License Statement This project is licensed under the GNU Affero General Public License v3.0 (AGPLv3).

• ✅ Permitted: free use, modification, and distribution
• 🔄 Requirement: derivative works must remain open source under the same license
• 🌐 Network services: if the project is used to provide online services, the modified source code must be made publicly available

Special Note on Network Services

If you use this project to provide online services (e.g., Web API, SaaS platform), you must:

• Make the modified source code publicly available to all users
• Provide a clear and accessible link to the source code in a prominent location (e.g., at the bottom of the service page)

Introduction to ssMOOD

The spatial and single-cell Major Depression Disease Omics Online Database (ssMOOD) is a comprehensive online resource designed to integrate and provide access to spatial transcriptomics and single-cell transcriptomic datasets related to major depressive disorder (MDD). Its primary aim is to facilitate in-depth exploration of the molecular mechanisms underlying MDD and to support the discovery of potential biomarkers for diagnosis and therapeutic development.

ssMOOD brings together data from both human studies and chronic social defeat stress (CSDS) mouse models, covering spatial transcriptomics and single-nucleus RNA sequencing (snRNA-seq). Currently, the database contains multiple curated projects, comprising more than six million entries, offering researchers a unified platform to query, visualize, and analyze depression-related omics data at both the spatial and single-cell levels.

From a technological perspective, ssMOOD is built upon a modern, high-performance web architecture. The frontend is developed with Vue.js and Element Plus, delivering a responsive and user-friendly interface with interactive visualization capabilities. The backend combines PHP and Python for efficient data processing and dynamic content generation, while MariaDB serves as the core database, providing robust and scalable data storage and management. Together, these technologies enable smooth user interaction, fast query responses, and reliable handling of large-scale omics data.

By integrating state-of-the-art data resources with a modern interface and optimized performance, ssMOOD aims to become a valuable tool for the neuroscience and psychiatry research communities. It empowers users to perform multi-dimensional exploration of MDD-related datasets, bridging spatial and single-cell omics to advance the understanding of this complex psychiatric disorder.

Overview of ssMOOD Page Functions

Home

The Home page provides a comprehensive overview of the database and highlights its core features:

• Bar Chart of Dataset Counts: Displays the number of datasets available across different categories, offering a quick snapshot of the data distribution.

• Species Proportion Pie Chart: Shows the distribution of species in the database, giving users a clear understanding of the species representation.

• Single-cell vs ST Proportion: A comparison chart illustrating the proportion of single-cell data versus spatial transcriptomics (ST) data within the database.

• UMAP of Human and Mouse Single-cell Data: Visualizes the clustering of single-cell data for both human and mouse species using UMAP (Uniform Manifold Approximation and Projection).

• ST Spatial Location Map for Human and Mouse: Displays the spatial positioning of human and mouse samples within the context of spatial transcriptomics.

• Integrated Datasets: Showcases the integration of various datasets, providing a holistic view of the available data across species and techniques.

Browse

The Browse section enables users to explore datasets in two primary categories:

• Single-cell datasets Includes both integrated datasets (aggregated from multiple studies) and individual datasets.As of August 2025, there are 626,425 cells.

• ST datasets Also includes both integrated and individual datasets, supporting both cross-study comparisons and single-study analyses.As of August 2025, there are 5,506,379 ST datas.

This section is designed to provide intuitive access to raw and processed data, facilitating downstream analyses.

About

The About section provides comprehensive background information:

• Methods Describes the experimental protocols and computational pipelines used for data generation, preprocessing, and integration.

• Usage Offers guidance on accessing and analyzing datasets, including search, filtering, and visualization features.

• FAQ Answers to frequently asked questions regarding data interpretation, usage, and troubleshooting.

• Contact Us Provides contact information for technical support, collaborative inquiries, and data contribution requests.

Download

The Download section provides direct access to:

• Raw datasets Publicly available single-cell and bulk RNA-seq datasets for offline analysis.

• Source code The complete source code of the web application, enabling reproducibility, local deployment, and further customization.

ssMOOD Runtime Environment

• Operating System: Ubuntu 22.04 LTS
• Server: Apache 2
• Backend: PHP 8.2, Python 3.10.12
• Database: MariaDB 10.6

ssMOOD project

src
├── App.vue                 # Vue root component, entry point and layout container for the entire application
├── assets                  # Static resources folder, such as images, icons, etc.
├── components              # Vue component directory
│   ├── AboutPage.vue       # About page component
│   ├── analyze             # Subcomponents for the analysis pages
│   ├── AnalyzePage.vue     # Main analysis page component
│   ├── backup              # Temporarily deprecated code
│   ├── color_map.js        # Plot color mapping
│   ├── ContactUsPage.vue   # Contact us page component
│   ├── css                 # Styles folder for components
│   ├── DocPage.vue         # Documentation page component
│   ├── DownloadPage.vue    # Download page component
│   ├── general             # General purpose components
│   ├── HomeView.vue        # Homepage component
│   ├── SingleCellList.vue  # Single-cell dataset list page
│   ├── SingleCellPage.vue  # Single-cell dataset detail page
│   ├── ssMOODPageTemplate.vue # Blank page template component
│   ├── STList.vue          # Spatial transcriptomics dataset list page
│   ├── STPage.vue          # Spatial transcriptomics dataset detail page
│   ├── study               # Integrated dataset list
│   ├── studySingleCellPage.vue # Single-cell integrated dataset detail page
│   ├── studySTPage.vue     # Spatial transcriptomics integrated dataset detail page
│   └── VisitLogPage.vue    # User visit log page
├── config                  # Configuration files folder
│   └── index.js            # Global project configuration, such as API endpoints, parameters, etc.
├── locales                 # Localization language files
│   ├── en.json             # English language pack
│   ├── zh-cn.json          # Simplified Chinese language pack
│   └── zh-tw.json          # Traditional Chinese language pack
├── main.js                 # Vue project entry file, mounts root component and routing
├── router                  # Routing configuration files folder
│   └── index.js            # Vue Router configuration file
└── styles                  # Global styles folder
    └── element-theme.css   # Element Plus UI framework theme styles

Project Setup and Usage

1. Installation

To get started, you need to install the project dependencies. Follow these steps:

1. Clone the repository to your local machine:

   https://github.com/YuLab-SMU/ssMOOD.git

2. Navigate to the project directory:

   cd ssMOOD-master

3. Install the required dependencies using npm or yarn:

   • Using npm:

     npm install

   • Or using yarn (if you have yarn installed):

     yarn install

This will install all necessary dependencies listed in package.json.

2. Build

To create a production build of the application, run the following command:

1. Build the project:

   • Using npm:

     npm run build

   • Or using yarn:

     yarn build

This will generate optimized and minified files for production in the dist/ directory.

3. Serve

To run the application locally in development mode, follow these steps:

1. Start the development server:

   • Using npm:

     npm run serve

   • Or using yarn:

     yarn serve

2. Once the server starts, open your browser and go to the following URL:

   http://localhost:8787

This will launch the app on the default port 8787. You can modify the port in the vue.config.js file if needed.

Dependencies and Tools

• Vue.js: Frontend framework
• Element Plus: UI framework
• Vue Router: Routing management
• npm/yarn: Package managers

Citation for ssMOOD (to be updated)

• Once the article is published, this section will be updated with the full bibliographic information and DOI. For now, please reference the project URL: https://ssmood.genomics.cn