SILO website

The public homepage, documentation, exercises, and browser-based query Console for SILO. The site is a fully client-side React and TypeScript application built with Vite, Tailwind CSS, and daisyUI. It can be hosted as static files and has no backend of its own.

Site areas

• / introduces SILO, its use cases, and the available learning and query tools.
• /docs explains SILO's data and query model and provides the query-language and HTTP API references.
• /exercises teaches the query language through tasks on a fixed SARS-CoV-2 staging dataset. Exercise and reference queries always use the configured exercise server.
• /console connects to a listed public SILO instance or a browser-accessible custom URL, displays /info and default.schema(), runs queries, and renders the results. Deployments may also enable browser-local SILO for preprocessing and querying files that remain on the visitor's device.

The Console sends requests directly from the visitor's browser. The target SILO instance must be reachable from that browser and allow the site's origin through its CORS policy. The site does not collect credentials or proxy requests. Shared Console links store the server and query in the URL fragment, which is not sent to the static site host.

When browser-local SILO is enabled, uploaded files, preprocessing, state loading, and queries remain in the current browser tab. The local database is cleared when the visitor reloads or closes the tab. Processed data can be downloaded as a ZIP and opened again later.

Development

npm install
npm run dev          # http://localhost:5001
npm run typecheck
npm test
npm run check-format
npm run build

Run npm run format before committing formatting-sensitive changes.

npm run build typechecks the application, builds it into dist/, and creates a real index.html for every route. This allows direct loads and browser refreshes on static hosts without SPA fallback rules.

Configuration

Vite reads these variables at build time:

Variable	Default	Purpose
VITE_SILO_DEFAULT_SERVER	GenSpectrum staging SILO	Initial server shown by the Console. Visitors may connect another instance.
VITE_SILO_EXERCISE_SERVER	GenSpectrum staging SILO	Fixed server used by exercises and reference answers. It is not editable in the UI.
VITE_SILO_WASM_ENABLED	false	Adds the opt-in browser-local SILO target. Requires administrator-supplied WASM assets and isolation headers.
VITE_BASE	/	Public base path, such as /silo-console/ for a GitHub Pages project site.

Example:

VITE_SILO_DEFAULT_SERVER=https://silo.example.org npm run build

Browser-local SILO

The pthread-enabled SILO WASM files are supplied separately at build time. Their source commit and GitHub Actions artifact are recorded in silo-wasm-source.txt. Download that artifact and place its two files in .silo-wasm/, or point SILO_WASM_ASSET_DIR at another directory:

gh run download 30373590930 --repo GenSpectrum/LAPIS-SILO --name silo-wasm --dir .silo-wasm
VITE_SILO_WASM_ENABLED=true npm run build
VITE_SILO_WASM_ENABLED=true npm run serve -- --host 127.0.0.1 --port 5001

An enabled build fails when silo_wasm.js or silo_wasm.wasm is absent. Disabled builds omit both files and the local-data tab. GitHub Pages uses the disabled default.

WASM threads require a secure, cross-origin-isolated page. The development/preview server sets the headers when the feature flag is enabled, and the included nginx configuration sets them for container deployments:

Cross-Origin-Opener-Policy: same-origin
Cross-Origin-Embedder-Policy: require-corp

To build the container with local SILO, place the files in .silo-wasm/ before building:

docker build --build-arg VITE_SILO_WASM_ENABLED=true -t silo-website .

Raw preprocessing accepts one preprocessing YAML and the files it references: one plain NDJSON or .zst input, the database configuration, the reference genome, and any configured lineage-definition or phylogenetic-tree files. The browser matches references by filename and reports missing or duplicate selections before loading WASM. Inputs above 500 MB are allowed with a memory warning; whether they fit depends on the resulting SILO indexes and the browser's 2 GiB WASM memory ceiling.

Query results

The Console requests NDJSON and infers a few presentation details from the returned values:

• Uppercase biological strings of at least 40 characters are displayed as sequences.
• Equally sized aligned sequence values can be opened together in the alignment viewer.
• Queries without a top-level .limit(...) are bounded to 100 rows for interactive use. If SILO rejects that limit for an unordered aggregate, the Console retries the original query.
• Long values are collapsed in the result table and can be expanded on demand.

SILO compatibility

silo-version.txt records the SILO commit against which the language reference, syntax highlighting, examples, and exercises were checked. When updating it, compare the site with SILO's documentation/query_documentation.md and validate exercise answers against the configured staging server.

Docker

The multi-stage image builds the static site and serves it with nginx on port 5001.

docker build -t silo-website .
docker run -p 5001:5001 silo-website