diff --git a/.github/workflows/example-data-seeder.yml b/.github/workflows/example-data-seeder.yml
index 1b06a9f8c..c759a77e3 100644
--- a/.github/workflows/example-data-seeder.yml
+++ b/.github/workflows/example-data-seeder.yml
@@ -6,8 +6,24 @@ env:
   DOCKER_IMAGE_NAME: ghcr.io/genspectrum/dashboards/example-data-seeder
 
 jobs:
+  test:
+    name: Test Example Data Seeder
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+
+      - uses: prefix-dev/setup-pixi@v0.9.6
+        with:
+          manifest-path: collection-seeding/pixi.toml
+          environments: test
+
+      - name: Run tests
+        working-directory: ./collection-seeding
+        run: pixi run -e test test
+
   dockerImage:
     name: Build Example Data Seeder Docker Image
+    needs: test
     runs-on: ubuntu-latest
     permissions:
       contents: read
@@ -37,7 +53,7 @@ jobs:
       - name: Build and push image
         uses: docker/build-push-action@v7
         with:
-          context: ./example-data
+          context: ./collection-seeding
           tags: ${{ steps.dockerMetadata.outputs.tags }}
           cache-from: type=gha,scope=example-data-seeder-${{ github.ref }}
           cache-to: type=gha,mode=max,scope=example-data-seeder-${{ github.ref }}
diff --git a/.gitignore b/.gitignore
index 35cd109ad..7ac7e8013 100644
--- a/.gitignore
+++ b/.gitignore
@@ -13,3 +13,10 @@ logs
 node_modules/
 
 .env
+
+# Python
+__pycache__/
+*.pyc
+
+# pixi
+.pixi/
diff --git a/backend/src/main/kotlin/org/genspectrum/dashboardsbackend/controller/CollectionsController.kt b/backend/src/main/kotlin/org/genspectrum/dashboardsbackend/controller/CollectionsController.kt
index b11e366df..d596c76a1 100644
--- a/backend/src/main/kotlin/org/genspectrum/dashboardsbackend/controller/CollectionsController.kt
+++ b/backend/src/main/kotlin/org/genspectrum/dashboardsbackend/controller/CollectionsController.kt
@@ -24,16 +24,19 @@ class CollectionsController(private val collectionModel: CollectionModel) {
     @Operation(
         summary = "Get collections",
         description = "Returns collections filtered by optional userId and/or organism parameters. " +
-            "Set includeVariants=true to include the full variant list; by default only variantCount is returned.",
+            "Set includeVariants=true to include the full variant list; by default only variantCount is returned. " +
+            "Set excludeSystemCollections=true to exclude collections owned by the system user.",
     )
     fun getCollections(
         @RequestParam(required = false) userId: Long?,
         @RequestParam(required = false) organism: String?,
         @RequestParam(required = false, defaultValue = "false") includeVariants: Boolean,
+        @RequestParam(required = false, defaultValue = "false") excludeSystemCollections: Boolean,
     ): List<Collection> = collectionModel.getCollections(
         userId = userId,
         organism = organism,
         includeVariants = includeVariants,
+        excludeSystemCollections = excludeSystemCollections,
     )
 
     @GetMapping("/collections/{id}", produces = [MediaType.APPLICATION_JSON_VALUE])
diff --git a/backend/src/main/kotlin/org/genspectrum/dashboardsbackend/model/collection/CollectionModel.kt b/backend/src/main/kotlin/org/genspectrum/dashboardsbackend/model/collection/CollectionModel.kt
index 958dc06dd..7b645d8d7 100644
--- a/backend/src/main/kotlin/org/genspectrum/dashboardsbackend/model/collection/CollectionModel.kt
+++ b/backend/src/main/kotlin/org/genspectrum/dashboardsbackend/model/collection/CollectionModel.kt
@@ -11,12 +11,14 @@ import org.genspectrum.dashboardsbackend.controller.BadRequestException
 import org.genspectrum.dashboardsbackend.controller.ForbiddenException
 import org.genspectrum.dashboardsbackend.controller.NotFoundException
 import org.genspectrum.dashboardsbackend.model.user.UserEntity
+import org.genspectrum.dashboardsbackend.model.user.UserModel
 import org.genspectrum.dashboardsbackend.util.now
 import org.jetbrains.exposed.v1.core.JoinType
 import org.jetbrains.exposed.v1.core.Op
 import org.jetbrains.exposed.v1.core.and
 import org.jetbrains.exposed.v1.core.count
 import org.jetbrains.exposed.v1.core.eq
+import org.jetbrains.exposed.v1.core.neq
 import org.jetbrains.exposed.v1.core.notInList
 import org.jetbrains.exposed.v1.jdbc.deleteWhere
 import org.jetbrains.exposed.v1.jdbc.select
@@ -27,8 +29,13 @@ import kotlin.time.Instant
 
 @Service
 @Transactional
-class CollectionModel(private val dashboardsConfig: DashboardsConfig) {
-    fun getCollections(userId: Long?, organism: String?, includeVariants: Boolean = false): List<Collection> {
+class CollectionModel(private val dashboardsConfig: DashboardsConfig, private val userModel: UserModel) {
+    fun getCollections(
+        userId: Long?,
+        organism: String?,
+        includeVariants: Boolean = false,
+        excludeSystemCollections: Boolean = false,
+    ): List<Collection> {
         if (userId != null) {
             UserEntity.findById(userId) ?: throw NotFoundException("User $userId not found")
         }
@@ -44,6 +51,12 @@ class CollectionModel(private val dashboardsConfig: DashboardsConfig) {
         if (organism != null) {
             collectionConditions = collectionConditions and (CollectionTable.organism eq organism)
         }
+        if (excludeSystemCollections) {
+            val systemUserId = userModel.getSystemUserId()
+            if (systemUserId != null) {
+                collectionConditions = collectionConditions and (CollectionTable.ownedBy neq systemUserId)
+            }
+        }
 
         val join = CollectionTable.join(VariantTable, JoinType.LEFT)
 
diff --git a/backend/src/main/kotlin/org/genspectrum/dashboardsbackend/model/user/UserModel.kt b/backend/src/main/kotlin/org/genspectrum/dashboardsbackend/model/user/UserModel.kt
index d372430b4..07301699a 100644
--- a/backend/src/main/kotlin/org/genspectrum/dashboardsbackend/model/user/UserModel.kt
+++ b/backend/src/main/kotlin/org/genspectrum/dashboardsbackend/model/user/UserModel.kt
@@ -3,6 +3,7 @@ package org.genspectrum.dashboardsbackend.model.user
 import org.genspectrum.dashboardsbackend.api.PublicUser
 import org.genspectrum.dashboardsbackend.api.User
 import org.genspectrum.dashboardsbackend.api.UserSyncRequest
+import org.genspectrum.dashboardsbackend.config.DashboardsConfig
 import org.genspectrum.dashboardsbackend.controller.NotFoundException
 import org.genspectrum.dashboardsbackend.util.now
 import org.springframework.stereotype.Service
@@ -10,7 +11,19 @@ import org.springframework.transaction.annotation.Transactional
 
 @Service
 @Transactional
-class UserModel {
+class UserModel(private val dashboardsConfig: DashboardsConfig) {
+    // Not `lazy {}` — needs @Transactional to run inside a DB transaction.
+    @Volatile
+    private var systemUserId: Long? = null
+
+    fun getSystemUserId(): Long? {
+        systemUserId?.let { return it }
+        val githubId = dashboardsConfig.systemUser?.githubId ?: return null
+        val id = UserEntity.findByGithubId(githubId)?.id?.value ?: return null
+        systemUserId = id
+        return id
+    }
+
     fun syncUser(request: UserSyncRequest): User {
         val now = now()
         val existing = UserEntity.findByGithubId(request.githubId)
diff --git a/backend/src/test/kotlin/org/genspectrum/dashboardsbackend/controller/CollectionsClient.kt b/backend/src/test/kotlin/org/genspectrum/dashboardsbackend/controller/CollectionsClient.kt
index 067123e73..7e0115666 100644
--- a/backend/src/test/kotlin/org/genspectrum/dashboardsbackend/controller/CollectionsClient.kt
+++ b/backend/src/test/kotlin/org/genspectrum/dashboardsbackend/controller/CollectionsClient.kt
@@ -31,12 +31,14 @@ class CollectionsClient(private val mockMvc: MockMvc, private val objectMapper:
         userId: Long? = null,
         organism: String? = null,
         includeVariants: Boolean = false,
+        excludeSystemCollections: Boolean = false,
     ): ResultActions {
         val params = buildString {
             val queryParams = mutableListOf<String>()
             if (userId != null) queryParams.add("userId=$userId")
             if (organism != null) queryParams.add("organism=$organism")
             if (includeVariants) queryParams.add("includeVariants=true")
+            if (excludeSystemCollections) queryParams.add("excludeSystemCollections=true")
             if (queryParams.isNotEmpty()) {
                 append("?")
                 append(queryParams.joinToString("&"))
@@ -49,8 +51,9 @@ class CollectionsClient(private val mockMvc: MockMvc, private val objectMapper:
         userId: Long? = null,
         organism: String? = null,
         includeVariants: Boolean = false,
+        excludeSystemCollections: Boolean = false,
     ): List<Collection> = deserializeJsonResponse(
-        getCollectionsRaw(userId, organism, includeVariants)
+        getCollectionsRaw(userId, organism, includeVariants, excludeSystemCollections)
             .andExpect(status().isOk),
     )
 
diff --git a/backend/src/test/kotlin/org/genspectrum/dashboardsbackend/controller/CollectionsExcludeSystemCollectionsTest.kt b/backend/src/test/kotlin/org/genspectrum/dashboardsbackend/controller/CollectionsExcludeSystemCollectionsTest.kt
new file mode 100644
index 000000000..e00193bef
--- /dev/null
+++ b/backend/src/test/kotlin/org/genspectrum/dashboardsbackend/controller/CollectionsExcludeSystemCollectionsTest.kt
@@ -0,0 +1,63 @@
+package org.genspectrum.dashboardsbackend.controller
+
+import org.genspectrum.dashboardsbackend.KnownTestOrganisms
+import org.genspectrum.dashboardsbackend.dummyCollectionRequest
+import org.genspectrum.dashboardsbackend.model.user.UserModel
+import org.hamcrest.MatcherAssert.assertThat
+import org.hamcrest.Matchers.hasItem
+import org.hamcrest.Matchers.not
+import org.junit.jupiter.api.Test
+import org.springframework.beans.factory.annotation.Autowired
+import org.springframework.boot.test.autoconfigure.web.servlet.AutoConfigureMockMvc
+import org.springframework.boot.test.context.SpringBootTest
+import org.springframework.context.annotation.Import
+import org.springframework.test.context.TestPropertySource
+
+@SpringBootTest
+@AutoConfigureMockMvc
+@TestPropertySource(
+    properties = [
+        "dashboards.system-user.github-id=test-system-user-exclude-test",
+        "dashboards.system-user.name=Test Bot",
+    ],
+)
+@Import(CollectionsClient::class, UsersClient::class)
+class CollectionsExcludeSystemCollectionsTest(
+    @param:Autowired private val collectionsClient: CollectionsClient,
+    @param:Autowired private val usersClient: UsersClient,
+    @param:Autowired private val userModel: UserModel,
+) {
+    @Test
+    fun `GIVEN system and regular user collections WHEN excludeSystemCollections=true THEN only regular returned`() {
+        val systemUserId = requireNotNull(userModel.getSystemUserId())
+        val regularUserId = usersClient.createUser()
+
+        val systemCollection = collectionsClient.postCollection(
+            dummyCollectionRequest.copy(name = "System Collection", organism = KnownTestOrganisms.Covid.name),
+            systemUserId,
+        )
+        val regularCollection = collectionsClient.postCollection(
+            dummyCollectionRequest.copy(name = "Regular Collection", organism = KnownTestOrganisms.Covid.name),
+            regularUserId,
+        )
+
+        val collections = collectionsClient.getCollections(includeVariants = true, excludeSystemCollections = true)
+
+        assertThat(collections, hasItem(regularCollection))
+        assertThat(collections, not(hasItem(systemCollection)))
+    }
+
+    @Test
+    fun `GIVEN system user collection WHEN not excluding system collections THEN system collection is included`() {
+        val systemUserId = requireNotNull(userModel.getSystemUserId())
+
+        val systemCollection = collectionsClient.postCollection(
+            dummyCollectionRequest.copy(name = "System Collection Visible", organism = KnownTestOrganisms.Covid.name),
+            systemUserId,
+        )
+
+        val collections = collectionsClient.getCollections(includeVariants = true, excludeSystemCollections = false)
+
+        assertThat(collections, hasItem(systemCollection))
+    }
+}
diff --git a/backend/src/test/kotlin/org/genspectrum/dashboardsbackend/controller/CollectionsGetTest.kt b/backend/src/test/kotlin/org/genspectrum/dashboardsbackend/controller/CollectionsGetTest.kt
index 2b9818448..0ecf366ef 100644
--- a/backend/src/test/kotlin/org/genspectrum/dashboardsbackend/controller/CollectionsGetTest.kt
+++ b/backend/src/test/kotlin/org/genspectrum/dashboardsbackend/controller/CollectionsGetTest.kt
@@ -300,6 +300,20 @@ class CollectionsGetTest(
             .andExpect(jsonPath("$[0].variants").doesNotExist())
     }
 
+    @Test
+    fun `GIVEN no system user configured WHEN getting with excludeSystemCollections THEN returns all collections`() {
+        val userId = usersClient.createUser()
+        val collection = collectionsClient.postCollection(dummyCollectionRequest.copy(name = "No System User"), userId)
+
+        val collections = collectionsClient.getCollections(
+            userId = userId,
+            includeVariants = true,
+            excludeSystemCollections = true,
+        )
+
+        assertThat(collections, hasItem(collection))
+    }
+
     @Test
     fun `WHEN getting collections with includeVariants=true THEN variantCount and variants are both present`() {
         val userId = usersClient.createUser()
diff --git a/collection-seeding/.dockerignore b/collection-seeding/.dockerignore
new file mode 100644
index 000000000..2688cbdae
--- /dev/null
+++ b/collection-seeding/.dockerignore
@@ -0,0 +1,7 @@
+*
+!pixi.toml
+!pixi.lock
+!seed.py
+!api.py
+!models.py
+!sources/
diff --git a/collection-seeding/Dockerfile b/collection-seeding/Dockerfile
new file mode 100644
index 000000000..da7b06e63
--- /dev/null
+++ b/collection-seeding/Dockerfile
@@ -0,0 +1,13 @@
+# Stage 1: use pixi to resolve and install dependencies
+FROM ghcr.io/prefix-dev/pixi:0.58.0 AS builder
+WORKDIR /app
+COPY pixi.toml pixi.lock .
+RUN pixi install --frozen
+
+# Stage 2: slim runtime image — copy only the installed site-packages
+FROM python:3.13-slim AS final
+WORKDIR /app
+COPY --from=builder /app/.pixi/envs/default/lib/python3.13/site-packages \
+                    /usr/local/lib/python3.13/site-packages
+COPY . .
+CMD ["python", "seed.py"]
diff --git a/collection-seeding/README.md b/collection-seeding/README.md
new file mode 100644
index 000000000..3ed909a5f
--- /dev/null
+++ b/collection-seeding/README.md
@@ -0,0 +1,59 @@
+# collection-seeding
+
+Seeds the backend with example collections:
+
+- **covid-resistance-mutations** — resistance mutation data for 3CLpro, RdRp, and Spike mAb
+- **covid-pango-lineages** — one collection per pango lineage, with nucleotide substitutions as variants
+- **covid-pango-lineages-sample** — same as above but limited to 10 lineages, for quick testing
+
+The script is idempotent — re-running it will create new collections or update existing ones (matched by name). If a collection's name changes in the source, the old entry is orphaned and a new one is created.
+
+Use `--repeat-interval-hours N` (or `$REPEAT_INTERVAL_HOURS`) to run on a loop — re-seeds every N hours. Without it, the script runs once and exits.
+
+## Via Docker Compose
+
+The seeder runs automatically as part of Docker Compose:
+
+```bash
+BACKEND_TAG=latest WEBSITE_TAG=latest SEEDER_TAG=latest docker compose up
+```
+
+## Running locally
+
+Requires [pixi](https://pixi.sh). Install dependencies once:
+
+```bash
+pixi install
+```
+
+Then use the provided tasks:
+
+```bash
+pixi run seed                    # all sources
+pixi run seed-resistance         # resistance mutations only
+pixi run seed-lineages           # pango lineages only
+pixi run seed-lineages-sample    # first 10 pango lineages (quick test)
+```
+
+To target a different backend:
+
+```bash
+pixi run seed --url http://localhost:4321
+```
+
+Run `pixi run seed --help` for all options, including `--source`, `--list`, `--repeat-interval-hours`, and `--url`.
+
+## Adding a new source
+
+1. Create `sources/your_source.py` and implement the `Source` ABC:
+   ```python
+   from sources import Source
+   from models import Collection
+
+   class YourSource(Source):
+       name = "your-source-name"  # used with --source flag
+
+       def get_collections(self) -> list[Collection]:
+           ...
+   ```
+2. Register it in `sources/registry.py` by adding it to `ALL_SOURCES`.
diff --git a/collection-seeding/api.py b/collection-seeding/api.py
new file mode 100644
index 000000000..bce08cdb3
--- /dev/null
+++ b/collection-seeding/api.py
@@ -0,0 +1,83 @@
+"""Shared backend API client for collection seeders."""
+
+import time
+
+import requests
+
+from models import Collection, ExistingCollection
+
+RETRY_ATTEMPTS = 30
+RETRY_DELAY_S = 2
+
+
+class ApiClient:
+    def __init__(self, base_url: str, api_key: str):
+        self.base_url = base_url.rstrip("/")
+        self._collections_url = f"{self.base_url}/api/collections"
+        self._auth_headers = {"Authorization": f"Bearer {api_key}"}
+
+    def wait_for_api(
+        self, attempts: int = RETRY_ATTEMPTS, delay: float = RETRY_DELAY_S
+    ):
+        """Poll until the API is ready by checking the collections endpoint."""
+        for attempt in range(1, attempts + 1):
+            try:
+                r = requests.get(self._collections_url, timeout=10)
+                if r.ok:
+                    return
+            except requests.RequestException:
+                pass
+            print(f"Waiting for API... (attempt {attempt}/{attempts})")
+            time.sleep(delay)
+        raise RuntimeError(
+            f"API at {self.base_url} did not become ready after {attempts} attempts."
+        )
+
+    def fetch_existing_collections(self, organism: str) -> list[ExistingCollection]:
+        r = requests.get(
+            self._collections_url,
+            params={"organism": organism},
+            headers=self._auth_headers,
+            timeout=10,
+        )
+        if not r.ok:
+            raise RuntimeError(f"GET /api/collections failed: {r.status_code} {r.text}")
+        return r.json()
+
+    def create_collection(self, collection: Collection) -> int:
+        r = requests.post(
+            self._collections_url,
+            headers=self._auth_headers,
+            json=collection,
+            timeout=10,
+        )
+        if r.status_code != 201:
+            raise RuntimeError(
+                f"POST /api/collections failed: {r.status_code} {r.text}"
+            )
+        return r.json()["id"]
+
+    def delete_collection(self, collection_id: int) -> None:
+        r = requests.delete(
+            f"{self._collections_url}/{collection_id}",
+            headers=self._auth_headers,
+            timeout=10,
+        )
+        if not r.ok:
+            raise RuntimeError(
+                f"DELETE /api/collections/{collection_id} failed: {r.status_code} {r.text}"
+            )
+
+    def update_collection(self, collection_id: int, collection: Collection) -> None:
+        # CollectionUpdate has no organism field; sending it causes a 400 (fail-on-unknown-properties=true)
+        body = {k: v for k, v in collection.items() if k != "organism"}
+        r = requests.put(
+            f"{self._collections_url}/{collection_id}",
+            headers=self._auth_headers,
+            json=body,
+            timeout=10,
+        )
+        if not r.ok:
+            raise RuntimeError(
+                f"PUT /api/collections/{collection_id} failed: {r.status_code} {r.text}"
+            )
diff --git a/collection-seeding/models.py b/collection-seeding/models.py
new file mode 100644
index 000000000..e0e636282
--- /dev/null
+++ b/collection-seeding/models.py
@@ -0,0 +1,29 @@
+"""Shared type definitions for collection seeding."""
+
+from typing import TypedDict
+
+
+class FilterObject(TypedDict, total=False):
+    aminoAcidMutations: list[str]
+    nucleotideMutations: list[str]
+
+
+class Variant(TypedDict):
+    type: str
+    name: str
+    filterObject: FilterObject
+
+
+class Collection(TypedDict):
+    name: str
+    organism: str
+    description: str
+    variants: list[Variant]
+
+
+class ExistingCollection(TypedDict):
+    """A collection as returned by the backend (includes the assigned id)."""
+
+    id: int
+    name: str
+    description: str | None
diff --git a/collection-seeding/pixi.lock b/collection-seeding/pixi.lock
new file mode 100644
index 000000000..37e2e83f2
--- /dev/null
+++ b/collection-seeding/pixi.lock
@@ -0,0 +1,1159 @@
+version: 6
+environments:
+  default:
+    channels:
+    - url: https://conda.anaconda.org/conda-forge/
+    indexes:
+    - https://pypi.org/simple
+    packages:
+      linux-64:
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_9.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.4.22-hbd8a1cb_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.45.1-default_hbd61a6d_102.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.8.0-hecca717_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libffi-3.5.2-h3435931_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-he0feb66_18.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-he0feb66_18.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.3-hb03c661_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libmpdec-4.0.0-hb03c661_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.53.1-h0c1763c_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.42-h5347b49_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.2-h25fd6f3_2.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.6-hdb14827_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/openssl-3.6.2-h35e630c_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/python-3.13.13-h6add32d_100_cp313.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/python_abi-3.13-8_cp313.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/readline-8.3-h853b02a_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h366c992_103.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/tzdata-2025c-hc9c84f9_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb78ec9c_6.conda
+      - pypi: https://files.pythonhosted.org/packages/22/30/7cd8fdcdfbc5b869528b079bfb76dcdf6056b1a2097a662e5e8c04f42965/certifi-2026.4.22-py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/fa/07/330e3a0dda4c404d6da83b327270906e9654a24f6c546dc886a0eb0ffb23/charset_normalizer-3.4.7-cp313-cp313-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl
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diff --git a/collection-seeding/pixi.toml b/collection-seeding/pixi.toml
new file mode 100644
index 000000000..f495ccb5b
--- /dev/null
+++ b/collection-seeding/pixi.toml
@@ -0,0 +1,30 @@
+[workspace]
+name = "collection-seeding"
+version = "0.1.0"
+channels = ["conda-forge"]
+platforms = ["linux-64", "osx-arm64", "osx-64", "linux-aarch64"]
+
+[dependencies]
+python = "3.13.*"
+
+[pypi-dependencies]
+requests = ">=2.33.1"
+
+[tasks]
+seed = "python seed.py"
+seed-lineages = "python seed.py --source covid-pango-lineages"
+seed-lineages-sample = "python seed.py --source covid-pango-lineages-sample"
+seed-resistance = "python seed.py --source covid-resistance-mutations"
+
+[feature.test.pypi-dependencies]
+pytest = ">=9.0.3"
+responses = ">=0.26.0"
+ruff = ">=0.9"
+
+[feature.test.tasks]
+test = "pytest"
+lint = "ruff check ."
+format = "ruff format ."
+
+[environments]
+test = { features = ["test"] }
diff --git a/collection-seeding/pytest.ini b/collection-seeding/pytest.ini
new file mode 100644
index 000000000..c7b23ecb1
--- /dev/null
+++ b/collection-seeding/pytest.ini
@@ -0,0 +1,3 @@
+[pytest]
+pythonpath = .
+testpaths = tests
diff --git a/collection-seeding/seed.py b/collection-seeding/seed.py
new file mode 100644
index 000000000..c52140a55
--- /dev/null
+++ b/collection-seeding/seed.py
@@ -0,0 +1,172 @@
+#!/usr/bin/env python3
+"""Seeds example collections into the backend from one or more data sources.
+
+Idempotent: upserts collections by name — creates new ones, updates existing ones.
+
+Run with --help for usage.
+"""
+
+import argparse
+import os
+import sys
+import time
+
+from api import ApiClient
+from models import Collection
+from sources import Source
+from sources.registry import ALL_SOURCES
+
+
+def main():
+    parser = make_parser()
+    args = parser.parse_args()
+
+    source_map = {cls.name: cls() for cls in ALL_SOURCES}
+
+    if args.list:
+        for name in source_map:
+            print(name)
+        return
+
+    if args.source and args.source not in source_map:
+        print(
+            f"Unknown source '{args.source}'. Use --list to see available sources.",
+            file=sys.stderr,
+        )
+        sys.exit(1)
+
+    if not args.api_key:
+        print("Error: --api-key is required (or set $API_KEY).", file=sys.stderr)
+        sys.exit(1)
+
+    client = ApiClient(args.url, args.api_key)
+    print(f"Seeding collections against {args.url} ...")
+
+    active = (
+        [source_map[args.source]]
+        if args.source
+        else [s for s in source_map.values() if s.include_in_default_run]
+    )
+
+    try:
+        if args.wait:
+            client.wait_for_api()
+
+        while True:
+            total_created = 0
+            total_updated = 0
+            total_deleted = 0
+            for source in active:
+                c, u, d = seed_source(client, source)
+                total_created += c
+                total_updated += u
+                total_deleted += d
+            if len(active) > 1:
+                print(
+                    f"\nTotal — created: {total_created}, updated: {total_updated}, deleted: {total_deleted}."
+                )
+            if not args.repeat_interval_hours:
+                break
+            print(f"\nSleeping for {args.repeat_interval_hours}h ...")
+            time.sleep(args.repeat_interval_hours * 3600)
+    except Exception as e:
+        print(f"Error: {e}", file=sys.stderr)
+        sys.exit(1)
+
+
+def seed_source(client: ApiClient, source: Source) -> tuple[int, int, int]:
+    """Upsert collections for one source. Returns (created, updated, deleted) counts.
+    Matching is by name — if a collection's name changes in the source, the old entry is orphaned and a new one is created."""
+    collections = source.get_collections()
+    print(f"\n[{source.name}]")
+
+    existing = client.fetch_existing_collections(source.organism)
+    existing_by_name = {
+        c["name"]: c for c in existing if source.owned_tag in (c["description"] or "")
+    }
+
+    created = 0
+    updated = 0
+    for collection in collections:
+        c, u = _upsert_collection(client, collection, existing_by_name)
+        existing_by_name.pop(collection["name"], None)
+        created += c
+        updated += u
+
+    orphan_ids = [e["id"] for e in existing_by_name.values()]
+    deleted = _delete_collections(client, orphan_ids)
+
+    print(f"  Created: {created}, updated: {updated}, deleted: {deleted}.")
+    return created, updated, deleted
+
+
+def _upsert_collection(
+    client: ApiClient,
+    collection: Collection,
+    existing_by_name: dict,
+) -> tuple[int, int]:
+    existing_entry = existing_by_name.get(collection["name"])
+    if existing_entry:
+        client.update_collection(existing_entry["id"], collection)
+        print(f"  UPDATE id={existing_entry['id']}  {collection['name']}")
+        return 0, 1
+    else:
+        col_id = client.create_collection(collection)
+        print(f"  CREATE id={col_id}  {collection['name']}")
+        return 1, 0
+
+
+def _delete_collections(client: ApiClient, collection_ids: list[int]) -> int:
+    for col_id in collection_ids:
+        client.delete_collection(col_id)
+        print(f"  DELETE id={col_id}")
+    return len(collection_ids)
+
+
+def make_parser() -> argparse.ArgumentParser:
+    parser = argparse.ArgumentParser(
+        description=__doc__,
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+    )
+    parser.add_argument(
+        "-u",
+        "--url",
+        default=os.environ.get("API_URL", "http://localhost:4321"),
+        help="Website base URL serving /api/* (default: $API_URL or http://localhost:4321)",
+    )
+    parser.add_argument(
+        "-k",
+        "--api-key",
+        default=os.environ.get("API_KEY"),
+        help="API key for authentication (default: $API_KEY)",
+    )
+    parser.add_argument(
+        "--wait",
+        action="store_true",
+        default=not sys.stdout.isatty(),
+        help="Retry until API is ready (auto-enabled when no TTY)",
+    )
+    parser.add_argument(
+        "--source",
+        metavar="NAME",
+        help="Only run this source (default: all). Use --list to see available sources.",
+    )
+    parser.add_argument(
+        "--list",
+        action="store_true",
+        help="List available sources and exit",
+    )
+    parser.add_argument(
+        "--repeat-interval-hours",
+        type=float,
+        default=float(os.environ["REPEAT_INTERVAL_HOURS"])
+        if os.environ.get("REPEAT_INTERVAL_HOURS")
+        else None,
+        metavar="HOURS",
+        help="Re-seed every N hours instead of exiting (default: $REPEAT_INTERVAL_HOURS or run once)",
+    )
+    return parser
+
+
+if __name__ == "__main__":
+    main()
diff --git a/collection-seeding/sources/__init__.py b/collection-seeding/sources/__init__.py
new file mode 100644
index 000000000..5f898d4a5
--- /dev/null
+++ b/collection-seeding/sources/__init__.py
@@ -0,0 +1,33 @@
+from abc import ABC, abstractmethod
+
+from models import Collection
+
+
+class Source(ABC):
+    """A data source that produces collections to be seeded into the backend.
+
+    Implement this to add a new source: set a unique `name` (used as the --source flag value),
+    an `organism`, an `owned_tag` (appended to each description and used to identify orphaned
+    collections for deletion), and implement `get_collections` to return the collections to upsert.
+    Then register it in sources/registry.py.
+
+    Set `include_in_default_run = False` for sources that should only be used via --source
+    (e.g. demo/sample sources that overlap with a full source).
+    """
+
+    include_in_default_run: bool = True
+
+    @property
+    @abstractmethod
+    def name(self) -> str: ...
+
+    @property
+    @abstractmethod
+    def organism(self) -> str: ...
+
+    @property
+    @abstractmethod
+    def owned_tag(self) -> str: ...
+
+    @abstractmethod
+    def get_collections(self) -> list[Collection]: ...
diff --git a/collection-seeding/sources/pango_lineages.py b/collection-seeding/sources/pango_lineages.py
new file mode 100644
index 000000000..048d89b64
--- /dev/null
+++ b/collection-seeding/sources/pango_lineages.py
@@ -0,0 +1,92 @@
+import requests
+
+from models import Collection, Variant
+from sources import Source
+
+DATA_URL = (
+    "https://raw.githubusercontent.com/corneliusroemer/pango-sequences"
+    "/refs/heads/main/data/pango-consensus-sequences_summary.json"
+)
+
+
+class PangoLineagesSource(Source):
+    """Source: Pango lineage definitions from corneliusroemer/pango-sequences.
+
+    Creates one collection per lineage, with nucleotide substitutions as variants.
+    """
+
+    name = "covid-pango-lineages"
+    organism = "covid"
+    owned_tag = "#pango-lineage"
+
+    def __init__(self, limit: int | None = None):
+        self._limit = limit
+
+    def get_collections(self) -> list[Collection]:
+        print(f"Fetching lineage data from {DATA_URL} ...")
+        response = requests.get(DATA_URL, timeout=60)
+        response.raise_for_status()
+        entries = list(response.json().values())
+        if self._limit is not None:
+            entries = entries[: self._limit]
+        print(f"  Loaded {len(entries)} lineage(s).")
+        return [self._build_collection(e) for e in entries]
+
+    def _build_collection(self, entry: dict) -> Collection:
+        lineage: str = entry["lineage"]
+        parent: str = entry.get("parent") or "—"
+        clade: str = entry.get("nextstrainClade") or "—"
+        date: str = entry.get("designationDate") or "unknown"
+
+        nuc_subs = [s for s in entry.get("nucSubstitutions", []) if s]
+        aa_subs = [s for s in entry.get("aaSubstitutions", []) if s]
+        nuc_subs_new = [s for s in entry.get("nucSubstitutionsNew", []) if s]
+        aa_subs_new = [s for s in entry.get("aaSubstitutionsNew", []) if s]
+
+        variants: list[Variant] = [
+            {
+                "type": "filterObject",
+                "name": "Nucleotide substitutions",
+                "filterObject": {"nucleotideMutations": nuc_subs},
+            },
+            {
+                "type": "filterObject",
+                "name": "Amino acid substitutions",
+                "filterObject": {"aminoAcidMutations": aa_subs},
+            },
+            {
+                "type": "filterObject",
+                "name": "New nucleotide substitutions",
+                "filterObject": {"nucleotideMutations": nuc_subs_new},
+            },
+            {
+                "type": "filterObject",
+                "name": "New amino acid substitutions",
+                "filterObject": {"aminoAcidMutations": aa_subs_new},
+            },
+        ]
+
+        description = (
+            f"Pango lineage {lineage}. "
+            f"Parent: {parent}. "
+            f"Nextstrain clade: {clade}. "
+            f"Designated: {date}. "
+            f"{self.owned_tag}"
+        )
+
+        return {
+            "name": lineage,
+            "organism": "covid",
+            "description": description,
+            "variants": variants,
+        }
+
+
+class PangoLineagesSampleSource(PangoLineagesSource):
+    """Same as PangoLineagesSource but limited to the first 10 lineages, for quick testing."""
+
+    name = "covid-pango-lineages-sample"
+    include_in_default_run = False
+
+    def __init__(self):
+        super().__init__(limit=10)
diff --git a/collection-seeding/sources/registry.py b/collection-seeding/sources/registry.py
new file mode 100644
index 000000000..88d704005
--- /dev/null
+++ b/collection-seeding/sources/registry.py
@@ -0,0 +1,15 @@
+"""Registry of all available seeding sources.
+
+To add a new source, import it here and add it to ALL_SOURCES. This is the only
+place that needs to change — seed.py discovers sources exclusively through this list.
+"""
+
+from sources.pango_lineages import PangoLineagesSource, PangoLineagesSampleSource
+from sources.resistance_mutations import ResistanceMutationsSource
+from sources import Source
+
+ALL_SOURCES: list[type[Source]] = [
+    ResistanceMutationsSource,
+    PangoLineagesSource,
+    PangoLineagesSampleSource,
+]
diff --git a/collection-seeding/sources/resistance_mutations.py b/collection-seeding/sources/resistance_mutations.py
new file mode 100644
index 000000000..30ca66501
--- /dev/null
+++ b/collection-seeding/sources/resistance_mutations.py
@@ -0,0 +1,335 @@
+from models import Collection, Variant
+from sources import Source
+
+
+class ResistanceMutationsSource(Source):
+    """Source: SARS-CoV-2 antiviral resistance mutations (ported from seed.mjs).
+
+    Three collections covering 3CLpro, RdRp, and Spike mAb resistance mutations
+    as per the Stanford Coronavirus Antiviral & Resistance database.
+    """
+
+    name = "covid-resistance-mutations"
+    organism = "covid"
+    owned_tag = "#resistance-mutation"
+
+    def get_collections(self) -> list[Collection]:
+        return [
+            {
+                "name": "3CLpro resistance mutations",
+                "organism": "covid",
+                "description": (
+                    "SARS-CoV-2 3C-like protease (3CLpro/Mpro) inhibitor resistance mutations "
+                    "as per Stanford Coronavirus Antiviral & Resistance database "
+                    f"(last updated 21 August 2024). {self.owned_tag}"
+                ),
+                "variants": _build_variants(CLPRO_MUTATIONS, "3CLpro", -3263),
+            },
+            {
+                "name": "RdRp resistance mutations",
+                "organism": "covid",
+                "description": (
+                    "SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) inhibitor resistance mutations "
+                    "as per Stanford Coronavirus Antiviral & Resistance database "
+                    f"(last updated 21 August 2024). {self.owned_tag}"
+                ),
+                "variants": _build_variants(RDRP_MUTATIONS, "RdRp", 9),
+            },
+            {
+                "name": "Spike mAb resistance mutations",
+                "organism": "covid",
+                "description": (
+                    "SARS-CoV-2 Spike monoclonal antibody (mAb) resistance mutations "
+                    "as per Stanford Coronavirus Antiviral & Resistance database "
+                    f"(last updated 21 August 2024). {self.owned_tag}"
+                ),
+                "variants": _build_variants(SPIKE_MUTATIONS, "Spike", 0),
+            },
+        ]
+
+
+def _mature_name(mutation: str, set_name: str, offset: int) -> str:
+    """Convert a genomic mutation code to a mature protein name with the given offset.
+
+    e.g. _mature_name("ORF1a:T3284I", "3CLpro", -3263) -> "3CLpro:T21I"
+    """
+    mut_part = mutation[mutation.index(":") + 1 :]
+    original_base = mut_part[0]
+    new_base = mut_part[-1]
+    position = int("".join(c for c in mut_part if c.isdigit()))
+    return f"{set_name}:{original_base}{position + offset}{new_base}"
+
+
+def _build_variants(mutations: list[str], set_name: str, offset: int) -> list[Variant]:
+    return [
+        {
+            "type": "filterObject",
+            "name": _mature_name(m, set_name, offset),
+            "filterObject": {"aminoAcidMutations": [m]},
+        }
+        for m in mutations
+    ]
+
+
+CLPRO_MUTATIONS = [
+    "ORF1a:T3284I",
+    "ORF1a:T3288A",
+    "ORF1a:T3288N",
+    "ORF1a:T3308I",
+    "ORF1a:D3311Y",
+    "ORF1a:M3312I",
+    "ORF1a:M3312L",
+    "ORF1a:M3312T",
+    "ORF1a:M3312-",
+    "ORF1a:L3313F",
+    "ORF1a:G3401S",
+    "ORF1a:F3403L",
+    "ORF1a:F3403S",
+    "ORF1a:N3405D",
+    "ORF1a:N3405L",
+    "ORF1a:N3405S",
+    "ORF1a:G3406S",
+    "ORF1a:S3407A",
+    "ORF1a:S3407E",
+    "ORF1a:S3407L",
+    "ORF1a:S3407P",
+    "ORF1a:C3423F",
+    "ORF1a:M3428R",
+    "ORF1a:M3428T",
+    "ORF1a:E3429A",
+    "ORF1a:E3429G",
+    "ORF1a:E3429K",
+    "ORF1a:E3429Q",
+    "ORF1a:E3429V",
+    "ORF1a:L3430F",
+    "ORF1a:P3431-",
+    "ORF1a:T3432I",
+    "ORF1a:H3435L",
+    "ORF1a:H3435N",
+    "ORF1a:H3435Q",
+    "ORF1a:H3435Y",
+    "ORF1a:A3436T",
+    "ORF1a:A3436V",
+    "ORF1a:V3449A",
+    "ORF1a:R3451G",
+    "ORF1a:R3451S",
+    "ORF1a:Q3452I",
+    "ORF1a:Q3452K",
+    "ORF1a:T3453I",
+    "ORF1a:A3454T",
+    "ORF1a:A3454V",
+    "ORF1a:Q3455A",
+    "ORF1a:Q3455C",
+    "ORF1a:Q3455D",
+    "ORF1a:Q3455E",
+    "ORF1a:Q3455F",
+    "ORF1a:Q3455G",
+    "ORF1a:Q3455H",
+    "ORF1a:Q3455I",
+    "ORF1a:Q3455K",
+    "ORF1a:Q3455L",
+    "ORF1a:Q3455N",
+    "ORF1a:Q3455P",
+    "ORF1a:Q3455R",
+    "ORF1a:Q3455S",
+    "ORF1a:Q3455T",
+    "ORF1a:Q3455V",
+    "ORF1a:Q3455W",
+    "ORF1a:Q3455Y",
+    "ORF1a:A3456P",
+    "ORF1a:A3457S",
+    "ORF1a:P3515L",
+    "ORF1a:V3560A",
+    "ORF1a:S3564P",
+    "ORF1a:T3567I",
+    "ORF1a:F3568L",
+]
+
+RDRP_MUTATIONS = [
+    "ORF1b:V157A",
+    "ORF1b:V157L",
+    "ORF1b:N189S",
+    "ORF1b:R276C",
+    "ORF1b:A367V",
+    "ORF1b:A440V",
+    "ORF1b:F471L",
+    "ORF1b:D475Y",
+    "ORF1b:A517V",
+    "ORF1b:V548L",
+    "ORF1b:G662S",
+    "ORF1b:S750A",
+    "ORF1b:V783I",
+    "ORF1b:E787G",
+    "ORF1b:C790F",
+    "ORF1b:C790R",
+    "ORF1b:E793A",
+    "ORF1b:E793D",
+    "ORF1b:M915R",
+]
+
+SPIKE_MUTATIONS = [
+    "S:P337H",
+    "S:P337L",
+    "S:P337R",
+    "S:P337S",
+    "S:P337T",
+    "S:E340A",
+    "S:E340D",
+    "S:E340G",
+    "S:E340K",
+    "S:E340Q",
+    "S:E340V",
+    "S:T345P",
+    "S:R346G",
+    "S:R346I",
+    "S:R346K",
+    "S:R346S",
+    "S:R346T",
+    "S:K356Q",
+    "S:K356T",
+    "S:S371F",
+    "S:S371L",
+    "S:D405E",
+    "S:D405N",
+    "S:E406D",
+    "S:K417E",
+    "S:K417H",
+    "S:K417I",
+    "S:K417M",
+    "S:K417N",
+    "S:K417R",
+    "S:K417S",
+    "S:K417T",
+    "S:D420A",
+    "S:D420N",
+    "S:N439K",
+    "S:N440D",
+    "S:N440E",
+    "S:N440I",
+    "S:N440K",
+    "S:N440R",
+    "S:N440T",
+    "S:N440Y",
+    "S:S443Y",
+    "S:K444E",
+    "S:K444F",
+    "S:K444I",
+    "S:K444L",
+    "S:K444M",
+    "S:K444N",
+    "S:K444R",
+    "S:K444T",
+    "S:V445A",
+    "S:V445D",
+    "S:V445F",
+    "S:V445I",
+    "S:V445L",
+    "S:G446A",
+    "S:G446D",
+    "S:G446I",
+    "S:G446N",
+    "S:G446R",
+    "S:G446S",
+    "S:G446T",
+    "S:G446V",
+    "S:G447C",
+    "S:G447D",
+    "S:G447F",
+    "S:G447S",
+    "S:G447V",
+    "S:N448D",
+    "S:N448K",
+    "S:N448T",
+    "S:N448Y",
+    "S:Y449D",
+    "S:N450D",
+    "S:N450K",
+    "S:L452M",
+    "S:L452Q",
+    "S:L452R",
+    "S:L452W",
+    "S:Y453F",
+    "S:Y453H",
+    "S:L455F",
+    "S:L455M",
+    "S:L455S",
+    "S:L455W",
+    "S:F456C",
+    "S:F456L",
+    "S:F456V",
+    "S:S459P",
+    "S:N460D",
+    "S:N460H",
+    "S:N460I",
+    "S:N460K",
+    "S:N460S",
+    "S:N460T",
+    "S:N460Y",
+    "S:A475D",
+    "S:A475V",
+    "S:G476D",
+    "S:G476R",
+    "S:G476T",
+    "S:V483A",
+    "S:E484A",
+    "S:E484D",
+    "S:E484G",
+    "S:E484K",
+    "S:E484P",
+    "S:E484Q",
+    "S:E484R",
+    "S:E484S",
+    "S:E484T",
+    "S:E484V",
+    "S:G485D",
+    "S:G485R",
+    "S:F486D",
+    "S:F486I",
+    "S:F486L",
+    "S:F486N",
+    "S:F486P",
+    "S:F486S",
+    "S:F486T",
+    "S:F486V",
+    "S:N487D",
+    "S:N487H",
+    "S:N487S",
+    "S:Y489H",
+    "S:Y489W",
+    "S:F490G",
+    "S:F490I",
+    "S:F490L",
+    "S:F490R",
+    "S:F490S",
+    "S:F490V",
+    "S:F490Y",
+    "S:Q493D",
+    "S:Q493E",
+    "S:Q493H",
+    "S:Q493K",
+    "S:Q493L",
+    "S:Q493R",
+    "S:Q493V",
+    "S:S494P",
+    "S:S494R",
+    "S:G496S",
+    "S:Q498H",
+    "S:P499H",
+    "S:P499R",
+    "S:P499S",
+    "S:P499T",
+    "S:N501T",
+    "S:N501Y",
+    "S:G504C",
+    "S:G504D",
+    "S:G504I",
+    "S:G504L",
+    "S:G504N",
+    "S:G504R",
+    "S:G504V",
+    "S:P507A",
+    "S:N856K",
+    "S:N969K",
+    "S:E990A",
+    "S:T1009I",
+]
diff --git a/collection-seeding/tests/__init__.py b/collection-seeding/tests/__init__.py
new file mode 100644
index 000000000..e69de29bb
diff --git a/collection-seeding/tests/mock_source.py b/collection-seeding/tests/mock_source.py
new file mode 100644
index 000000000..05e9bc9a7
--- /dev/null
+++ b/collection-seeding/tests/mock_source.py
@@ -0,0 +1,14 @@
+from models import Collection
+from sources import Source
+
+
+class MockSource(Source):
+    name = "mock-source"
+    organism = "covid"
+    owned_tag = "#mock-tag"
+
+    def __init__(self, collections: list[Collection]):
+        self._collections = collections
+
+    def get_collections(self) -> list[Collection]:
+        return self._collections
diff --git a/collection-seeding/tests/test_pango_lineages.py b/collection-seeding/tests/test_pango_lineages.py
new file mode 100644
index 000000000..057301e30
--- /dev/null
+++ b/collection-seeding/tests/test_pango_lineages.py
@@ -0,0 +1,152 @@
+import responses as rsps_lib
+
+from sources.pango_lineages import PangoLineagesSource, DATA_URL
+
+SAMPLE_DATA = {
+    "BA.2": {
+        "lineage": "BA.2",
+        "unaliased": "B.1.1.529.2",
+        "parent": "BA",
+        "nextstrainClade": "22C",
+        "nucSubstitutions": ["C241T", "A23403G", ""],
+        "aaSubstitutions": ["S:N501Y", ""],
+        "nucSubstitutionsNew": ["A23403G"],
+        "aaSubstitutionsNew": ["S:N501Y"],
+        "designationDate": "2022-01-20",
+    },
+    "XBB": {
+        "lineage": "XBB",
+        "unaliased": "XBB",
+        "parent": "",
+        "nextstrainClade": "",
+        "nucSubstitutions": [""],
+        "aaSubstitutions": [""],
+        "nucSubstitutionsNew": [""],
+        "aaSubstitutionsNew": [""],
+        "designationDate": "",
+    },
+    "BA.5": {
+        "lineage": "BA.5",
+        "unaliased": "B.1.1.529.5",
+        "parent": "BA",
+        "nextstrainClade": "22B",
+        "nucSubstitutions": ["C241T", "T19955C"],
+        "aaSubstitutions": ["S:L452R"],
+        "nucSubstitutionsNew": ["T19955C"],
+        "aaSubstitutionsNew": [],
+        "designationDate": "2022-05-06",
+    },
+}
+
+
+def test_name():
+    assert PangoLineagesSource.name == "covid-pango-lineages"
+
+
+# --- _build_collection ---
+
+
+def test_build_collection_basic():
+    col = PangoLineagesSource()._build_collection(SAMPLE_DATA["BA.2"])
+    assert col["name"] == "BA.2"
+    assert col["organism"] == "covid"
+
+
+def test_build_collection_description_format():
+    col = PangoLineagesSource()._build_collection(SAMPLE_DATA["BA.2"])
+    assert "BA.2" in col["description"]
+    assert "BA" in col["description"]  # parent
+    assert "22C" in col["description"]  # clade
+    assert "2022-01-20" in col["description"]
+
+
+def test_build_collection_missing_fields_use_defaults():
+    col = PangoLineagesSource()._build_collection(SAMPLE_DATA["XBB"])
+    assert "—" in col["description"]  # parent and clade fallback
+    assert "unknown" in col["description"]  # date fallback
+
+
+def test_build_collection_always_four_variants():
+    col = PangoLineagesSource()._build_collection(SAMPLE_DATA["BA.2"])
+    assert len(col["variants"]) == 4
+
+
+def test_build_collection_variant_names():
+    col = PangoLineagesSource()._build_collection(SAMPLE_DATA["BA.2"])
+    names = [v["name"] for v in col["variants"]]
+    assert names == [
+        "Nucleotide substitutions",
+        "Amino acid substitutions",
+        "New nucleotide substitutions",
+        "New amino acid substitutions",
+    ]
+
+
+def test_build_collection_variant_filter_keys():
+    col = PangoLineagesSource()._build_collection(SAMPLE_DATA["BA.2"])
+    variants = col["variants"]
+    assert "nucleotideMutations" in variants[0]["filterObject"]
+    assert "aminoAcidMutations" in variants[1]["filterObject"]
+    assert "nucleotideMutations" in variants[2]["filterObject"]
+    assert "aminoAcidMutations" in variants[3]["filterObject"]
+
+
+def test_build_collection_variant_contents():
+    col = PangoLineagesSource()._build_collection(SAMPLE_DATA["BA.2"])
+    variants = col["variants"]
+    assert variants[0]["filterObject"]["nucleotideMutations"] == ["C241T", "A23403G"]
+    assert variants[1]["filterObject"]["aminoAcidMutations"] == ["S:N501Y"]
+    assert variants[2]["filterObject"]["nucleotideMutations"] == ["A23403G"]
+    assert variants[3]["filterObject"]["aminoAcidMutations"] == ["S:N501Y"]
+
+
+def test_build_collection_filters_blank_subs():
+    col = PangoLineagesSource()._build_collection(SAMPLE_DATA["BA.2"])
+    # nucSubstitutions has ["C241T", "A23403G", ""] — blank should be dropped
+    nuc = col["variants"][0]["filterObject"]["nucleotideMutations"]
+    assert "" not in nuc
+    assert len(nuc) == 2
+
+
+def test_build_collection_empty_lists_when_all_blanks():
+    col = PangoLineagesSource()._build_collection(SAMPLE_DATA["XBB"])
+    assert len(col["variants"]) == 4
+    for v in col["variants"]:
+        lists = list(v["filterObject"].values())
+        assert lists == [[]]
+
+
+# --- get_collections ---
+
+
+@rsps_lib.activate
+def test_get_collections_fetches_data_url():
+    rsps_lib.add(rsps_lib.GET, DATA_URL, json=SAMPLE_DATA, status=200)
+    PangoLineagesSource().get_collections()
+    assert len(rsps_lib.calls) == 1
+    assert rsps_lib.calls[0].request.url == DATA_URL
+
+
+@rsps_lib.activate
+def test_get_collections_includes_all_lineages():
+    rsps_lib.add(rsps_lib.GET, DATA_URL, json=SAMPLE_DATA, status=200)
+    cols = PangoLineagesSource().get_collections()
+    # All lineages included regardless of empty subs
+    names = [c["name"] for c in cols]
+    assert "BA.2" in names
+    assert "XBB" in names
+    assert "BA.5" in names
+
+
+@rsps_lib.activate
+def test_get_collections_respects_limit():
+    rsps_lib.add(rsps_lib.GET, DATA_URL, json=SAMPLE_DATA, status=200)
+    cols = PangoLineagesSource(limit=1).get_collections()
+    assert len(cols) <= 1
+
+
+@rsps_lib.activate
+def test_get_collections_no_limit_returns_all():
+    rsps_lib.add(rsps_lib.GET, DATA_URL, json=SAMPLE_DATA, status=200)
+    cols = PangoLineagesSource().get_collections()
+    assert len(cols) == 3
diff --git a/collection-seeding/tests/test_resistance_mutations.py b/collection-seeding/tests/test_resistance_mutations.py
new file mode 100644
index 000000000..c708f7673
--- /dev/null
+++ b/collection-seeding/tests/test_resistance_mutations.py
@@ -0,0 +1,49 @@
+from sources.resistance_mutations import ResistanceMutationsSource, _mature_name
+
+
+def test_name():
+    assert ResistanceMutationsSource.name == "covid-resistance-mutations"
+
+
+# --- _mature_name ---
+
+
+def test_mature_name_clpro_offset():
+    # ORF1a position 3284, offset -3263 → position 21
+    assert _mature_name("ORF1a:T3284I", "3CLpro", -3263) == "3CLpro:T21I"
+
+
+def test_mature_name_rdrp_offset():
+    # ORF1b position 157, offset +9 → position 166
+    assert _mature_name("ORF1b:V157A", "RdRp", 9) == "RdRp:V166A"
+
+
+def test_mature_name_spike_zero_offset():
+    assert _mature_name("S:E484K", "Spike", 0) == "Spike:E484K"
+
+
+def test_mature_name_deletion():
+    # Deletions use '-' as new base
+    assert _mature_name("ORF1a:M3312-", "3CLpro", -3263) == "3CLpro:M49-"
+
+
+# --- get_collections ---
+
+
+def test_get_collections_returns_three():
+    cols = ResistanceMutationsSource().get_collections()
+    assert len(cols) == 3
+
+
+def test_get_collections_all_covid():
+    for col in ResistanceMutationsSource().get_collections():
+        assert col["organism"] == "covid"
+
+
+def test_get_collections_variant_structure():
+    for col in ResistanceMutationsSource().get_collections():
+        assert col["variants"], f"'{col['name']}' has no variants"
+        for v in col["variants"]:
+            assert v["type"] == "filterObject"
+            assert "aminoAcidMutations" in v["filterObject"]
+            assert len(v["filterObject"]["aminoAcidMutations"]) == 1
diff --git a/collection-seeding/tests/test_seed.py b/collection-seeding/tests/test_seed.py
new file mode 100644
index 000000000..9a474dc73
--- /dev/null
+++ b/collection-seeding/tests/test_seed.py
@@ -0,0 +1,149 @@
+from unittest.mock import MagicMock
+
+from seed import seed_source
+from tests.mock_source import MockSource
+
+COLLECTIONS = [
+    {
+        "name": "Mock Collection A",
+        "organism": "covid",
+        "description": "A mock collection for testing.",
+        "variants": [
+            {
+                "type": "filterObject",
+                "name": "C123T",
+                "filterObject": {"nucleotideMutations": ["C123T"]},
+            }
+        ],
+    },
+    {
+        "name": "Mock Collection B",
+        "organism": "covid",
+        "description": "Another mock collection for testing.",
+        "variants": [],
+    },
+]
+
+
+def make_client(existing=None):
+    client = MagicMock()
+    client.fetch_existing_collections.return_value = existing or []
+    client.create_collection.return_value = 99
+    return client
+
+
+# --- seed_source: create / update / mixed ---
+
+
+def test_all_new_creates_all():
+    client = make_client(existing=[])
+    created, updated, deleted = seed_source(client, MockSource(COLLECTIONS))
+    assert created == len(COLLECTIONS)
+    assert updated == 0
+    assert deleted == 0
+    assert client.create_collection.call_count == len(COLLECTIONS)
+    client.update_collection.assert_not_called()
+
+
+def existing_entry(id: int, name: str) -> dict:
+    return {
+        "id": id,
+        "name": name,
+        "description": f"A collection. {MockSource.owned_tag}",
+    }
+
+
+def test_all_existing_updates_all():
+    existing = [existing_entry(i + 1, c["name"]) for i, c in enumerate(COLLECTIONS)]
+    client = make_client(existing=existing)
+    created, updated, deleted = seed_source(client, MockSource(COLLECTIONS))
+    assert created == 0
+    assert updated == len(COLLECTIONS)
+    assert deleted == 0
+    assert client.update_collection.call_count == len(COLLECTIONS)
+    client.create_collection.assert_not_called()
+
+
+def test_mixed_creates_and_updates():
+    existing = [existing_entry(10, COLLECTIONS[0]["name"])]
+    client = make_client(existing=existing)
+    created, updated, deleted = seed_source(client, MockSource(COLLECTIONS))
+    assert created == len(COLLECTIONS) - 1
+    assert updated == 1
+
+
+def test_update_uses_correct_id():
+    existing = [existing_entry(42, COLLECTIONS[0]["name"])]
+    client = make_client(existing=existing)
+    seed_source(client, MockSource([COLLECTIONS[0]]))
+    client.update_collection.assert_called_once_with(42, COLLECTIONS[0])
+
+
+def test_create_passes_full_collection():
+    client = make_client(existing=[])
+    seed_source(client, MockSource([COLLECTIONS[0]]))
+    client.create_collection.assert_called_once_with(COLLECTIONS[0])
+
+
+def test_returns_zero_counts_for_empty_collections():
+    client = make_client(existing=[])
+    created, updated, deleted = seed_source(client, MockSource([]))
+    assert created == 0
+    assert updated == 0
+    assert deleted == 0
+
+
+# --- seed_source: orphan deletion ---
+
+TAG = "#test-tag"
+
+
+class TaggedMockSource(MockSource):
+    owned_tag = TAG
+
+
+def tagged(name: str, description: str = "") -> dict:
+    return {
+        "name": name,
+        "organism": "covid",
+        "description": description or f"A collection. {TAG}",
+        "variants": [],
+    }
+
+
+def test_orphan_with_tag_is_deleted():
+    existing = [
+        {"id": 5, "name": "OldLineage", "description": f"Old. {TAG}"},
+        {"id": 6, "name": "CurrentLineage", "description": f"Current. {TAG}"},
+    ]
+    client = make_client(existing=existing)
+    created, updated, deleted = seed_source(
+        client, TaggedMockSource([tagged("CurrentLineage")])
+    )
+    assert deleted == 1
+    client.delete_collection.assert_called_once_with(5)
+
+
+def test_orphan_without_tag_is_not_deleted():
+    existing = [{"id": 5, "name": "ManualCollection", "description": "No tag here."}]
+    client = make_client(existing=existing)
+    created, updated, deleted = seed_source(client, TaggedMockSource([]))
+    assert deleted == 0
+    client.delete_collection.assert_not_called()
+
+
+def test_no_deletion_when_owned_tag_is_none():
+    existing = [{"id": 5, "name": "OldLineage", "description": f"Old. {TAG}"}]
+    client = make_client(existing=existing)
+    created, updated, deleted = seed_source(client, MockSource([]))
+    assert deleted == 0
+    client.delete_collection.assert_not_called()
+
+
+def test_current_collections_are_not_deleted():
+    col = tagged("ExistingLineage")
+    existing = [{"id": 5, "name": "ExistingLineage", "description": col["description"]}]
+    client = make_client(existing=existing)
+    created, updated, deleted = seed_source(client, TaggedMockSource([col]))
+    assert deleted == 0
+    client.delete_collection.assert_not_called()
diff --git a/docker-compose.yml b/docker-compose.yml
index a5c499de7..16e0848a5 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -19,6 +19,8 @@ services:
       - "127.0.0.1:9021:8080"
     depends_on:
       - database
+    environment:
+      DASHBOARDS_SYSTEM_USER_API_KEY: dummy-system-user-api-key-insecure
     command:
       - --spring.datasource.url=jdbc:postgresql://database:5432/dashboards-backend-db
       - --spring.datasource.username=postgres
@@ -39,11 +41,12 @@ services:
   example-data-seeder:
     image: ghcr.io/genspectrum/dashboards/example-data-seeder:${SEEDER_TAG}
     depends_on:
-      - backend
+      - website
     environment:
-      BACKEND_URL: http://backend:8080
-      SEED_USER_ID: example-data-seeder
-    restart: "no"
+      API_URL: http://website:4321
+      API_KEY: dummy-system-user-api-key-insecure
+      REPEAT_INTERVAL_HOURS: 8
+    restart: always
 
 volumes:
   database-data:
diff --git a/docs/arc42/09-architecture-decisions.md b/docs/arc42/09-architecture-decisions.md
index 6f0853a9c..32e4c44f1 100644
--- a/docs/arc42/09-architecture-decisions.md
+++ b/docs/arc42/09-architecture-decisions.md
@@ -29,3 +29,25 @@ We would have needed to host it on one of our servers and configure it properly.
 Although is it relatively easy to get a Keycloak Docker image running,
 it is still difficult to get the configuration right.
 None of the team members was an expert in Keycloak and misconfigurations can lead to security issues.
+
+## Auto-creation of collections
+
+### Context
+
+As GenSpectrum, we want to provide a few collections that we create based on other online resources.
+Ideally, others would maintain their own collections, but for now we want to do it ourselves.
+For example, we create collections for mutations that are relevant for vaccine resistance, based
+on online lists. Or we create collections based on canonical lineage definitions.
+
+Since we want others to also be able to easily generate collections, the code should also serve
+as a kind of reference implementation on how one would generate collections. Therefore, we want the
+code to be completely independent of the rest of the codebase, and also understandable to
+bioinformatics researchers.
+
+### Decision
+
+We decided to write the code in Python.
+The alternative would have been to use JavaScript, since we already have that. But since we want
+researchers to reuse or copy the code, Python is better suited.
+Kotlin was not considered — it is heavier than both Python and JavaScript and even less familiar
+to the target audience.
diff --git a/example-data/Dockerfile b/example-data/Dockerfile
deleted file mode 100644
index 4ebbbed8e..000000000
--- a/example-data/Dockerfile
+++ /dev/null
@@ -1,4 +0,0 @@
-FROM node:24-alpine
-WORKDIR /app
-COPY seed.mjs .
-CMD ["node", "seed.mjs"]
diff --git a/example-data/README.md b/example-data/README.md
deleted file mode 100644
index 3c33232c0..000000000
--- a/example-data/README.md
+++ /dev/null
@@ -1,27 +0,0 @@
-# example-data
-
-Seeds the backend with example collections (resistance mutation data for 3CLpro, RdRp, and Spike mAb).
-
-The script is idempotent — re-running it will skip collections that already exist.
-
-## Via Docker Compose
-
-The seeder runs automatically as part of Docker Compose:
-
-```bash
-BACKEND_TAG=latest WEBSITE_TAG=latest SEEDER_TAG=latest docker compose up
-```
-
-## Running locally by hand
-
-Requires a current version of NodeJS. No `npm install` needed.
-
-```bash
-# Local backend running on :8080
-node seed.mjs
-
-# Local backend on a different port
-node seed.mjs --url http://localhost:9021
-```
-
-Run `node seed.mjs --help` for all options.
diff --git a/example-data/seed.mjs b/example-data/seed.mjs
deleted file mode 100644
index 3ecdb4dc9..000000000
--- a/example-data/seed.mjs
+++ /dev/null
@@ -1,261 +0,0 @@
-#!/usr/bin/env node
-// Seeds example collections into the backend.
-// Idempotent: skips any collection whose name already exists for the seed user.
-//
-// Run with --help for usage.
-
-import { parseArgs } from 'node:util';
-
-const HELP = `\
-Usage: node seed.mjs [options]
-
-Options:
-  -u, --url <url>    Backend base URL (default: $BACKEND_URL or http://localhost:8080)
-      --user-id <id> User ID (default: $SEED_USER_ID or example-data-seeder)
-      --wait         Retry until backend is ready (auto-enabled when no TTY)
-  -h, --help         Show this help
-
-Examples:
-  # Local backend running on :8080
-  node seed.mjs
-
-  # Local backend on a different port
-  node seed.mjs --url http://localhost:9021
-`;
-
-let parsedArgs;
-try {
-    parsedArgs = parseArgs({
-        options: {
-            url:       { type: 'string',  short: 'u' },
-            'user-id': { type: 'string' },
-            wait:      { type: 'boolean' },
-            help:      { type: 'boolean', short: 'h' },
-        },
-    });
-} catch (err) {
-    console.error(`Error: ${err.message}\n`);
-    console.error(HELP);
-    process.exit(1);
-}
-
-const { values } = parsedArgs;
-
-if (values.help) {
-    console.log(HELP);
-    process.exit(0);
-}
-
-const BACKEND_URL  = values.url        ?? process.env.BACKEND_URL  ?? 'http://localhost:8080';
-const SEED_USER_ID = values['user-id'] ?? process.env.SEED_USER_ID ?? 'example-data-seeder';
-// Auto-enable wait when there's no TTY (e.g. running inside Docker).
-const WAIT         = values.wait ?? !process.stdout.isTTY;
-
-const RETRY_ATTEMPTS   = 30;
-const RETRY_DELAY_MS   = 2000;
-const COLLECTIONS_BASE = `${BACKEND_URL}/collections`;
-
-// Converts a genomic mutation code to a mature protein name with the given offset.
-// e.g. matureName("ORF1a:T3284I", "3CLpro", -3263) => "3CLpro:T21I"
-function matureName(mutation, setName, offset) {
-    const mutationPart = mutation.slice(mutation.indexOf(':') + 1);
-    const originalBase = mutationPart[0];
-    const newBase = mutationPart[mutationPart.length - 1];
-    const position = parseInt(mutationPart.match(/\d+/)[0], 10);
-    return `${setName}:${originalBase}${position + offset}${newBase}`;
-}
-
-function buildVariants(mutations, setName, offset) {
-    return mutations.map((mutation) => ({
-        type: 'filterObject',
-        name: matureName(mutation, setName, offset),
-        filterObject: { aminoAcidMutations: [mutation] },
-    }));
-}
-
-// --- Collection definitions ---
-
-const CLPRO_MUTATIONS = [
-    'ORF1a:T3284I', 'ORF1a:T3288A', 'ORF1a:T3288N', 'ORF1a:T3308I', 'ORF1a:D3311Y',
-    'ORF1a:M3312I', 'ORF1a:M3312L', 'ORF1a:M3312T', 'ORF1a:M3312-', 'ORF1a:L3313F',
-    'ORF1a:G3401S', 'ORF1a:F3403L', 'ORF1a:F3403S', 'ORF1a:N3405D', 'ORF1a:N3405L',
-    'ORF1a:N3405S', 'ORF1a:G3406S', 'ORF1a:S3407A', 'ORF1a:S3407E', 'ORF1a:S3407L',
-    'ORF1a:S3407P', 'ORF1a:C3423F', 'ORF1a:M3428R', 'ORF1a:M3428T', 'ORF1a:E3429A',
-    'ORF1a:E3429G', 'ORF1a:E3429K', 'ORF1a:E3429Q', 'ORF1a:E3429V', 'ORF1a:L3430F',
-    'ORF1a:P3431-', 'ORF1a:T3432I', 'ORF1a:H3435L', 'ORF1a:H3435N', 'ORF1a:H3435Q',
-    'ORF1a:H3435Y', 'ORF1a:A3436T', 'ORF1a:A3436V', 'ORF1a:V3449A', 'ORF1a:R3451G',
-    'ORF1a:R3451S', 'ORF1a:Q3452I', 'ORF1a:Q3452K', 'ORF1a:T3453I', 'ORF1a:A3454T',
-    'ORF1a:A3454V', 'ORF1a:Q3455A', 'ORF1a:Q3455C', 'ORF1a:Q3455D', 'ORF1a:Q3455E',
-    'ORF1a:Q3455F', 'ORF1a:Q3455G', 'ORF1a:Q3455H', 'ORF1a:Q3455I', 'ORF1a:Q3455K',
-    'ORF1a:Q3455L', 'ORF1a:Q3455N', 'ORF1a:Q3455P', 'ORF1a:Q3455R', 'ORF1a:Q3455S',
-    'ORF1a:Q3455T', 'ORF1a:Q3455V', 'ORF1a:Q3455W', 'ORF1a:Q3455Y', 'ORF1a:A3456P',
-    'ORF1a:A3457S', 'ORF1a:P3515L', 'ORF1a:V3560A', 'ORF1a:S3564P', 'ORF1a:T3567I',
-    'ORF1a:F3568L',
-];
-
-const RDRP_MUTATIONS = [
-    'ORF1b:V157A', 'ORF1b:V157L', 'ORF1b:N189S', 'ORF1b:R276C', 'ORF1b:A367V',
-    'ORF1b:A440V', 'ORF1b:F471L', 'ORF1b:D475Y', 'ORF1b:A517V', 'ORF1b:V548L',
-    'ORF1b:G662S', 'ORF1b:S750A', 'ORF1b:V783I', 'ORF1b:E787G', 'ORF1b:C790F',
-    'ORF1b:C790R', 'ORF1b:E793A', 'ORF1b:E793D', 'ORF1b:M915R',
-];
-
-const SPIKE_MUTATIONS = [
-    'S:P337H', 'S:P337L', 'S:P337R', 'S:P337S', 'S:P337T',
-    'S:E340A', 'S:E340D', 'S:E340G', 'S:E340K', 'S:E340Q', 'S:E340V',
-    'S:T345P',
-    'S:R346G', 'S:R346I', 'S:R346K', 'S:R346S', 'S:R346T',
-    'S:K356Q', 'S:K356T',
-    'S:S371F', 'S:S371L',
-    'S:D405E', 'S:D405N', 'S:E406D',
-    'S:K417E', 'S:K417H', 'S:K417I', 'S:K417M', 'S:K417N', 'S:K417R', 'S:K417S', 'S:K417T',
-    'S:D420A', 'S:D420N',
-    'S:N439K',
-    'S:N440D', 'S:N440E', 'S:N440I', 'S:N440K', 'S:N440R', 'S:N440T', 'S:N440Y',
-    'S:S443Y',
-    'S:K444E', 'S:K444F', 'S:K444I', 'S:K444L', 'S:K444M', 'S:K444N', 'S:K444R', 'S:K444T',
-    'S:V445A', 'S:V445D', 'S:V445F', 'S:V445I', 'S:V445L',
-    'S:G446A', 'S:G446D', 'S:G446I', 'S:G446N', 'S:G446R', 'S:G446S', 'S:G446T', 'S:G446V',
-    'S:G447C', 'S:G447D', 'S:G447F', 'S:G447S', 'S:G447V',
-    'S:N448D', 'S:N448K', 'S:N448T', 'S:N448Y',
-    'S:Y449D',
-    'S:N450D', 'S:N450K',
-    'S:L452M', 'S:L452Q', 'S:L452R', 'S:L452W',
-    'S:Y453F', 'S:Y453H',
-    'S:L455F', 'S:L455M', 'S:L455S', 'S:L455W',
-    'S:F456C', 'S:F456L', 'S:F456V',
-    'S:S459P',
-    'S:N460D', 'S:N460H', 'S:N460I', 'S:N460K', 'S:N460S', 'S:N460T', 'S:N460Y',
-    'S:A475D', 'S:A475V',
-    'S:G476D', 'S:G476R', 'S:G476T',
-    'S:V483A',
-    'S:E484A', 'S:E484D', 'S:E484G', 'S:E484K', 'S:E484P', 'S:E484Q', 'S:E484R', 'S:E484S', 'S:E484T', 'S:E484V',
-    'S:G485D', 'S:G485R',
-    'S:F486D', 'S:F486I', 'S:F486L', 'S:F486N', 'S:F486P', 'S:F486S', 'S:F486T', 'S:F486V',
-    'S:N487D', 'S:N487H', 'S:N487S',
-    'S:Y489H', 'S:Y489W',
-    'S:F490G', 'S:F490I', 'S:F490L', 'S:F490R', 'S:F490S', 'S:F490V', 'S:F490Y',
-    'S:Q493D', 'S:Q493E', 'S:Q493H', 'S:Q493K', 'S:Q493L', 'S:Q493R', 'S:Q493V',
-    'S:S494P', 'S:S494R',
-    'S:G496S',
-    'S:Q498H',
-    'S:P499H', 'S:P499R', 'S:P499S', 'S:P499T',
-    'S:N501T', 'S:N501Y',
-    'S:G504C', 'S:G504D', 'S:G504I', 'S:G504L', 'S:G504N', 'S:G504R', 'S:G504V',
-    'S:P507A',
-    'S:N856K', 'S:N969K', 'S:E990A', 'S:T1009I',
-];
-
-const COLLECTIONS = [
-    {
-        name: '3CLpro resistance mutations',
-        organism: 'covid',
-        description:
-            'SARS-CoV-2 3C-like protease (3CLpro/Mpro) inhibitor resistance mutations as per Stanford Coronavirus Antiviral & Resistance database (last updated 21 August 2024).',
-        variants: buildVariants(CLPRO_MUTATIONS, '3CLpro', -3263),
-    },
-    {
-        name: 'RdRp resistance mutations',
-        organism: 'covid',
-        description:
-            'SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) inhibitor resistance mutations as per Stanford Coronavirus Antiviral & Resistance database (last updated 21 August 2024).',
-        variants: buildVariants(RDRP_MUTATIONS, 'RdRp', 9),
-    },
-    {
-        name: 'Spike mAb resistance mutations',
-        organism: 'covid',
-        description:
-            'SARS-CoV-2 Spike monoclonal antibody (mAb) resistance mutations as per Stanford Coronavirus Antiviral & Resistance database (last updated 21 August 2024).',
-        variants: buildVariants(SPIKE_MUTATIONS, 'Spike', 0),
-    },
-];
-
-// --- API helpers ---
-
-async function sleep(ms) {
-    return new Promise((resolve) => setTimeout(resolve, ms));
-}
-
-async function waitForBackend() {
-    for (let attempt = 1; attempt <= RETRY_ATTEMPTS; attempt++) {
-        try {
-            const response = await fetch(
-                `${BACKEND_URL}/collections?userId=${SEED_USER_ID}&organism=covid`,
-            );
-            if (response.ok || response.status === 404) return;
-        } catch {
-            // backend not ready yet
-        }
-        console.log(`Waiting for backend... (attempt ${attempt}/${RETRY_ATTEMPTS})`);
-        await sleep(RETRY_DELAY_MS);
-    }
-    console.error(`Backend at ${BACKEND_URL} did not become ready after ${RETRY_ATTEMPTS} attempts.`);
-    process.exit(1);
-}
-
-async function fetchExistingCollections(organism) {
-    const url = `${COLLECTIONS_BASE}?userId=${encodeURIComponent(SEED_USER_ID)}&organism=${encodeURIComponent(organism)}`;
-    const response = await fetch(url);
-    if (!response.ok) {
-        throw new Error(`GET /collections failed: ${response.status} ${await response.text()}`);
-    }
-    return response.json();
-}
-
-async function createCollection(collection) {
-    const url = `${COLLECTIONS_BASE}?userId=${encodeURIComponent(SEED_USER_ID)}`;
-    const response = await fetch(url, {
-        method: 'POST',
-        headers: { 'Content-Type': 'application/json' },
-        body: JSON.stringify(collection),
-    });
-    if (response.status !== 201) {
-        throw new Error(`POST /collections failed: ${response.status} ${await response.text()}`);
-    }
-    const created = await response.json();
-    return created.id;
-}
-
-// --- Main ---
-
-async function main() {
-    console.log(`Seeding example data against ${BACKEND_URL} as user '${SEED_USER_ID}'...`);
-
-    if (WAIT) {
-        await waitForBackend();
-    }
-
-    // Group collections by organism to minimise GET requests
-    const byOrganism = {};
-    for (const collection of COLLECTIONS) {
-        (byOrganism[collection.organism] ??= []).push(collection);
-    }
-
-    let created = 0;
-    let skipped = 0;
-
-    for (const [organism, collections] of Object.entries(byOrganism)) {
-        const existing = await fetchExistingCollections(organism);
-        const existingNames = new Set(existing.map((c) => c.name));
-
-        for (const collection of collections) {
-            if (existingNames.has(collection.name)) {
-                console.log(`  SKIP  ${collection.name}`);
-                skipped++;
-            } else {
-                const id = await createCollection(collection);
-                console.log(`  OK    id=${id}  ${collection.name}`);
-                created++;
-            }
-        }
-    }
-
-    console.log(`\nDone. Created: ${created}, skipped (already exist): ${skipped}.`);
-}
-
-try {
-    await main();
-} catch (err) {
-    console.error(err);
-    process.exit(1);
-}
diff --git a/website/routeMocker.ts b/website/routeMocker.ts
index 1058170fb..9551e1d75 100644
--- a/website/routeMocker.ts
+++ b/website/routeMocker.ts
@@ -30,11 +30,27 @@ export class AstroApiRouteMocker {
         this.workerOrServer.use(http.post(`${ASTRO_SERVER_URL}/log`, () => Response.json({})));
     }
 
-    mockGetCollectionSummaries(response: CollectionSummary[], organism?: string, statusCode = 200) {
+    mockGetCollectionSummaries(
+        response: CollectionSummary[],
+        organism?: string,
+        statusCode = 200,
+        excludeSystemCollections?: boolean,
+    ) {
         this.workerOrServer.use(
             http.get(
                 `${ASTRO_SERVER_URL}/collections`,
-                resolver([{ statusCode, response, requestParam: organism !== undefined ? { organism } : undefined }]),
+                resolver([
+                    {
+                        statusCode,
+                        response,
+                        requestParam: {
+                            ...(organism !== undefined ? { organism } : {}),
+                            ...(excludeSystemCollections !== undefined
+                                ? { excludeSystemCollections: String(excludeSystemCollections) }
+                                : {}),
+                        },
+                    },
+                ]),
             ),
         );
     }
@@ -215,15 +231,6 @@ export class BackendRouteMocker {
             }),
         );
     }
-
-    mockGetCollectionSummaries(response: CollectionSummary[], organism?: string, statusCode = 200) {
-        this.workerOrServer.use(
-            http.get(
-                `${DUMMY_BACKEND_URL}/collections`,
-                resolver([{ statusCode, response, requestParam: organism !== undefined ? { organism } : undefined }]),
-            ),
-        );
-    }
 }
 
 function resolver(cases: MockCase[]) {
diff --git a/website/src/backendApi/backendService.spec.ts b/website/src/backendApi/backendService.spec.ts
index 39fea2bbe..3a3605e40 100644
--- a/website/src/backendApi/backendService.spec.ts
+++ b/website/src/backendApi/backendService.spec.ts
@@ -3,7 +3,6 @@ import { describe, expect, test } from 'vitest';
 import { BackendError, BackendService, UnknownBackendError } from './backendService.ts';
 import { DUMMY_BACKEND_URL } from '../../routeMocker.ts';
 import { backendRouteMocker } from '../../vitest.setup.ts';
-import type { CollectionSummary } from '../types/Collection.ts';
 import type { SubscriptionRequest, SubscriptionResponse, TriggerEvaluationResponse } from '../types/Subscription.ts';
 
 describe('backendService', () => {
@@ -171,27 +170,4 @@ describe('backendService', () => {
             new UnknownBackendError('Bad Request', 400, '/subscriptions'),
         );
     });
-
-    const aCollection: CollectionSummary = {
-        id: 1,
-        name: 'Test collection',
-        ownedBy: 123,
-        organism: 'covid',
-        description: 'A test collection',
-        variantCount: 0,
-    };
-
-    test('should GET collection summaries without organism filter', async () => {
-        backendRouteMocker.mockGetCollectionSummaries([aCollection]);
-
-        await expect(backendService.getCollectionSummaries()).resolves.to.deep.equal([aCollection]);
-    });
-
-    test('should GET collection summaries filtered by organism', async () => {
-        backendRouteMocker.mockGetCollectionSummaries([aCollection], 'covid');
-
-        await expect(backendService.getCollectionSummaries({ organism: 'covid' })).resolves.to.deep.equal([
-            aCollection,
-        ]);
-    });
 });
diff --git a/website/src/backendApi/backendService.ts b/website/src/backendApi/backendService.ts
index 3b829a0c2..8019e6d9d 100644
--- a/website/src/backendApi/backendService.ts
+++ b/website/src/backendApi/backendService.ts
@@ -22,7 +22,7 @@ const X_REQUEST_ID_HEADER = 'x-request-id';
 
 type EndpointParameters<Response> = {
     url: string;
-    requestParams?: Record<string, string>;
+    requestParams?: Record<string, string | boolean | undefined>;
     schema: ZodSchema<Response>;
 };
 
@@ -177,8 +177,7 @@ export class BackendService extends ApiService {
         return this.get({ url: `/users/${id}`, schema: publicUserSchema });
     }
 
-    public async getCollectionSummaries({ organism }: { organism?: string } = {}) {
-        const requestParams = organism !== undefined ? { organism } : undefined;
+    public async getCollectionSummaries(requestParams: { organism?: string; excludeSystemCollections?: boolean } = {}) {
         return this.get({ url: '/collections', requestParams, schema: z.array(collectionSummarySchema) });
     }
 
diff --git a/website/src/components/collections/overview/CollectionsOverview.browser.spec.tsx b/website/src/components/collections/overview/CollectionsOverview.browser.spec.tsx
index a36ce8a2a..b83c358f0 100644
--- a/website/src/components/collections/overview/CollectionsOverview.browser.spec.tsx
+++ b/website/src/components/collections/overview/CollectionsOverview.browser.spec.tsx
@@ -29,7 +29,7 @@ const mockCollections = [
 
 describe('CollectionsOverview', () => {
     it('shows the headline and collections table on success', async ({ routeMockers: { astro } }) => {
-        astro.mockGetCollectionSummaries(mockCollections, ORGANISM);
+        astro.mockGetCollectionSummaries(mockCollections, ORGANISM, 200, true);
 
         const { getByText, getByRole } = render(<CollectionsOverview organism={ORGANISM} isLoggedIn={false} />);
 
@@ -42,7 +42,7 @@ describe('CollectionsOverview', () => {
     });
 
     it('shows the headline and empty message when there are no collections', async ({ routeMockers: { astro } }) => {
-        astro.mockGetCollectionSummaries([], ORGANISM);
+        astro.mockGetCollectionSummaries([], ORGANISM, 200, true);
 
         const { getByText } = render(<CollectionsOverview organism={ORGANISM} isLoggedIn={false} />);
 
@@ -51,7 +51,7 @@ describe('CollectionsOverview', () => {
     });
 
     it('shows the headline and error message when the fetch fails', async ({ routeMockers: { astro } }) => {
-        astro.mockGetCollectionSummaries([], ORGANISM, 500);
+        astro.mockGetCollectionSummaries([], ORGANISM, 500, true);
         astro.mockLog();
 
         const { getByText } = render(<CollectionsOverview organism={ORGANISM} isLoggedIn={false} />);
diff --git a/website/src/components/collections/overview/CollectionsOverview.tsx b/website/src/components/collections/overview/CollectionsOverview.tsx
index 2daf07383..5f83635b1 100644
--- a/website/src/components/collections/overview/CollectionsOverview.tsx
+++ b/website/src/components/collections/overview/CollectionsOverview.tsx
@@ -21,7 +21,8 @@ function CollectionsOverviewInner({ organism, isLoggedIn }: { organism: Organism
         error,
     } = useQuery({
         queryKey: ['collections', organism],
-        queryFn: () => getBackendServiceForClientside().getCollectionSummaries({ organism }),
+        queryFn: () =>
+            getBackendServiceForClientside().getCollectionSummaries({ organism, excludeSystemCollections: true }),
     });
 
     if (isError) {
diff --git a/website/src/components/views/wasap/WasapPage.tsx b/website/src/components/views/wasap/WasapPage.tsx
index 59de27440..85b5be6a4 100644
--- a/website/src/components/views/wasap/WasapPage.tsx
+++ b/website/src/components/views/wasap/WasapPage.tsx
@@ -1,4 +1,3 @@
-import type { MeanProportionInterval } from '@genspectrum/dashboard-components/util';
 import { useMemo } from 'react';
 import { type FC } from 'react';
 
@@ -6,6 +5,7 @@ import { CollectionInfo } from './components/CollectionInfo';
 import { NoDataHelperText } from './components/NoDataHelperText';
 import { VariantFetchInfo } from './components/VariantFetchInfo';
 import { WasapStats } from './components/WasapStats';
+import { getInitialMeanProportionInterval } from './initialMeanProportionInterval';
 import type { ResistanceData } from './resistanceData';
 import { useWasapPageData } from './useWasapPageData';
 import type { WasapPageConfig } from './wasapPageConfig';
@@ -39,10 +39,7 @@ export const WasapPageInner: FC<WasapPageProps> = ({ config, resistanceData }) =
     // fetch which mutations should be analyzed
     const { data, isPending, isError } = useWasapPageData(config, displayMutationsBySet, analysis);
 
-    let initialMeanProportionInterval: MeanProportionInterval = { min: 0.0, max: 1.0 };
-    if (analysis.mode === 'manual' && analysis.mutations === undefined) {
-        initialMeanProportionInterval = { min: 0.05, max: 0.95 };
-    }
+    const initialMeanProportionInterval = getInitialMeanProportionInterval(analysis);
 
     const lapisFilter = {
         ...(base.locationName && { locationName: base.locationName }),
diff --git a/website/src/components/views/wasap/initialMeanProportionInterval.spec.ts b/website/src/components/views/wasap/initialMeanProportionInterval.spec.ts
new file mode 100644
index 000000000..03f38a240
--- /dev/null
+++ b/website/src/components/views/wasap/initialMeanProportionInterval.spec.ts
@@ -0,0 +1,40 @@
+import { describe, expect, test } from 'vitest';
+
+import { getInitialMeanProportionInterval } from './initialMeanProportionInterval';
+import type { WasapAnalysisFilter } from './wasapPageConfig';
+
+describe('getInitialMeanProportionInterval', () => {
+    test('resistance mutations initially show mean proportion from 5 to 100 percent', () => {
+        const analysis: WasapAnalysisFilter = {
+            mode: 'resistance',
+            sequenceType: 'amino acid',
+            resistanceSet: 'Spike',
+        };
+
+        expect(getInitialMeanProportionInterval(analysis)).toEqual({ min: 0.05, max: 1.0 });
+    });
+
+    test('manual mode without mutations keeps the previous 5 to 95 percent default', () => {
+        const analysis: WasapAnalysisFilter = {
+            mode: 'manual',
+            sequenceType: 'nucleotide',
+            mutations: undefined,
+        };
+
+        expect(getInitialMeanProportionInterval(analysis)).toEqual({ min: 0.05, max: 0.95 });
+    });
+
+    test('other analysis states initially show the full mean proportion range', () => {
+        const analysis: WasapAnalysisFilter = {
+            mode: 'variant',
+            sequenceType: 'nucleotide',
+            variant: 'XFG*',
+            minProportion: 0.8,
+            minCount: 15,
+            minJaccard: 0.75,
+            timeFrame: 'all',
+        };
+
+        expect(getInitialMeanProportionInterval(analysis)).toEqual({ min: 0.0, max: 1.0 });
+    });
+});
diff --git a/website/src/components/views/wasap/initialMeanProportionInterval.ts b/website/src/components/views/wasap/initialMeanProportionInterval.ts
new file mode 100644
index 000000000..ec9a42773
--- /dev/null
+++ b/website/src/components/views/wasap/initialMeanProportionInterval.ts
@@ -0,0 +1,13 @@
+import type { MeanProportionInterval } from '@genspectrum/dashboard-components/util';
+
+import type { WasapAnalysisFilter } from './wasapPageConfig';
+
+export function getInitialMeanProportionInterval(analysis: WasapAnalysisFilter): MeanProportionInterval {
+    if (analysis.mode === 'resistance') {
+        return { min: 0.05, max: 1.0 };
+    }
+    if (analysis.mode === 'manual' && analysis.mutations === undefined) {
+        return { min: 0.05, max: 0.95 };
+    }
+    return { min: 0.0, max: 1.0 };
+}
diff --git a/website/src/components/views/wasap/wasapPageConfig.ts b/website/src/components/views/wasap/wasapPageConfig.ts
index 878798e87..2c4cbfe69 100644
--- a/website/src/components/views/wasap/wasapPageConfig.ts
+++ b/website/src/components/views/wasap/wasapPageConfig.ts
@@ -38,6 +38,8 @@ export type WasapPageConfigBase = {
 
     browseDataUrl: string;
     browseDataDescription: string;
+
+    defaultAnalysisMode?: WasapAnalysisMode;
 };
 
 /**
diff --git a/website/src/layouts/base/header/getPathogenMegaMenuSections.ts b/website/src/layouts/base/header/getPathogenMegaMenuSections.ts
index fcad22493..70015a43c 100644
--- a/website/src/layouts/base/header/getPathogenMegaMenuSections.ts
+++ b/website/src/layouts/base/header/getPathogenMegaMenuSections.ts
@@ -1,5 +1,5 @@
 import type { MenuIconType } from '../../../components/iconCss.ts';
-import { getOrganismConfig, isStaging } from '../../../config.ts';
+import { getOrganismConfig } from '../../../config.ts';
 import { type Organism, organismConfig, paths } from '../../../types/Organism.ts';
 import { Page } from '../../../types/pages.ts';
 import {
@@ -51,8 +51,7 @@ export function getPathogenMegaMenuSections(): PathogenMegaMenuSections {
 
         const supplementaryEntries: MegaMenuSection[] = [];
 
-        // only on staging for now, remove when enabling on prod: https://github.com/GenSpectrum/dashboards/issues/1108
-        if (isStaging() && getOrganismConfig(config.organism).hasCollections) {
+        if (getOrganismConfig(config.organism).hasCollections) {
             supplementaryEntries.push({
                 label: 'Collections',
                 href: Page.collectionsForOrganism(config.organism),
diff --git a/website/src/pages/collections/[organism]/index.astro b/website/src/pages/collections/[organism]/index.astro
index f4999df09..043eddf84 100644
--- a/website/src/pages/collections/[organism]/index.astro
+++ b/website/src/pages/collections/[organism]/index.astro
@@ -1,16 +1,10 @@
 ---
 import { CollectionsOverview } from '../../../components/collections/overview/CollectionsOverview';
-import { isStaging } from '../../../config';
 import { defaultBreadcrumbs } from '../../../layouts/Breadcrumbs';
 import ContaineredPageLayout from '../../../layouts/ContaineredPage/ContaineredPageLayout.astro';
 import { organismConfig, organismSchema } from '../../../types/Organism';
 import { Page } from '../../../types/pages';
 
-// only on staging for now, remove when enabling on prod: https://github.com/GenSpectrum/dashboards/issues/1108
-if (!isStaging()) {
-    return Astro.redirect('/404');
-}
-
 const { organism } = Astro.params;
 
 const parsedOrganism = organismSchema.safeParse(organism);
diff --git a/website/src/pages/collections/index.astro b/website/src/pages/collections/index.astro
index 031dfbabd..760f56910 100644
--- a/website/src/pages/collections/index.astro
+++ b/website/src/pages/collections/index.astro
@@ -1,14 +1,9 @@
 ---
-import { getOrganismConfig, isStaging } from '../../config';
+import { getOrganismConfig } from '../../config';
 import { defaultBreadcrumbs } from '../../layouts/Breadcrumbs';
 import ContaineredPageLayout from '../../layouts/ContaineredPage/ContaineredPageLayout.astro';
 import { allOrganisms, organismConfig } from '../../types/Organism';
 import { Page } from '../../types/pages';
-
-// only on staging for now, remove when enabling on prod: https://github.com/GenSpectrum/dashboards/issues/1108
-if (!isStaging()) {
-    return Astro.redirect('/404');
-}
 ---
 
 <ContaineredPageLayout
diff --git a/website/src/types/wastewaterConfig.spec.ts b/website/src/types/wastewaterConfig.spec.ts
index 93d774339..4671138a5 100644
--- a/website/src/types/wastewaterConfig.spec.ts
+++ b/website/src/types/wastewaterConfig.spec.ts
@@ -1,6 +1,7 @@
 import { describe, expect, test } from 'vitest';
 
-import { wastewaterOrganismConfigs } from './wastewaterConfig';
+import { wastewaterOrganismConfigs, wastewaterOrganisms } from './wastewaterConfig';
+import { enabledAnalysisModes } from '../components/views/wasap/wasapPageConfig';
 
 describe.each(Object.entries(wastewaterOrganismConfigs))('wastewaterConfig %s', (_configName, config) => {
     test('default resistance set name is valid', () => {
@@ -10,4 +11,25 @@ describe.each(Object.entries(wastewaterOrganismConfigs))('wastewaterConfig %s',
             expect(resistanceSetNames).include(defaultSetName);
         }
     });
+
+    test('configured default mode must be enabled', () => {
+        const defaultMode = config.defaultAnalysisMode;
+        if (defaultMode === undefined) {
+            return;
+        }
+
+        // Prevent configs from pointing the URL-less page state at a disabled mode.
+        expect(enabledAnalysisModes(config)).include(defaultMode);
+    });
+});
+
+test('COVID wastewater opens on Spike resistance mutations by default', () => {
+    const covidConfig = wastewaterOrganismConfigs[wastewaterOrganisms.covid];
+
+    // This pins the default requested for the COVID wastewater dashboard landing state.
+    expect(covidConfig.defaultAnalysisMode).toBe('resistance');
+    if (!covidConfig.resistanceAnalysisModeEnabled) {
+        throw new Error('COVID wastewater resistance analysis mode must be enabled.');
+    }
+    expect(covidConfig.filterDefaults.resistance.resistanceSet).toBe('Spike');
 });
diff --git a/website/src/types/wastewaterConfig.ts b/website/src/types/wastewaterConfig.ts
index 5c298ad6e..495ab0a08 100644
--- a/website/src/types/wastewaterConfig.ts
+++ b/website/src/types/wastewaterConfig.ts
@@ -29,6 +29,7 @@ export const wastewaterOrganismConfigs: Record<WastewaterOrganismName, WasapPage
         resistanceAnalysisModeEnabled: true,
         untrackedAnalysisModeEnabled: true,
         collectionAnalysisModeEnabled: true,
+        defaultAnalysisMode: 'resistance',
         resistanceMutationCollections: [
             {
                 collectionId: 1,
@@ -85,7 +86,7 @@ export const wastewaterOrganismConfigs: Record<WastewaterOrganismName, WasapPage
             resistance: {
                 mode: 'resistance',
                 sequenceType: 'amino acid',
-                resistanceSet: '3CLpro',
+                resistanceSet: 'Spike',
             },
             untracked: {
                 mode: 'untracked',
diff --git a/website/src/views/pageStateHandlers/WasapPageStateHandler.spec.ts b/website/src/views/pageStateHandlers/WasapPageStateHandler.spec.ts
index 37d580272..6656024f4 100644
--- a/website/src/views/pageStateHandlers/WasapPageStateHandler.spec.ts
+++ b/website/src/views/pageStateHandlers/WasapPageStateHandler.spec.ts
@@ -93,6 +93,19 @@ describe('WasapPageStateHandler', () => {
             const url = handler.getDefaultPageUrl();
             expect(url).toBe('/wastewater/covid');
         });
+
+        it('uses configured default mode when URL has no analysisMode', () => {
+            const handlerWithDefaultMode = new WasapPageStateHandler({
+                ...config,
+                defaultAnalysisMode: 'resistance',
+            });
+
+            // A bare URL should use the configured mode instead of the first enabled mode.
+            const filter = handlerWithDefaultMode.parsePageStateFromUrl(new URL('http://example.com/wastewater/covid'));
+
+            expect(filter.analysis.mode).toBe('resistance');
+            expect((filter.analysis as WasapResistanceFilter).resistanceSet).toBe('3CLpro');
+        });
     });
 
     describe('base filter', () => {
diff --git a/website/src/views/pageStateHandlers/WasapPageStateHandler.ts b/website/src/views/pageStateHandlers/WasapPageStateHandler.ts
index ecc35e731..37f6909a4 100644
--- a/website/src/views/pageStateHandlers/WasapPageStateHandler.ts
+++ b/website/src/views/pageStateHandlers/WasapPageStateHandler.ts
@@ -35,7 +35,7 @@ export class WasapPageStateHandler implements PageStateHandler<WasapFilter> {
         const providedMode = texts.analysisMode as WasapAnalysisMode | undefined;
 
         // config provided defaults
-        const defaultMode = enabledAnalysisModes(this.config)[0];
+        const defaultMode = this.config.defaultAnalysisMode ?? enabledAnalysisModes(this.config)[0];
 
         const mode = providedMode ?? defaultMode;