DyHealthNet Backend Repository

Django backend for the DyHealthNet Masters project (2024) to build a prototype for an interactive multi-omics network which aims to include both data from the Cooperative Health Research in South Tyrol (CHRIS) study and public data from external databases.

Usage guide

1. Clone the repository using one of the following options:

   git clone https://github.com/DyHealthNet/backend_django.git #https
   git clone git@github.com:DyHealthNet/backend_django.git #ssh
   

2. Create a conda environment including all package dependencies and activate it:

   conda env create -f environment.yml -n dyhealthnet_env
   conda activate dyhealthnet_env
   
   # if you encounter any issues with the environment.yml file, create a python 3.11 environment and install
   # the required packages manually:
   # pip install -r requirements.txt
   # pip install --no-deps numba-scipy==0.4.0

3. Set the secret key in the .env.example file manually and rename the file afterwards:

   cd backend_django/dyhealthnet_project
   vi .env.example #Edit secret key variable
   mv .env.example .env
   

4. Install and run redis server:

   sudo apt update && sudo apt install redis-server

5. Install and run celery worker:

   celery -A dyhealthnet_project worker -l info

6. Run the server and access it on your browser according to the instructions:

   cd ..
   python manage.py runserver

Format specifications

Phenotypes

Phenotypes are not optional.

Your phenotype file must use columns as variables and rows as samples. One (usually the first) column must be the sample ID, specified by the PATIENT_ID_COLUMN variable in the .env file. Furthermore, there must exist a meta file, which contains a column PHENOTYPE_TYPE_COLUMN which specifies the numeric type of the variable. Allowed types are boolean, categorical, float and integer. These types are used to determine the statistical tests that will be performed on the data.

Proteins

Proteins are optional.

Your protein file must use columns as proteins and rows as samples. Ensure that you have a consistent column with the sample ID, specified by the PATIENT_ID_COLUMN variable in the .env file.

Metabolites

Metabolites are optional.

Your metabolite file must use columns as metabolites and rows as samples. Ensure that you have a consistent column with the sample ID, specified by the PATIENT_ID_COLUMN variable in the .env file.