Research Workflow Assistant

An open-source, modular AI research assistant that runs inside VS Code + GitHub Copilot. It connects to academic databases via MCP (Model Context Protocol) servers and encodes research best practices through custom Copilot agents. Built for reproducibility, ICMJE compliance, and human-centered research.

All RWA outputs — manuscripts, protocols, reports, analysis scripts, dashboards, and progress briefs — use Quarto (by Posit) as the default document format. Quarto supports R and Python code execution, multi-format rendering (HTML, PDF, Word, PowerPoint, dashboards, websites, books, slides), native Mermaid diagrams, and built-in bibliography management. See docs/posit-quarto-guide.md for the full ecosystem guide.

Model note: This project was developed and tested using Claude Opus 4.6 and GPT-5.3-Codex in GitHub Copilot agent mode. You can switch between models depending on task type and preference. Other models available in Copilot (model comparison) may also work, but behavior can vary by agent workflow, so validate critical outputs after switching.

First time here? Start with docs/quick-start.md, or open Copilot Chat and type @setup for an interactive guided setup. If setup is complete and something is not working, use @troubleshooter for diagnostics and issue resolution. For the full walkthrough, see docs/getting-started.md.

Important: Before using non-setup agents, you must accept the user disclaimer once via @setup.

Philosophy

The question isn't which AI research tool to adopt. It's whether researchers have the right tech stack to build their own.

RWA is a proof of concept for what becomes possible when researchers have a capable IDE, open-source tools, and access to a capable LLM. If your researchers already have VS Code, R, Python, Quarto, Markdown, and git, they have the building blocks. Give them LLM access, and someone on the team could build a custom, organization-compliant research workflow assistant in a few weeks, with MCP servers tailored to their specific needs.

Any specific implementation is going to be opinionated. This one integrates with Zotero, enforces ICMJE authorship guidelines, and defaults to Quarto for reproducible documents. Your organization might make entirely different choices, and that's fine.

What matters is not locking researchers into a single platform. Tools that sound impressive but limit you to one documentation system, one output format, one way of working are the kind of constraint that slows people down. The better path: meet researchers where they already are. Make their existing environment AI-capable. Don't replace their tools; connect them.

The stack already exists:

• Positron / VS Code for the IDE
• R and Python for analysis
• Quarto and Markdown for reproducible documents
• Git for version control and collaboration
• MCP for connecting LLMs to structured data sources

The missing piece for most organizations isn't a new product. It's access to a capable LLM within the tools researchers already use, and permission to experiment.

Read the launch post on LinkedIn for the full backstory.

Who Is This For?

Any researcher who wants AI-assisted support without surrendering intellectual ownership:

• NGO and public sector researchers managing evidence reviews or program evaluations
• Government analysts producing policy briefs backed by systematic evidence
• Academic faculty and postdocs running systematic reviews or multi-study projects
• Independent researchers and consultants needing structured, reproducible workflows
• Research organizations wanting standardized, auditable research processes

No PhD required. If you do research, this tool is for you.

What It Does

| Capability | How | |---|---| | Systematic literature reviews | @systematic-reviewer agent guides PRISMA-compliant workflows: question refinement (PICO/PEO/SPIDER), search strategy development, database searching, screening, data extraction, risk of bias | | Academic database access | MCP servers for PubMed, OpenAlex, Semantic Scholar, Europe PMC, CrossRef, Scopus (institutional) | | Reference management | Zotero MCP server: search library, add items by DOI, tag, organize collections, export BibTeX | | Data analysis | @data-analyst agent generates reproducible R or Python analysis scripts in Quarto documents | | Academic writing | @academic-writer agent scaffolds IMRaD manuscripts, manages citations, enforces ICMJE AI disclosure | | Research planning | @research-planner agent helps with protocols, ethics applications, study design, grant writing | | Project management | @project-manager agent tracks phases, milestones, tasks, decisions; generates progress briefs for colleagues | | End-to-end orchestration | @research-orchestrator routes workflows across specialist agents, tracks stage progression, and provides ready-to-run handoff prompts | | Troubleshooting and support | @troubleshooter agent diagnoses environment and MCP issues, validates API keys, and provides practical how-to help for day-to-day RWA usage | | Development and bug fixes | @developer agent gathers requirements for bug fixes, feature requests, and codebase improvements, then directs to plan mode for implementation | | Chat session export | Export Copilot Chat conversations to QMD for reproducibility via scripts/export_chat_session.py or chat-exporter MCP server | | ICMJE compliance | Built into every agent: human-in-the-loop mandate, audit trail, AI disclosure generation, authorship checklist |

Architecture

graph TB
    YOU["👤 You · the Researcher<br/>All decisions · All ownership · All accountability"]

    VSCODE["VS Code + GitHub Copilot Chat"]

    YOU --> VSCODE

    subgraph AGENTS["Specialist AI Agents"]
        direction LR
        ORCH["@research-orchestrator<br/>End-to-end<br/>workflow routing"] ~~~ SR["@systematic-reviewer<br/>PRISMA-compliant<br/>evidence reviews"] ~~~ RP["@research-planner<br/>Protocols &<br/>study design"] ~~~ DA["@data-analyst<br/>Reproducible R / Python<br/>analysis scripts"] ~~~ AW["@academic-writer<br/>Manuscript drafting<br/>& citations"] ~~~ PM["@project-manager<br/>Milestones, decisions<br/>& progress briefs"] ~~~ TS["@troubleshooter<br/>Diagnostics &<br/>environment fixes"] ~~~ DEV["@developer<br/>Bug fixes &<br/>feature planning"]
    end

    VSCODE --> AGENTS

    ICMJE["🔒 ICMJE Compliance Layer<br/>Human-in-the-loop · Audit trail · AI disclosure"]

    AGENTS --> ICMJE

    subgraph MCP["MCP Servers · Model Context Protocol"]
        direction LR
        subgraph LITERATURE["Literature Databases"]
            direction LR
            PUB["PubMed<br/>NCBI E-utilities"] ~~~ OA["OpenAlex<br/>REST API"] ~~~ SS["Semantic Scholar<br/>Academic Graph"] ~~~ EPMC["Europe PMC<br/>REST API"] ~~~ CR["CrossRef<br/>DOI metadata"]
        end
        subgraph REFERENCE["Reference Management"]
            direction LR
            ZOT["Zotero Web<br/>API v3"] ~~~ ZLOC["Zotero Local<br/>PDFs & annotations"]
        end
        subgraph TRACKING["Project Tracking"]
            direction LR
            PRISMA["PRISMA Tracker<br/>flow diagrams"] ~~~ PROJ["Project Tracker<br/>tasks & milestones"] ~~~ CHATEX["Chat Exporter<br/>session audit trails"]
        end
    end

    ICMJE --> MCP

    subgraph OUTPUTS["Research Outputs"]
        direction LR
        QMD["📄 Quarto Documents<br/>Manuscripts · Protocols · Reports"] ~~~ SCRIPTS["📊 Analysis Scripts<br/>R · Python · Reproducible"] ~~~ PFLOW["📋 PRISMA Flow<br/>Diagrams & Checklists"] ~~~ BRIEFS["📝 Progress Briefs<br/>Decision logs · Meeting notes"]
    end

    MCP --> OUTPUTS

    %% ── Styles ──
    classDef researcher fill:#2563eb,stroke:#1e40af,color:#fff,font-weight:bold
    classDef vscode fill:#007acc,stroke:#005a9e,color:#fff,font-weight:bold
    classDef agent fill:#7c3aed,stroke:#5b21b6,color:#fff
    classDef compliance fill:#dc2626,stroke:#991b1b,color:#fff,font-weight:bold
    classDef litdb fill:#10b981,stroke:#047857,color:#fff
    classDef refmgmt fill:#14b8a6,stroke:#0d9488,color:#fff
    classDef tracking fill:#06b6d4,stroke:#0891b2,color:#fff
    classDef output fill:#d97706,stroke:#b45309,color:#fff

    class YOU researcher
    class VSCODE vscode
    class ORCH,SR,RP,DA,AW,PM,TS,DEV agent
    class ICMJE compliance
    class PUB,OA,SS,EPMC,CR litdb
    class ZOT,ZLOC refmgmt
    class PRISMA,PROJ tracking
    class QMD,SCRIPTS,PFLOW,BRIEFS output

Also available as SVG, rendered HTML (quarto render docs/architecture-diagram.qmd), or Mermaid source.

ICMJE Compliance: You Are the Author

This tool is designed around the ICMJE authorship criteria. AI cannot be an author. You must meet all four criteria:

1. Substantial contributions to conception, design, data acquisition, analysis, or interpretation
2. Drafting or critically revising the work for important intellectual content
3. Final approval of the version to be published
4. Accountability for all aspects of the work

The tool enforce