Montage

Montage is a web-based visualization platform, featuring several interactive dashboards of single cell genomics data. Key features include:

Getting Started

These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. See deployment for notes on how to deploy the project on a live system.

Prerequisites

• ElasticSearch
• Python 2.7
• pip
• virtualenv
• yarn or npm

Installing

Extract the ElasticSearch archive, and add these to the config/elasticsearch.yml file to enable CORS

http.cors.enabled : true
http.cors.allow-origin : "*"

Also install the mapper-size plugin

./bin/elasticsearch-plugin install mapper-size

Then start the ElasticSearch instance

./bin/elasticsearch

Clone the Montage repository and install the necessary dependencies, then start development mode.

yarn install
yarn start

OR

npm install
npm start

Go into /src/api/config.js and point the HOST to your local ElasticSearch instance

const config = {
  HOST: "http://localhost:9200/",
  SEARCH: "/_search",

  ANALYSIS_INDEX: "tree_analysis"
};

Loading Data

Create a Python virtualenv and install the required packages

virtualenv ~/pythonenv
source ~/pythonenv/bin/activate
pip install -r <MONTAGE_REPO_DIR>/loader/pip-requires.txt

Load using the appropriate dashboard loader with the correct YAML file. For example:

python tree_cellscape_loader.py -y directory/to/yaml/data_metadata.yaml

This will load an entry into the Analysis index, as well as the appropriate data files. You can view the README in /loader to see more information about the data types.

Built With

• Create React App
• Redux

Authors

This project was designed and built in Dr. Sohrab Shah's laboratory at BC Cancer under the leadership of Dr. Cydney Nielsen and in close collaboration with Dr. Samuel Aparicio's research team. The following dedicated students and software developers (ordered alphabetically) created the codebase:

• Samantha Leung

Acknowledgments

We are grateful for the following funding:

• The Canadian Cancer Society Research Institute - Innovation Grant
• Genome Canada / Genome BC - Disruptive Innovation in Genomics Grant
• CANARIE - Research Software Program