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Interactive open-code computer simulation exercises promote a deeper understanding of quantitative phenomena in bioanalytics
Prof. Paola Picotti | D-BIOL

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We will design interactive, open-code simulations to enable student exploration of non-intuitive quantitative phenomena in bioanalytics. The simulations will be built on the LET’s JupyterHub platform. With this project, we acquire the competence to develop such teaching tools in-house to boost the computational reasoning skills of our students.
Abstract
Technically sophisticated analytical techniques play an increasingly important role in biological research. Confident use of these techniques requires a solid comprehension of the underlying quantitative phenomena. But, in the 3rd semester Bioanalytics course we observe that many students struggle to develop an intuitive understanding of these phenomena and their rigorous mathematical treatments tends to be too complex to be taught effectively at the introductory level. As a middle ground between a purely descriptive and a rigorous mathematical treatment, we will develop open-code simulations, that allow students to explore the relevant quantitative phenomena interactively. These simulations will be based on strongly simplified models. The goal of these simulations is to convey the nature of the modelled phenomena rather than the detailed replication of all their nuances. These simulation exercise will be implemented as Python-code in Jupyter Notebooks and make use of the Emerging Educational Media Hub’s JupyterHub. This architecture enables students to explore, analyze and modify the data generated by the simulations as well as the code of the simulations themselves. This will allow students to explore the simulated phenomena at multiple levels of engagement and in the process develop their computational and quantitative reasoning skills.
Project goals
The project has two main goals: 1) The first goal is to develop interactive simulations and the corresponding visualizations that support interactive exercises that will develop students' quantitative intuition about selected quantitative phenomena taught in the 3rd semester Bioanalytics course. 2) The second goal is to acquire, at the DBIOL’s Center for Active Learning (CAL), the competence to develop such simulations / visualizations in the framework of the LET-supported JupyterHub platform. This competence will allow us to develop, at short notice, similar simulations, visualizations and exercises as teaching tools for other departmental courses.
Effects of the project
Students will have access to a new category of learning material that synergizes with the existing lecture- and text-based material. In particular the new learning material will allow students to explore quantitative and dynamic phenomena that may be difficult to grasp based on the existing training materials (linear narratives and static images). The ability to directly interact with the simulation’s code and data will allow students to apply and consolidate the computational skills they are acquiring in their introductory informatics course. This transfer will be facilitated by the fact that the simulations will use the same programming language and similar development environments as the introductory informatics course. The students will develop the habit of using computational approaches to think about and explore new areas of their study outside of their informatics courses. Lecturers will have a newl class of teaching material at their disposal, which is particularly useful for the type of phenomena and effects they have to convey to the students in this course. At the level of the Biology Bachelor degree program, the increase of computational competencies, in particular the ability to explore problems or phenomena computationally, is a long-term goal that is well aligned with the ETH computational competency initiative. Establishing the expertise for the development of simulations and computation-based exercises on the ETH-preferred computation platform (iPython / Jupyter Hub) to the DBIOL’s Center for Active Learning (CAL) will facilitate the development and routine use of this type of simulation / exercise throughout the DBIOL curriculum. In the past the CAL has already catalyzed the widespread adoption of other modern teaching tools in the department. Examples include the use of Moodle pages, blended / flipped-classroom course formats and electronic exams.



Applicant Prof. Paola Picotti | Manager Dr. Ulrich Genick | Contact person Prof. Paola Picotti
picotti@imsb.biol.ethz.ch
| Department D-BIOL | Institute Institute of Molecular Systems Biology | | Filing date 30.09.2022 | Period 15.11.2022 to 31.5.2024

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