Autoprotocol experiment plan starter

Skill ma-compbio-lab/SkillFoundry/skills/robotics-lab-automation-and-scientific-instrumentation/autoprotocol-experiment-plan-starter

A framework for discovering, compiling, and validating reusable skills for scientific agents.

Install

npx -y skills add ma-compbio-lab/SkillFoundry --skill autoprotocol-experiment-plan-starter

Assembled from the repository path, not quoted from the project. Check it against their README if it does not work.

SKILL.md

1.3 KB, 290 tokens by cl100k_base, as published. Nobody here has run it

Autoprotocol Experiment Plan Starter

Use this skill to generate a deterministic Autoprotocol JSON plan for a small liquid-handling experiment and inspect a concise execution summary.

What This Skill Does

reads a simple transfer plan from TSV
constructs an Autoprotocol Protocol with source and assay plates
emits machine-readable protocol JSON plus a compact summary of refs and operations

When To Use It

when you need a runnable robotic-experiment-planning starter
when you want a local machine-readable lab plan before targeting a specific robot platform
when you need deterministic protocol artifacts for repository tests

Run

./slurm/envs/instrumentation/bin/python skills/robotics-lab-automation-and-scientific-instrumentation/autoprotocol-experiment-plan-starter/scripts/build_autoprotocol_experiment_plan.py \
  --transfers skills/robotics-lab-automation-and-scientific-instrumentation/autoprotocol-experiment-plan-starter/examples/toy_transfers.tsv \
  --protocol-json scratch/instrumentation/autoprotocol_plan.json \
  --summary-out scratch/instrumentation/autoprotocol_plan_summary.json

Notes

This skill only creates a protocol specification; it does not execute wet-lab work.
The transfer plan is intentionally small and deterministic so the generated JSON stays stable across runs.

Gives 0 of the 12 instructions most plan spec skills give in 290 tokens

Counted across 1,100 of the 1,860 authors here whose files we hold, read 2026-08-06

ask one question at a timein 46 of 1100, across 38 files
Break plans into vertical slicesin 28 of 1100, across 10 files
Publish issues in dependency orderin 27 of 1100, across 9 files
Iterate until user approves the breakdownin 24 of 1100, across 6 files
Explore the repository to understand the codebase statein 24 of 1100, across 7 files
Use domain glossary vocabularyin 23 of 1100, across 5 files
Apply correct triage labels to published issuesin 23 of 1100, across 5 files
Write failing tests before implementation codein 23 of 1100, across 18 files
Prefer AFK slices over HITLin 22 of 1100, across 7 files
ask clarifying questions until requirements are concretein 21 of 1100, across 13 files
Respect existing architecture decision recordsin 20 of 1100, across 5 files
write a specification before writing any codein 20 of 1100, across 12 files

Said here and by no other author read

read a transfer plan from TSV
construct an Autoprotocol Protocol with source plates
emit machine-readable protocol JSON
emit a compact summary of refs and operations

Grouped from the skills themselves: near-identical wordings counted once, and counted by distinct author, so one author publishing three of these counts once. Length counted with cl100k_base; the agent that loads this file may tokenize it differently.