BioTools Explorer

A live, searchable app for discovering and comparing bioinformatics tools. Search by name to instantly aggregate metadata from GitHub, Docker Hub, and scholarly literature (Europe PMC / PubMed) — all in one view.

Live demo:

• biotools-explorer
• biotools-explorer (PC ONLY)

Table of Contents

• Features
• Architecture
• Prerequisites
• Installation
• Running in Development
• Building for Production
• Project Structure
• API Reference
• External APIs Used
• Usage Guide
• Configuration
• Troubleshooting
• Author

Features

• Tool search — Type any bioinformatics tool name (e.g. STAR, HISAT2, Seurat, Samtools, BWA, DESeq2) to fetch live data.
• GitHub metadata — Stars, forks, open/closed issues, latest version, release notes, creation date, last update, language, license, topics, and homepage link.
• Docker Hub images — Container name, namespace, pull count, star count, latest tag, last update date, with direct links to Docker Hub.
• Publications — Scholarly references from Europe PMC (covers PubMed, PMC, and preprints) with title, authors, year, journal, DOI/PMID links, and auto-classified usage summaries (alignment, benchmarking, pipeline, single-cell, etc.).
• Side-by-side comparison — Compare 2+ tools in a sortable/filterable table. Sort by stars, recency, open issues, publication count, or Docker availability. Filter by "has Docker" or "has publications."
• Dark / Light mode — System-aware theme with manual toggle.
• Responsive — Works on mobile, tablet, and desktop.
• No database required — All data is fetched live from public APIs. No sign-up or API keys needed.

Architecture

┌─────────────────────────────────────────────────┐
│                    Browser                      │
│  React 18 + Tailwind CSS + shadcn/ui + Recharts │
│  Hash routing (wouter) · TanStack React Query   │
└────────────────────┬────────────────────────────┘
                     │ HTTP (fetch)
┌────────────────────▼─────────────────────────────┐
│              Express 5 Server                    │
│         GET /api/search?q=<tool_name>            │
│                                                  │
│  Parallel fan-out to:                            │
│   ├── GitHub REST API (repos, releases, tags,    │
│   │   closed-issues search)                      │
│   ├── Docker Hub v2 API (search, tags)           │
│   └── Europe PMC REST API (literature search)    │
└──────────────────────────────────────────────────┘

The server acts as a lightweight proxy/aggregator — it makes parallel requests to three public APIs, normalizes the responses, and returns a unified JSON payload to the frontend. No database, no authentication, no persistent state.

Prerequisites

Requirement	Minimum Version	Check Command
Node.js	18.x or higher	node --version
npm	9.x or higher	npm --version
Git	2.x	git --version

Note: This project uses Node.js fetch() (available from Node 18+). No Python or other runtimes are required.

Installation

1. Clone the repository

git clone https://github.com/bhagesh-h/biotools-dashboard.git
cd biotools-dashboard

2. Install dependencies

npm install

This installs all dependencies listed in package.json — both runtime and development. There is no separate requirements.txt because this is a JavaScript/TypeScript project managed entirely by npm.

Running in Development

npm run dev

This starts a single process that serves both the Express backend (API routes) and the Vite frontend (React with hot module replacement) on the same port.

• Open http://localhost:5000 in your browser.
• Frontend changes hot-reload automatically.
• Backend changes require restarting the command.

Building for Production

Build

npm run build

This compiles:

• Frontend → dist/public/ (static HTML/CSS/JS bundle via Vite)
• Backend → dist/index.cjs (bundled Express server via esbuild)

Run production server

npm start

Or explicitly:

NODE_ENV=production node dist/index.cjs

The production server serves the static frontend and the API on port 5000.

API Reference

GET /api/search?q=<tool_name>

Searches GitHub, Docker Hub, and Europe PMC in parallel for the given tool name.

Query parameters:

Param	Type	Required	Description
q	string	Yes	Tool name to search (e.g. "STAR", "samtools")

Response (200 OK):

{
  "searchQuery": "STAR",
  "github": [
    {
      "name": "STAR",
      "fullName": "alexdobin/STAR",
      "description": "RNA-seq aligner",
      "url": "https://github.com/alexdobin/STAR",
      "homepage": "https://github.com/alexdobin/STAR",
      "stars": 1850,
      "forks": 520,
      "openIssues": 45,
      "closedIssues": 890,
      "latestVersion": "2.7.11b",
      "latestReleaseDate": "2024-01-15T...",
      "latestReleaseNotes": "Bug fixes...",
      "firstReleaseDate": "2015-03-01T...",
      "createdAt": "2013-05-01T...",
      "updatedAt": "2024-12-01T...",
      "language": "C++",
      "license": "MIT",
      "topics": ["rna-seq", "aligner", "bioinformatics"]
    }
  ],
  "docker": [
    {
      "name": "star",
      "namespace": "alexdobin",
      "description": "Docker image for STAR aligner",
      "url": "https://hub.docker.com/r/alexdobin/star",
      "starCount": 2,
      "pullCount": 30987,
      "lastUpdated": "2024-06-01T...",
      "latestTag": "latest"
    }
  ],
  "publications": [
    {
      "title": "STAR: ultrafast universal RNA-seq aligner.",
      "authors": "Dobin A, Davis CA, ...",
      "year": "2013",
      "journal": "Bioinformatics",
      "doi": "10.1093/bioinformatics/bts635",
      "pmid": "23104886",
      "url": "https://doi.org/10.1093/bioinformatics/bts635",
      "usageSummary": "Sequence alignment / read mapping",
      "source": "PubMed"
    }
  ],
  "fetchedAt": "2026-03-14T06:13:00.000Z"
}

Error responses:

• 400 — Missing or empty q parameter.
• 500 — Server-side error during API fetching.

External APIs Used

All APIs are public and require no authentication for basic usage.

API	Purpose	Rate Limits
GitHub REST API	Repository search, releases, tags, issues	60 req/hour unauthenticated; 5,000/hour with token
Docker Hub API v2	Image search, tag listing	Varies; generally generous for reads
Europe PMC REST API	Literature search (covers PubMed, PMC)	No hard limit; be respectful

Optional: Add a GitHub token for higher rate limits

If you hit GitHub's 60-requests-per-hour limit, add a personal access token:

# In your terminal before starting the server:
export GITHUB_TOKEN=ghp_your_token_here

Then update server/routes.ts to include the token in the Authorization header:

headers: {
  Accept: "application/vnd.github.v3+json",
  "User-Agent": "BioTools-Dashboard",
  "Authorization": `Bearer ${process.env.GITHUB_TOKEN}`,
},

Usage Guide

Searching for a tool

1. Type a tool name (e.g. STAR, HISAT2, Seurat) in the search bar at the top.
2. Press Enter or click Search.
3. The dashboard fetches data from all three sources in parallel and displays results.

Alternatively, click any of the suggestion buttons on the landing page (STAR, HISAT2, Seurat, Samtools, BWA, DESeq2) for one-click searching.

Adding multiple tools

Search for additional tools — each is added as a badge below the search bar. You can search for as many tools as you want.

Exploring results

For each tool, the Explore tab shows three sections:

• Repositories — Cards showing the top GitHub matches. Each card includes:

  • Stars, forks, open issues, closed issues
  • Latest version tag with relative timestamp
  • Last update and creation dates
  • Language, license, and website badges
  • Expandable release notes (click "Release notes")

• Docker Images — Cards for Docker Hub matches, showing pull count, star count, latest tag, and direct links.

• Publications — Compact cards for each scholarly paper, showing:

  • Title (linked to DOI/PubMed)
  • Authors and year
  • Journal/source badge
  • Auto-classified usage type (e.g. "Sequence alignment / read mapping", "Benchmarking / comparative analysis", "Single-cell analysis", "Part of an analysis pipeline")
  • Click "Show all X publications" to expand the full list.

Comparing tools side-by-side

When 2 or more tools are loaded, a Compare tab appears. It shows:

• A sortable table with columns: Tool, Repository, Stars, Forks, Version, Last Update, Created, Open Issues, Closed Issues, Docker availability, Publication count, and Language.
• Sort dropdown — Sort by: Most stars, Recently updated, Most open issues, Most publications, Docker available.
• Filter buttons — Toggle "Has Docker" and "Has Publications" to narrow results.
• The highest-starred tool and most recently updated tool are highlighted.
• A Docker Comparison section below the table shows Docker image details for tools that have container images.

Removing a tool

Click the × on any tool badge in the header, or click Remove in the tool's result section.

Dark / Light mode

Click the sun/moon icon in the top-right corner of the header. The theme defaults to your system preference.

Configuration

Environment Variables

Variable	Default	Description
NODE_ENV	—	Set to production for production builds
PORT	5000	Server port (optional; defaults to 5000)
GITHUB_TOKEN	—	Optional GitHub personal access token for higher rate limits

Customization

• Add more suggestion buttons — Edit client/src/components/empty-state.tsx, update the suggestions array.
• Change theme colors — Edit client/src/index.css. The --primary variable controls the accent color (currently teal 174 72% 32%).
• Increase API results — In server/routes.ts, change per_page=5 (GitHub), page_size=5 (Docker), or pageSize=8 (Europe PMC) to higher values.

Troubleshooting

"GitHub API rate limit exceeded"

The unauthenticated GitHub API allows 60 requests/hour. Each tool search makes ~3-6 requests (search + releases/tags + closed issues per repo). Solutions:

1. Wait for the rate limit to reset (shown in the X-RateLimit-Reset response header).
2. Add a GITHUB_TOKEN environment variable (see Configuration).

"Module not found" or "Cannot find module" errors

Run npm install again. If the error persists, delete node_modules and package-lock.json, then reinstall:

rm -rf node_modules package-lock.json
npm install

Port 5000 already in use

# Find and kill the process using port 5000:
lsof -i :5000
kill -9 <PID>

Or set a different port: PORT=3000 npm run dev

Docker/publications not showing for a tool

Some tools may not have Docker images or indexed publications. The sections only appear when results are found.

Available npm Scripts

Command	Description
npm run dev	Start development server (Vite HMR + Express)
npm run build	Build production frontend + backend bundles
npm start	Run the production server from dist/
npm run check	Run TypeScript type checking

Author

Bhagesh Hunakunti