Research Assistant — Academic Research Assistance Pipeline

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

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

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

Data Transfer Protocol

Error Handling

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: