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Rubabel: wrapping open Babel with Ruby

2013; BioMed Central; Volume: 5; Issue: 1 Linguagem: Inglês

10.1186/1758-2946-5-35

1758-2946

Rob Smith, Ryan C. Williamson, Dan Ventura, John T. Prince,

Topic Modeling

The number and diversity of wrappers for chemoinformatic toolkits suggests the diverse needs of the chemoinformatic community. While existing chemoinformatics libraries provide a broad range of utilities, many chemoinformaticians find compiled language libraries intimidating, time-consuming, arcane, and verbose. Although high-level language wrappers have been implemented, more can be done to leverage the intuitiveness of object-orientation, the paradigms of high-level languages, and the extensibility of languages such as Ruby. We introduce Rubabel, an intuitive, object-oriented suite of functionality that substantially increases the accessibily of the tools in the Open Babel chemoinformatics library.Rubabel requires fewer lines of code than any other actively developed wrapper, providing better object organization and navigation, and more intuitive object behavior than extant solutions. Moreover, Rubabel provides a convenient interface to the many extensions currently available in Ruby, greatly streamlining otherwise onerous tasks such as creating web applications that serve up Rubabel functionality.Rubabel is powerful, intuitive, concise, freely available, cross-platform, and easy to install. We expect it to be a platform of choice for new users, Ruby users, and some users of current solutions.