CellCycleBrowser

The Human Cell Cycle Browser (hCCB) is an interactive web tool for visualizing and simulating the human cell cycle to explore the timeline of molecular events during cell cycle progression. It was implemented using the Docker platform and Django web framework on the server back. The client front-end visualization was created using D3 JavaScript library. To use the tool, go to https://cellcycle.renci.org and follow the tutorial.

Install

This section is aimed for developers interested in working on the code. It provides guidance for setting up docker-based Django server local development environment for the CellCycleBrowser.

Prerequisite

Docker and Docker Compose need to be installed. On Windows, a Linux VM is needed.

Steps to run Cell Cycle Browser Django web server in your local development environment

• git clone source code from this repo.
• Modify config/cc-config.yaml file to change CC_PATH to point to the root directory of the source tree for CellCycleBrowser.
• Copy local_settings.py from cellcycledev.renci.org and put it under the cellcycle directory. This local_settings.py holds sensitive information, so should not be exposed to the outside world.
• Create a directory data which holds csv dataset, and subdirectories config and model. Refer to cellcycledev.renci.org and copy config, model input, and dataset to your local development environment.
• Modify docker-compose-dev.yml file to replace all occurrences of /home/ccbuild/CellCycleBrowser with the corresponding path in your local environment.
• cd cc_docker_base directory and run docker build -t cc_base . to build the base image. This only needs to be done once to build the environment unless you want to install more libraries/packages into your development environment.
• cd .. to get back to the root directory of the source tree, and run ./ccctl deploy_dev_nodb to build all containers.
• Rebuild index_bundle.js using npm and drop it under cc_core/static/cc_core/js directory, then run docker exec -ti cellcycle python manage.py collectstatic to collect the updated index_bundle.js file into the static directory that can be served to the client by the Django server.
• At this point you should be able to open up your browser to get to the Cell Cycle Browser page: http://localhost:8000 from within the VM, or http://192.168.56.101:8000/ from the host if host-only adaptor is set up in VirtualBox for the Linux VM.

Useful docker-compose commands to manage docker containers

• docker-compose up --- bring up all containers
• docker-compose stop --- shut down all containers
• docker-compose ps --- check status of all containers
• docker rm -fv $(docker ps -a -q --- remove all containers
• docker rmi -f <image_id> where <image_id> is the image id output from docker images command which you want to remove.

Troubleshooting notes

• You may need to run docker-compose stop followed by docker-compose up when you run into issues when bringing up containers the first time.
• To run ./ccctl command again, you need to clean up existing containers and images by running docker rm -fv $(docker ps -a -q to remove all containers and docker rmi -f <image_id> to remove images that need to be rebuilt.

License

CellCycleBrowser is released under the BSD 3-Clause License. This means that you can do what you want, so long as you don't mess with the trademark, and as long as you keep the license with the source code.

©2017. This material is based upon work supported by a medical research grant from W. M. Keck Foundation. Any opinions, findings, conclusions, or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the foundation.