3D ViralHuman Interactome Web Server

Source code for the Django Web Server, data is not included. To build and run the web server, v2h_binary_list_with_ires_iseq_category_seq_20231012.txt, v2h_binary_ppi_info_complete_20230814.txt, and v2h_bincocomp_with_coverage.csv are necessary in the folder static/downloads/interface/. To show the structures, docked structures and single structures are necessary in the folders static/docked_models/ and static/single_models/, respectively. To support download, docked_models.tar.gz and single_models.tar.gz are necessary in the folder static/downloads/. The running server site is https://3d-viralhuman.yulab.org.

Build and run servers:

1. With docker-compose or docker compose command
   • Setup docker-compose.yml and Dockerfile (also with .env and requirements.txt, see these file under BASEDIR)
   • Build images. Go to BASEDIR, run
     • docker-compose build (or docker compose build if docker-compose does not exist)
   • Run containers. After building the image, run
     • docker-compose up (or docker compose up). Use -d to run the container in the background
2. With docker and manually link the web server and database server (if both docker-compose and docker compose do not work)
   • Build web image
     • docker build -t vh3d .
   • Create an image and container for the database (if port 5432 is not available, change the first 5432 to another one and change .env accordingly)
     • docker run -d --name db -e POSTGRES_DB=postgres -e POSTGRES_USER=postgres -e POSTGRES_PASSWORD=postgres -e TZ=UTC -p 5432:5432 postgres
   • Run web container with the link to database container (8888 is the host port, 8020 is the internal port)
     • docker run -t -d --name web --link [database_container_id]:db -v $BASEDIR:$BASEDIR -p 8888:8020 -e DJANGO_DB_HOST=db -e DJANGO_DB_PORT=5432 -e DJANGO_DB_NAME=postgres -e DJANGO_DB_USER=postgres -e DJANGO_DB_PASSWORD=postgres [web_image_id]

Post-setup:

1. Make migrations after running the containers
   • Log in to the server bash shell:
     • `docker exec -it [web_container_id] bash
   • Make migrations:
     • python manage.py makemigrations
     • python manage.py migrate
2. Update database (inside the server bash)
   • python manage.py update_Protein
   • python manage.py update_SingleModel
   • python manage.py update_DockedModel
   • python manage.py update_Interface
   • python manage.py update_InterfaceSimilarity

Access the webserver:

1. Locally (development):
   • [server ip]:[host port] (for example, if I run the containers on the server with address xxx.xxx.xxx, then the address of the webserver is xxx.xxx.xxx:8888)
2. Publicly (production):
   • Make sure the webserver is running smoothly on your server
   • Contact the server owner/technician to set up the proxy to the public domain

Contact

Please contact [email protected] if you have any questions.