Diagen: A Model-driven Framework for Integrating Bioinformatic Tools

Abstract. Nowadays, the diagnosis of disease based on genomic information is feasible by searching genetic variations on DNA sequences. However, geneticists struggle with bioinformatic tools that are supposed to simplify DNA sequence analysis. As a universal tool to support every requirement is far from be implemented, geneticists themselves must solve the data exchange among several tools. Due to the fact that there are no standards to support this integration task, it must be managed in every analysis. This paper proposes addressing this integration by means of a model-driven framework. The Diagen framework is a software implementation based on conceptual modeling principles that formalizes data exchange and simpli es bioinformatic tool integration. First, we analyze how conceptual modeling can be used to deal with data exchange among tools. And then, as a proof of concept, the presented framework is used to search for variations on the BRCA2 gene using real DNA samples and a set of speci c bioinformatic tools. Keywords: Model-Driven Development, Tool Integration, DNA sequence analysi