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SpatialAI_MCP: Skill for Claude Code

.agents/skills/openproblems-submission/SKILL.md

openproblems-submission is a skill for Claude Code from Rebell-Leader/SpatialAI_MCP. It costs 55 tokens per session (636 once invoked), scanned A, original, Apache-2.0.

A submission workflow for contributing a spatial transcriptomics method to an OpenProblems benchmark, a shared system for comparing analysis methods. It guides creation of a Viash component, a portable benchmark program with defined inputs and outputs.

In plain words
What is it for?
Preparing a benchmark contribution, checking SpatialData or AnnData inputs, configuring Viash components, building containers, running test profiles, and getting a pull request ready.
Why use it?
It helps ensure the method matches the benchmark's data contract, builds correctly, uses fixed software versions, and can be reproduced by others.

Skill for Claude Code

Written for Claude Code: shipped in a Claude Code plugin. Also seen: installed under .agents/ (shared by several agents).

This is Rebell-Leader/SpatialAI_MCP's own configuration. It tells Claude Code how to work on SpatialAI_MCP itself, so it is not a mod to install elsewhere. Copy it as a starting point and replace the rules that are about this project. Everything SpatialAI_MCP configures →

Part of the openproblems-spatial plugin — 4 skills, 1 MCP server shipped together

not rated 4repo 2mo ago A scan 55 tokens original Apache-2.0
View source ↗ Rebell-Leader/SpatialAI_MCP
Reuse

Borrowing it

Nothing to install: this file belongs to Rebell-Leader/SpatialAI_MCP. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.

Copy the file
curl -O https://raw.githubusercontent.com/Rebell-Leader/SpatialAI_MCP/main/.agents/skills/openproblems-submission/SKILL.md
Clone the repo
git clone --depth 1 https://github.com/Rebell-Leader/SpatialAI_MCP

Made for: Claude Code.

Or install openproblems-spatial, the plugin that ships this one along with the rest of its 4 skills, 1 MCP server.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for openproblems-submission

README.md
[![agentmods](https://agentmods.dev/badge/skills/rebell-leader/spatialai_mcp/openproblems-submission/github.svg)](https://agentmods.dev/skills/rebell-leader/spatialai_mcp/openproblems-submission)
Your own site
<a href="https://agentmods.dev/skills/rebell-leader/spatialai_mcp/openproblems-submission"><img src="https://agentmods.dev/badge/skills/rebell-leader/spatialai_mcp/openproblems-submission/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for openproblems-submission

Your own site · 80×15
<a href="https://agentmods.dev/skills/rebell-leader/spatialai_mcp/openproblems-submission"><img src="https://agentmods.dev/badge/skills/rebell-leader/spatialai_mcp/openproblems-submission.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 55 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 636 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.
Origin original No closer match found in the catalogue.
Token cost

What 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.

ModelPer sessionOnce invoked
Fable 5.1 $0.00055 $0.00636
Opus 5 $0.00028 $0.00318
Sonnet 5 $0.00011 $0.00127
Haiku 4.5 $0.00006 $0.00064

Measured 10d ago against content hash 4fdd9a4d93bd, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-09, from the pricing page.

Security

Grade A, and why

openproblems-submission 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 10d 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.

.agents/skills/openproblems-submission/SKILL.md · 52 lines

How it starts

The opening of the file, as written. The whole thing — 52 lines — stays where its author put it; the contents beside it link to each section on GitHub.

OpenProblems submission

Goal: a Viash component that conforms to a task's API, builds cleanly, passes the test profile, and is reproducible — ready for a PR.

Checklist

  1. Repo setup. Clone the target task_* repo and initialize the common/ git submodule (git submodule update --init --recursive). Read the repo's CONTRIBUTING / README for current conventions.

  2. Conform to the component API. Your config.vsh.yaml must __merge__ the correct comp_<stage>.yaml interface and match its inputs/outputs and info/metadata fields. Run analyze_workflow_configuration on the config.

  3. Data contract. Inputs/outputs are SpatialData (zarr) / AnnData as the stage requires. Validate test data with validate_spatial_data and confirm the elements the stage needs are present (check_spatial_data_compatibility for multi-file). State raw-vs-normalized expectations explicitly.

  4. Reproducibility. Build on the shared base images (openproblems/base_python:1 / base_r:1) with __merge__-ed setup partials rather than raw python:*/r-base images. Pin base-image tags and package versions — no unpinned latest. Provide the standard metadata (label, summary, description, links, references/doi) and document every parameter with a default and biological rationale.

  5. Build & test locally (server doesn't run these — use the terminal):

    • viash ns build
    • viash run config.vsh.yaml -- --input <test>.zarr --output tmp/out.zarr
    • viash test config.vsh.yaml — a unit test (test_resources) is expected for every component
    • nextflow run main.nf -profile test,docker

  6. Dependency sanity. Run analyze_workflow_dependencies across the workflow files to catch missing/conflicting containers or libraries.

  7. PR hygiene. Include test data + expected output, document parameter choices, and confirm CI (GitHub Actions) builds and runs the component.

Don't

  • Don't claim the server can build/benchmark/validate-submission automatically — build_openproblems_method, run_openproblems_benchmark, and validate_openproblems_submission are roadmap. Use the validation/analysis tools that exist, and run the build/benchmark steps via local CLIs.

Read the full file on GitHub · 52 lines

Changes

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.

  1. 10d ago First seen · 52 lines · 55 tokens per session scan A 4fdd9a4d93bd

Subscribe to this mod's changes

openproblems-submission is a skill published in the GitHub repository Rebell-Leader/SpatialAI_MCP (4 stars, last pushed 2mo ago), licensed Apache-2.0. It adds 55 tokens to every session and 636 once invoked, about $0.0003 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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