Masters Projects

At the Control Theory and Systems Biology Laboratory, led by Prof. Dr. Mustafa Khammash, we are developing technology to enable a seamless interface between the biological and digital worlds. This enables the study of synthetic biological circuits, prototyping mixed controllers (cybergenetics), and ultimately the development of synthetic control systems implemented exclusively with biological parts, with a wide range of applications in medicine and biotechnology. A key aspect of this interface is the measurement of state information from biological samples. We are particularly interested in obtaining high-frequency data (in the context of biological timescales), with high throughput and quality, from samples in culture under controlled conditions. Optical measurements are versatile and widely useful for measuring a variety of parameters, for example, the concentration of cells, pH, or individual gene expression levels. This project focuses on extracting information from spectroscopy data using an interpretable data-driven method, and builds upon preliminary work that has been done in the lab, with a custom built, low-cost fluorescence spectrometer. In this ambitious project, the student will have the opportunity to creatively apply or create robust and interpretable methods to extract information from spectroscopy data. ## Tasks - Mathematical modelling of scattering, fluorescence and absorption in the context of spectroscopy - Data analysis, model selection, and fitting - Design of experiments - Automated interpretation of results from known spectra - Statistical guarantees on performance - Documentation and presentation of results ## Possible Extensions - User interface for the method and integration with automated experimental setups - Publication of results in a peer-reviewed journal or conference proceedings ## Candidates should - Be creative, independent, and self-motivated - Be familiar with system identification methods, optimization, and statistics - Be willing to perform experimental work in a biology lab (BSL1) with assistance from lab members - Have at least basic knowledge of optics, control theory and machine learning - Have strong programming skills. The project will be implemented preferably in Python. - Knowledge of biology is a plus but not required ### Deliverables - Written report - 20 minute presentation - Structured and well-documented code The project's earliest starting date is September 2025. It will remain open until a suitable candidate is found.

The primary goal is to develop and validate a comprehensive spectral unmixing framework that can automatically extract meaningful biological parameters from complex spectroscopy data. The successful completion of this project will significantly enhance the laboratory's capability to perform high-throughput, real-time biological measurements, advancing research in synthetic biology and cybergenetics.

For any questions regarding this posting please contact: Dr. Samuel Balula (samuel.balula@bsse.ethz.ch) In your application please include: - A brief (1-2 paragraphs) cover letter with your reasoning for applying to this project - Curriculum Vitae - Transcripts # Location The Control Theory and Systems Biology Laboratory is located in the new D-BSSE building in Basel. The student is expected to come in person to the lab to conduct experimental work whenever necessary. There is flexibility for online meetings and remote work.