bigomics/omicsplayground

Omics Playground: Explore Omics Data Freely

Omics Playground is a comprehensive self-service analytics platform for the visualization, analytics and exploration of Big Omics Data. It allows biologists to apply a multitude of state-of-the-art analysis tools to their own data to explore and discover underlying biology without coding.

How to use Omics Playground?

The detailed documentation on how to load data and how to use the functionalities of omics playground can be found here for text-based tutorials, or here for video tutorials.

Platform components

The platform consists of two main components. The first component is off-line and addresses the data importing and preprocessing, which includes preparing the input data, filtering, normalising and precomputing of statistics for some analyses. The second part is composed of the online interface, which supports the real-time visualisation and interaction with users. The interface is subdivided into Basic and Expert modes to provide a customisable experience suited to each user's background.

The docker image and the installation script will contain some example data sets. To analyze your own data you can use the upload function, or create/modify the scripts in the ``scripts/``folder. Creating a custom script is much more flexible and allows, if necessary, batch correction, quality filtering and/or translation of probe names.

More detailed information and feature explanation of Omics Playground is available in the online documentation.

Installation

You can either run the platform from the source code, or download the docker image. Running Omics Playground from the docker file is the easiest way.

Run using the Docker file

The docker file of the platform is available on Docker Hub. Follow the steps below to set up a running platform from the docker file:

1. Pull the docker image using the command:

   docker pull bigomics/omicsplayground
   

   Warning. The docker image requires about 5GB-8GB hard disk space. Note: download version v1.0 if you want the exact version of the NAR/GAB publication, otherwise docker will download the latest version by default.

2. Now run the docker with:

   docker run --rm -p 4000:3838 bigomics/omicsplayground
   

3. Then open http://localhost:4000 in your browser to access the platform.

Run from source code

Omics Playground is implemented using the R/Shiny web application framework. You will need R and Shiny Server installed to run Omics Playground. The source code of the platform is available on GitHub. You can download the latest release of the software by cloning the repository here.

Below, we explain the steps required to set up the platform from the source code:

1. Clone the GitHub repository using:

   git clone https://github.com/bigomics/omicsplayground.git
   

   Note: download version v1.0 if you want the exact version of the NAR/GAB publication, otherwise GitHub will download the latest version by default.

2. Install all necessary R packages by running the script in the R/ folder:

   Rscript requirements.R
   

3. Run the following command in the build/ folder to build the datasets:

   Rscript build-datasets.R
   

   Note: Building the datasets can vary from minutes to a couple of hours depending on their sizes.

4. Change the current directory into the shiny/ folder and execute the following command to run the platform:

   R -e "shiny::runApp(launch.browser=TRUE)"
   

   If you have Shiny Server installed you can create a link to the shiny folder in the system-wide shiny-server apps folder or in your ShinyApps user folder.