Composable Languages for Bioinformatics: The NYoSh experiment (1311.5550v2)

Abstract: Language workbenches are software engineering tools that help domain experts develop solutions to various classes of problems. Some of these tools focus on non-technical users and provide languages to help organize knowledge while other workbenches provide means to create new programming languages. A key advantage of language workbenches is that they support the composition of independently developed languages. This capability is useful when developing programs that can benefit from different levels of abstraction. We reasoned that language workbenches could be useful to develop bioinformatics software solutions. In order to evaluate the potential of language workbenches in bioinformatics, we tested a prominent workbench by developing an alternative to shell scripting. While shell scripts are widely used in bioinformatics to automate computational analysis, existing scripting languages do not provide many of the features present in modern programming languages. We report on our design of NYoSh (Not Your ordinary Shell). NYoSh was implemented as a collection of languages that can be composed to write programs as expressive and concise as shell scripts. NYoSh offers a concrete illustration of the advantages that language workbench technologies can bring to bioinformatics. For instance, NYoSh scripts can be edited with an environment-aware editor that provides semantic error detection and can be compiled interactively with an automatic build and deployment system. In contrast to shell scripts, NYoSh scripts can be written in a modern development environment, supporting context dependent intentions and can be extended seamlessly with new abstractions and language constructs. We demonstrate language extension and composition by presenting a tight integration of NYoSh scripts with the GobyWeb system. The NYoSh Workbench prototype is distributed at http://nyosh.campagnelab.org