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| author | Christoph Helma <helma@in-silico.ch> | 2011-03-09 12:31:05 +0100 |
|---|---|---|
| committer | Christoph Helma <helma@in-silico.ch> | 2011-03-09 12:31:05 +0100 |
| commit | c651fe10fe5e09dbfdf2b3abd420fc2fc0051937 (patch) | |
| tree | 30029f9c3246de739aaf7b66a490c01b7b147f04 /README.markdown | |
| parent | 5233ab341757557c536ed8cc8eefd79a936b4295 (diff) | |
| parent | 66f2ee967317954568562510111b0d832881547d (diff) | |
Merge branch 'release/v1.0.0'v1.0.0
Conflicts:
lib/dataset.rb
Diffstat (limited to 'README.markdown')
| -rw-r--r-- | README.markdown | 41 |
1 files changed, 41 insertions, 0 deletions
diff --git a/README.markdown b/README.markdown new file mode 100644 index 0000000..79bdab2 --- /dev/null +++ b/README.markdown @@ -0,0 +1,41 @@ +opentox-ruby +============ + +Ruby wrapper for the [OpenTox](http://www.opentox.org) REST API + +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/1.0.0/frames) +------------------------------------------------------------------- + +Copyright +--------- + +Copyright (c) 2009-2011 Christoph Helma, Martin Guetlein, Micha Rautenberg, Andreas Maunz, David Vorgrimmler, Denis Gebele. See LICENSE for details. |