README.markdown


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opentox-ruby
============

Ruby wrapper for the OpenTox REST API (http://www.opentox.org)

Installation
------------

opentox-ruby depends on many third party programs and libraries, which makes the setup complicated and error prone. For this reason we recommend to use the installer from (opentox-install)[http://github.com/opentox/opentox-install]. If you want to install manually you can find the necessary steps in the installation scripts.

Quickstart
----------

This example shows how to create a lazar model and predict a compound, it assumes that you have access to a working installation of OpenTox services with corresponding settings in $HOME/.opentox/config. Run the following code in irb or from a ruby script:

  require 'rubygems'
  require 'opentox-ruby'

  # Authenticate
  subjectid = OpenTox::Authorization.authenticate(USER,PASSWORD) 

  # Upload a dataset
  training_dataset = OpenTox::Dataset.create_from_csv_file(TRAINING_DATASET, subjectid)

  # Create a prediction model
  model_uri = OpenTox::Algorithm::Lazar.new.run({:dataset_uri => training_dataset.uri, :subjectid => subjectid}).to_s
  lazar = OpenTox::Model::Lazar.find model_uri, subjectid
  
  # Predict a compound
  compound = OpenTox::Compound.from_smiles("c1ccccc1NN")
  prediction_uri = lazar.run(:compound_uri => compound.uri, :subjectid => subjectid)
  prediction = OpenTox::LazarPrediction.find(prediction_uri, subjectid)
  puts prediction.to_yaml

API documentation
-----------------

http://rdoc.info/gems/opentox-ruby/0.0.2/frames

Copyright
--------

Copyright (c) 2009-2011 Christoph Helma. See LICENSE for details.