PaIntDB

Pseudomonas aeruginosa Interactions Database

PaIntDB contains more than 150K protein-protein (PPI) and protein-metabolite interactions in P. aeruginosa. It allows the integration and visualization of high-throughput (proteomics, RNASeq and/or TnSeq) experimental results, using a list of genes as input and mapping them onto a network using the PPI data. It is available at www.paintdb.ca.

If you use PaIntDB to analyze your data, please cite:

Castillo-Arnemann JJ, Solodova O, Dhillon BK, Hancock REW (2021). PaIntDB: Network-based omics integration and visualization using protein-protein interactions in Pseudomonas aeruginosa. Bioinformatics. doi: 10.1093/bioinformatics/btab363

You need Python 3 and pip installed to install and run the application locally. To install the app on Windows, you also need Microsoft Visual C++ Build Tools, this is a good installation tutorial.

Installation

1. Clone repo.
2. Navigate to the project root.
3. Create a new Python virtual environment: python -m venv env
4. Activate virtual environment: source env/bin/activate on MacOS/Linux, .\env\Scripts\activate on Windows.
5. Download and install required libaries: pip install -r requirements.txt
6. Run app: python -m dash_app.index, and go to http://127.0.0.1:8050/home.