diff --git a/.github/workflows/cypress_debug.yml b/.github/workflows/cypress_debug.yml
index 78d4e57ef..56c48923d 100644
--- a/.github/workflows/cypress_debug.yml
+++ b/.github/workflows/cypress_debug.yml
@@ -19,7 +19,7 @@ jobs:
         run: yarn --immutable
 
       - name: Get latest JBrowse
-        run: yarn run jbrowse create --nightly .jbrowse
+        run: yarn run jbrowse create .jbrowse
         working-directory: packages/jbrowse-plugin-apollo
 
       - name: Start MongoDB
diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
index 4da93cf59..c15b5b926 100644
--- a/.github/workflows/pull_request.yml
+++ b/.github/workflows/pull_request.yml
@@ -42,7 +42,7 @@ jobs:
 
       # Cypress tests
       - name: Get latest JBrowse
-        run: yarn run jbrowse create --nightly .jbrowse
+        run: yarn run jbrowse create .jbrowse
         working-directory: packages/jbrowse-plugin-apollo
       - name: Start MongoDB
         uses: supercharge/mongodb-github-action@1.12.1
diff --git a/packages/apollo-collaboration-server/package.json b/packages/apollo-collaboration-server/package.json
index f3ab1ca6f..ea6d2bb93 100644
--- a/packages/apollo-collaboration-server/package.json
+++ b/packages/apollo-collaboration-server/package.json
@@ -46,9 +46,9 @@
     "@emotion/styled": "^11.10.6",
     "@gmod/gff": "^2.1.0",
     "@gmod/indexedfasta": "^5.0.2",
-    "@jbrowse/core": "^4.1.1",
-    "@jbrowse/mobx-state-tree": "^5.5.0",
-    "@mui/material": "^7.3.7",
+    "@jbrowse/core": "^4.3.0",
+    "@jbrowse/mobx-state-tree": "^5.8.7",
+    "@mui/material": "^7.3.11",
     "@nestjs/common": "^10.1.0",
     "@nestjs/config": "^3.0.0",
     "@nestjs/core": "^10.1.0",
diff --git a/packages/apollo-common/package.json b/packages/apollo-common/package.json
index 7e2527f5a..06cda69ca 100644
--- a/packages/apollo-common/package.json
+++ b/packages/apollo-common/package.json
@@ -14,7 +14,7 @@
   },
   "dependencies": {
     "@apollo-annotation/schemas": "workspace:^",
-    "@jbrowse/core": "^4.1.1",
+    "@jbrowse/core": "^4.3.0",
     "bson-objectid": "^2.0.4",
     "tslib": "^2.3.1"
   },
@@ -29,8 +29,8 @@
     "typescript": "^5.5.3"
   },
   "peerDependencies": {
-    "@jbrowse/mobx-state-tree": "^5.5.0",
-    "@mui/material": "^7.3.7",
+    "@jbrowse/mobx-state-tree": "^5.8.7",
+    "@mui/material": "^7.3.11",
     "@mui/x-data-grid": "^8.0.0",
     "mobx": "^6.6.1",
     "mobx-react": "^7.2.1",
diff --git a/packages/apollo-mst/package.json b/packages/apollo-mst/package.json
index fa56e419b..a9a1539f3 100644
--- a/packages/apollo-mst/package.json
+++ b/packages/apollo-mst/package.json
@@ -13,8 +13,8 @@
     "build": "tsc"
   },
   "dependencies": {
-    "@jbrowse/core": "^4.1.1",
-    "@jbrowse/mobx-state-tree": "^5.5.0",
+    "@jbrowse/core": "^4.3.0",
+    "@jbrowse/mobx-state-tree": "^5.8.7",
     "mobx": "^6.6.1",
     "react-dom": "^18.2.0",
     "rxjs": "^7.4.0",
diff --git a/packages/apollo-shared/package.json b/packages/apollo-shared/package.json
index f297c6a60..c1965e0f1 100644
--- a/packages/apollo-shared/package.json
+++ b/packages/apollo-shared/package.json
@@ -22,14 +22,14 @@
     "@apollo-annotation/schemas": "workspace:^",
     "@gmod/gff": "^2.1.0",
     "@gmod/indexedfasta": "^5.0.2",
-    "@jbrowse/core": "^4.1.1",
+    "@jbrowse/core": "^4.3.0",
     "bson-objectid": "^2.0.4",
     "generic-filehandle2": "^2.0.18",
     "jwt-decode": "^3.1.2",
     "tslib": "^2.3.1"
   },
   "devDependencies": {
-    "@jbrowse/mobx-state-tree": "^5.5.0",
+    "@jbrowse/mobx-state-tree": "^5.8.7",
     "@nestjs/common": "^10.1.0",
     "@nestjs/core": "^10.1.0",
     "@types/chai": "^4.3.19",
@@ -46,8 +46,8 @@
     "typescript": "^5.5.3"
   },
   "peerDependencies": {
-    "@jbrowse/mobx-state-tree": "^5.5.0",
-    "@mui/material": "^7.3.7",
+    "@jbrowse/mobx-state-tree": "^5.8.7",
+    "@mui/material": "^7.3.11",
     "@mui/x-data-grid": "^8.0.0",
     "mobx": "^6.6.1",
     "mobx-react": "^7.2.1",
diff --git a/packages/jbrowse-plugin-apollo/package.json b/packages/jbrowse-plugin-apollo/package.json
index bcffe93c4..3bea4ce44 100644
--- a/packages/jbrowse-plugin-apollo/package.json
+++ b/packages/jbrowse-plugin-apollo/package.json
@@ -52,9 +52,9 @@
     "@emotion/react": "^11.10.6",
     "@emotion/styled": "^11.10.6",
     "@gmod/gff": "^2.1.0",
-    "@jbrowse/plugin-authentication": "^4.1.1",
-    "@jbrowse/plugin-linear-genome-view": "^4.1.1",
-    "@mui/icons-material": "^7.3.7",
+    "@jbrowse/plugin-authentication": "^4.3.0",
+    "@jbrowse/plugin-linear-genome-view": "^4.3.0",
+    "@mui/icons-material": "^7.3.11",
     "@types/jsonpath": "^0.2.0",
     "autosuggest-highlight": "^3.3.4",
     "bson-objectid": "^2.0.4",
@@ -72,12 +72,12 @@
     "@babel/core": "^7.28.6",
     "@babel/plugin-proposal-class-properties": "^7.18.6",
     "@babel/preset-env": "^7.28.6",
-    "@jbrowse/cli": "^4.1.1",
-    "@jbrowse/core": "^4.1.1",
+    "@jbrowse/cli": "^4.3.0",
+    "@jbrowse/core": "^4.3.0",
     "@jbrowse/development-tools": "^2.2.1",
-    "@jbrowse/mobx-state-tree": "^5.5.0",
+    "@jbrowse/mobx-state-tree": "^5.8.7",
     "@jest/globals": "^29.0.3",
-    "@mui/material": "^7.3.7",
+    "@mui/material": "^7.3.11",
     "@mui/x-data-grid": "^8.0.0",
     "@rollup/plugin-babel": "^6.1.0",
     "@rollup/plugin-commonjs": "^29.0.0",
@@ -133,9 +133,9 @@
     "typescript": "^5.5.3"
   },
   "peerDependencies": {
-    "@jbrowse/core": "^4.1.1",
-    "@jbrowse/mobx-state-tree": "^5.5.0",
-    "@mui/material": "^7.3.7",
+    "@jbrowse/core": "^4.3.0",
+    "@jbrowse/mobx-state-tree": "^5.8.7",
+    "@mui/material": "^7.3.11",
     "mobx": "^6.6.1",
     "mobx-react": "^9.0.0",
     "prop-types": "^15.8.1",
diff --git a/packages/jbrowse-plugin-apollo/src/ApolloJobModel.ts b/packages/jbrowse-plugin-apollo/src/ApolloJobModel.ts
index 0b928d2c8..98d9a008a 100644
--- a/packages/jbrowse-plugin-apollo/src/ApolloJobModel.ts
+++ b/packages/jbrowse-plugin-apollo/src/ApolloJobModel.ts
@@ -1,4 +1,3 @@
-/* eslint-disable @typescript-eslint/no-unsafe-assignment */
 /* eslint-disable @typescript-eslint/no-confusing-void-expression */
 import {
   type SessionWithWidgets,
diff --git a/packages/jbrowse-plugin-apollo/src/ApolloTextSearchAdapter/ApolloTextSearchAdapter.ts b/packages/jbrowse-plugin-apollo/src/ApolloTextSearchAdapter/ApolloTextSearchAdapter.ts
index 2ec579445..431389453 100644
--- a/packages/jbrowse-plugin-apollo/src/ApolloTextSearchAdapter/ApolloTextSearchAdapter.ts
+++ b/packages/jbrowse-plugin-apollo/src/ApolloTextSearchAdapter/ApolloTextSearchAdapter.ts
@@ -78,7 +78,7 @@ export class ApolloTextSearchAdapter
     const { assemblyManager } = session as unknown as AbstractSessionModel
     for (const assemblyName of this.assemblyNames) {
       const backendDriver = apolloDataStore.getBackendDriver(assemblyName)
-      const assembly = assemblyManager.get(assemblyName)
+      const assembly = assemblyManager.get(assemblyName) as Assembly | undefined
       if (!(backendDriver && assembly)) {
         continue
       }
diff --git a/packages/jbrowse-plugin-apollo/src/BackendDrivers/LocalDriver/LocalDriver.ts b/packages/jbrowse-plugin-apollo/src/BackendDrivers/LocalDriver/LocalDriver.ts
index e75cb9bda..ca301275b 100644
--- a/packages/jbrowse-plugin-apollo/src/BackendDrivers/LocalDriver/LocalDriver.ts
+++ b/packages/jbrowse-plugin-apollo/src/BackendDrivers/LocalDriver/LocalDriver.ts
@@ -74,7 +74,9 @@ export class LocalDriver extends BackendDriver {
   async getSequence(region: Region): Promise<{ seq: string; refSeq: string }> {
     const session = getSession(this.clientStore)
     const { assemblyManager } = session
-    const assembly = await assemblyManager.waitForAssembly(region.assemblyName)
+    const assembly = (await assemblyManager.waitForAssembly(
+      region.assemblyName,
+    )) as Assembly | undefined
     if (!assembly) {
       throw new Error(`Assembly not found: "${region.assemblyName}"`)
     }
@@ -109,7 +111,9 @@ export class LocalDriver extends BackendDriver {
   async getRegions(assemblyName: string): Promise<Region[]> {
     const session = getSession(this.clientStore)
     const { assemblyManager } = session
-    const assembly = await assemblyManager.waitForAssembly(assemblyName)
+    const assembly = (await assemblyManager.waitForAssembly(assemblyName)) as
+      | Assembly
+      | undefined
     if (!assembly) {
       throw new Error(`Assembly not found: "${assemblyName}"`)
     }
@@ -127,7 +131,9 @@ export class LocalDriver extends BackendDriver {
   async getRefNameAliases(assemblyName: string): Promise<RefNameAliases[]> {
     const session = getSession(this.clientStore)
     const { assemblyManager } = session
-    const assembly = await assemblyManager.waitForAssembly(assemblyName)
+    const assembly = (await assemblyManager.waitForAssembly(assemblyName)) as
+      | Assembly
+      | undefined
     if (!assembly) {
       throw new Error(`Assembly not found: "${assemblyName}"`)
     }
diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/components/CheckResultWarnings.tsx b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/components/CheckResultWarnings.tsx
index bad858035..13f361ea0 100644
--- a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/components/CheckResultWarnings.tsx
+++ b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/components/CheckResultWarnings.tsx
@@ -1,4 +1,5 @@
 import type { CheckResultI } from '@apollo-annotation/mst'
+import type { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 import { type AbstractSessionModel, doesIntersect2 } from '@jbrowse/core/util'
 import ErrorIcon from '@mui/icons-material/Error'
 import { Avatar, Badge, Box, Tooltip } from '@mui/material'
@@ -23,7 +24,9 @@ export const CheckResultWarnings = observer(function CheckResultWarnings({
   }
   return lgv.dynamicBlocks.contentBlocks.map((block) => {
     const widthBp = lgv.bpPerPx * apolloRowHeight
-    const assembly = assemblyManager.get(block.assemblyName)
+    const assembly = assemblyManager.get(block.assemblyName) as
+      | Assembly
+      | undefined
     if (!assembly) {
       return null
     }
diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/ExonGlyph.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/ExonGlyph.ts
index d68e83647..3de21ac92 100644
--- a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/ExonGlyph.ts
+++ b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/ExonGlyph.ts
@@ -106,7 +106,7 @@ function getContextMenuItems(
     session,
   } = display
   const [region] = regions
-  const currentAssemblyId = display.getAssemblyId(region.assemblyName)
+  const currentAssemblyId = display.getAssemblyId(region.assemblyName) as string
   const role = internetAccount ? internetAccount.role : 'admin'
   const admin = role === 'admin'
   const menuItems: MenuItem[] = []
diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/TranscriptGlyph.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/TranscriptGlyph.ts
index 604cb2ecd..42795b9db 100644
--- a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/TranscriptGlyph.ts
+++ b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/TranscriptGlyph.ts
@@ -205,7 +205,7 @@ function getContextMenuItems(
 ): MenuItem[] {
   const { changeManager, regions, selectedFeature, session } = display
   const [region] = regions
-  const currentAssemblyId = display.getAssemblyId(region.assemblyName)
+  const currentAssemblyId = display.getAssemblyId(region.assemblyName) as string
   const menuItems: MenuItem[] = []
   if (isSessionModelWithWidgets(session)) {
     menuItems.splice(1, 0, {
diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/base.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/base.ts
index 7dcf97e83..d9e075547 100644
--- a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/base.ts
+++ b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/base.ts
@@ -5,6 +5,7 @@
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import type { AnnotationFeature } from '@apollo-annotation/mst'
 import type PluginManager from '@jbrowse/core/PluginManager'
+import type { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 import {
   type AnyConfigurationSchemaType,
   ConfigurationReference,
@@ -137,7 +138,9 @@ export function baseModelFactory(
         const { assemblyName } = region
         const { assemblyManager } =
           self.session as unknown as AbstractSessionModel
-        const assembly = assemblyManager.get(assemblyName)
+        const assembly = assemblyManager.get(assemblyName) as
+          | Assembly
+          | undefined
         if (!assembly) {
           throw new Error(`No assembly found with name ${assemblyName}`)
         }
diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/layouts.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/layouts.ts
index 0605def88..bb902aca1 100644
--- a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/layouts.ts
+++ b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/layouts.ts
@@ -2,6 +2,7 @@
 
 import type { AnnotationFeature } from '@apollo-annotation/mst'
 import type PluginManager from '@jbrowse/core/PluginManager'
+import type { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration'
 import { type AbstractSessionModel, doesIntersect2 } from '@jbrowse/core/util'
 import { addDisposer, isAlive } from '@jbrowse/mobx-state-tree'
@@ -72,7 +73,9 @@ export function layoutsModelFactory(
       getCanonicalRefName(assemblyName: string, refSeq: string) {
         const { assemblyManager } =
           self.session as unknown as AbstractSessionModel
-        const assembly = assemblyManager.get(assemblyName)
+        const assembly = assemblyManager.get(assemblyName) as
+          | Assembly
+          | undefined
         if (!assembly) {
           throw new Error('no assembly in layout')
         }
diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/mouseEvents.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/mouseEvents.ts
index 8b9ce5eca..de2aecbd7 100644
--- a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/mouseEvents.ts
+++ b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/mouseEvents.ts
@@ -4,6 +4,7 @@ import {
   LocationStartChange,
 } from '@apollo-annotation/shared'
 import type PluginManager from '@jbrowse/core/PluginManager'
+import type { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration'
 import type { MenuItem } from '@jbrowse/core/ui'
 import { doesIntersect2 } from '@jbrowse/core/util'
@@ -189,7 +190,9 @@ export function mouseEventsModelFactory(
           }
           const { displayedRegions } = self.lgv
           const region = displayedRegions[start.regionNumber]
-          const assembly = self.getAssemblyId(region.assemblyName)
+          const assembly = self.getAssemblyId(region.assemblyName) as
+            | Assembly
+            | undefined
           const changes = getPropagatedLocationChanges(
             feature,
             current.bp,
diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloReferenceSequenceDisplay/stateModel/base.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloReferenceSequenceDisplay/stateModel/base.ts
index e4e92a454..c0659d538 100644
--- a/packages/jbrowse-plugin-apollo/src/LinearApolloReferenceSequenceDisplay/stateModel/base.ts
+++ b/packages/jbrowse-plugin-apollo/src/LinearApolloReferenceSequenceDisplay/stateModel/base.ts
@@ -5,6 +5,7 @@
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import type { AnnotationFeature } from '@apollo-annotation/mst'
 import type PluginManager from '@jbrowse/core/PluginManager'
+import type { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 import {
   type AnyConfigurationSchemaType,
   ConfigurationReference,
@@ -115,7 +116,9 @@ export function baseModelFactory(
         const { assemblyName } = region
         const { assemblyManager } =
           self.session as unknown as AbstractSessionModel
-        const assembly = assemblyManager.get(assemblyName)
+        const assembly = assemblyManager.get(assemblyName) as
+          | Assembly
+          | undefined
         if (!assembly) {
           throw new Error(`No assembly found with name ${assemblyName}`)
         }
diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/components/LinearApolloSixFrameDisplay.tsx b/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/components/LinearApolloSixFrameDisplay.tsx
index 6a9f17fcc..4033d6ef3 100644
--- a/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/components/LinearApolloSixFrameDisplay.tsx
+++ b/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/components/LinearApolloSixFrameDisplay.tsx
@@ -3,6 +3,7 @@
 /* eslint-disable @typescript-eslint/no-misused-promises */
 
 import type { CheckResultI } from '@apollo-annotation/mst'
+import type { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 import { Menu, type MenuItem } from '@jbrowse/core/ui'
 import {
   type AbstractSessionModel,
@@ -157,7 +158,9 @@ export const LinearApolloSixFrameDisplay = observer(
               />
               {lgv.displayedRegions.flatMap((region, idx) => {
                 const widthBp = lgv.bpPerPx * apolloRowHeight
-                const assembly = assemblyManager.get(region.assemblyName)
+                const assembly = assemblyManager.get(region.assemblyName) as
+                  | Assembly
+                  | undefined
                 if (showCheckResults) {
                   const filteredCheckResults = [
                     ...session.apolloDataStore.checkResults.values(),
diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/glyphs/GeneGlyph.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/glyphs/GeneGlyph.ts
index e9d418ec8..6edf7b29b 100644
--- a/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/glyphs/GeneGlyph.ts
+++ b/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/glyphs/GeneGlyph.ts
@@ -856,7 +856,7 @@ function getContextMenuItems(
     session,
   } = display
   const [region] = regions
-  const currentAssemblyId = display.getAssemblyId(region.assemblyName)
+  const currentAssemblyId = display.getAssemblyId(region.assemblyName) as string
   const menuItems: MenuItem[] = []
   const role = internetAccount ? internetAccount.role : 'admin'
   const readOnly = !(role && ['admin', 'user'].includes(role))
diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/base.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/base.ts
index 938c4e397..dc40c204c 100644
--- a/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/base.ts
+++ b/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/base.ts
@@ -5,6 +5,7 @@
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import type { AnnotationFeature } from '@apollo-annotation/mst'
 import type PluginManager from '@jbrowse/core/PluginManager'
+import type { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 import {
   type AnyConfigurationSchemaType,
   ConfigurationReference,
@@ -128,7 +129,9 @@ export function baseModelFactory(
         const { assemblyName } = region
         const { assemblyManager } =
           self.session as unknown as AbstractSessionModel
-        const assembly = assemblyManager.get(assemblyName)
+        const assembly = assemblyManager.get(assemblyName) as
+          | Assembly
+          | undefined
         if (!assembly) {
           throw new Error(`No assembly found with name ${assemblyName}`)
         }
diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/layouts.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/layouts.ts
index 43c8b15f3..7ee1f5794 100644
--- a/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/layouts.ts
+++ b/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/layouts.ts
@@ -2,6 +2,7 @@
 
 import type { AnnotationFeature } from '@apollo-annotation/mst'
 import type PluginManager from '@jbrowse/core/PluginManager'
+import type { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration'
 import {
   type AbstractSessionModel,
@@ -45,7 +46,9 @@ export function layoutsModelFactory(
         const { assemblyManager } =
           self.session as unknown as AbstractSessionModel
         return self.lgv.displayedRegions.map((region) => {
-          const assembly = assemblyManager.get(region.assemblyName)
+          const assembly = assemblyManager.get(region.assemblyName) as
+            | Assembly
+            | undefined
           let min: number | undefined
           let max: number | undefined
           const { end, refName, start } = region
@@ -101,7 +104,9 @@ export function layoutsModelFactory(
         const { assemblyManager } =
           self.session as unknown as AbstractSessionModel
         return self.lgv.displayedRegions.map((region, idx) => {
-          const assembly = assemblyManager.get(region.assemblyName)
+          const assembly = assemblyManager.get(region.assemblyName) as
+            | Assembly
+            | undefined
           const featureLayout = new Map<number, LayoutRow[]>()
           const minMax = self.featuresMinMax[idx]
           if (!minMax) {
diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/mouseEvents.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/mouseEvents.ts
index 2f479b2e1..5d3b4b2ab 100644
--- a/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/mouseEvents.ts
+++ b/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/mouseEvents.ts
@@ -202,7 +202,7 @@ export function mouseEventsModelFactory(
         }
         const { displayedRegions } = self.lgv
         const region = displayedRegions[start.regionNumber]
-        const assembly = self.getAssemblyId(region.assemblyName)
+        const assembly = self.getAssemblyId(region.assemblyName) as string
         const changes = getPropagatedLocationChanges(
           feature,
           current.bp,
diff --git a/packages/jbrowse-plugin-apollo/src/components/CopyFeature.tsx b/packages/jbrowse-plugin-apollo/src/components/CopyFeature.tsx
index 632bfedab..44b139d86 100644
--- a/packages/jbrowse-plugin-apollo/src/components/CopyFeature.tsx
+++ b/packages/jbrowse-plugin-apollo/src/components/CopyFeature.tsx
@@ -8,6 +8,7 @@ import type {
   AnnotationFeatureSnapshot,
 } from '@apollo-annotation/mst'
 import { AddFeatureChange } from '@apollo-annotation/shared'
+import type { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 import { readConfObject } from '@jbrowse/core/configuration'
 import type { AbstractSessionModel } from '@jbrowse/core/util'
 import { getSnapshot } from '@jbrowse/mobx-state-tree'
@@ -105,7 +106,9 @@ export function CopyFeature({
         setErrorMessage('No assemblies to copy to')
         return
       }
-      const assembly = await assemblyManager.waitForAssembly(selectedAssemblyId)
+      const assembly = (await assemblyManager.waitForAssembly(
+        selectedAssemblyId,
+      )) as Assembly | undefined
       if (!assembly) {
         return
       }
@@ -136,7 +139,9 @@ export function CopyFeature({
     event.preventDefault()
     setErrorMessage('')
     const featureLength = sourceFeature.length
-    const assembly = await assemblyManager.waitForAssembly(selectedAssemblyId)
+    const assembly = (await assemblyManager.waitForAssembly(
+      selectedAssemblyId,
+    )) as Assembly | undefined
     if (!assembly) {
       setErrorMessage(`Assembly not found: ${selectedAssemblyId}.`)
       return
diff --git a/packages/jbrowse-plugin-apollo/src/components/DownloadGFF3.tsx b/packages/jbrowse-plugin-apollo/src/components/DownloadGFF3.tsx
index 01f40e14f..31ebed9bc 100644
--- a/packages/jbrowse-plugin-apollo/src/components/DownloadGFF3.tsx
+++ b/packages/jbrowse-plugin-apollo/src/components/DownloadGFF3.tsx
@@ -3,6 +3,7 @@
 /* eslint-disable @typescript-eslint/no-misused-promises */
 import { annotationFeatureToGFF3 } from '@apollo-annotation/shared'
 import { GFFFormattingTransformer } from '@gmod/gff'
+import type { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 import { getConf } from '@jbrowse/core/configuration'
 import type { AbstractSessionModel } from '@jbrowse/core/util'
 import {
@@ -61,7 +62,7 @@ export function DownloadGFF3({
   }
 
   const { assemblyManager } = session as unknown as AbstractSessionModel
-  const assembly = assemblyManager.get(assemblyName)
+  const assembly = assemblyManager.get(assemblyName) as Assembly | undefined
   if (!assembly) {
     setErrorMessage(`Assembly "${assemblyName}" not found`)
     return
diff --git a/packages/jbrowse-plugin-apollo/src/components/ViewChangeLog.tsx b/packages/jbrowse-plugin-apollo/src/components/ViewChangeLog.tsx
index 1867ebf6a..c1aaa7c23 100644
--- a/packages/jbrowse-plugin-apollo/src/components/ViewChangeLog.tsx
+++ b/packages/jbrowse-plugin-apollo/src/components/ViewChangeLog.tsx
@@ -4,6 +4,7 @@
 /* eslint-disable @typescript-eslint/no-unsafe-member-access */
 /* eslint-disable @typescript-eslint/no-unsafe-return */
 import { changeRegistry } from '@apollo-annotation/common'
+import type { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 import type { AbstractSessionModel } from '@jbrowse/core/util'
 import { makeStyles } from '@jbrowse/core/util/tss-react'
 import {
@@ -102,7 +103,7 @@ export function ViewChangeLog({
 
   const { apolloDataStore } = session
   const { assemblyManager } = session as unknown as AbstractSessionModel
-  const assembly = assemblyManager.get(assemblyId)
+  const assembly = assemblyManager.get(assemblyId) as Assembly | undefined
   const assemblyName = assembly?.displayName ?? assemblyId
 
   const gridColumns: GridColDef[] = [
diff --git a/packages/jbrowse-plugin-apollo/src/session/ClientDataStore.ts b/packages/jbrowse-plugin-apollo/src/session/ClientDataStore.ts
index 98a9d80dd..603a2f933 100644
--- a/packages/jbrowse-plugin-apollo/src/session/ClientDataStore.ts
+++ b/packages/jbrowse-plugin-apollo/src/session/ClientDataStore.ts
@@ -12,6 +12,7 @@ import {
   CheckResult,
   type CheckResultSnapshot,
 } from '@apollo-annotation/mst'
+import type { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 import {
   type AnyConfigurationModel,
   getConf,
@@ -106,7 +107,9 @@ export function clientDataStoreFactory(
         let ref = apolloAssembly.refSeqs.get(feature.refSeq)
         if (!ref) {
           // maybe it's a valid refName that we haven't loaded yet
-          const assembly = assemblyManager.get(assemblyId)
+          const assembly = assemblyManager.get(assemblyId) as
+            | Assembly
+            | undefined
           if (!assembly) {
             throw new Error(
               `Could not find assembly "${assemblyId}" to add feature "${feature._id}"`,
diff --git a/packages/jbrowse-plugin-apollo/src/util/glyphUtils.ts b/packages/jbrowse-plugin-apollo/src/util/glyphUtils.ts
index 181570fd6..c05e0eed4 100644
--- a/packages/jbrowse-plugin-apollo/src/util/glyphUtils.ts
+++ b/packages/jbrowse-plugin-apollo/src/util/glyphUtils.ts
@@ -314,8 +314,8 @@ export function getContextMenuItemsForFeature(
   const role = internetAccount ? internetAccount.role : 'admin'
   const readOnly = !(role && ['admin', 'user'].includes(role))
   const [region] = regions
-  const sourceAssemblyId = display.getAssemblyId(region.assemblyName)
-  const currentAssemblyId = display.getAssemblyId(region.assemblyName)
+  const sourceAssemblyId = display.getAssemblyId(region.assemblyName) as string
+  const currentAssemblyId = display.getAssemblyId(region.assemblyName) as string
   menuItems.push(
     {
       label: makeFeatureLabel(sourceFeature),
diff --git a/yarn.lock b/yarn.lock
index 2376f1a5c..85e5ae804 100644
--- a/yarn.lock
+++ b/yarn.lock
@@ -374,9 +374,9 @@ __metadata:
     "@emotion/styled": "npm:^11.10.6"
     "@gmod/gff": "npm:^2.1.0"
     "@gmod/indexedfasta": "npm:^5.0.2"
-    "@jbrowse/core": "npm:^4.1.1"
-    "@jbrowse/mobx-state-tree": "npm:^5.5.0"
-    "@mui/material": "npm:^7.3.7"
+    "@jbrowse/core": "npm:^4.3.0"
+    "@jbrowse/mobx-state-tree": "npm:^5.8.7"
+    "@mui/material": "npm:^7.3.11"
     "@nestjs/cli": "npm:^10.1.10"
     "@nestjs/common": "npm:^10.1.0"
     "@nestjs/config": "npm:^3.0.0"
@@ -454,7 +454,7 @@ __metadata:
     "@apollo-annotation/mst": "workspace:^"
     "@apollo-annotation/schemas": "workspace:^"
     "@gmod/gff": "npm:^2.1.0"
-    "@jbrowse/core": "npm:^4.1.1"
+    "@jbrowse/core": "npm:^4.3.0"
     "@nestjs/common": "npm:^10.1.0"
     "@nestjs/core": "npm:^10.1.0"
     "@types/node": "npm:^24.10.9"
@@ -464,8 +464,8 @@ __metadata:
     tslib: "npm:^2.3.1"
     typescript: "npm:^5.5.3"
   peerDependencies:
-    "@jbrowse/mobx-state-tree": ^5.5.0
-    "@mui/material": ^7.3.7
+    "@jbrowse/mobx-state-tree": ^5.8.7
+    "@mui/material": ^7.3.11
     "@mui/x-data-grid": ^8.0.0
     mobx: ^6.6.1
     mobx-react: ^7.2.1
@@ -491,15 +491,15 @@ __metadata:
     "@emotion/react": "npm:^11.10.6"
     "@emotion/styled": "npm:^11.10.6"
     "@gmod/gff": "npm:^2.1.0"
-    "@jbrowse/cli": "npm:^4.1.1"
-    "@jbrowse/core": "npm:^4.1.1"
+    "@jbrowse/cli": "npm:^4.3.0"
+    "@jbrowse/core": "npm:^4.3.0"
     "@jbrowse/development-tools": "npm:^2.2.1"
-    "@jbrowse/mobx-state-tree": "npm:^5.5.0"
-    "@jbrowse/plugin-authentication": "npm:^4.1.1"
-    "@jbrowse/plugin-linear-genome-view": "npm:^4.1.1"
+    "@jbrowse/mobx-state-tree": "npm:^5.8.7"
+    "@jbrowse/plugin-authentication": "npm:^4.3.0"
+    "@jbrowse/plugin-linear-genome-view": "npm:^4.3.0"
     "@jest/globals": "npm:^29.0.3"
-    "@mui/icons-material": "npm:^7.3.7"
-    "@mui/material": "npm:^7.3.7"
+    "@mui/icons-material": "npm:^7.3.11"
+    "@mui/material": "npm:^7.3.11"
     "@mui/x-data-grid": "npm:^8.0.0"
     "@rollup/plugin-babel": "npm:^6.1.0"
     "@rollup/plugin-commonjs": "npm:^29.0.0"
@@ -566,9 +566,9 @@ __metadata:
     tss-react: "npm:^4.6.1"
     typescript: "npm:^5.5.3"
   peerDependencies:
-    "@jbrowse/core": ^4.1.1
-    "@jbrowse/mobx-state-tree": ^5.5.0
-    "@mui/material": ^7.3.7
+    "@jbrowse/core": ^4.3.0
+    "@jbrowse/mobx-state-tree": ^5.8.7
+    "@mui/material": ^7.3.11
     mobx: ^6.6.1
     mobx-react: ^9.0.0
     prop-types: ^15.8.1
@@ -583,8 +583,8 @@ __metadata:
   version: 0.0.0-use.local
   resolution: "@apollo-annotation/mst@workspace:packages/apollo-mst"
   dependencies:
-    "@jbrowse/core": "npm:^4.1.1"
-    "@jbrowse/mobx-state-tree": "npm:^5.5.0"
+    "@jbrowse/core": "npm:^4.3.0"
+    "@jbrowse/mobx-state-tree": "npm:^5.8.7"
     mobx: "npm:^6.6.1"
     react-dom: "npm:^18.2.0"
     rxjs: "npm:^7.4.0"
@@ -619,8 +619,8 @@ __metadata:
     "@apollo-annotation/schemas": "workspace:^"
     "@gmod/gff": "npm:^2.1.0"
     "@gmod/indexedfasta": "npm:^5.0.2"
-    "@jbrowse/core": "npm:^4.1.1"
-    "@jbrowse/mobx-state-tree": "npm:^5.5.0"
+    "@jbrowse/core": "npm:^4.3.0"
+    "@jbrowse/mobx-state-tree": "npm:^5.8.7"
     "@nestjs/common": "npm:^10.1.0"
     "@nestjs/core": "npm:^10.1.0"
     "@types/chai": "npm:^4.3.19"
@@ -640,8 +640,8 @@ __metadata:
     tsx: "npm:^4.6.2"
     typescript: "npm:^5.5.3"
   peerDependencies:
-    "@jbrowse/mobx-state-tree": ^5.5.0
-    "@mui/material": ^7.3.7
+    "@jbrowse/mobx-state-tree": ^5.8.7
+    "@mui/material": ^7.3.11
     "@mui/x-data-grid": ^8.0.0
     mobx: ^6.6.1
     mobx-react: ^7.2.1
@@ -5705,6 +5705,13 @@ __metadata:
   languageName: node
   linkType: hard
 
+"@babel/runtime@npm:^7.28.6":
+  version: 7.29.2
+  resolution: "@babel/runtime@npm:7.29.2"
+  checksum: 10c0/30b80a0140d16467792e1bbeb06f655b0dab70407da38dfac7fedae9c859f9ae9d846ef14ad77bd3814c064295fe9b1bc551f1541ea14646ae9f22b71a8bc17a
+  languageName: node
+  linkType: hard
+
 "@babel/template@npm:^7.22.15, @babel/template@npm:^7.22.5, @babel/template@npm:^7.3.3":
   version: 7.22.15
   resolution: "@babel/template@npm:7.22.15"
@@ -7081,12 +7088,12 @@ __metadata:
   languageName: node
   linkType: hard
 
-"@floating-ui/core@npm:^1.7.3":
-  version: 1.7.3
-  resolution: "@floating-ui/core@npm:1.7.3"
+"@floating-ui/core@npm:^1.7.5":
+  version: 1.7.5
+  resolution: "@floating-ui/core@npm:1.7.5"
   dependencies:
-    "@floating-ui/utils": "npm:^0.2.10"
-  checksum: 10c0/edfc23800122d81df0df0fb780b7328ae6c5f00efbb55bd48ea340f4af8c5b3b121ceb4bb81220966ab0f87b443204d37105abdd93d94846468be3243984144c
+    "@floating-ui/utils": "npm:^0.2.11"
+  checksum: 10c0/f9c52205e198b231d63a387b09c659aab08c46a1899e0b0bbe147b8b4f048b546f15ba17cb5d2a471da9534f1883d979425e13e5c4ceee67be63e4b0abd4db5d
   languageName: node
   linkType: hard
 
@@ -7100,13 +7107,13 @@ __metadata:
   languageName: node
   linkType: hard
 
-"@floating-ui/dom@npm:^1.7.4":
-  version: 1.7.4
-  resolution: "@floating-ui/dom@npm:1.7.4"
+"@floating-ui/dom@npm:^1.7.6":
+  version: 1.7.6
+  resolution: "@floating-ui/dom@npm:1.7.6"
   dependencies:
-    "@floating-ui/core": "npm:^1.7.3"
-    "@floating-ui/utils": "npm:^0.2.10"
-  checksum: 10c0/da6166c25f9b0729caa9f498685a73a0e28251613b35d27db8de8014bc9d045158a23c092b405321a3d67c2064909b6e2a7e6c1c9cc0f62967dca5779f5aef30
+    "@floating-ui/core": "npm:^1.7.5"
+    "@floating-ui/utils": "npm:^0.2.11"
+  checksum: 10c0/5c098e0d7b58c9bc769f276cca1766994c2c9c70c92d091a61bba8b3e9be53c011e0a79a8457fc2fb2f3d91697a26eb52e0a4962ef936dc963b45f58613c212f
   languageName: node
   linkType: hard
 
@@ -7122,29 +7129,29 @@ __metadata:
   languageName: node
   linkType: hard
 
-"@floating-ui/react-dom@npm:^2.1.6":
-  version: 2.1.6
-  resolution: "@floating-ui/react-dom@npm:2.1.6"
+"@floating-ui/react-dom@npm:^2.1.8":
+  version: 2.1.8
+  resolution: "@floating-ui/react-dom@npm:2.1.8"
   dependencies:
-    "@floating-ui/dom": "npm:^1.7.4"
+    "@floating-ui/dom": "npm:^1.7.6"
   peerDependencies:
     react: ">=16.8.0"
     react-dom: ">=16.8.0"
-  checksum: 10c0/6654834a8e73ecbdbc6cad2ad8f7abc698ac7c1800ded4d61113525c591c03d2e3b59d3cf9205859221465ea38c87af4f9e6e204703c5b7a7e85332d1eef2e18
+  checksum: 10c0/26260ca4bb23b57c73b824062505abf977a008ce6e0463bdacca74f7e49853c4cd1d2bbf1a77c6caa17fa37dfffda2c6c4cd07a8737ebd7474aaff7818401d75
   languageName: node
   linkType: hard
 
-"@floating-ui/react@npm:^0.27.16":
-  version: 0.27.16
-  resolution: "@floating-ui/react@npm:0.27.16"
+"@floating-ui/react@npm:^0.27.19":
+  version: 0.27.19
+  resolution: "@floating-ui/react@npm:0.27.19"
   dependencies:
-    "@floating-ui/react-dom": "npm:^2.1.6"
-    "@floating-ui/utils": "npm:^0.2.10"
+    "@floating-ui/react-dom": "npm:^2.1.8"
+    "@floating-ui/utils": "npm:^0.2.11"
     tabbable: "npm:^6.0.0"
   peerDependencies:
     react: ">=17.0.0"
     react-dom: ">=17.0.0"
-  checksum: 10c0/a026266d8875e69de1ac1e1a00588660c8ee299c1e7d067c5c5fd1d69a46fd10acff5dd6cb66c3fe40a3347b443234309ba95f5b33d49059d0cda121f558f566
+  checksum: 10c0/2a2cdfd3e67e0606833b63f922ad2a9037974f22b944e1cb8c0991b4c40450f8413d69745c0bbf4646e5ba283747f60d2fdc9a8d289b68b24448e59d81a3a96d
   languageName: node
   linkType: hard
 
@@ -7155,10 +7162,10 @@ __metadata:
   languageName: node
   linkType: hard
 
-"@floating-ui/utils@npm:^0.2.10":
-  version: 0.2.10
-  resolution: "@floating-ui/utils@npm:0.2.10"
-  checksum: 10c0/e9bc2a1730ede1ee25843937e911ab6e846a733a4488623cd353f94721b05ec2c9ec6437613a2ac9379a94c2fd40c797a2ba6fa1df2716f5ce4aa6ddb1cf9ea4
+"@floating-ui/utils@npm:^0.2.11":
+  version: 0.2.11
+  resolution: "@floating-ui/utils@npm:0.2.11"
+  checksum: 10c0/f4bcea1559bdbb721ecc8e8ead423ac58d6a5b6e70b602cf0810ba6ad4ed1c77211b207faa88b278a9042f0c743133de08a203ed6741c1b6443423332884d5b3
   languageName: node
   linkType: hard
 
@@ -7176,7 +7183,18 @@ __metadata:
   languageName: node
   linkType: hard
 
-"@gmod/bgzf-filehandle@npm:^6.0.12, @gmod/bgzf-filehandle@npm:^6.0.3":
+"@gmod/bgzf-filehandle@npm:^6.0.19":
+  version: 6.0.26
+  resolution: "@gmod/bgzf-filehandle@npm:6.0.26"
+  dependencies:
+    "@jbrowse/quick-lru": "npm:^7.3.5"
+    generic-filehandle2: "npm:^2.1.4"
+    pako-esm2: "npm:^2.0.2"
+  checksum: 10c0/cbae7673a7fd99e2e1a9d571a6bc9c172d974041f0e7497db013d258437e16705fa3000a0827c30b9cefe30bf353977a6a71b94b8bba32025eb03523e4a77d33
+  languageName: node
+  linkType: hard
+
+"@gmod/bgzf-filehandle@npm:^6.0.3":
   version: 6.0.12
   resolution: "@gmod/bgzf-filehandle@npm:6.0.12"
   dependencies:
@@ -7396,104 +7414,59 @@ __metadata:
   languageName: node
   linkType: hard
 
-"@jbrowse/cli@npm:^4.1.1":
-  version: 4.1.3
-  resolution: "@jbrowse/cli@npm:4.1.3"
+"@jbrowse/cli@npm:^4.3.0":
+  version: 4.3.0
+  resolution: "@jbrowse/cli@npm:4.3.0"
   dependencies:
-    "@jbrowse/text-indexing-core": "npm:^4.1.3"
+    "@jbrowse/text-indexing-core": "npm:^4.3.0"
     cli-progress: "npm:^3.12.0"
     command-exists: "npm:^1.2.9"
     cors: "npm:^2.8.6"
     decompress: "npm:^4.2.1"
     express: "npm:^5.2.1"
-    ixixx: "npm:^3.0.3"
+    ixixx: "npm:^3.0.4"
     json-parse-better-errors: "npm:^1.0.2"
     tmp: "npm:^0.2.5"
   bin:
     jbrowse: dist/bin.js
-  checksum: 10c0/bb1609b2b46636c7a055980d07dbf41d00902239664618c80b65a27f7dcc166e4e58233bd74f61acd0fe150f88bf2e9f799ba6c0affe0e6a5d770bc6198d86bc
-  languageName: node
-  linkType: hard
-
-"@jbrowse/core@npm:^4.1.1":
-  version: 4.1.1
-  resolution: "@jbrowse/core@npm:4.1.1"
-  dependencies:
-    "@emotion/react": "npm:^11.14.0"
-    "@emotion/serialize": "npm:^1.3.3"
-    "@emotion/utils": "npm:^1.4.2"
-    "@floating-ui/react": "npm:^0.27.16"
-    "@gmod/abortable-promise-cache": "npm:^3.0.4"
-    "@gmod/bgzf-filehandle": "npm:^6.0.12"
-    "@gmod/http-range-fetcher": "npm:^5.0.7"
-    "@jbrowse/jexl": "npm:^3.0.1"
-    "@jbrowse/mobx-state-tree": "npm:^5.5.0"
-    "@jbrowse/quick-lru": "npm:^7.3.5"
-    "@leeoniya/ufuzzy": "npm:^1.0.19"
-    "@mui/icons-material": "npm:^7.3.7"
-    "@mui/material": "npm:^7.3.7"
-    "@mui/system": "npm:^7.3.7"
-    "@mui/types": "npm:^7.4.10"
-    "@mui/x-data-grid": "npm:^8.26.0"
-    "@types/file-saver-es": "npm:^2.0.3"
-    canvas-sequencer-ts: "npm:^3.1.3"
-    canvas2svg: "npm:^1.0.16"
-    copy-to-clipboard: "npm:^3.3.3"
-    deepmerge: "npm:^4.3.1"
-    detect-node: "npm:^2.1.0"
-    dompurify: "npm:^3.3.1"
-    escape-html: "npm:^1.0.3"
-    fast-deep-equal: "npm:^3.1.3"
-    file-saver-es: "npm:^2.0.5"
-    generic-filehandle2: "npm:^2.0.18"
-    idb: "npm:^8.0.3"
-    librpc-web-mod: "npm:^2.1.1"
-    mobx: "npm:^6.15.0"
-    mobx-react: "npm:^9.2.1"
-    react-draggable: "npm:^4.5.0"
-    rxjs: "npm:^7.8.2"
-    source-map-js: "npm:^1.2.1"
-  peerDependencies:
-    react: ">=18.0.0"
-    react-dom: ">=18.0.0"
-  checksum: 10c0/4a3293387ff4b48f8036711fdfb4ff5131770fdcde9090318dd519937b8a0091273c537b42bf4ab6c5e6ca21758d6c7012ba69ef0068c22f66c8760784759595
+  checksum: 10c0/4171e7dd309d77f919a052aec1a3dbf247e22937685213fb65de2c1231cf273df837ee00c940667f30b9bbbec2c23c4ecdf97dff8f501f9e9fa74b1961611db7
   languageName: node
   linkType: hard
 
-"@jbrowse/core@npm:^4.1.3":
-  version: 4.1.3
-  resolution: "@jbrowse/core@npm:4.1.3"
+"@jbrowse/core@npm:^4.3.0":
+  version: 4.3.0
+  resolution: "@jbrowse/core@npm:4.3.0"
   dependencies:
     "@emotion/react": "npm:^11.14.0"
     "@emotion/serialize": "npm:^1.3.3"
     "@emotion/utils": "npm:^1.4.2"
-    "@floating-ui/react": "npm:^0.27.16"
+    "@floating-ui/react": "npm:^0.27.19"
     "@gmod/abortable-promise-cache": "npm:^3.0.4"
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+  version: 8.28.7
+  resolution: "@mui/x-data-grid@npm:8.28.7"
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     "@mui/utils": "npm:^7.3.5"
     "@mui/x-internals": "npm:8.26.0"
-    "@mui/x-virtualizer": "npm:0.3.3"
+    "@mui/x-virtualizer": "npm:0.3.5"
     clsx: "npm:^2.1.1"
     prop-types: "npm:^15.8.1"
     use-sync-external-store: "npm:^1.6.0"
@@ -8543,7 +8547,7 @@ __metadata:
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     "@emotion/styled":
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@@ -8589,9 +8593,9 @@ __metadata:
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-"@mui/x-virtualizer@npm:0.3.3":
-  version: 0.3.3
-  resolution: "@mui/x-virtualizer@npm:0.3.3"
+"@mui/x-virtualizer@npm:0.3.5":
+  version: 0.3.5
+  resolution: "@mui/x-virtualizer@npm:0.3.5"
   dependencies:
     "@babel/runtime": "npm:^7.28.4"
     "@mui/utils": "npm:^7.3.5"
@@ -8599,7 +8603,7 @@ __metadata:
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     react-dom: ^17.0.0 || ^18.0.0 || ^19.0.0
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-  version: 4.2.0
-  resolution: "crypto-js@npm:4.2.0"
-  checksum: 10c0/8fbdf9d56f47aea0794ab87b0eb9833baf80b01a7c5c1b0edc7faf25f662fb69ab18dc2199e2afcac54670ff0cd9607a9045a3f7a80336cccd18d77a55b9fdf0
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   resolution: "crypto-random-string@npm:4.0.0"
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-"dompurify@npm:^3.3.1":
-  version: 3.3.1
-  resolution: "dompurify@npm:3.3.1"
+"dompurify@npm:^3.4.2":
+  version: 3.4.5
+  resolution: "dompurify@npm:3.4.5"
   dependencies:
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   dependenciesMeta:
     "@types/trusted-types":
       optional: true
-  checksum: 10c0/fa0a8c55a436ba0d54389195e3d2337e311f56de709a2fc9efc98dbbc7746fa53bb4b74b6ac043b77a279a8f2ebd8685f0ebaa6e58c9e32e92051d529bc0baf8
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   languageName: node
   linkType: hard
 
+"generic-filehandle2@npm:^2.1.4, generic-filehandle2@npm:^2.1.7":
+  version: 2.1.9
+  resolution: "generic-filehandle2@npm:2.1.9"
+  checksum: 10c0/5acaa4ee0c04e5c97b31b65fb685c04d788601956bbc5e9888b5c468eccf1da61d8ca0ed86e094d72de7a5891144151d5bff04702640476adc535811e7ebd8e5
+  languageName: node
+  linkType: hard
+
 "gensync@npm:^1.0.0-beta.2":
   version: 1.0.0-beta.2
   resolution: "gensync@npm:1.0.0-beta.2"
@@ -22831,16 +22835,14 @@ __metadata:
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-"ixixx@npm:^3.0.3":
-  version: 3.0.3
-  resolution: "ixixx@npm:3.0.3"
+"ixixx@npm:^3.0.4":
+  version: 3.0.9
+  resolution: "ixixx@npm:3.0.9"
   dependencies:
-    command-exists: "npm:^1.2.9"
-    split2: "npm:^4.1.0"
-    tmp: "npm:^0.2.1"
+    split2: "npm:^4.2.0"
   bin:
     ixixxjs: dist/bin.js
-  checksum: 10c0/cdb6517e823ec8bc83d558694303c41d700c5ed27edf280f3f7cc447ff81f55ee594c9564f5252470c43e749a6cb4d5f2e3d74d949d3eff6caea799fb4dc6b3c
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@@ -25887,10 +25889,10 @@ __metadata:
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-"mobx@npm:^6.15.0":
-  version: 6.15.0
-  resolution: "mobx@npm:6.15.0"
-  checksum: 10c0/afbfdc5659caac4ba620d1caca8eb471bbe56746403a8023ae402e27f9e04856394e1529ccf46feb7fdad0c6d695fa1972e8421e7fbfcb1cf453131739a12ac4
+"mobx@npm:^6.15.3":
+  version: 6.15.3
+  resolution: "mobx@npm:6.15.3"
+  checksum: 10c0/3a49d0d9ad2d9f9d28842b1f49147a2b074629120150f9cbe3d99b5c1d84528f8f43a72d084e97892407238d4f5140e03c90e434d7004c4167efd2d11fb198b1
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@@ -26253,7 +26255,7 @@ __metadata:
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-"node-fetch@npm:^2.6.1, node-fetch@npm:^2.6.12, node-fetch@npm:^2.6.7, node-fetch@npm:^2.7.0":
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   resolution: "node-fetch@npm:2.7.0"
   dependencies:
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-"split2@npm:^4.1.0":
+"split2@npm:^4.2.0":
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   resolution: "split2@npm:4.2.0"
   checksum: 10c0/b292beb8ce9215f8c642bb68be6249c5a4c7f332fc8ecadae7be5cbdf1ea95addc95f0459ef2e7ad9d45fd1064698a097e4eb211c83e772b49bc0ee423e91534
@@ -32305,7 +32307,14 @@ __metadata:
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   linkType: hard
 
-"tmp@npm:^0.2.1, tmp@npm:~0.2.1":
+"tmp@npm:^0.2.5":
+  version: 0.2.5
+  resolution: "tmp@npm:0.2.5"
+  checksum: 10c0/cee5bb7d674bb4ba3ab3f3841c2ca7e46daeb2109eec395c1ec7329a91d52fcb21032b79ac25161a37b2565c4858fefab927af9735926a113ef7bac9091a6e0e
+  languageName: node
+  linkType: hard
+
+"tmp@npm:~0.2.1":
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   resolution: "tmp@npm:0.2.1"
   dependencies:
@@ -32314,13 +32323,6 @@ __metadata:
   languageName: node
   linkType: hard
 
-"tmp@npm:^0.2.5":
-  version: 0.2.5
-  resolution: "tmp@npm:0.2.5"
-  checksum: 10c0/cee5bb7d674bb4ba3ab3f3841c2ca7e46daeb2109eec395c1ec7329a91d52fcb21032b79ac25161a37b2565c4858fefab927af9735926a113ef7bac9091a6e0e
-  languageName: node
-  linkType: hard
-
 "tmpl@npm:1.0.5":
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   resolution: "tmpl@npm:1.0.5"