research-assistant

name

research-assistant

description

A pipeline where an agent team systematically performs academic research assistance. Use this skill for requests such as 'search for papers,' 'literature review,' 'organize research materials,' 'academic research,' 'organize references,' 'prior research analysis,' 'research trend analysis,' 'literature search,' or 'academic note organization.' Note: experiment execution, statistical analysis execution, final paper writing, and journal submission are outside the scope of this skill.

Research Assistant — Academic Research Assistance Pipeline

An agent team collaborates to execute: literature search, note-taking, critical synthesis, and reference management.

Execution Mode

Agent Team — Five agents communicate directly via SendMessage and perform cross-validation.

Agent Composition

Agent	File	Role	Type
literature-searcher	.claude/agents/literature-searcher.md	Literature search, relevance filtering	general-purpose
note-taker	.claude/agents/note-taker.md	Structured reading note creation	general-purpose
critic-synthesizer	.claude/agents/critic-synthesizer.md	Critical analysis, thematic synthesis	general-purpose
reference-manager	.claude/agents/reference-manager.md	Bibliographic information, citation format management	general-purpose
research-coordinator	.claude/agents/research-coordinator.md	Quality verification, final summary	general-purpose

Workflow

Phase 1: Preparation (Performed Directly by Orchestrator)

1. Extract from user input:
   • Research Topic/Question: What to investigate
   • Research Purpose (optional): Paper writing, presentation, report, etc.
   • Citation Format (optional): APA, MLA, Chicago, etc. (default: APA 7th)
   • Scope Limitations (optional): Time period, language, field, number of sources
   • Existing Materials (optional): Already collected papers, notes
2. Create the _workspace/ directory in the project root
3. Organize inputs and save to _workspace/00_input.md
4. If existing materials are provided, copy them to _workspace/ and skip the relevant phase
5. Determine the execution mode based on the scope of the request

Phase 2: Team Assembly and Execution

Order	Task	Owner	Dependencies	Deliverable
1	Literature Search	literature-searcher	None	_workspace/01_literature_search.md
2a	Reading Notes	note-taker	Task 1	_workspace/02_reading_notes.md
2b	Draft Bibliography	reference-manager	Task 1	_workspace/04_bibliography.md (draft)
3	Critical Synthesis	critic-synthesizer	Task 2a	_workspace/03_critical_synthesis.md
4	Final Bibliography	reference-manager	Task 3	_workspace/04_bibliography.md (final)
5	Research Coordination	research-coordinator	Tasks 2a, 3, 4	_workspace/05_research_summary.md

Tasks 2a (notes) and 2b (draft bibliography) are executed in parallel.

Inter-agent Communication Flow:

• literature-searcher completes -> Delivers source list and priorities to note-taker; delivers bibliographic info to reference-manager
• note-taker completes -> Delivers notes and connections to critic-synthesizer
• critic-synthesizer completes -> Delivers citation list to reference-manager
• research-coordinator cross-verifies all deliverables. When RED issues are found, sends correction requests to the relevant agent -> rework -> re-verification (up to 2 rounds)

Phase 3: Integration and Final Deliverables

1. Review all files in _workspace/
2. Confirm all RED items from the research coordination report have been addressed
3. Present the final summary to the user:
   • Literature Search Results — 01_literature_search.md
   • Reading Notes — 02_reading_notes.md
   • Critical Synthesis — 03_critical_synthesis.md
   • Bibliography — 04_bibliography.md
   • Research Report — 05_research_summary.md

Execution Modes by Request Scope

User Request Pattern	Execution Mode	Deployed Agents
"Do a literature review," "Prior research analysis"	Full Pipeline	All 5 agents
"Just search for papers"	Search Mode	literature-searcher + reference-manager
"Organize these papers" (existing sources provided)	Note Mode	note-taker + critic-synthesizer + reference-manager
"Change the reference format"	Bibliography Mode	reference-manager solo
"Synthesize and analyze these sources"	Synthesis Mode	critic-synthesizer + research-coordinator

Using Existing Files: If the user provides a paper list or notes, copy them to _workspace/ and skip the corresponding phase.

Data Transfer Protocol

Strategy	Method	Purpose
File-based	_workspace/ directory	Primary deliverable storage and sharing
Message-based	SendMessage	Real-time critical information transfer, revision requests
Web exploration	WebSearch/WebFetch	Academic resource search and collection

Error Handling

Error Type	Strategy
Web search failure	Recommend based on known major journals and authors; note "search limitations"
Full text inaccessible	Work based on abstracts; mark "full text unverified"
Insufficient sources	Expand search to adjacent fields; label as "preliminary synthesis"
Agent failure	Retry once; if still failing, proceed without that deliverable; note omission in report
Citation format unknown	Apply APA 7th as default; request confirmation from the user

Test Scenarios

Normal Flow

Prompt: "Do a literature review on 'hallucination mitigation techniques in large language models.' Use APA format." Expected Results:

• Literature Search: 10+ sources, Boolean query documented, core/supporting/background classification
• Reading Notes: Structured notes per source, methodology analysis, key quote extraction
• Critical Synthesis: Thematic synthesis, research gap identification, temporal development trajectory
• Bibliography: APA 7th format, in-text citation guide, BibTeX
• Research Report: All consistency matrix items verified

Existing Materials Flow

Prompt: "Organize and synthesize these 5 papers" + paper list provided Expected Results:

• Skip literature search; organize provided paper list as 01_literature_search.md
• Focus on note-taker + critic-synthesizer + reference-manager

Error Flow

Prompt: "Find papers on the intersection of quantum computing and machine learning" Expected Results:

• Switch to search mode
• Search for related papers via web search
• If results are limited, expand to adjacent fields + label as "preliminary search"

Agent Extension Skills

Extension skills that enhance each agent's domain expertise:

Agent	Extension Skill	Role
literature-searcher, critic-synthesizer	systematic-review-protocol	PRISMA flow diagram, PICO queries, Boolean strategies, literature quality assessment, thematic synthesis
reference-manager	citation-formatter	APA/MLA/Chicago formats, BibTeX conversion, citation quality checks