CSE490B1: Software Engineering for Biologists
Description: Biology has transitioned from a descriptive enterprise to a quantitative science. This transition has been driven by a combination of low cost sequencing technology and radical reductions in the cost of computing. Indeed, modern biology relies heavily on computational artifacts, both code and data, to produce scientific results (e.g., genomic data sets and computational tools for biochemical pathways). This course is intended for biology students who want to create reproducible and extensible computational artifacts for the quantitative analysis of biological systems. The course focuses on applications drawn from molecular and cell biology (MCB). The course teaches skills in biochemical modeling and software engineering that are needed to work in biological sciences in the 21st century. The software skills include: programming basics, databases, and software process (e.g., design, testing, software packaging). No prior exposure to programming is required (although students who lack programming experience will find the course more challenging). The course is more software intensive than AMATH 301, but the course does not cover the breadth of numerical techniques taught in AMATH 301. The course does not include the breadth of concepts and techniques covered in a computer science introduction to programming, such as CSE 142, CSE 160, and CSE 190P. Rather, the course focuses on practical skills for building software that operates efficiently and can be used and extended by others.
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