Your function

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

Your profile

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

What do we offer?

A challenging position in a socially engaged organisation. At VU Amsterdam, you contribute to education, research and service for a better world. And that is valuable. So in return for your efforts, we offer you:

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

About us

Faculty of Science
Working at the Faculty of Science means collaborating with students, lecturers and researchers who are focused on their field, yet have a broad view of the world. We are proud of a positive and inclusive workplace culture within the faculty, where we work together with great energy and a pragmatic attitude to tackle social challenges. At the Faculty of Science, scientists and students work on fundamental and complex societal issues for a sustainable, healthy and just future.

From forest fires to big data, from obesity to malnutrition, from helium to the universe and from genetics to medicine: our education and research cover the full breadth of science, from molecules to mankind. Our academic education and research are highly experimental, technical and interdisciplinary in nature. That is why we collaborate extensively with leading scientific institutes and industry. The faculty has more than 8,000 students studying in one of the 39 programms and employs more than 1,400 staff across 10 scientific departments, making us one of the largest science faculties in the Netherlands.

Vrije Universiteit Amsterdam
Vrije Universiteit Amsterdam stands for values-driven education and research. We are open-minded experts with the ability to think freely - a broader mind. Maintaining an entrepreneurial perspective and concentrating on diversity, significance and humanity, we work on sustainable solutions with social impact. By joining forces, across the boundaries of disciplines, we work towards a better world for people and planet. Together we create a safe and respectful working and study climate, and an inspiring environment for education and research. Learn more about our codes of conduct

We are located on one physical campus, in the heart of Amsterdam's Zuidas business district, with excellent location and accessibility. Over 6,150 staff work at the VU and over 31,000 students attend academic education.

Diversity
Diversity is the driving force of VU Amsterdam. VU wants to be accessible and receptive to diversity in disciplines, cultures, ideas, nationalities, beliefs, preferences and worldviews. We believe that trust, respect, interest and differences lead to new insights and innovation, to sharpness and clarity, to excellence and a broader understanding.

We stand for an inclusive community and believe that diversity and internationalisation contribute to the quality of education, research and our services.

Therefore, we are always searching for people whose backgrounds and experience contribute to the diversity of the VU community.

Interested

Are you interested in this position and do you believe that your experience will contribute to the excellence of our services? In that case, we encourage you to submit your application, even if you don't meet all requirements.

Submitting a diploma and a reference check are part of the application process.

Applications received by e-mail will not be considered.

Acquisition in response to this advertisement is not appreciated.

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