server import MCPServer

Two consequences worth knowing before you start: resource.uri is a plain str rather than an AnyUrl, and there are no server-initiated requests, so ctx.elicit() only works on legacy connections — use a Resolve(...) resolver instead. The cheat sheet covers the rest.

Development

uv sync
uv run pytest                          # plugins/ and tests/
uv run python scripts/check_servers.py # launches every plugin's server over stdio

tests/test_plugin_structure.py is the structural checker from the spawning-agent-plugins skill: it guards against drift such as a version mismatch between a plugin's manifests, a plugin missing from the marketplace, or a root .mcp.json reappearing.

To regenerate the manifests after editing plugin.spec.json, use the spawning-agent-plugins skill's generator. Three classes of hand-edit survive generation and a regeneration reports them as kept, which is expected: the ${PLUGIN_ROOT} placeholder in each plugins/*/mcp.json, the relative-path source strings in .claude-plugin/marketplace.json, and the missing $schema in each root plugins/*/plugin.json (see Plugin formats).

Licence

MIT — see LICENSE.