Epibricks MCP servers for pathogen analysis agents.

This host publishes seven Streamable HTTP MCP servers: primer design intelligence, Delphy phylogenetics, read-only Pathoplexus sequence access, Nextstrain context, Virological.org post intelligence, and gget genomic reference lookup, and JUNIPER outbreak reconstruction recipes. Agents can discover the tools directly from the endpoints below.

HTTPS online Streamable HTTP MCP Pathoplexus-Agent reports 73 tools mounted

MCP Servers

Each endpoint is independently discoverable by MCP clients. Use the trailing slash URLs for direct Streamable HTTP connections.

Primer MCP

Primer design and primer intelligence tools.

31 tools

Heavy workflow mode: returns local execution recipes

qPrimer ADAPT RAZOR PrimerDB IDT handoff

https://epibricks.sentinel-ai-relay.org/mcp/primer/

Delphy MCP

Delphy phylogenetic inference discovery, run-planning heuristics, and local-run recipes.

11 tools

Heavy workflow mode: returns local execution recipes

version/help inference recipe run heuristics MCC recipe BEAST conversion

https://epibricks.sentinel-ai-relay.org/mcp/delphy/

Pathoplexus MCP

Read-only Pathoplexus sequence metadata and FASTA access.

7 tools

Write access: disabled; read-only LAPIS-backed tools

organisms counts metadata FASTA

https://epibricks.sentinel-ai-relay.org/mcp/pathoplexus/

Nextstrain MCP

Read-only Nextstrain dataset context plus phylogenetic workflow guidance and Nextclade/Augur execution recipes.

8 tools

Execution mode: returns local Nextclade and Augur recipes

Auspice JSON data files clade context Augur-first guidance Nextclade recipe Augur recipe

https://epibricks.sentinel-ai-relay.org/mcp/nextstrain/

Virological MCP

Read-only Virological.org post search, topic fetches, and outbreak-analysis playbook context.

5 tools

Access: public read-only Discourse endpoints

search latest/top topic text analysis playbook

https://epibricks.sentinel-ai-relay.org/mcp/virological/

gget MCP

Curated gget genomic reference lookup and sequence-fetching tools.

6 tools

Access: curated gget modules with bounded MCP responses

Ensembl search gene metadata sequences reference URLs NCBI Virus

https://epibricks.sentinel-ai-relay.org/mcp/gget/

JUNIPER MCP

JUNIPER outbreak reconstruction input guidance, run heuristics, and local R execution recipes.

5 tools

Execution mode: returns local R execution recipes

input checks R install MCMC recipe summaries run heuristics

https://epibricks.sentinel-ai-relay.org/mcp/juniper/

Access

Configure your MCP-capable agent with one or more of these Streamable HTTP URLs. The service currently exposes public read/discovery endpoints over HTTPS.

Connection details

Choose the domain endpoint that matches the work: Primer, Delphy, Pathoplexus, Nextstrain, Virological, gget, or JUNIPER.
Use transport streamable-http.
Use the exact URL with the trailing slash.
Ask the agent to list MCP tools, then call the relevant tool by name.

{
  "mcpServers": {
    "epibricks-primer": {
      "url": "https://epibricks.sentinel-ai-relay.org/mcp/primer/",
      "transport": "streamable-http"
    },
    "epibricks-delphy": {
      "url": "https://epibricks.sentinel-ai-relay.org/mcp/delphy/",
      "transport": "streamable-http"
    },
    "epibricks-pathoplexus": {
      "url": "https://epibricks.sentinel-ai-relay.org/mcp/pathoplexus/",
      "transport": "streamable-http"
    },
    "epibricks-nextstrain": {
      "url": "https://epibricks.sentinel-ai-relay.org/mcp/nextstrain/",
      "transport": "streamable-http"
    },
    "epibricks-virological": {
      "url": "https://epibricks.sentinel-ai-relay.org/mcp/virological/",
      "transport": "streamable-http"
    },
    "epibricks-gget": {
      "url": "https://epibricks.sentinel-ai-relay.org/mcp/gget/",
      "transport": "streamable-http"
    },
    "epibricks-juniper": {
      "url": "https://epibricks.sentinel-ai-relay.org/mcp/juniper/",
      "transport": "streamable-http"
    }
  }
}

Raw discovery check

This JSON-RPC request verifies that an MCP endpoint is reachable and can list tools.

curl -sS -X POST "https://epibricks.sentinel-ai-relay.org/mcp/primer/" \
  -H "Content-Type: application/json" \
  -H "Accept: application/json, text/event-stream" \
  --data '{"jsonrpc":"2.0","id":1,"method":"tools/list","params":{}}'

Primer, Delphy, and JUNIPER design/inference workflows are intentionally recipe-only on this host. The user's agent receives commands and setup instructions, then runs expensive jobs locally or on a worker it controls.

Operational Notes

These notes describe the hosted behavior so agents and users know what will run on the server.

Runs directly here

Primer database searches against enabled public endpoints.
IDT order handoff preparation without purchase submission.
Read-only Pathoplexus metadata and FASTA requests.
Read-only Nextstrain dataset JSON summaries and data file fetches.
Read-only Virological.org public post search, topic fetches, and analysis playbook context.
Curated gget search, info, seq, ref, and guarded virus sequence fetches.

Returned as recipes

qPrimer and ADAPT design workflows.
Delphy inference and postprocessing commands.
Nextclade clade/QC/mutation analysis commands and Augur tree/refine/export commands.
JUNIPER R installation, initialization, MCMC, summarize, and plot workflows.
Any workflow that can become CPU, disk, or runtime intensive, including broad unfiltered gget virus downloads.

Pathoplexus-Agent Reports

A static report index shows agent-authored findings after calling these MCP tools.

AI report gallery

The gallery lists generated reports as clickable cards. It currently contains the June 9, 2026 Pathoplexus Yellow Fever Virus analysis with primer checks, Delphy context-tree output, and downloadable reproducibility files.

https://epibricks.sentinel-ai-relay.org/pathoplexus-agent/

Open the Pathoplexus-Agent reports