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README.md

IsoStamp 2.0 Website

Background for the IsoStamp project & website

Isotopic signature transfer and mass pattern prediction (IsoStamp) is an enabling technique for chemically-directed proteomics. Specifically, it is an algorithm for the targeted detection and identification of modified species by mass spectrometry (MS).

This repository contains the code for isostamp.herokuapp.com, a web application that enables other people to use IsoStamp to upload and analyze their own data.

For more information: Interview with postdocs David Spiciarich and Christina Woo

History of the code base

This repo contains the code for isostamp.herokuapp.com, version 2 of the website. The original and current official site will eventually be deprecated in favor of this new site, and you can find its code at github.com/cmwoo/mass-spectrometry.

Ownership

As of July 2016:

Deployment Pipeline

isostamp relies upon Heroku's deployment pipeline. The structure is as follows:

  1. Local development.
  2. Deploy to isostamp-staging (staging heroku app) by running $ rb deploy_staging.rb.
  3. Promote isostamp-staging to isostamp (production heroku app) by running $ rb deploy_production.rb.

Setup

Note: the $ at the beginning code snippets indicates the command should be run in your terminal. The $ should not be included in the actual command.

  1. Setup Ruby on Rails on your computer.
  2. In your terminal, navigate to the directory in which you'd like to store this repository: $ cd ~/path/to/parent/dir. Then, run $ git clone https://github.com/devonzuegel/isostamp-web-v2.git.
  3. Run $ bundle install
  4. In ~/path/to/parent/dir/isostamp-web-v2, run $ bundle install to install the required Ruby gems.
  5. Run $ guard to start the server and continuous testing.

Contact

If you come across any problems with the site, please create a Github issue with specific details and screenshots of the problem.

Developed by the Bertozzi Group, 2016.

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Web interface for Isostamp project (V2)

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