/clawpathy-autoresearch
Tuned skill/SKILL.md plus history.jsonl, snapshots, executor_runs
Claude Code
$ npx -y skills add ClawBio/ClawBio --skill clawpathy-autoresearch --agent claude-code
Codex
$ npx skills add ClawBio/ClawBio --skill clawpathy-autoresearch -a codex -y
Cursor
$ npx skills add ClawBio/ClawBio --skill clawpathy-autoresearch -a cursor -y
Gemini CLI
$ npx skills add ClawBio/ClawBio --skill clawpathy-autoresearch -a gemini-cli -y
GitHub Copilot
$ npx skills add ClawBio/ClawBio --skill clawpathy-autoresearch -a github-copilot -y
OpenCode
$ npx skills add ClawBio/ClawBio --skill clawpathy-autoresearch -a opencode -y
Windsurf
$ npx skills add ClawBio/ClawBio --skill clawpathy-autoresearch -a windsurf -y
SKILL.md
clawpathy-autoresearch.SKILL.mdname: clawpathy-autoresearch
description: 'Eval-driven skill tuning. Given a task and an LLM-judge rubric, iteratively rewrites a SKILL.md until a downstream executor agent performs well against the judge. Low-code: all evaluation
is LLM-as-judge, not deterministic Python.'
license: MIT
metadata:
openclaw:
requires:
bins:
- python3
- claude
always: false
emoji: 🔁
homepage: https://github.com/ClawBio/ClawBio
os:
- darwin
- linux
trigger_keywords:
- auto research
- autoresearch
- tune a skill
- skill tuning
- improve a skill
- eval-driven
- clawpathy
- replicate paper
- reproduce paper
author: Jay Moore
inputs:
- name: paper_query_or_task
type: string
description: Paper title/URL/PMID/DOI, or a freeform task description
required: true
outputs:
- name: workspace/
type: directory
description: Tuned skill/SKILL.md plus history.jsonl, snapshots, executor_runs
tags:
- meta
- autoresearch
- skill-tuning
- llm-judge
- eval-driven
version: 1.0.0clawpathy-autoresearch
Eval-driven skill development. The system iteratively rewrites a `SKILL.md` so a downstream executor agent performs better at a task class, as judged by an LLM against a paper/task-specific rubric.
Core idea
propose (sonnet) → execute (sonnet, shell) → judge (opus, rubric)
↑ │
└──────── feedback: verdict + recommended edits ────────┘- **Proposer** rewrites SKILL.md based on the last judge verdict.
- **Executor** runs the new SKILL.md end-to-end inside a workspace.
- **Judge** scores methodology (primary) and outputs (secondary) against
a per-task rubric. Lower is better; 0 = perfect.
- Keep the new SKILL.md only if it strictly beats the best score; else
revert. Stop on target_score or on `early_stop_n` consecutive regressions.
You are the orchestrator
You (the agent reading this) don't run the loop yourself. You dispatch subagents to build the workspace, then hand off to the Python loop.
Phase 1 — Scout
Dispatch a subagent with `prompts/scout.md` to research the paper/task. Report key findings to the user in a few lines.
Phase 2 — Scope (you + user)
Have a conversation. Ask ONE question at a time, multiple-choice where helpful. Agree on:
- what to reproduce / what success looks like
- which data sources are in-bounds
- what methodology expectations belong in the rubric
- iteration budget and target_score (if any)
Present a summary and get approval.
Phase 3 — Build
Dispatch a builder subagent with `prompts/builder.md` and the agreed scope. It writes:
- `task.json`
- `rubric.md` — **the authoritative scoring rubric for the LLM judge**
- `reference/` (optional; judge-only)
- `skill/SKILL.md` — seed
Validate:
from skills.clawpathy_autoresearch import validate_workspace
print(validate_workspace(Path("WORKSPACE"))) # [] means validPhase 4 — Loop
python -m skills.clawpathy_autoresearch WORKSPACE_DIR
# or with custom models:
python -m skills.clawpathy_autoresearch WORKSPACE_DIR \
--proposer-model sonnet --executor-model sonnet --judge-model opus
The loop streams progress to `WORKSPACE/history.jsonl`, snapshots every iteration's skill to `WORKSPACE/snapshots/iter-NNN.md`, and writes the executor's full transcript to `WORKSPACE/executor_runs/iter-NNN.log`.
Workspace layout
workspace/
task.json # task metadata + loop knobs
rubric.md # LLM-judge rubric (the heart of the system)
reference/ # optional ground truth, judge-only
skill/SKILL.md # iterated by the loop
output/ # executor outputs (cleared each iter)
executor_runs/iter-NNN.log # transcripts (judge reads these)
snapshots/iter-NNN.md # per-iter SKILL.md snapshots
history.jsonl # one row per iter: score, kept, verdict
Key principles
- **LLM judge only.** No deterministic Python scorers. All evaluation goes
through `judge.md` + opus. This keeps the system low-code and lets the rubric carry paper-specific nuance without adding code.
- **Methodology is primary.** The rubric weights "did the agent use sound
methods?" above "did the numbers match?". Ground-truth match is a signal, not the objective — the goal is better SKILL.md files.
- **Never leak ground truth.** `reference/` is judge-only. The executor
prompt says not to read it, and the judge penalises leakage.
- **No hardcoded answers in SKILL.md.** The proposer prompt and the judge
both enforce this. The executor must derive results by running methods.
- **Snapshots + strict-better revert.** Score on the first iter becomes the
floor. Later iters that tie or regress revert to the best.
Safety
- All processing is local except scout web fetches for public resources.
- ClawBio disclaimer: research/education tool, not a medical device.
Gotchas
- **Do not skip scoping.** The rubric is paper-specific; a generic rubric
tunes nothing. Get the user to agree on methodology expectations.
- **Do not write a Python scorer.** Earlier versions of this project did.
They rewarded API-fetching, not methodology. The judge is the scorer.
- **Do not hand-pick the "best" snapshot yourself.** Trust the loop. If
the judge is calibrated wrong, fix the rubric, not the history.
Read more
name: clawpathy-autoresearch
description: 'Eval-driven skill tuning. Given a task and an LLM-judge rubric, iteratively rewrites a SKILL.md until a downstream executor agent performs well against the judge. Low-code: all evaluation
is LLM-as-judge, not deterministic Python.'
license: MIT
metadata:
openclaw:
requires:
bins:
- python3
- claude
always: false
emoji: 🔁
homepage: https://github.com/ClawBio/ClawBio
os:
- darwin
- linux
trigger_keywords:
- auto research
- autoresearch
- tune a skill
- skill tuning
- improve a skill
- eval-driven
- clawpathy
- replicate paper
- reproduce paper
author: Jay Moore
inputs:
- name: paper_query_or_task
type: string
description: Paper title/URL/PMID/DOI, or a freeform task description
required: true
outputs:
- name: workspace/
type: directory
description: Tuned skill/SKILL.md plus history.jsonl, snapshots, executor_runs
tags:
- meta
- autoresearch
- skill-tuning
- llm-judge
- eval-driven
version: 1.0.0clawpathy-autoresearch
Eval-driven skill development. The system iteratively rewrites a `SKILL.md` so a downstream executor agent performs better at a task class, as judged by an LLM against a paper/task-specific rubric.
Core idea
propose (sonnet) → execute (sonnet, shell) → judge (opus, rubric)
↑ │
└──────── feedback: verdict + recommended edits ────────┘- **Proposer** rewrites SKILL.md based on the last judge verdict.
- **Executor** runs the new SKILL.md end-to-end inside a workspace.
- **Judge** scores methodology (primary) and outputs (secondary) against
a per-task rubric. Lower is better; 0 = perfect.
- Keep the new SKILL.md only if it strictly beats the best score; else
revert. Stop on target_score or on `early_stop_n` consecutive regressions.
You are the orchestrator
You (the agent reading this) don't run the loop yourself. You dispatch subagents to build the workspace, then hand off to the Python loop.
Phase 1 — Scout
Dispatch a subagent with `prompts/scout.md` to research the paper/task. Report key findings to the user in a few lines.
Phase 2 — Scope (you + user)
Have a conversation. Ask ONE question at a time, multiple-choice where helpful. Agree on:
- what to reproduce / what success looks like
- which data sources are in-bounds
- what methodology expectations belong in the rubric
- iteration budget and target_score (if any)
Present a summary and get approval.
Phase 3 — Build
Dispatch a builder subagent with `prompts/builder.md` and the agreed scope. It writes:
- `task.json`
- `rubric.md` — **the authoritative scoring rubric for the LLM judge**
- `reference/` (optional; judge-only)
- `skill/SKILL.md` — seed
Validate:
from skills.clawpathy_autoresearch import validate_workspace
print(validate_workspace(Path("WORKSPACE"))) # [] means validPhase 4 — Loop
python -m skills.clawpathy_autoresearch WORKSPACE_DIR # or with custom models: python -m skills.clawpathy_autoresearch WORKSPACE_DIR \ --proposer-model sonnet --executor-model sonnet --judge-model opus
The loop streams progress to `WORKSPACE/history.jsonl`, snapshots every iteration's skill to `WORKSPACE/snapshots/iter-NNN.md`, and writes the executor's full transcript to `WORKSPACE/executor_runs/iter-NNN.log`.
Workspace layout
workspace/ task.json # task metadata + loop knobs rubric.md # LLM-judge rubric (the heart of the system) reference/ # optional ground truth, judge-only skill/SKILL.md # iterated by the loop output/ # executor outputs (cleared each iter) executor_runs/iter-NNN.log # transcripts (judge reads these) snapshots/iter-NNN.md # per-iter SKILL.md snapshots history.jsonl # one row per iter: score, kept, verdict
Key principles
- **LLM judge only.** No deterministic Python scorers. All evaluation goes
through `judge.md` + opus. This keeps the system low-code and lets the rubric carry paper-specific nuance without adding code.
- **Methodology is primary.** The rubric weights "did the agent use sound
methods?" above "did the numbers match?". Ground-truth match is a signal, not the objective — the goal is better SKILL.md files.
- **Never leak ground truth.** `reference/` is judge-only. The executor
prompt says not to read it, and the judge penalises leakage.
- **No hardcoded answers in SKILL.md.** The proposer prompt and the judge
both enforce this. The executor must derive results by running methods.
- **Snapshots + strict-better revert.** Score on the first iter becomes the
floor. Later iters that tie or regress revert to the best.
Safety
- All processing is local except scout web fetches for public resources.
- ClawBio disclaimer: research/education tool, not a medical device.
Gotchas
- **Do not skip scoping.** The rubric is paper-specific; a generic rubric
tunes nothing. Get the user to agree on methodology expectations.
- **Do not write a Python scorer.** Earlier versions of this project did.
They rewarded API-fetching, not methodology. The judge is the scorer.
- **Do not hand-pick the "best" snapshot yourself.** Trust the loop. If
the judge is calibrated wrong, fix the rubric, not the history.
🦖 ClawBio - The first bioinformatics-native AI agent skill library. Local-first. Reproducible. Open. Free.
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Questions about clawpathy-autoresearch.
- Which coding agents can use clawpathy-autoresearch?
- clawpathy-autoresearch installs in Claude Code, Codex, Cursor, Gemini CLI, GitHub Copilot, OpenCode and Windsurf with the skills CLI, using each agent's flag shown on this page. Flowy's auto-invocation, which fires a skill when your prompt matches, runs in Claude Code only.

