Oscars Postdoctoral Fellowship: Tracking and
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Postdoctoral Fellowships
EMBL Heidelberg
EMBL is Europe’s life sciences laboratory - an intergovernmental organisation with more than 110 independent research groups and service teams covering the spectrum of molecular biology. It operates across six sites in Heidelberg (headquarters), Barcelona, Cambridge, Grenoble, Hamburg and Rome. Our mission is to perform basic research in molecular biology; train scientists, students and visitors at all levels; offer vital services to scientists in the public and private sectors within the member states; develop new instruments and methods; and engage actively in technology transfer.
Your role
- Implement new features in the LabID Python command line interface (CLI) and in the server back end (Python Django) to enable (1) the import of workflow run results (e.g. Galaxy, Nextflow, Snakemake, CWL) and (2) the export of stored derived data as RO-Crate objects following the Workflow and Workflow Run RO-Crate profiles,
- Implement use cases using both omics and imaging data, reflecting real-world scenarios, to demonstrate the integration of the new LabID capabilities into the existing Open Science landscape (submission/retrieval of WF to/from WorkflowHub, publication of RO-Crate objects to Zenodo ),
- Generate online LabID tutorials demonstrating best practices in WF development and the FAIR dissemination of associated derived data with their provenance,
- Organize a LabID-PROV workshop at the end of the project,
- Join the relevant communities (e.g. RO-Crate, Nextflow, Snakemake, WorkflowHub, Galaxy, Zenodo) to (1) ensure the compatibility of the implemented solutions and (2) work in collaboration with the communities on missing features if needed,
- Join relevant events (e.g. workshops, conferences) to promote and disseminate LabID-PROV,
- Write final reports
**Closing date**: 15 November 2024
Contract duration: 20 Months
Grading: Postdoc/Stipend
Reference number: HD02740
You have
- PhD in e.g. Bioinformatics, Computational Biology or similar disciplines
- Strong commands in programming with Python & REST APIs
- Experience with Git and good software development practices (Unit Testing, CI/CD) in general
- Experience and strong interest in Scientific Data Management, FAIR concepts and Open Science in general
- Experience in omics and/or image data analysis using workflow management systems such as Galaxy, Snakemake, Nextflow or CWL
- Experience in writing workflows with e.g. Galaxy, Snakemake, Nextflow or CWL
- Strong interest in Open Source projects
- Ability to work in a team
- Good written and oral communication skills in English
You might also have
- Experience with Django Development
- Experience with web front end development with Vue.js
- Experience in submitting data to public repositories (e.g. EBI)
Why join us
We are Europe’s research laboratory for the life sciences - an intergovernmental organisation performing scientific research in disciplines including molecular biology, physics, chemistry and computer science. We are an international, innovative and interdisciplinary laboratory.
This is a great opportunity to develop expertise at the interface of data analysis and translational epigenetics, and to develop computational methods to advance our understanding of life. You will be part of a very interactive, collaborative and intercultural team.
EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organization with a very collegial and family friendly working environment. We are committed to diversity and equality, and encourage women and underrepresented groups to apply. Competitive salary and social security benefits, financial support for relocation, a relaxed culture, professional development, an on-site nursery, canteen and other staff facilities make EMBL a great place to work.
What else you need to know
- **EMBL is a signatory of DORA.** Find out how we implement best practices in research assessment in our recruitment processes here
- **Job location**: This role is based in Heidelberg, Germany.
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