Method design

Skill BioTender-max/awesome-bio-agent-skills/skills/neuroclaw/method-design

A curated collection of AI agent skills for biomedical research, covering genomics, proteomics, single-cell analysis, clinical AI, and protein design.

Install

npx -y skills add BioTender-max/awesome-bio-agent-skills --skill method-design

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What its author says it does

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Use this skill whenever the user wants to formalize a network architecture and derive theoretical components from a research idea. Triggers include: 'method design', 'design method', 'network architecture', 'formula derivation', 'method-design', 'theoretical framework', 'derive equations', or any request to transform IDEA.md into a detailed METHOD.md. This skill is the **mandatory interface-layer method formalizer** in NeuroClaw: it reads IDEA.md, designs concrete network structures (layers, modules, connections), performs mathematical derivations (equations, loss functions, proofs), and always outputs a structured METHOD.md.

The file declares its own license as MIT License (NeuroClaw custom skill – freely modifiable within the project). That is the author’s claim about this one file, and it is not the same thing as the license GitHub reports for the repository, which is listed with the other numbers below.

SKILL.md

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Method Design

Overview

This skill implements the Framework Formalization & Theoretical Derivation process for the NeuroClaw method-design phase.

It acts as the Method Architect within the multi-agent framework:

Reads the latest IDEA.md from the workspace.
Designs the specific neural network structure (e.g., CNN backbone, attention modules, MRI-specific layers) tailored to the neuroscience task.
Derives all necessary formulas (loss functions, gradients, convergence proofs, etc.) using symbolic or step-by-step reasoning.
Produces a clean, publication-ready METHOD.md with sections: Architecture Diagram (text description), Detailed Layers, Mathematical Formulation, Implementation Notes, and Pseudocode.

If any part is ambiguous, it asks the user for clarification before proceeding.
Research use only — the output is a mathematically rigorous METHOD.md ready for experiment-controller and paper-writing.

Quick Reference (Method Flow)

Step	Description	Output File
1. Read & Parse	Load and analyze IDEA.md	01_idea_summary.md
2. Architecture Design	Define network layers & modules	02_architecture.md
3. Formula Derivation	Derive equations & proofs	03_formulas.md
4. Pseudocode & Notes	Generate implementation details	04_pseudocode.md
5. Finalize	Compile and polish	METHOD.md

Installation

# Place files in: skills/method-design/

Important Notes & Limitations

Always starts from the latest IDEA.md; stops and prompts if missing.
Every step saved as numbered .md files for transparency and resumption.
Uses symbolic derivation (no hallucinated math); can call claw-shell or code tools internally for verification.
Final output always saved as METHOD.md in workspace root.
Diagrams are described in text (PlantUML/Mermaid ready); no image generation here.

When to Call This Skill

Immediately after research-idea skill completes IDEA.md
When the user wants to specify network details or mathematical foundation
Before experiment-controller or paper-writing

Complementary / Related Skills

research-idea → provides IDEA.md (input)
experiment-controller → consumes METHOD.md
paper-writing → consumes METHOD.md

Reference

NeuroClaw architecture (section 1.5 method-design skill).
Flow: IDEA.md parsing → architecture design → equation derivation → pseudocode → METHOD.md

Created At: 2026-03-24 00:00 HKT Last Updated At: 2026-03-26 00:14 HKT
Author: chengwang96

What ships with it

Read from the repository

Just SKILL.md. No reference files, no scripts.