Research Software Engineer for Computational Mass Spectrometry

80%-100%, Zurich, fixed-term

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The Functional Genomics Center Zurich (FGCZ) is a joint state-of-the-art research and training facility of the ETH Zurich and the University of Zurich. With the latest technologies and key expertise for omics research, the FGCZ provides research services and project support to the Zurich life science research community.

We are looking for a Research Software Engineer at Functional Genomics Center Zurich as soon as possible or upon agreement.

Project background

This position is centered on mass spectrometry data, with a primary focus on bioinformatics analysis and interpretation in support of researchers at the FGCZ. Within that field, the team covers raw data processing, high-performance computing, statistical evaluation, interpretation, and integrated analysis. The unit maintains a portfolio of commercial and open-source applications operating on our infrastructure and establishes novel data processing and analysis pipelines. An integral part of the work is integrating the data into our data management system and ensuring the reproducibility of the analysis.

Job Description

• You will support the FGCZ proteomics and metabolomics user community by maintaining existing and developing new mass spectrometric data processing and analysis pipelines
• In this role, you will apply your expertise in informatics and data science to ensure the reproducibility of the data analysis performed
• As a member of the FGCZ bioinformatics group, you will have back-office and user-desk tasks to support our collaborators at ETH and the University of Zurich with data interpretation and bioinformatics projects

Profile

Required Skills And Experiences

• Team player - working closely with wet-lab scientists and translating their needs into analysis
• Academic degree in any of the relevant areas, including (but not limited to) computer science, statistics, or biology
• A master’s degree in a relevant field; candidates with a Ph.D. are equally welcome to apply
• Proficiency in Microsoft Windows and Linux operating systems, including command-line interfaces
• Practical knowledge of at least one programming language (C++, C#, Java, Python) and tools such as Git
• Responsible and informed use of AI-assisted tools in a scientific context

Preferred Skills And Experiences

• Familiarity with the management and analysis of large-scale datasets, in particular omics-related data
• Background in bioinformatics, ideally in mass spectrometry
• Experience in imaging, spatial, or cross-omics disciplines
• Proven track record of writing and maintaining code
• Experience in R/Bioconductor and client-side web programming
• Experience with UI/UX design, particularly the development of web-based or desktop interfaces for scientific data visualization
• Experience with virtualization tools, e.g., Docker, Apptainer
• Experience with resource managment software, e.g., Slurm

The ability to work independently is a prerequisite, as is the ability to interact effectively with the center's research and technical staff and external research groups in a team-oriented manner Advanced knowledge of English is essential, as this is the working language of the center.

We particularly encourage applications from early-career candidates eager to develop their skills in a stimulating research environment.

Workplace

Workplace

We offer

A highly interesting position at the intersection of technology and life science research. Employment conditions are according to the regulations of ETH Zurich and the University of Zurich. Working at the FGCZ allows collaboration with our international, multicultural group in a motivating, friendly, and flexible atmosphere. Employment will be at ETH Zurich; the position is available immediately.

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We value diversity and sustainability

In line with our values, ETH Zurich encourages an inclusive culture. We promote equality of opportunity, value diversity and nurture a working and learning environment in which the rights and dignity of all our staff and students are respected. Visit our Equal Opportunities and Diversity website to find out how we ensure a fair and open environment that allows everyone to grow and flourish. Sustainability is a core value for us – we are consistently working towards a climate-neutral future.

Curious? So are we.

We look forward to receiving your online application with the following documents:

• CV
• Motivation letter
• Diplomas, and employment certificates
• Reference letters (in case of former employment)

Further information about FGCZ can be found on our Website. Questions regarding the position should be directed to Christian Panse, [email protected] (no applications).

Please note that we exclusively accept applications submitted through our online application portal. Applications via email or postal services will not be considered. Please submit your application by August 30, 2026.

About ETH Zürich ETH Zurich is one of the world’s leading universities specialising in science and technology. We are renowned for our excellent education, cutting-edge fundamental research and direct transfer of new knowledge into society. Over 30,000 people from more than 120 countries find our university to be a place that promotes independent thinking and an environment that inspires excellence. Located in the heart of Europe, yet forging connections all over the world, we work together to develop solutions for the global challenges of today and tomorrow.