Skip to content

README.md

Latest commit

 

History

History
56 lines (40 loc) · 1.51 KB

README.md

File metadata and controls

56 lines (40 loc) · 1.51 KB

Autoprotocol Ruby Library

Autoprotocol is a standard way to express experiments in life science. This repository contains a Ruby library for generating Autoprotocol.

This library is heavily inspired from the Python Autoprotocol library

Installation

To install, simply:

`gem install autoprotocol`

Bundler

Or you can install via bundler with the following addition to your Gemfile:

source 'https://rubygems.org'

gem 'autoprotocol'

Requirements

  • Ruby 2.0.0 or above

Status

Only some of the autoprotocol spec has been currently implemented. If there's a portion missing that you need, open an issue or even better open a pull request.

Instructions implemented

[x] Dispense [x] Incubate [ ] Distribute [ ] Cover

Building a Protocol

A basic protocol object has empty "refs" and "instructions" stanzas. Various helper methods in the Protocol class are used to append Instructions and Refs to the Protocol object such as in the simple protocol below:

require 'json'
require 'autoprotocol'

# instantiate new Protocol Object
protocol = Protocol.new

# append refs (containers) to Protocol object
bacteria = protocol.ref('bacteria', cont_type: '96-pcr', storage: 'cold-4')
media = protocol.ref('media', cont_type: 'micro-1.5', storage: 'cold-4')
reaction_plate = protocol.ref('reaction_plate', cont_type: '96-flat', storage: 'warm_37')

...

Development

The tests can be run with bundle exec rake test