Software Engineer / Software Engineeress

Software Engineer (Viral and Bacterial Sequence Database)

100%, Basel, fixed-term

The Computational Evolution Group, led by Prof. Dr. Tanja Stadler, in the Department of Biosystems Science and Engineering (D-BSSE) at ETH Zürich, operates at the interface of mathematics, computer science, and evolutionary biology. Our mission is to develop innovative methods that unravel evolutionary, ecological, epidemiological, and developmental processes across various scales using genetic data.

We are on the cutting edge of science, transitioning research into production-ready software. Our focus includes developing genomic databases, web applications, and APIs to enable real-time monitoring of pathogen variants and address critical epidemiological questions. We maintain strong collaborations with public health agencies and scientists globally.

Project Background

The projects stem from the urgent needs identified during the SARS-CoV-2 pandemic. As the volume of genome sequences surged, the necessity to track emerging variants became paramount. Our team has developed software solutions to assist in the detection and tracking of new variants, while enhancing the management and sharing of pathogen sequencing data.

Initially focused on viral data, our database system is built using TypeScript, React, Kotlin, and Python. In this role, you will both extend this existing system and develop a novel database for bacterial pangenome data, based on a prototype created during a previous research project. The backend of the prototype is implemented in Python (with some C++ bindings), and the frontend in TypeScript and React.

We closely collaborate with various research groups both in Basel and internationally, including public health agencies like the Federal Office of Public Health (FOPH) in Switzerland and the Centers for Disease Control and Prevention (CDC) in the United States.

Commitment to solid software engineering practices is essential in our group. We conduct code reviews, maintain automated testing pipelines, and strive to produce modern, clean, and maintainable code. Our agile work environment encourages continuous improvement and collaboration.

Job Description

• You will collaborate with other software engineers and researchers in our group and among our partners.
• Your primary responsibilities will include extending an existing database system used for viral sequencing data.
• You will design, implement, and test a new scalable database system for bacterial pangenome data based on an existing research prototype.
• Engagement with users and scientists will be vital to identify and refine needs and requirements.

Profile

We seek a highly motivated professional who is eager to learn and contribute to public health and genomic epidemiology. The ideal candidate will have:

• Experience in bacterial bioinformatics, specifically with pangenome data (relevant publications are beneficial).
• Strong proficiency in Python, with familiarity in tools like mypy, black, and ruff being advantageous.
• Experience in web development, ideally using TypeScript and React.
• Background in developing database engines and a solid understanding of core database properties and their implementations; C++ expertise is a plus.
• Experience in phylogenetics and (Bayesian) phylodynamics.
• A Master's degree in computer science, bioinformatics, or a related field.
• An interest in working within an interdisciplinary and international team, contributing to a welcoming and inclusive group culture.
• Fluency in English; knowledge of German is not required.

We welcome candidates from all experience levels, as we are committed to maintaining an inclusive workplace that promotes equal opportunities for individuals from all backgrounds.

Workplace

We provide a vibrant and supportive work environment with flexible hours, coupled with exciting projects that contribute directly to public health. We value personal growth and offer support for career development through funding for courses, workshops, and other relevant events.

Living in Switzerland means enjoying an exceptional quality of life, highlighted by stunning natural landscapes and an excellent infrastructure. We invite you to explore Basel, a dynamically international city ranked the tenth most livable city globally by Mercer, and see why it is an excellent place to live and work!

We Value Diversity and Sustainability

At ETH Zurich, we promote an inclusive culture where equality of opportunity and respect for all are paramount. We are committed to a diverse workplace that fosters positive growth and collaboration. Sustainability is integral to our mission, and we actively work towards a climate-neutral future.

Curious? So are we.

We invite you to apply online using the form below. Please ensure your application includes the following documents:

• A letter of motivation outlining your interest in the position and what makes you an excellent fit.
• A Curriculum Vitae that details your publication record and familiarity with specific programming languages and frameworks.
• Links to code samples or open-source projects are appreciated.

Only applications matching the job profile will be considered.

For additional information about our group, please visit our website. If you have any questions (no applications), feel free to contact Chaoran Chen at chaoran.chen@bsse.ethz.ch.

About ETH Zürich

ETH Zurich stands as one of the world's leading universities specializing in science and technology. Our reputation is built on an outstanding education system, fundamental research breakthroughs, and direct societal impact through the transfer of knowledge. With over 30,000 individuals from more than 120 countries, our university fosters independent thinking and an inspiring academic environment. Situated in the heart of Europe while nurturing global connections, we work collaboratively to tackle the pressing challenges of today and tomorrow.