Simple ruby library for accessing myExperiment via REST


The myExperiment workflow repository (www.myexperiment.org) provides a REST API to access its information. This is a simple library to access some of the workflow and user data available in myExperiment and make them available as ruby objects. It provides a subset of what is available, particularly what was needed from my other projects. However, it is easy to extend so contact me if you want more information exposed.


  1. myExperiment: a repository and social network for the sharing of bioinformatics workflows. Nucleic acids research, Vol. 38 (suppl 2): W677-W682, 2010.
  2.  http://www.myexperiment.org


The tool is implemented in Ruby, so a Ruby development environment needs to be available. Native packages of libxml, libopenssl and zlib may be required. Please use your favorite package manager to install them (an apt-get example is given). Note that some of the following native packages might already be installed in your system. For Debian-based systems, use this command:

$ sudo apt-get install ruby rubygems gcc build-essential libopenssl-ruby ruby1.8-dev libxml2-dev

To install the myexperiment-rest library type the following command:

$ sudo gem install myexperiment-rest


Test that it is correctly installed by typing:

$ get_workflow_data.rb

Note that in some systems the executable will not be automatically in the path. Run:

$ gem environment

and add the value of EXECUTABLE DIRECTORY to your PATH.


  • Kostas Karasavvas -- kostas (dot) karasavvas (at) nbic (dot) nl
  • Marco Roos -- m (dot) roos1 (at) uva (dot) nl

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