🧪 TDEase - an Open-Source Data Visualization Software Framework for Targeted Proteoform Characterization by Top-Down Proteomics

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English | 中文

✨ Introduction

✨ TDEase is an automated data processing and interactive visualization toolkit designed specifically for top-down proteomics research.

It helps laboratories quickly build the data processing and visualization components of a top-down proteomics workflow.

It consists of two core modules:

• 🛠️ TDPipe: Automated data processing engine
• 📊 TDVis: Interactive data visualization platform

The demo data for TDVis is available at Zenodo.

🌟 Key Features

1. One-Click Deployment 🚀
   Both modules provide ready-to-use exe packages, requiring no complex configuration, see releases.
2. Thoughtful UI Design:
   • TDpipe uses PyQt to create a sophisticated workflow control interface, allowing platform administrators high flexibility.
   • TDvis uses Streamlit to provide a minimalist, almost parameter-free interface, making it easy for users to quickly get started with data viewing.
3. Intranet Web Deployment:
   • The visualization module can be deployed on an intranet using Python's http.server, allowing collaborators to access results remotely without transferring large mass spectrometry files.
   • ⚠️ Note: Due to HTTP's plaintext nature, public internet deployment is not recommended.
   • For external collaborators, you can simply send the result files, and users can view them locally with TDvis.

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Quick Start

📥 Installation

Download the released setup package, double-click the corresponding exe to run:

• TDPipe.exe: automated data processing engine
• TDVis.exe: standalone data visualization platform
• TDVisWeb.exe: web data visualization platform

🌐 to access the web data visualization platform:

1. click the visualization button in TDPipe
2. run TDVisWeb.exe/TDVis.exe and enter the url http://{your_ip}:8501 in explorer

TDPipe Workflow Configuration

TDPipe is a GUI-based top-down proteomics data processing workflow integration tool. With a rich set of buttons, you can easily invoke each module, set workflow parameters, and run the workflow automatically.

TDVis Database Configuration

If you do not need user authentication, you can skip this section.

PostgreSQL

The TDVisWeb version uses PostgreSQL by default for user management.

PostgreSQL provides detailed official documentation. Simply follow the guide to create an initial database using pgAdmin, then configure it in TDVis/DBUtils/dbconfig.toml!

SQLite

If you want to use SQLite for quick testing, simply modify the parameter file as follows:

[database]
mode = "sqlite"
dbname = "{your_path}/TDEase/TDVis/src/DBUtils/TDVis_sqlite3.db"

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For Developers

If you have unique feature requirements, we welcome your contributions!

Recommended steps for collaborative development:

1. Source Code Download

git clone https://github.com/Elcherneske/TDEase.git && cd TDEase

2. Dependency Installation

We recommend using uv for fast deployment instead of pip.

uv install -r requirements.txt

or

uv pip install -r requirements.txt --index-url https://pypi.tuna.tsinghua.edu.cn/simple

Alternatively, you can use conda for environment management (slower, but reusable across projects):

conda create -n tdease python=3.12 -y
conda activate tdease
pip install -r requirements.txt

TDpipe

To run TDPipe:

cd TDEase/TDPipe
python src/TDPipe.py

TDvis

Our web service is built on Streamlit. For collaborative development and debugging, run the following command in the TDVis folder:

cd TDEase/TDVis
streamlit run MainPage.py

Publications && Citation

If you find our work helpful, please consider citing us in your publications.

Liao Y, Qian R, Zhang M, et al. TDEase: An Open‐Source Data Visualization Software Framework for Targeted Proteoform Characterization by Top‐Down Proteomics[J]. Proteomics, 2025: e70031.