How do I use research-workbench?

1. Click on "Install Server". 2. Wait a few minutes for the server to deploy. Once ready, it will show a "Started" state. 3. In the chat, type @ followed by the MCP server name and your instructions, e.g., "@research-workbench Align avGFP, EGFP, and EBFP and highlight chromophore residues." That's it! The server will respond to your query, and you can continue using it as needed. Here is a step-by-step guide with screenshots.

Research Workbench MCP

In-chat scientific viewers for Langdock (or any MCP Apps host). Same job as the Rosalind Workbench viewers, without GPT-Rosalind.

Rosalind’s model is gated. The interesting part of that product is not the model. It is that the structure, the alignment, and the slide stay in the same thread as the question. That is an MCP App problem, and we can ship it.

What Rosalind actually ships

From the Rosalind Workbench post:

Rosalind surface	What it is	What they demo
Molecular Structure Viewer	3D protein / ligand scene next to the interpretation and sequence	PDB `5LF3` proteasome + bortezomib; GLP1R + semaglutide movie
Biological Sequence & Alignment Viewer	MSA with functional residues marked	avGFP / EGFP / EBFP / ECFP, chromophore 65–67
Slide Viewer	Pan/zoom tissue image with regions to review	Pathology ROI handoff
NGS Analysis Workbench	Plan-first sequencing pipeline	FASTQ → QC → bulk RNA-seq or single-cell

The custom biology model and NVIDIA BioNeMo skills (OpenFold3, Boltz-2, MSA-Search, Parabricks) sit behind those viewers. We do not need them to rebuild the viewers. We do need them if we later want folding, docking, or real NGS compute.

Relevant tools (what we wrap vs what we skip)

Viewers we can own

Mol * — same family of viewer Rosalind is showing. RCSB and PDBe already run it in production.
Custom MSA canvas — no need for a heavy MSA widget; conservation coloring plus residue highlights covers the GFP demo.
OpenSeadragon — the standard WSI / deep-zoom viewer.

Public data APIs (no keys)

RCSB Data + Search API — metadata, sequences, ligands, assemblies.
UniProt REST — accessions and gene searches.
EBI Clustal Omega — real MSA, with a local Needleman–Wunsch fallback.

Not in v1 (compute, not viewing)

BioNeMo / OpenFold / Boltz — structure prediction. Claude Science already wires these; we can add them later as optional tools.
FastQC / salmon / DESeq2 / scanpy — plan_ngs_analysis drafts the Rosalind-style plan. It does not run FASTQ.
Docking and movie export — Mol* can do both; they need more scene-state work than a first demo.

MCP tools

Data tools return JSON. UI tools open an MCP App in the chat.

Tool	Kind	Role
`search_structures`	data	PDB keyword search
`fetch_structure`	data	RCSB metadata + sequences + ligands
`render_structure`	UI	Mol* structure viewer
`fetch_sequences`	data	UniProt fetch / search
`align_sequences`	data	Clustal or local MSA
`render_alignment`	UI	Sequence & alignment viewer
`render_slide`	UI	OpenSeadragon slide viewer
`plan_ngs_analysis`	data	Reviewable NGS plan, no pipeline run

Pattern matches the Langdock cookbook drawio / google-maps apps: data in, HTML resource out, host renders the iframe.

Setup

cd research-workbench
pnpm install
pnpm dev

Server listens on 8787 (3000 is usually the Langdock app). MCP endpoint is /mcp. Health is /health. Set PORT to override.

Optional: CLUSTALO_EMAIL (defaults to research-workbench@langdock.com) for EBI Clustal Omega.

{
  "mcpServers": {
    "research-workbench": {
      "type": "streamable-http",
      "url": "http://localhost:8787/mcp"
    }
  }
}

In Langdock, add it as a custom MCP server with that URL (or the Railway URL after deploy). The host must support MCP Apps for the viewers to render inline.

Demo prompts (Rosalind’s own examples)

Proteasome + bortezomib

Open biological assembly 1 of PDB 5LF3. Color the outer alpha rings teal, the inner beta rings coral, and bortezomib gold. Label the alpha-ring entrance, the catalytic chamber, and a beta5-bound inhibitor.

Expected tool path: fetch_structure → render_structure with assemblyId: "1", chain colors, ligand color, labels.

GFP variants

Align avGFP, EGFP, EBFP, and ECFP. Highlight the chromophore-forming residues and explain how the substitutions change fluorescent color.

Expected tool path: fetch_sequences (P42212 and variants, or a UniProt search) → render_alignment with a highlight on columns 65–67.

Slide review

Open this tissue image and mark regions a pathologist should review.

Pass a JPEG/PNG imageUrl, or a DZI / IIIF tileSource. OpenSeadragon’s public demo tiles work: https://openseadragon.github.io/example-images/highsmith/highsmith.dzi.

NGS plan