Intersect-Collaborations-LLC/research-workflow-assistant

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Open-source AI research assistant for VS Code + GitHub Copilot. Connects to PubMed, OpenAlex, Semantic Scholar, Europe PMC, CrossRef, and Zotero via MCP servers. Custom agents guide systematic reviews, academic writing, data analysis, and project management — all ICMJE-compliant with full audit trails.

23 ★6 forksHTMLUpdated 2mo ago

What you need to know

An open-source, modular AI research assistant integrated into VS Code + GitHub Copilot. It bundles 12 MCP servers for literature databases (PubMed, OpenAlex, Semantic Scholar, Europe PMC, CrossRef), Zotero, PRISMA tracking and Google Workspace, plus custom Copilot agents and Quarto outputs.

Install

git clone the repo and open it in VS Code
python -m venv .venv && pip install -e mcp-servers/_shared -e mcp-servers/pubmed-server ... (12 servers)
cp .env.example .env and configure API keys

Usage

  • •Run @setup for guided configuration, then use @systematic-reviewer, @data-analyst, @academic-writer, etc.
  • •@research-orchestrator coordinates the full workflow

Key features

  • ✓12 bundled MCP servers for literature, references, tracking and Google Workspace
  • ✓Specialist Copilot agents (systematic review, data analysis, academic writing, planning, project management)
  • ✓ICMJE compliance, audit trail and AI disclosure generation
  • ✓Quarto-based reproducible documents (IMRaD, protocols, reports)

Best for

Researchers running systematic reviews and reproducible research in VS Code

Caveats

  • ⚠Designed for VS Code + GitHub Copilot with agent mode enabled
  • ⚠Assumes researchers already have or adopt R/Python/Quarto tooling
Platforms: macOS · Windows · LinuxClients: VS Code · GitHub Copilot

Reviewed 2026-08-11

Topics

academic-writingcrossrefeurope-pmcgithub-copiloticmjeliterature-reviewmcp-servermeta-analysismodel-context-protocolopenalexprismapubmedquartoreference-managementreproducible-researchresearch-assistantsemantic-scholarsystematic-reviewvscodezotero
Stars
23★
Forks
6
Language
HTML
License
MIT
Created
2026-03-08
Last push
2026-06-30