Exploring Life: Answer Set Programming in Bioinformatics

This chapter provides a broad overview of howlogic programming, and more specifically Answer Set Programming (ASP), can be used to model and solve some popular and challenging classes of problems in the general domain of bioinformatics. In particular, the chapter explores the use of ASP in Genomics studies, such as Haplotype inference and Phylogenetic inference, in Structural studies, such as RNA secondary structure prediction and Protein structure prediction, and in Systems Biology. The chapter offers a brief introduction to biology and bioinformatics and working ASP code fragments for the various problems investigated. The chapter serves a dual role: (1) it offers a declarative characterization of a number of core problems in bioinformatics, making them easily understandable; and (2) it provides an "entry point" to the extensive literature on the use of logic-based methods to address such bioinformatics problems, by offering the basic modeling of the problem and pointers to the relevant literature.