Applied software engineering for life sciences

• Python (object types, statements, functions, packages, object oriented programming)
• Distributed version control via git
• Debugging, profiling, refactoring
• Unit, integration and functional testing
• Project and code documentation
• Models of developmental biology and neuroscience

The first part of the semester is devoted to acquiring the necessary skills and tools (Week 1-4). In the second part, biological problems are presented and the students form groups of (typically) 3 students to create a python repository that addresses one biological question. The software has to meet various specifications with regard to the application programming interface, documentation and performance. The hours of practical work will be devoted to planning, coding and presenting. A detailed class schedule can be found here.