Software Engineer

About Swiss TPH: The Swiss Tropical and Public Health Institute (Swiss TPH) is a world-leading institute in global health, associated with the University of Basel. It combines research, education, and services to address health challenges in low- and middle-income countries. Swiss TPH focuses on infectious and non-communicable diseases, with a strong commitment to open-source tools for data sharing and genomic surveillance. The institute is at the forefront of developing technologies like Pathoplexus and ARTIC2, which aim to make pathogen sequencing data more accessible, interpretable, and equitable worldwide.

About the Role: We are seeking a Software Engineer to join our Epidemiology & Virus Evolution (EVE) group. This role involves extending the Loculus software infrastructure, which powers the Pathoplexus platform—a pioneering open-source database for sharing viral genomic data globally. You will contribute to the development of tools that enable rapid virus identification, tracking, and vaccine development. This position offers a unique opportunity to work at the intersection of cutting-edge software engineering and global public health, creating infrastructure used by public health labs, outbreak responders, and researchers worldwide.

Responsibilities:

• Extend Loculus, a modular genomic data platform, including frontend (TypeScript/React/astro), backend (Spring Boot/Kotlin/Python/Postgres), and REST API systems.
• Build integrations with analytical tools like Nextclade and interface with systems like Cephalopod (ARTIC2 analytic system).
• Wire Loculus into the ARTIC2 sequencing pipeline to support easy local data storage and enhance its interaction with Pathoplexus for one-button global data sharing.
• Develop features for decentralized data control, embargo settings, submission portals, and federated querying.
• Support the Loculus/Pathoplexus team with international rollouts, community feedback integration, and platform documentation.

Requirements:

• Professional experience in software engineering, preferably with open-source contributions.
• Proficiency in 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 to engage with stakeholders from diverse backgrounds.

What We Offer:

• Your work will directly impact global health by supporting more equitable access to genomic data infrastructure and shaping standards for open, FAIR data sharing.
• A state-of-the-art workplace in our new building with a canteen on the BaseLink site in Allschwil, Switzerland.
• A diverse institute with staff from various backgrounds, working on world-leading open-source public health software.
• Attractive employment conditions, versatile further education opportunities, and mentoring programs.

Job Conditions:

• 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: Necessary for conferences and meetings.

Life in Switzerland: Switzerland consistently ranks high in quality of life. The Basel area is international, with universities, pharmaceutical industry, and excellent public transport. It offers a blend of urban and natural beauty, with proximity to France and Germany.

Apply: Submit your application online, including CV, motivational letter, GitHub links or portfolio, and references. Apply by 31 August 2025. For informal questions, email applications@hodcroft.com.