Skip to contents


SigRepo_Server

SigRepo_Server is the server half of SigRepo, a platform for storing, sharing, and comparing omic signatures. It is a reproducible framework for deploying a SigRepo instance — locally or on a Linux-based cloud host — and for interacting with it through a REST API, a web interface, and an MCP server for AI agents.

The client half is the SigRepo R package; signatures themselves are represented as R6 objects defined by OmicSignature, our in-house package.

Architecture

The server is a set of containerized services:

  • MySQL database — initializes and manages the SigRepo schema, storing signatures, collections, users, controlled vocabularies (organisms, platforms, sample types, assay types), and gene set resources. Per-signature differential-expression (difexp) tables are held in a companion object store.
  • Plumber REST API — the single access path to the data. It defines the schema, loads reference tables, stores and retrieves difexp objects, authenticates every call by api_key, and exposes the analysis endpoints (signature comparison, enrichment) so that analysis runs server-side rather than requiring users to download whole signatures.
  • Web interface — a React single-page app, built to static assets and served by nginx, which also proxies /api to the API container so the browser talks to a single origin. It replaced the R Shiny dashboard, which is archived in SigRepo_Server_Legacy.
  • MCP server — a Model Context Protocol endpoint that lets AI agents search signatures, retrieve signature context, compare signatures, browse gene sets, and run enrichment, grounded in the stored data. It sits behind a rate-limiting reverse proxy and is reachable at https://sigrepo.org/mcp/.

Because analyses are exposed as discrete API endpoints over a common signature representation, additional analysis engines and external gene-set resources can be added as new endpoints without changing the database schema.

Our deployed instance

Our team runs a SigRepo server on DigitalOcean.

Analysis endpoints

Beyond storage and retrieval, the API supports analysis over stored signatures:

  • Signature comparison — any set of signatures can be compared by feature overlap (Jaccard index with Fisher exact tests), by rank-based Kolmogorov–Smirnov statistics, or by GSEA, returning similarity matrices and, for GSEA, per-pair leading-edge data. Bi-directional signatures are compared per matched group label.
  • Gene set enrichment — over-representation and rank-based enrichment against MSigDB via hypeR, with MSigDB collections cached server-side.

In development

Active work, not yet part of the deployed stack:

  • AI-assisted signature authoring — an agent service that reads a study’s differential-expression output and description, proposes metadata from SigRepo’s controlled vocabularies, and emits a validated OmicSignature for the depositor to review, so contributing a signature becomes a review step rather than a curation task.
  • Additional external gene-set resources for matching stored signatures against published gene sets.

Deployment

See the installation guide for standing up your own instance. The stack is defined with docker compose; the MySQL service, the API, the web app, and the MCP server each run as their own container on a shared internal network, with only the intended ports published.