Software Engineer – Open Source Pathogen Data Platforms (80 – 100%)

The Swiss Tropical and Public Health Institute (Swiss TPH) is a world-leading institute in global health with a particular focus on low- and middle-income countries. Associated with the University of Basel, Swiss TPH combines research, education and services at local, national and international levels. 950 people from 95 nations work at Swiss TPH focusing on infectious and non-communicable diseases, environment, society and health as well as health systems and interventions.

The Department of Medical Parasitology and Infection Biology (MPI) investigates the biology and transmission of pathogens. Findings from this research inform the development of new diagnostics, treatments, and vaccines against malaria, tuberculosis, schistosomiasis, Chagas and other neglected tropical diseases.

For the Epidemiology & Virus Evolution (EVE) group at Swiss TPH, we are seeking a Software Engineer – Open Source Pathogen Data Platforms (80 – 100%) to help shape the tools that underpin pathogen data generation and sharing in the 21st century. You will help expand Loculus, the software infrastructure powering Pathoplexus, and contribute to the ARTIC2 global surveillance toolkit.

Are you excited by the idea of building global infrastructure to make pathogen sequencing more accessible, interpretable, and equitable? This software developer position offers a unique opportunity to work at the intersection of two world-leading efforts:

• ARTIC2, the latest evolution of the renowned ARTIC project, enabling affordable, portable, and real-time genetic sequencing in low-resource settings
• Pathoplexus, a pioneering open-source platform redefining how viral sequence data is shared and governed globally, powered by the modular, federated backend database software Loculus

Your position

• Extending Loculus, a modular genomic data platform, including frontend (TypeScript/React/astro), backend (springboot/Kotlin/python/Postgres), and REST API systems
• Building integrations with analytical tools like Nextclade, and interfacing with systems like Cephalopod (ARTIC2 analytic system)
• Wiring Loculus into the ARTIC2 sequencing pipeline to support easy local data storage, while extending its interaction with Pathoplexus to ensure 'one-button' global data sharing
• Developing features for decentralized data control, embargo settings, submission portals, and federated querying
• Supporting the Loculus/Pathoplexus team with international rollouts, community feedback integration, and platform documentation

Your profile

• Professional experience in software engineering, preferably with open-source contributions
• Proficiency in at least some of our stack: JavaScript/TypeScript, Kotlin, React, Python
• Familiarity with REST APIs, database architecture, and CI/CD tools like GitHub Actions
• Experience with or interest in scientific computing, bioinformatics, or data governance
• Comfortable working in a distributed team, communicating asynchronously, and collaborating via GitHub
• Excellent communication and interpersonal skills, with the ability to engage and collaborate effectively with stakeholders from diverse backgrounds - including technical and non-technical teams - to gather requirements, align on goals, and co-design practical, user-centered solutions.
• Desired: Experience with Docker, Kubernetes, or cloud systems
• Desired: Experience developing data pipelines for biological data (snakemake/python/bash scripting)
• Desired: Experience working on public health or non-profit technology initiatives

We offer you

• Your work will be used by public health labs, outbreak responders, and research teams around the world. It directly supports more equitable access to genomic data infrastructure, and helps shape global standards for open, FAIR, and community-aligned data sharing.
• A state-of-the-art workplace in our new building with its own canteen on the dynamic BaseLink site in Allschwil
• A diverse institute with people from a wide variety of backgrounds
• Being part of a world-leading team developing open-source public health software, with close links to other renowned research groups in the Basel area
• Attractive employment conditions, versatile further education opportunities and mentoring

• Start Date: Flexible, ideally late 2025 or early 2026
• Duration: Fixed-term contract for up to 2 years
• Percentage: 80- 100%
• Location: Allschwil, Switzerland (located minutes outside of Basel)
• Travel required: Necessary only for conferences and meetings
• Internal job title: Software Engineer

• CV
• Motivational letter, including your background and experience, any GitHub links or portfolio, and what you envision you could bring to the project
• Names and contact information (email) of 2-3 references
• Degrees and/or certifications achieved