Heidelberg

Software Development and Engineering
EMBL Heidelberg

EMBL is seeking a software developer / system architect to join the new EMBL Data Science Centre, co-headed by Jan Korbel, and to actively participate in the recently funded infrastructure initiative German Human Genome Phenome Archive (GHGA, http://www.ghga.de). GHGA is funded within the framework of Germany’s national research data infrastructure (NFDI, https://www.nfdi.de/). The goal of GHGA is to establish a national infrastructure for the archival, analysis and the dissemination of human omics data. GHGA is implemented as a federated infrastructure, which currently connects six data centers across Germany to the federated network of the European Genome Phenome Archive (EGA, https://www.ebi.ac.uk/ega). To enable long-term scalability and respect national data security regulations, the EGA is undergoing a transition to a federated model, with GHGA operating as an EGA node for Germany. GHGA has an ambitious long-term concept with an initial focus on providing technological infrastructure and services for rare disease genetics and oncology. With its 16 partners the GHGA network spans all major omics centers in Germany.

This position can be located at any of the EMBL sites, but may require some travel to EMBL’s five other sites. 

Your role

The successful candidate will design, implement, and operate the main GHGA infrastructure, and identify and realise synergies with EMBL’s Data Science data management strategies. As part of an interdisciplinary research, software development, and data management team he or she will develop and apply a diverse range of state-of-the-art technologies.The candidate will take part in national and international collaborations through many partner projects around GHGA. As a young project, GHGA offers its employees room to shape the software development from the start. Your input will help GHGA reach its mission to make omics data more accessible and help drive genome research forwards.

The candidate will be responsible to/for:

  • Contribute to the development (backend/frontend) of the GHGA software tools
  • Develop a data portal and interface it with underlying software services
  • Design and specification of features, aligned with international standards such as GA4GH
  • Collaboration with local and international developers

Apply now

Closing date: 16 July 2022

  • Contract duration: 3 years
  • Grading: 4, 5 or 6 depending on experience and qualifications
  • Reference number: HD02216

Related

You have

  • BSc, or alternatively, a higher degree in Computer Science, Bioinformatics statistics, Mathematics, Physics, and/or Engineering, or a degree in biological science with demonstrated experience in Computational Biology/Bioinformatics/Software development.
  • Proficiency with python based web frameworks (e.g., FastAPIDjango, Flask, Django)
  • Familiarity with database and search engine setups (like PostgreSQL, MongoDB, ElasticSearch)
  • Familiarity with test driven software development
  • Experience or interest in microservice design patterns and domain-driven design and familiarity with using docker containers for development and deployment is a plus

The ideal applicant should have demonstrated the ability to work independently and creatively. The candidate should have excellent communications skills and be able to articulate clearly the technical needs, set clear goals and work within an interdisciplinary setting, communicating with other partners.

We encourage candidates with all levels of expertise to apply.

You might also have

  • Interest in computational biology and/or data science
  • Expertise in informatics
  • Expertise in (agile) software development
  • Expertise in system architecture
  • Expertise in cloud computing 
  • Expertise in IT-Security

Why join us

EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation with a very collegial and family friendly working environment. The remuneration package comprises from a competitive salary, a comprehensive pension scheme, medical, educational and other social benefits, and the availability of an excellent child care facility on campus. You will be involved in many ongoing cutting-edge projects and activities and will collaborate with experts from the scientific community and have the possibility to acquire new state-of-the-art skills.

What else you need to know

The Korbel group at the European Molecular Biology Laboratory (EMBL), within the Genome Biology Unit, is a ‘hybrid’ laboratory in which computational biologists and experimentalist collaborate tightly to obtain new insights into human disease and molecular mechanisms. By combining experimental and computational approaches, including single-cell sequencing technology, we aim to unravel determinants and consequences of germline and somatic genetic variation. Our group is using bulk as well as single cell-based omics approaches for investigating mechanisms behind complex phenotypes in humans, ranging from common diseases including cancer to ageing. An overarching theme centers on the formation and selection of germline and somatic genetic variation in health and disease states, in particular genomic structural variation (SV).