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Seten (web interface)

A tool for systematic identification and comparison of processes, phenotypes and diseases associated with RNA-binding proteins from condition-specific CLIP-seq profiles

Production server

Seten's production server is running on https://sysbio.sitehost.iu.edu/seten/.

Development server

Requirements

  • Node.js version 5.x

      # remove if an old version was installed
  # sudo apt-get remove nodejs
  curl -sL https://deb.nodesource.com/setup_5.x | sudo -E bash -
  sudo apt-get install -y nodejs

  • Node Package Manager (NPM) latest version

      sudo apt-get install npm
  sudo npm install -g npm # upgrades itself to the latest version

Setup

git clone https://github.com/gungorbudak/seten.git
cd seten/
# download and untar the resources (around 300 MB)
wget https://sysbio.sitehost.iu.edu/seten/assets/resources.tar.gz
tar xzf resources.tar.gz -C assets/ && rm resources.tar.gz
npm install --production
npm start

After the server setup, Seten will run on http://localhost:3000

Modification

The source code files is under assets/js/src/. After installing development dependencies, you can modify and live test them or bundle them for production. Run following commands to install dependencies:

npm install --dev

Live test

Live test uses webpack-dev-server that tracks changes in the source code files in assets/js/src/ and updates the pages automatically. Run following command to start it:

npm run devel

Bundling for production

You can then bundle source code files inside assets/js/build/ for production.

npm run bundle

Switching between two in index.html

For live test, you should be using unminified version of the bundle, assets/js/build/bundle.js in index.html. After bundling for production, the minified version assets/js/build/bundle.min.js should be used.

Tutorial

A tutorial that can guide you through Seten's features can be found on https://sysbio.sitehost.iu.edu/seten/tutorial.html

Documentation

Seten's documentation can be found on https://sysbio.sitehost.iu.edu/seten/docs.html

Command line interface

For those who would like to run Seten in command line, there is a Python version of the same implementation that can be found on https://github.com/gungorbudak/seten-cli