PhageExpressionAtlas

The PhageExpressionAtlas is a web application for interactive exploration of various bacteriophage infections on the transcriptional level based on publicly available dual RNA-seq data.

The aim of the Atlas is to facilitate transcriptomics-based discoveries and validations of hypotheses in phage-host interaction research. The PhageExpressionAtlas offers functionalities such as gene expression visualization of phage-host interactions, phage gene classification and exploration of phage gene expression in the genomic context.

Access:

The PhageExpressionAtlas can be accessed online via https://phageexpressionatlas.cs.uni-tuebingen.de, or by running it locally on your machine.

How to run the Altas locally:

After installing the requirements in the requirements.txt file, run the following command in your terminal: (Note: before running, make sure you are inside the inner PhageExpressionAtlas folder which contains the app.py file)

python app.py

or

flask run

Subsequently, you will see something like this:

* Serving Flask app 'app'
* Debug mode: on
WARNING: This is a development server. Do not use it in a production deployment.
* Running on http://127.0.0.1:5000
Press CTRL+C to quit

This means that the app is running locally on your machine at http://127.0.0.1:5000.

To view the the Atlas, open your web browser and visit http://127.0.0.1:5000.

Implement a custom database

Replace the database file PhageExpressionAtlas/instance/db.sqlite3 with your custom database(, which should be processed and generate identically to the one present in the current atlas). To create your custom database, adapt and use the script Create_database/Create_database.ipynb, which details how the current database was successively filled. Make sure, when filling the database, that all data normalization types are added to the database, since they are required for the functionality of the atlas. In PhageExpressionAtlas/models.py the entire database classes are defined. All of the required database and backend code elements required to create and fill the database are also gathered in Create_database/app.py.

Contact

Please contact Maik Wolfram-Schauerte for questions and feedback.