Modeling Biological Problems in Computer Science: A Case Study in Genome Assembly

Abstract

As computer scientists working in bioinformatics/computational biology, we often face the challenge of coming up with an algorithm to answer a biological question. This occurs in many areas, such as variant calling, alignment, and assembly. In this tutorial, we use the example of the genome assembly problem to demonstrate how to go from a question in the biological realm to a solution in the computer science realm. We show the modeling process step-by-step, including all the intermediate failed attempts.