Runs a 13-agent deep research pipeline for rigorous academic work on any topic across 7 modes (full research, quick brief, paper review, lit-review, fact-check, Socratic guided research dialogue, and systematic review with optional meta-analysis), covering research-question formulation, Socratic mentoring, methodology design, systematic literature search, source verification, cross-source synthesis, risk-of-bias assessment, meta-analysis, APA 7.0 report compilation, editorial and devil's-advocate review, ethics review, and post-research literature monitoring. Use when the request mentions research, deep research, literature review, systematic review, meta-analysis, PRISMA, evidence synthesis, fact-check, guide my research, help me think through, or 研究, 深度研究, 文獻回顧, 文獻探討, 系統性回顧, 後設分析, 事實查核, 引導我的研究, 幫我釐清, 幫我想想, 我不確定要研究什麼, 研究方向, 研究主題. Part of the AlterLab Academic Skills suite.
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SKILL.md
Instructions source · Aperçu en lecture seule
name
alterlab-deep-research
description
Runs a 13-agent deep research pipeline for rigorous academic work on any topic across 7 modes (full research, quick brief, paper review, lit-review, fact-check, Socratic guided research dialogue, and systematic review with optional meta-analysis), covering research-question formulation, Socratic mentoring, methodology design, systematic literature search, source verification, cross-source synthesis, risk-of-bias assessment, meta-analysis, APA 7.0 report compilation, editorial and devil's-advocate review, ethics review, and post-research literature monitoring. Use when the request mentions research, deep research, literature review, systematic review, meta-analysis, PRISMA, evidence synthesis, fact-check, guide my research, help me think through, or 研究, 深度研究, 文獻回顧, 文獻探討, 系統性回顧, 後設分析, 事實查核, 引導我的研究, 幫我釐清, 幫我想想, 我不確定要研究什麼, 研究方向, 研究主題. Part of the AlterLab Academic Skills suite.
license
MIT
allowed-tools
Read Write Edit Bash WebFetch WebSearch
compatibility
Uses built-in Claude tools only (Read/Write/Edit/Bash/WebFetch/WebSearch); no external API key or account required
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:
Scoping — Research question + methodology blueprint
Investigation — Systematic literature search + source verification
Analysis — Cross-source synthesis + bias check
Composition — Full APA 7.0 report
Review — Editorial + ethics + vulnerability scan
Revision — Final polished report
Trigger Conditions
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
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):
User has no clear research question and wants guided thinking
User asks to be "led", "guided", or "mentored" through research
User expresses uncertainty about what to research or where to start
User wants to brainstorm, explore, or clarify a research direction
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
Scenario
Use Instead
Writing a paper (not researching)
alterlab-paper-writer
Reviewing a paper (structured review)
alterlab-paper-reviewer
Full research-to-paper pipeline
alterlab-research-pipeline
Quick Mode Selection Guide
Your Situation 你的狀況
Recommended Mode
Vague idea, need guidance / 有模糊想法，需要引導
socratic
Clear RQ, need comprehensive research / 有明確 RQ，需要完整研究
full
Need a quick brief (30 min) / 需要快速摘要
quick
Have a paper to evaluate before citing / 有論文需要評估
review
Need literature review for a topic / 需要文獻回顧
lit-review
Need to verify specific claims / 需要查核特定事實
fact-check
Need systematic review / meta-analysis / 系統性回顧或後設分析
systematic-review
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)
#
Agent
Role
Phase
1
research_question_agent
Transforms vague topics into precise, FINER-scored research questions with scope boundaries
Challenges assumptions, tests for logical fallacies, finds alternative explanations, confirmation bias checks
Phase 1, 3, 5, Socratic Layer 2, 4
9
ethics_review_agent
AI-assisted research ethics, attribution integrity, dual-use screening, fair representation
Phase 5
10
socratic_mentor_agent
Q1 journal editor persona; guides research thinking through Socratic questioning across 5 layers
Socratic Mode (Layer 1-5)
11
risk_of_bias_agent
Assesses risk of bias using RoB 2 (RCTs) and ROBINS-I (non-randomized); traffic-light visualization
Systematic Review (Phase 2)
12
meta_analysis_agent
Designs and executes meta-analysis or narrative synthesis; effect sizes, heterogeneity, GRADE
Systematic Review (Phase 3)
13
monitoring_agent
Post-research literature monitoring: digests, retraction alerts, contradictory findings detection
Optional (post-pipeline)
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
Devil's Advocate has 3 mandatory checkpoints; Critical-severity issues block progression
Revision loops capped at 2 iterations; remaining issues become "acknowledged limitations"
Ethics Review can halt delivery for Critical ethics concerns
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
All standard checkpoint rules apply (see Checkpoint Rules below)
Protocol must be registered (or registration recommended) before Phase 2
Risk of bias must be completed for all studies before Phase 3
GRADE assessment required for every pooled outcome
PRISMA checklist compliance verified in Phase 5
Operational Modes
Mode
Agents Active
Output
Word Count
full (default)
All 9 core (excluding socratic_mentor, risk_of_bias, meta_analysis, monitoring)
Full PRISMA 2020 report + forest plot data + GRADE table
5,000-15,000
Failure Paths
See references/failure_paths.md for all failure scenarios, trigger conditions, and recovery strategies across all modes.
Key failure path summary:
Failure Scenario
Trigger Condition
Recovery Strategy
RQ cannot converge
Phase 1 / Layer 1 exceeds multiple rounds while still vague
Provide 3 candidate RQs or suggest lit-review
Insufficient literature
bibliography_agent finds < 5 sources
Expand search strategy, alternative keywords
Methodology mismatch
RQ type misaligned with method capability
Return to Phase 1, suggest 3 alternative methods
Devil's Advocate CRITICAL
Fatal logical flaw discovered
STOP, explain the issue, require correction
Ethics BLOCKED
Serious ethical issue
STOP, list issues and remediation path
Socratic non-convergence
> 10 rounds without convergence
Suggest switching to full mode
User abandons mid-process
Explicitly states they don't want to continue
Save progress, provide re-entry path
Only Chinese-language literature
English search returns empty
Switch to Chinese academic databases
Literature Monitoring (Optional Post-Pipeline)
After any research mode is complete, users can optionally activate the monitoring_agent to set up post-research literature monitoring. This is not part of the main pipeline — it is an auxiliary capability triggered on demand.
See agents/monitoring_agent.md for the detailed agent definition.
See references/literature_monitoring_strategies.md for platform-specific setup guides.
Trigger: "monitor this topic", "set up alerts", "track new publications on this"
Capabilities:
Weekly/monthly monitoring digest generation
Retraction alerts for cited sources
Contradictory findings detection
Key author tracking
Keyword evolution tracking
Input: Completed bibliography + search strategy from any research mode
Output: Monitoring configuration + digest template (markdown)
Limitation: The monitoring agent produces configurations and templates for the user to act on. It cannot run autonomous background monitoring.
Contradiction disclosure — if sources disagree, report both sides with evidence quality comparison
Limitation transparency — every report must have an explicit limitations section
AI disclosure — all reports include a statement that AI-assisted research tools were used
Reproducibility — search strategies, inclusion criteria, and analytical methods must be documented for replication
Socratic integrity — in socratic mode, never give direct answers; always guide through questions
Cross-Agent Quality Alignment
Unified definitions to prevent inconsistency across agents:
Concept
Definition
Applies To
Peer-reviewed
Published in a journal with formal peer review process (editorial review alone does not qualify). Conference proceedings count only if explicitly peer-reviewed
bibliography_agent, source_verification_agent
Currency Rule
Default: published within 5 years. Override by domain: CS/AI = 3 years, History/Philosophy = 20 years, Law = depends on jurisdiction changes. Seminal works exempt regardless of age
bibliography_agent, ethics_review_agent
CRITICAL severity
Issue that, if unresolved, would invalidate a core conclusion or constitute academic misconduct. Requires immediate resolution before pipeline can proceed
All agents
Source Tier
tier_1 = top-quartile peer-reviewed journal; tier_2 = other peer-reviewed; tier_3 = academic but not peer-reviewed; tier_4 = grey literature
bibliography_agent, source_verification_agent
Minimum Source Count
full = 15+, quick = 5-8, lit-review = 25+, systematic-review = all eligible (no limit), fact-check = 3+ per claim
bibliography_agent
Verification Threshold
100% DOI check + 50% WebSearch spot-check
source_verification_agent, ethics_review_agent
Cross-Skill Reference: See shared/handoff_schemas.md for inter-stage data exchange formats.
Integration with Other Skills
This skill is domain-agnostic but composes with other AlterLab skills:
alterlab-deep-research + alterlab-paper-2-web -> Disseminate research as a website / video / poster
alterlab-deep-research + alterlab-paper-writer -> Full research-to-publication pipeline
alterlab-deep-research (socratic) + alterlab-paper-writer (plan) -> Guided research + paper planning
alterlab-deep-research (systematic-review) + alterlab-paper-writer -> PRISMA systematic review paper
alterlab-deep-research -> alterlab-research-pipeline -> End-to-end research → review → finalize workflow
Version History
Current: v2.3 (see frontmatter metadata.version). Latest change: added the
systematic-review mode (PRISMA 2020 pipeline with risk_of_bias_agent and
meta_analysis_agent, PRISMA protocol/report templates, systematic_review_toolkit
reference) and the optional post-pipeline monitoring_agent, bringing the team to
13 agents and 7 modes.
