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"resolved": "https://registry.npmjs.org/xml-name-validator/-/xml-name-validator-5.0.0.tgz", - "integrity": "sha512-EvGK8EJ3DhaHfbRlETOWAS5pO9MZITeauHKJyb8wyajUfQUenkIg2MvLDTZ4T/TgIcm3HU0TFBgWWboAZ30UHg==", + "version": "4.0.0", + "resolved": "https://registry.npmjs.org/xml-name-validator/-/xml-name-validator-4.0.0.tgz", + "integrity": "sha512-ICP2e+jsHvAj2E2lIHxa5tjXRlKDJo4IdvPvCXbXQGdzSfmSpNVyIKMvoZHjDY9DP0zV17iI85o90vRFXNccRw==", "dev": true, "license": "Apache-2.0", "engines": { - "node": ">=18" + "node": ">=12" } }, "node_modules/xmlchars": { @@ -10631,6 +11046,16 @@ "node": ">=12" } }, + "node_modules/yn": { + "version": "3.1.1", + "resolved": "https://registry.npmjs.org/yn/-/yn-3.1.1.tgz", + "integrity": "sha512-Ux4ygGWsu2c7isFWe8Yu1YluJmqVhxqK2cLXNQA5AcC3QfbGNpM7fu0Y8b/z16pXLnFxZYvWhd3fhBY9DLmC6Q==", + "dev": true, + "license": "MIT", + "engines": { + "node": ">=6" + } + }, "node_modules/yocto-queue": { "version": "0.1.0", "resolved": "https://registry.npmjs.org/yocto-queue/-/yocto-queue-0.1.0.tgz", diff --git a/package.json b/package.json index 1f881f56..0457d7f4 100644 --- a/package.json +++ b/package.json @@ -7,12 +7,8 @@ "build": "next build", "start": "next start", "lint": "next lint", -<<<<<<< Updated upstream -}, -======= "test": "./node_modules/.bin/jest" }, ->>>>>>> Stashed changes "dependencies": { "leaflet": "^1.9.4", "next": "^15.5.3", @@ -22,21 +18,24 @@ "react-leaflet-cluster": "^3.1.0" }, "devDependencies": { - "@testing-library/dom": "^10.4.1", - "@testing-library/jest-dom": "^6.9.1", - "@testing-library/react": "^16.3.2", - "@types/jest": "^30.0.0", - "@types/leaflet": "^1.9.21", + "@tailwindcss/postcss": "^4.2.2", + "@testing-library/dom": "^10.4.0", + "@testing-library/jest-dom": "^6.6.3", + "@testing-library/react": "^16.3.0", + "@types/jest": "^29.5.14", + "@types/leaflet": "^1.9.18", "@types/node": "24.3.3", "@types/react": "19.1.13", "@typescript-eslint/eslint-plugin": "^8.39.1", "@typescript-eslint/parser": "^8.39.1", + "autoprefixer": "^10.4.27", "eslint": "^8.57.1", "eslint-config-next": "^15.4.6", - "jest": "^30.3.0", - "jest-environment-jsdom": "^30.3.0", + "jest": "^29.7.0", + "jest-environment-jsdom": "^29.7.0", "prettier": "^3.6.2", - "ts-jest": "^29.4.6", + "ts-jest": "^29.4.0", + "ts-node": "^10.9.2", "typescript": "^5.9.2" } } diff --git a/paper.bib b/paper.bib new file mode 100644 index 00000000..6173eabb --- /dev/null +++ b/paper.bib @@ -0,0 +1,74 @@ +@article{Hadfield2018, + author = {Hadfield, James and Megill, Colin and Bell, Sidney M. and + Huddleston, John and Potter, Barney and Callender, Charlton and + Sagulenko, Pavel and Bedford, Trevor and Neher, Richard A.}, + title = {Nextstrain: real-time tracking of pathogen evolution}, + journal = {Bioinformatics}, + year = {2018}, + volume = {34}, + number = {23}, + pages = {4121--4123}, + doi = {10.1093/bioinformatics/bty407}, + pmid = {29790939}, + pmcid = {PMC6247931} +} + +@article{Argimon2016, + author = {Argim{\'o}n, Silvia and Abudahab, Khalil and Goater, Richard J. E. and + Fedosejev, Artemij and Bhai, Jyothish and Glasner, Corinna and + Feil, Edward J. and Holden, Matthew T. 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Built on Next.js 15 and TypeScript, it renders interactive +Leaflet-based maps with automatic marker clustering, supports search and filter +operations across outbreak records, and runs without server-side infrastructure beyond +standard static file hosting. The v0.1.0 release establishes the geographic +surveillance interface and the application architecture on which phylogenetic tree +visualization, data parsers, and external API integrations are being built. EvoMap +targets researchers, public health practitioners, and educators who need accessible +outbreak visualization without the installation overhead of desktop bioinformatics +tools. + +# Statement of Need + +Pathogen genomic and epidemiological data is generated at scale across low- and +middle-income countries, but the infrastructure to interpret it is unevenly +distributed. Most phylogenetic and outbreak visualization workflows, including IQ-TREE +[@Nguyen2015], BEAST, and the Nextstrain augur pipeline [@Hadfield2018], require local +software installation, command-line literacy, and computational hardware unavailable to +much of the global public health workforce. A district epidemiologist tracking an +outbreak cluster in a resource-constrained setting needs to answer spatial questions +about case concentration, spread, and geographic clustering without first configuring +a pipeline to do it. + +Existing browser-based platforms address parts of this gap. Nextstrain [@Hadfield2018] +combines phylogenetic inference with geographic visualization, but a custom Nextstrain +workflow requires managing augur and auspice installations with meaningful compute +overhead. Microreact [@Argimon2016] provides a polished linked tree-and-map viewer but +requires pre-computed inputs and has no integration with public sequence repositories. +iTOL [@Letunic2019] handles phylogenetic annotation well but was not built for spatial +outbreak tracking. None of these platforms is designed for rapid deployment by teams +without dedicated bioinformatics staff. + +EvoMap sits between these tools: a web-native geographic visualization layer that runs +from a URL, requires no installation, and is built from the start to receive +phylogenetic and API layers as the platform grows. At v0.1.0, EvoMap delivers the +geographic map interface, the search and filter system, and the full application +scaffold. This paper describes what is functional now, what is planned, and how the +architecture supports that roadmap. + +# Implementation + +## Technology Stack + +EvoMap is implemented in TypeScript 5.9 using the Next.js 15 App Router. The +production build outputs static assets deployable to any CDN or static host, including +free-tier services like Vercel and Netlify, which matters for research groups without +hosting budgets. TypeScript strict mode is enforced throughout to catch data ingestion +errors early, since silent failures on malformed files erode user trust faster than +almost any other class of bug. + +Geographic visualization runs on Leaflet 1.9.4 via react-leaflet 5 and +react-leaflet-cluster 3.1. Leaflet was chosen over Mapbox GL because its default +OpenStreetMap configuration requires no API token, removing a setup barrier that +disproportionately affects users in institutions without managed developer accounts. +Marker clustering via react-leaflet-cluster keeps dense outbreak datasets readable. +TailwindCSS handles the responsive layout. The application starts with a standard +`npm install && npm run dev` with no environment variables required for the core +geographic interface. + +![EvoMap v0.1.0 geographic interface. The Leaflet map renders outbreak markers over an +OpenStreetMap basemap with zoom and pan controls. Navigation provides access to the +map, phylogenetic, search, and dashboard routes.](fig1.png) + +## Application Architecture + +The repository follows the Next.js App Router convention. Route segments under +`src/app/` cover the geographic map, phylogenetic viewer (scaffolded), dashboard, and +API routes. Supporting modules in `src/lib/` handle mock data and shared types. +Custom React hooks in `src/hooks/` manage data fetching for outbreaks, pathogens, +phylogenetic data, and search. The current structure is: + +``` +src/ +├── __tests__/ +│ └── outbreak-data.test.ts +├── app/ +│ └── api/ +│ ├── outbreaks/ +│ ├── pathogens/ +│ ├── phylogenetic/ +│ ├── search/ +│ └── upload/ +├── components/ +│ ├── charts/ +│ │ └── Timeline.tsx +│ ├── maps/ +│ │ └── GlobalMap.tsx +│ └── upload/ +│ └── DataUpload.tsx +├── data/ +│ └── mockApi.ts +├── hooks/ +│ ├── useOutbreaks.ts +│ ├── usePathogens.ts +│ ├── usePhylogeneticData.ts +│ └── useSearch.ts +└── lib/ + ├── data/ + │ └── mockData.ts + ├── mongodb.ts + ├── store.ts + └── types.ts +``` + +The map, hooks, and data layers are functional in v0.1.0. The phylogenetic viewer, +parsers, and API integrations are scaffolded for v0.2.0 and v1.0.0. + +## Current Functionality + +The following are implemented and verified in v0.1.0: an interactive Leaflet map with +OpenStreetMap tiles, zoom and pan controls, and automatic marker clustering; a search +and filter panel for querying the loaded outbreak dataset; a responsive layout that +adapts from desktop to mobile without functional loss; a clean production build +deployable via the included `vercel.json`; a Dockerfile and `nginx.conf` for +containerised institutional deployment; and an MIT licence, `CONTRIBUTING.md` with +Conventional Commits, `CODE_OF_CONDUCT.md`, and GitHub Actions CI. + +## Planned Functionality + +Phase 2 (v0.2.0) covers D3.js phylogenetic tree rendering with rectangular, radial, +and circular layouts; client-side parsers for Newick, phyloXML, and FASTA; Zustand +state management; SWR data fetching; and bidirectional selection linking between the +tree and map panels. + +Phase 3 (v1.0.0) covers NCBI Entrez API integration for automated sequence retrieval, +Nextstrain JSON endpoint support [@Hadfield2018], direct ingestion of GISAID-formatted +datasets [@Shu2017], replacement of mock data with live repository feeds, SVG and CSV +export, and Progressive Web App offline capability for field use. + +# Limitations + +Three limitations are worth stating plainly. The current map renders mock data only; +EvoMap connects to no live data source at v0.1.0, and custom data ingestion requires +manual modification of the mock data layer until the parsers planned for v0.2.0 land. +The phylogenetic tree page exists as a navigable route but renders no content yet. +The test suite covers coordinate validation and search logic but not component-level +rendering; broader coverage is a Phase 2 priority. + +# Acknowledgements + +The author thanks the Nextstrain and Microreact development teams for the design +precedents that shaped EvoMap's architecture, and the open-source communities behind +Next.js, React, Leaflet, and D3.js. NCBI and WHO data resources underpin the planned +real-data layer. Portions of the implementation were developed with Cursor, an +AI-powered code editor, used for boilerplate scaffolding and iterative debugging. All +research design, architectural decisions, and scientific framing were made by the +author, who takes full responsibility for all code in the repository. + +# References