A graphical programming system for molecular motif search

Authors:
Janina Reeder;Robert Giegerich
Affiliations:
Bielefeld University, Bielefeld, Germany;Bielefeld University, Bielefeld, Germany
Venue:
Proceedings of the 5th international conference on Generative programming and component engineering
Year:
2006

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Abstract

We describe a graphical programming system for a domain specific language in biosequence analysis. It supports the development of programs for RNA structure prediction and motif search, created by biologists with little or no programming skills. The system combines several programming paradigms in a productive way. It has a client - server architecture, with a transport layer in XML. The graphical front-end is implemented in the object-oriented paradigm (using Java). Graphics are compiled into a declarative domain-specific language for dynamic programming (ADP) that is embedded in Haskell. Finally, motif search programs expressed in ADP are compiled to imperative code in C, a step which includes substantial domain-specific optimization.