Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx agentmods add rules/rebell-leader/spatialai_mcp/openproblemsgit clone --depth 1 https://github.com/Rebell-Leader/SpatialAI_MCPWhat it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5 | $0.01429 | $0.01429 |
| Opus 5 | $0.00714 | $0.00714 |
| Sonnet 5 | $0.00286 | $0.00286 |
| Haiku 4.5 | $0.00143 | $0.00143 |
Grade A, and why
openproblems scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 2d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 113 lines — stays where its author put it; the contents beside it link to each section on GitHub.
AGENTS.md — OpenProblems Spatial Transcriptomics Co-pilot
Canonical, provider-neutral instructions for any AI coding agent working in this repository (Claude Code, OpenAI Codex, Cursor, GitHub Copilot, and others). This is the single source of truth. Tool-specific files (
CLAUDE.md,.cursor/rules/,.github/copilot-instructions.md) are generated from this file and theskills/directory byinstaller/— do not edit them by hand.
What this project is
A co-pilot for computational biologists working on the OpenProblems spatial transcriptomics benchmarks. It ships two things:
- An MCP server (
src/openproblems_mcp/) — domain-aware validation and analysis tools for spatial data and bioinformatics workflows, exposed over the Model Context Protocol so any MCP-capable agent can call them. - A provider-agnostic skill installer (
skills/,context/,installer/) — author rules/skills/context once here, then project them into whichever agent the user runs.
Ground truth: which MCP tools actually exist
Only call tools that are registered. As of now the server is read-only analysis — it validates and inspects, it does not execute pipelines.
Available now:
health_check, list_tools_status, get_server_info,
validate_spatial_data, validate_multiple_spatial_files,
analyze_spatial_metadata, check_spatial_data_compatibility,
extract_bioinformatics_metadata, analyze_workflow_configuration,
assess_data_quality, analyze_workflow_dependencies.
Roadmap — NOT implemented, do not call:
run_nextflow_workflow, run_viash_component, build_docker_image,
run_nf_test, analyze_nextflow_log, create_spatial_component,
setup_spatial_environment, and the OpenProblems build/benchmark/submission
tools. For these actions, drive the user's local nextflow / viash / docker
CLIs directly via the terminal instead, and say so plainly.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 2d ago First seen · 113 lines · 1,429 tokens per session scan A 1d8488dd662c
openproblems is a cursor rule published in the GitHub repository Rebell-Leader/SpatialAI_MCP (4 stars, last pushed 2mo ago), licensed Apache-2.0. It adds 1,429 tokens to every session, about $0.0071 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.
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cli-error-handling
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prefer-direct-imports-over-module-mocks
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control-plane-descriptors
Control plane descriptor and instance implementation patterns.
family-instance-domain-actions
Family instance domain action implementation patterns.