2024-07-10 –, Method (1.5)
Teaching a structural bioinformatics course is challenging as the audience typically consists of diverse academic backgrounds. Here, we describe our experience on teaching a course based on our framework BiochemicalAlgorithms.jl, which is a redesign of the open source C++-framework Biochemical Algorithms Library (BALL). The use of Julia allowed to focus more on the actual teaching goals, while the students of the former C++-based course were distracted by complex development cycles.
Structural Bioinformatics is a highly interdisciplinary research area. A teaching course in this field typically covers topics from various disciplines such as physics(e.g., Newtonian mechanics), mathematics(numerical optimization) and biochemistry (molecular entities like atoms, molecules,...) etc. In order to run and develop applications successfully a profound knowledge of programming and software development is required.
In our course, the switch from C++ to Julia enabled the students to focus on learning the algorithms and data structures implemented in BiochemicalAlgorithms.jl. The usage of C++ often impeded learning progress starting already at the level of setting up a development environment for BALL, which is a nontrivial task. In contrast, using Julia resulted in accelerated development times for applications -- based on students feedback -- in more fun.
09/2012 - B.Sc. Molecular Biology, Johannes Gutenberg University Mainz
03/2015 - M.Sc. Applied Bioinformatics, Johannes Gutenberg University Mainz
03/2016 - present Research associate in computer science Johannes Gutenberg University Mainz
04/2015 - present PhD candidate in computer science Johannes Gutenberg University Mainz
I am interested in structural bioinformatics and development of software for applications in this and related fields.
