README.md

LINEX - The Lipid Network EXplorer

Flexible Django webapp, to compute and visualize lipid metabolic networks with statistical properties.

Publications:

• LINEX version 2: Rose and Köhler et al. Lipid network and moiety analysis for revealing enzymatic dysregulation and mechanistic alterations from lipidomics data. Briefings in Bioinformatics, 2023, bbac572

• LINEX: Köhler and Rose et al. Investigating Global Lipidome Alterations with the Lipid Network Explorer. Metabolites 2021, 11, 488

We recommend running LINEX in a docker environment, to avoid compatibility issues. Below are instructions to run in with and without Docker:

Deployment with Docker

docker and docker-compose need to be installed.

Depending on your installation you might need to execute the docker commands with sudo (or as administrator)

To start LINEX, run the following command:

docker-compose up -d

Open your browser at: http://127.0.0.1:8084

To shut down the server run:

docker-compose down

(Changing the code of the django app requires rebuilding of the web container.)

Deployment without Docker

1. Requirements

• python: >= 3.8
• LipidLynxX (version from October 2020)
  • download lynx folder from github
  • move folder into the site-packages directory of your current environment
    • if you need to find the site-packages dir run (assuming numpy is installed):

      python3 -c "import numpy as np; import os; print(os.path.dirname(os.path.dirname(np.__file__)))"

2. Setup

2.1. Installation

cd lipid_network_project  # directory containing manage.py
python3 manage.py makemigrations lipid_network
python3 manage.py makemigrations
python3 manage.py migrate lipid_network
python3 manage.py migrate

2.2. Running

Important: runserver and process_tasks need to be run in different threads!

python3 manage.py runserver 7000 &
python3 manage.py process_tasks

2.3. Admin Account

To view the content of the database and saved userdata, you need an admin account, which you can create with:

python3 manage.py createsuperuser

3. View application

Open your browser at: http://127.0.0.1:7000

License

LINEX is free software published under the AGPLv3 license.