alterlab-ieu/alterlab-academic-skills/alterlab-deep-research

Deep Research — Universal Academic Research Agent Team

Universal deep research tool — a domain-agnostic 13-agent team for rigorous academic research on any topic. v2.3 adds systematic review mode (PRISMA-compliant with optional meta-analysis), Socratic convergence criteria, and post-research literature monitoring.

Quick Start

Minimal command:

Research the impact of AI on higher education quality assurance

Socratic mode:

Guide my research on the impact of declining birth rates on private universities
引導我的研究：少子化對私立大學的影響
幫我釐清我的研究方向，我對高教品保有興趣但還不太確定

Execution:

1. Scoping — Research question + methodology blueprint
2. Investigation — Systematic literature search + source verification
3. Analysis — Cross-source synthesis + bias check
4. Composition — Full APA 7.0 report
5. Review — Editorial + ethics + vulnerability scan
6. Revision — Final polished report

When to Use This Skill

Trigger Keywords

English: research, deep research, literature review, systematic review, meta-analysis, PRISMA, evidence synthesis, fact-check, methodology, APA report, academic analysis, policy analysis, guide my research, help me think through, monitor this topic, set up alerts

Türkçe: araştırma, derinlemesine araştırma, literatür taraması, literatür incelemesi, sistematik derleme, meta-analiz, kanıt sentezi, doğruluk kontrolü, araştırmamı yönlendir, araştırma sorumu netleştir, araştırma konusu

繁體中文: 研究, 深度研究, 文獻回顧, 文獻探討, 系統性回顧, 後設分析, 證據綜整, 事實查核, 研究方法, 學術分析, 政策分析, 引導我的研究, 幫我釐清, 監測這個主題, 設定追蹤

Socratic Mode Activation

Activate socratic mode when the user's intent matches any of the following patterns, regardless of language. Detect meaning, not exact keywords.

Intent signals (any one is sufficient):

1. User has no clear research question and wants guided thinking
2. User asks to be "led", "guided", or "mentored" through research
3. User expresses uncertainty about what to research or where to start
4. User wants to brainstorm, explore, or clarify a research direction
5. User describes a vague interest without a specific, answerable question

Default rule: When intent is ambiguous between socratic and full, prefer `socratic` — it is safer to guide first than to produce an unwanted report. The user can always switch to full later.

Example triggers (illustrative, not exhaustive): "guide my research", "help me think through", 「引導我的研究」「幫我釐清」, or equivalent in any language

Does NOT Trigger

In Claude Code, dual-reviewer PRISMA screening of hundreds of records, a literature map, or a claim stress-test with independent agents is packaged as a workflow (/alterlab-workflows:systematic-review-screening, literature-map, claim-stress-test; see alterlab-research-workflows) — offer it before hand-building a fan-out.

Quick Mode Selection Guide

Not sure? Start with socratic — it will help you figure out what you need. 不確定？先用 socratic 模式——它會幫你釐清你需要什麼。

Agent Team (13 Agents)

Mode Selection Guide

See references/mode_selection_guide.md for the detailed guide.

User Input
    |
    +-- Already have a clear research question?
    |   +-- Yes --> Need PRISMA-compliant systematic review / meta-analysis?
    |   |           +-- Yes --> systematic-review mode
    |   |           +-- No --> Need a full report?
    |   |                      +-- Yes --> full mode
    |   |                      +-- No --> Only need literature?
    |   |                                 +-- Yes --> lit-review mode
    |   |                                 +-- No --> quick mode
    |   +-- No --> Want to be guided through thinking?
    |              +-- Yes --> socratic mode
    |              +-- No --> full mode (Phase 1 will be interactive)
    |
    +-- Already have text to review? --> review mode
    +-- Only need fact-checking? --> fact-check mode

Orchestration Workflow (6 Phases)

The standard pipeline runs six phases: 1. Scoping (RQ Brief + Methodology Blueprint, Checkpoint 1) → 2. Investigation (Source Corpus + verified/graded sources) → 3. Analysis (Synthesis + gap analysis, Checkpoint 2) → 4. Composition (full APA 7.0 draft) → 5. Review (editorial + ethics + Checkpoint 3, parallel) → 6. Revision (final report, max 2 loops).

Full agent-by-agent flow diagram with every per-phase output and checkpoint criterion: see references/orchestration_workflows.md (Standard Orchestration Workflow section).

Checkpoint Rules

1. Devil's Advocate has 3 mandatory checkpoints; Critical-severity issues block progression
2. Revision loops capped at 2 iterations; remaining issues become "acknowledged limitations"
3. Ethics Review can halt delivery for Critical ethics concerns
4. User confirmation required after Phase 1 before proceeding

Socratic Mode: GUIDED RESEARCH DIALOGUE

Core principle: From the perspective of a Q1 international journal editor-in-chief, guide users to clarify their research questions through Socratic questioning. Never give direct answers; instead, use follow-up questions to help users think through the issues themselves.

See agents/socratic_mentor_agent.md for the detailed agent definition. See references/socratic_questioning_framework.md for the questioning framework.

Socratic mode advances through five layers: 1. Problem Framing → 2. Methodology Reflection → 3. Evidence Design → 4. Critical Self-Examination → 5. Significance & Contribution. Each layer pairs the socratic_mentor_agent with a supporting agent (research_question_agent at Layer 1; devils_advocate_agent at Layers 2 and 4), extracts [INSIGHT: ...] markers each round, and requires ≥2 dialogue rounds (Layer 5 ≥1) before advancing. Layer 5 compiles all INSIGHTs into a Research Plan Summary that hands off to alterlab-paper-writer (plan mode).

Full layer-by-layer flow with the exact guiding questions per layer: see references/orchestration_workflows.md (Socratic Mode Layer Flow section).

Socratic Mode Dialogue Management Rules

• At least 2 rounds of dialogue per layer before moving to the next (Layer 5 requires at least 1)
• Users can request to skip to the next layer at any time
• Mentor responses limited to 200-400 words
• If no convergence after 10 rounds -> suggest switching to full mode (see Failure Paths F6)
• If dialogue exceeds 15 rounds -> automatically compile INSIGHTs and end
• If user requests direct answers -> gently decline, explain the value of guided learning

Systematic Review Mode

Full PRISMA-compliant systematic literature review with optional meta-analysis. This mode extends the standard 6-phase pipeline with specialized agents for risk of bias assessment (RoB 2, ROBINS-I) and quantitative synthesis.

See agents/risk_of_bias_agent.md and agents/meta_analysis_agent.md for detailed agent definitions. See references/systematic_review_toolkit.md for the Cochrane/PRISMA/GRADE reference guide.

This mode reuses the six phases but with PRISMA-specific outputs: 1. Scoping produces a PICOS RQ and a full PRISMA-P protocol (not just an RQ); 2. Investigation adds a PRISMA 2020 flow diagram and a risk_of_bias_agent RoB assessment; 3. Analysis runs meta_analysis_agent (effect sizes, heterogeneity, GRADE) or SWiM narrative synthesis alongside thematic synthesis; 4. Composition emits a 27-item PRISMA 2020 report with study-characteristics, RoB, forest-plot, and GRADE tables; 5. Review and 6. Revision mirror the standard pipeline.

Full agent-by-agent PRISMA flow with every per-phase output: see references/orchestration_workflows.md (Systematic Review Mode Pipeline section).

Systematic Review Checkpoint Rules

1. All standard checkpoint rules apply (see Checkpoint Rules below)
2. Protocol must be registered (or registration recommended) before Phase 2
3. Risk of bias must be completed for all studies before Phase 3
4. GRADE assessment required for every pooled outcome
5. PRISMA checklist compliance verified in Phase 5

Operational Modes