From d1f555bdb0368fc82a2bb379ab7857bae727072a Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Wed, 9 Mar 2011 11:37:57 +0100 Subject: README updated and converted to markdown --- README.markdown | 43 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 README.markdown (limited to 'README.markdown') diff --git a/README.markdown b/README.markdown new file mode 100644 index 0000000..8f18598 --- /dev/null +++ b/README.markdown @@ -0,0 +1,43 @@ +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. -- cgit v1.2.3