Michal Ziemski

About Me

The intersection of biochemistry, computational biophysics, and software engineering.

Download CV (PDF)

I am a software engineer with a background in biochemistry and biophysics. My work sits at the intersection of scientific computing, open-source software, backend systems, and developer tooling.

I started in experimental and computational biology, earning my Ph.D. in Biophysics at ETH Zürich, then transitioned into dedicated software engineering. That non-traditional path fundamentally shaped how I think about code: I believe software should act as a force-multiplier. Good tools should hide unnecessary complexity, making complex data and computational systems easier to understand, use, reproduce, and extend.

Currently, at **ETH Zürich**, I lead the engineering of production-grade open-source scientific software, primarily within the Rachis (formerly QIIME 2) bioinformatics ecosystem. In addition to contributing to core frameworks, my role involves establishing engineering standards around testing, documentation, thorough code review, CI/CD, and long-term maintainability, alongside mentoring junior developers and coordinating across institutional stakeholders.

Recently, I have been focused on exploring practical ways to make scientific software ecosystems easier to discover, navigate, and build on using structured metadata, retrieval-based documentation, and developer-facing tools. This includes building **Model Context Protocol (MCP)** metadata servers, creating provenance-aware terminal interfaces, and documenting reusable development patterns for open-source contributors.

I am interested in software engineering roles involving backend systems, developer tools, data-intensive systems, scientific computing, open-source ecosystems, and ML-adjacent infrastructure—especially in environments that value high code quality, developer productivity, and scientific rigor.

Technical Leadership Highlights

Open-Source Engineering Mentoring 8+ junior developers, coordinating multi-institution releases, and establishing versioning, testing, and CI/CD standards across 15+ repositories.
AI & Developer Productivity Leading design of retrieval-based documentation metadata layers, Model Context Protocol (MCP) servers, and custom agentic workspace developer tools.
Michal Ziemski

Quick Facts

Location Zürich, Switzerland
Languages English, Polish, German
Current Role Research Software Engineer at ETH Zürich
Academic Background Ph.D. in Biophysics, ETH Zürich

Technical Skills

Programming Languages
Python (Primary) JavaScript Rust Go
Frameworks & Tools
Django REST APIs gRPC Docker Kubernetes AWS CI/CD Slurm Nextflow

Education

2013 - 2018 Ph.D. in Biophysics ETH Zürich
2018 Data Science Bootcamp Propulsion Academy, Zürich
2009 - 2011 M.Sc. in Biotechnology University of Silesia, Poland