Scientific Programmer (Bioinformatics Software Developer)

The research group of Danielle Posthuma within the Complex Traits Genetics laboratory at the Centre of Neurogenomics and Cognitive Research (CNCR) of Vrije Universiteit Amsterdam is looking for a Scientific Programmer to contribute to the continued development and maintenance of widely used genetic web-tool called FUMA (Functional Mapping and Annotation of GWAS).

FUMA is a heavily used web platform that enables researchers worldwide to perform functional interpretation and downstream analysis of genome-wide association study (GWAS) results. Thousands of researchers use FUMA every year to analyze genetic data through an interactive web interface supported by a robust computational backend. The webtool is built on Laravel, the tool utilizes PHP, JavaScript, Python, and R.

You will play a key role in the technical development and maintenance of FUMA, with possible involvement in the scientific development as well (i.e. suggesting novel additions).

Your responsibilities include:

• Develop and implement existing and new analysis modules and visualizations within FUMA, including integration of statistical pipelines developed by the Complex Traits Genetics group
• Integrate large-scale biological reference datasets for use within FUMA. These resources including molecular QTLs, chromatin interaction, functional annotation, and single-cell transcriptomic resources from the latest scientific literature
• Maintain and improve the production infrastructure, including software dependencies, databases, Linux servers, job scheduling, storage management, and automated data update pipelines
• Optimize performance, scalability, and reliability of the web platform and backend analysis pipelines
• Be responsible for maintaining reproducible workflows for preprocessing, harmonizing, and updating biological datasets
• Resolve software bugs, improve code quality, and modernize components of the codebase when needed
• Provide user support by troubleshooting analyses and answering technical questions from researchers worldwide
• Collaborate closely with computational biologists and statistical geneticists within the department to translate new research methods into user-friendly software

We are looking for a software engineer interested in applying their skills to computational genomics and statistical genetics. Alternatively the position would also fit someone with a bioinformatics background who enjoys software development.

• Master’s degree (or equivalent) in Computer Science, Bioinformatics, Computational Biology, or a related field
• Strong programming skills in Python and/or R
• Experience with version control using Git
• Experience with Linux environments and command-line tools
• Experience with SQL and relational databases
• Good command of English
• Enjoy translating new scientific methods into practical, robust software
• Take ownership of long-term software projects and continuously seek improvements
• Are proactive, self-motivated, reliable, and enthusiastic
• Enjoy working in an interdisciplinary research environment alongside statistical geneticists, bioinformaticians, neuroscientists, and experimental researchers
• Like improving both the scientific capabilities and user experience of a widely used research platform, whether by adding new visualizations, improving usability, increasing computational efficiency, or expanding biological resources

Additional preferred skills, or with a strong willingness to learn:

• Experience with Docker or other containerization technologies
• Experience with web development (PHP/Laravel, JavaScript, HTML/CSS)
• Familiarity with workflow management systems (e.g. Snakemake or Nextflow)
• Knowledge of bioinformatics, statistical genetics, GWAS, or functional genomics

• a salary of minimum € 3.706,00 (Scale 10) and maximum € 5.760,00 (Scale 10) gross per month, on a full-time basis. This is based on UFO profile Education and Research Technician - O profile 2. The exact salary depends on your education and experience
• a position for at least 0.5 FTE
• Your employment contract will initially last 1 year. Afterwards, the possibility of expansion exists

We also offer you attractive fringe benefits and regulations. Some examples:

• 8% holiday allowance and 8.3% end-of-year bonus
• contribution to commuting expenses
• solid pension scheme (ABP)
• optional model for designing a personalized benefits package

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