BioModels — the public repository of curated, executable mathematical models of biological systems (SBML, CellML, BioPAX and more), searchable by pathway, disease, organism, gene or author, with the model files themselves and the paper each model came from.
Setup
Choose your client, copy the config, then fill in any required environment variables.
claude mcp add --transport http biomodels https://gateway.pipeworx.io/biomodels/mcp~/.codex/config.toml
[mcp_servers.biomodels]
url = "https://gateway.pipeworx.io/biomodels/mcp"
# codex mcp add biomodels --url https://gateway.pipeworx.io/biomodels/mcp~/.cursor/mcp.json
{
"mcpServers": {
"biomodels": {
"url": "https://gateway.pipeworx.io/biomodels/mcp"
}
}
}.vscode/mcp.json
{
"servers": {
"biomodels": {
"type": "http",
"url": "https://gateway.pipeworx.io/biomodels/mcp"
}
}
}~/.gemini/settings.json
{
"mcpServers": {
"biomodels": {
"httpUrl": "https://gateway.pipeworx.io/biomodels/mcp"
}
}
}claude_desktop_config.json · Customize › Connectors › Add custom connector
{
"mcpServers": {
"biomodels": {
"command": "npx",
"args": [
"-y",
"mcp-remote",
"https://gateway.pipeworx.io/biomodels/mcp"
]
}
}
}.trae/mcp.json
{
"mcpServers": {
"biomodels": {
"url": "https://gateway.pipeworx.io/biomodels/mcp"
}
}
}