Data Engineer/Software developer
SIB Institut Suisse de Bioinformatique
Publication date:
06 January 2025Workload:
100%Contract type:
Permanent position- Place of work:Basel
The SIB Swiss Institute of Bioinformatics is an internationally recognized non-profit organization, dedicated to biological and biomedical data science. Its data scientists are passionate about creating knowledge and solving complex questions in many fields, from biodiversity and evolution to medicine. They provide essential databases and software platforms as well as bioinformatics expertise and services to academic, clinical, and industry groups. SIB federates the Swiss bioinformatics community of some 900 scientists, encouraging collaboration and knowledge sharing. The Institute contributes to keeping Switzerland at the forefront of innovation by fostering progress in biological research and enhancing health.
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To reinforce our team in Basel, Switzerland, we are seeking an experienced Data Engineer/Software Developer to help build and improve the innovative tools and technologies at the core of the SPHN FAIR data tool stack and BioMedIT central services.
Data Engineer/Software developer
Job description
Who we are
To leverage the potential of health-related data for better disease prevention, improved medical practice and innovative treatments, data needs to be interoperable and accessible to researchers in various disciplines. The Swiss Personalized Health Network (SPHN), a government-funded research infrastructure, was launched in 2017 with the mandate to create coordinated infrastructures to efficiently and securely manage, exchange and process consented health data in accordance with legal and ethical requirements.
We are seeking a skilled and motivated Data Engineer/Software Developer to join our dynamic team. Your role will be to develop and especially maintain the open-source tools developed in the context of BioMedIT and the SPHN FAIR Data tool stack https://www.biomedit.ch/home/tools-and-resources.html to enhance accessibility, interoperability and usability of data by the stakeholders. This role will involve working closely with data scientists, bioinformaticians, and other stakeholders from hospitals and BioMedIT nodes.
Responsibility/Task
- Feature Development: Design, implement, optimize, and test new features for the SPHN DCC Toolstack, including components such as SPHN Connector, Schema Forge, Schema Scope, BioMedIT toolstack, Portal, sett and the Terminology Service.
- Testing and Quality Assurance: Develop and maintain automated tests to ensure the robustness of the tools.
- Security Implementation: Regularly review and update the software to ensure it meets the latest security standards and best practices.
- Documentation: Contribute to the technical documentations and user guides as different tools get released.
- Bug Fixes: Actively monitor and resolve issues reported by users or identified through automated testing. Provide timely and effective support to users, ensuring minimal disruption to their work.
Profile requirements
Education and Experience
- Minimum of a degree in Computer Science or Bioinformatics and two years experience in building data engineering and integration pipelines and/or software development.
Technical requirements
- Proficiency in programming languages: Python and JavaScript/TypeScript. Java, Rust and R are a plus.
- Proficiency with following JavaScript frameworks is a plus: React, Redux & NextJS.
- Proficiency in the following related technologies is a plus: fast-api, Jinja2, svelte & Django.
- Familiarity working with APIs.
- Proficiency in using computational reproducibility tools and collaborative/management frameworks (e.g., GitHub, Docker Compose, Kubernetes, Airflow).
- Proficiency working with modern stacks containing tools like postgres or traefik Understanding of CI/CD practices and tools (e.g., GitLab CI/CD & Ansible).
- Knowledge of system interfaces, protocols, and standards and object storage systems (e.g., MinIO).
Nice to have
- Familiarity with Semantic Web Technologies (RDF, RDFS, SPARQL, SHACL, RML).
- Familiarity with Python-based tools for working with RDF such as rdflib and oxigraph.
- Familiarity with database ecosystems, especially graph databases related to the Semantic Web Technologies (e.g., GraphDB, Apache Jena Fuseki, Virtuoso)
- Familiarity with Django, KeyCloak, Opensearch & Prometheus.
Soft skills
- Self-starter with an ability to work independently as well as in a group
- Strong problem-solving and analytical skills, detail-oriented
- Ability to work in an agile environment
- Excellent communication and teamwork capabilities
- Proficiency in English both oral and writing. French, German or Italian is a plus
- Eager to learn new technologies.
How to apply
SIB is committed to ensuring and fostering diversity and equal opportunities in the workplace as well as in the scientific ecosystem. If you are interested in this challenging and highly interesting position, please submit your application including CV, letter of motivation, certification and any other documentation, through our online portal by clicking the "Apply" button.
If you would like more information about this role or the activities of the PHI Group, check the links below or contact Regan Geissmann at E-Mail schreiben.
