fjukstad/mixt repository overview

⁠MIxT

Matched Interaction Across Tissues (MIxT) is a system designed for exploring and comparing transcriptional profiles from two or more matched tissues across individuals. Here, the MIxT system is applied to tumor and blood transcriptional profiles from breast cancer patients from the Norwegian Women and Cancer study.

Users can browse through all the results generated for this study, visualize gene co-expression networks and expression heatmaps, and search for genes, gene lists, and pathways.

The application runs at mixt-blood-tumor.bci.mcgill.ca⁠.

⁠System

MIxT consist of two main components: the web application and the compute backend. The compute backend provides data and analyses, and the web application allows users to view and explore the results. We use the r package in Kvik⁠ to run the compute backend.

⁠Install and run

There are two options for installing and running the MIxT web application, either compile and run on your machine, or use the Docker Image.

⁠Compile and run

• First install go⁠
• $ go get github.com/fjukstad/mixt
• $ cd $GOPATH/src/github.com/fjukstad/mixt
• $ mixt
• Open localhost:8004⁠

⁠Docker

First, install Docker⁠ then you can either start the two components separately or together using docker-compose⁠.

⁠Docker

First start the compute-service

$ docker run --name=compute -t fjukstad/mixt-compute-service 

then the web application

$ docker run -p 8000:80 --link compute -e COMPUTE_SERVICE=compute:80 --name=mixt -t fjukstad/mixt-stroma 

which is now running on localhost:8000⁠.

⁠Docker Compose

Run

$ git clone github.com/fjukstad/mixt
$ cd mixt
$ docker-compose up

and open localhost:8000⁠.