scSAID

Single-Cell Skin & Appendages Integrated Database

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Unifying the world's single-cell skin transcriptomics data in one place.

Overview

scSAID is a comprehensive web platform for exploring single-cell RNA sequencing (scRNA-seq) data from skin and appendage tissues. We aggregate, harmonize, and visualize data from over 1,000,000 cells across 600+ samples, spanning both human and mouse species in healthy and disease conditions.

Whether you're investigating keratinocyte differentiation, immune cell infiltration in psoriasis, or hair follicle stem cell dynamics — scSAID gives you the tools to explore it all.

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Features

Feature	Description
Browse	Explore datasets with advanced filtering, sorting, and pagination
Gene Search	Query expression patterns across cell types and conditions
Interactive Visualization	Embedded UMAP plots with real-time cell type exploration
DEG Analysis	Filter differentially expressed genes by p-value, fold change, and cell type
CellPhoneDB	Visualize cell-cell communication networks and receptor interactions
Enrichment Analysis	Gene set enrichment using MSigDB pathways
Gene Set Scoring	Score cells using Reactome pathways with AUCell, GSVA, or mean expression
Data Export	Download filtered results as Excel files

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Tech Stack

┌─────────────────────────────────────────────────────────┐
│                      Frontend                           │
│   JSP  ·  CSS3  ·  JavaScript  ·  ECharts  ·  DataTables│
├─────────────────────────────────────────────────────────┤
│                      Backend                            │
│   Java Servlets  ·  Apache POI  ·  Python Dash          │
├─────────────────────────────────────────────────────────┤
│                   Infrastructure                        │
│   Maven  ·  Tomcat 9  ·  Nginx  ·  GitHub Actions       │
└─────────────────────────────────────────────────────────┘

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Quick Start

# Clone the repository
git clone https://github.com/Dostoyevsky7/SkinDB_web.git
cd SkinDB_web

# Make Maven wrapper executable
chmod +x mvnw

# Run locally
./mvnw tomcat7:run

Open http://localhost:8080 in your browser.

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Project Structure

src/main/
├── java/
│   ├── Servlet/          # HTTP request handlers
│   ├── Utils/            # Data processing utilities
│   └── Entity/           # Data models
├── webapp/
│   ├── CSS/              # Design system & component styles
│   ├── JS/               # Interactive charts & micro-interactions
│   ├── images/           # Static assets
│   ├── WEB-INF/          # Configuration & data files
│   └── *.jsp             # Page templates
└── resources/
    └── mapping.json      # Field mappings

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Requirements

• Java 11+
• Maven 3.6+

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Production Deployment

Dash App Integration

The enrichment and gene set scoring modules are embedded via iframes expecting same-origin paths:

• /enrichment/ → Dash app on localhost:8051
• /gene-scoring/ → Dash app on localhost:8052

Configure your nginx reverse proxy to forward these paths:

map $http_upgrade $connection_upgrade {
    default upgrade;
    ''      close;
}

location /enrichment/ {
    proxy_pass http://127.0.0.1:8051/enrichment/;
    proxy_http_version 1.1;
    proxy_set_header Host $host;
    proxy_set_header Upgrade $http_upgrade;
    proxy_set_header Connection $connection_upgrade;
}

location /gene-scoring/ {
    proxy_pass http://127.0.0.1:8052/gene-scoring/;
    proxy_http_version 1.1;
    proxy_set_header Host $host;
    proxy_set_header Upgrade $http_upgrade;
    proxy_set_header Connection $connection_upgrade;
}

Use a process manager (systemd, supervisor, pm2) to keep Dash apps running.

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License

Zhejiang University · ZJE

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_{Built with care for skin biology research}