Basic Research Design

Basic Research Topic Design

This skill helps users design a biomedical research topic by generating progressive subtitles and a detailed experimental outline.

When to Use

• Use this skill when the request matches its documented task boundary.
• Use it when the user can provide the required inputs and expects a structured deliverable.
• Prefer this skill for repeatable, checklist-driven execution rather than open-ended brainstorming.

Key Features

• Scope-focused workflow aligned to: A biomedical research topic designer that generates progressive experimental subtitles and detailed research outlines based on a given subject. Use when the user wants to design a research proposal, outline experiments for a topic, or structure a biomedical study.
• Documentation-first workflow with no packaged script requirement.
• Reference material available in references/ for task-specific guidance.
• Structured execution path designed to keep outputs consistent and reviewable.

Dependencies

• Python: 3.10+. Repository baseline for current packaged skills.
• Third-party packages: not explicitly version-pinned in this skill package. Add pinned versions if this skill needs stricter environment control.

Example Usage

Skill directory: 20260316/scientific-skills/Protocol Design/basic-research-design
No packaged executable script was detected.
Use the documented workflow in SKILL.md together with the references/assets in this folder.

Example run plan:

1. Read the skill instructions and collect the required inputs.
2. Follow the documented workflow exactly.
3. Use packaged references/assets from this folder when the task needs templates or rules.
4. Return a structured result tied to the requested deliverable.

Implementation Details

See ## Workflow above for related details.

• Execution model: validate the request, choose the packaged workflow, and produce a bounded deliverable.
• Input controls: confirm the source files, scope limits, output format, and acceptance criteria before running any script.
• Primary implementation surface: instruction-only workflow in SKILL.md.
• Reference guidance: references/ contains supporting rules, prompts, or checklists.
• Parameters to clarify first: input path, output path, scope filters, thresholds, and any domain-specific constraints.
• Output discipline: keep results reproducible, identify assumptions explicitly, and avoid undocumented side effects.

Workflow

Follow these steps to generate the research design.

Step 1: Generate Subtitles

1. Identify the Subject (keywords) from the user's request (e.g., "PD-1 in lung cancer").
2. Use the Subtitle Generation Prompt (see references/prompt_templates.md) to generate 6 progressive subtitles.
3. Input for Prompt:
   • <Subject>: The user's subject.

Step 2: Generate Research Outline

1. Take the Subject and the Subtitles generated in Step 1.
2. Use the Research Outline Generation Prompt (see references/prompt_templates.md) to generate the detailed outline.
3. Input for Prompt:
   • <Subject>: The original subject.
   • <Subtitles>: The output from Step 1.

Quality Rules

• Progressive Logic: Ensure the subtitles and experiments show a clear logical progression (screening -> verification -> mechanism -> in vivo).
• Specific Methods: The outline must include specific experimental method names.
• No Summary: Do not output a summary at the end.
• Exact Count: Ensure exactly 6 subtitles are generated in Step 1.

Output Format

Present the final result in Markdown, following the format specified in the prompt templates.

When Not to Use

• Do not use this skill when the required source data, identifiers, files, or credentials are missing.
• Do not use this skill when the user asks for fabricated results, unsupported claims, or out-of-scope conclusions.
• Do not use this skill when a simpler direct answer is more appropriate than the documented workflow.

Required Inputs

• A clearly specified task goal aligned with the documented scope.
• All required files, identifiers, parameters, or environment variables before execution.
• Any domain constraints, formatting requirements, and expected output destination if applicable.

Output Contract

• Return a structured deliverable that is directly usable without reformatting.
• If a file is produced, prefer a deterministic output name such as basic_research_design_result.md unless the skill documentation defines a better convention.
• Include a short validation summary describing what was checked, what assumptions were made, and any remaining limitations.

Validation and Safety Rules

• Validate required inputs before execution and stop early when mandatory fields or files are missing.
• Do not fabricate measurements, references, findings, or conclusions that are not supported by the provided source material.
• Emit a clear warning when credentials, privacy constraints, safety boundaries, or unsupported requests affect the result.
• Keep the output safe, reproducible, and within the documented scope at all times.

Failure Handling

• If validation fails, explain the exact missing field, file, or parameter and show the minimum fix required.
• If an external dependency or script fails, surface the command path, likely cause, and the next recovery step.
• If partial output is returned, label it clearly and identify which checks could not be completed.

Quick Validation

Run this minimal verification path before full execution when possible:

No local script validation step is required for this skill.

Expected output format:

Result file: basic_research_design_result.md
Validation summary: PASS/FAIL with brief notes
Assumptions: explicit list if any