You will join a integrated data & compute team, consisting of field experts, data stewards and HPC engineers, to facilitate the storage, processing, integration and sharing of scientific research data according to the FAIR principles. You will work closely with the staff of the imaging, flow cytometry, and omics core facilities (genomics, proteomics, metabolomics) and develop tools & resources to enable data integration for multi-omics and AI-based research. Specific tasks include:

• Optimise performance and operations of the HPC cluster.
• Monitor and improve system safety and security following international standards (ISO/IEC).
• Provide HPC training and support for users.
• Provide a shared resource CPU and GPU intensive workloads.
• Provide a shared resource for sophisticated domain specific applications.
• Identify current and future compute needs of researchers in their domain.
• Co-develop domain specific data analysis pipelines.
• Implement and standardise data analysis pipelines.
• Provide data analysis workshops and training for users.
• Act as technical consultant for core facility users.
• Take part in development of HPC infrastructure e.g. specialised compute, GPU, storage or connectivity hardware.
• Organise the HPC spoke network of domain experts. Connect and align to identify common ground and synergetic opportunities.
• Integrate data management solutions within our high-performance clusters HPC(s) platforms.
• Advise researchers about the available HPC facilities at Amsterdam UMC, onboard and support them in using the suitable facility.

• You have a completed MSc or PhD in computer science or exact science.
• You have experience and affinity with imaging, flow cytometry, and OMICs research.
• You have excellent communicative skills and organisational talents.
• You have working experience with Linux and HPC.
• You have experience with Linux system administration.
• You are proficient with bash and python.
• You have experience with software engineering.
• You have knowledge about programming languages such as Rust, C++, and Java.

• One-year contract with the prospect of a permanent contract.
• Classification in salary scale 10: € 3.493 tot € 5.504 Gross for full-time employment (depending on education and experience).
• In addition to a good basic salary, we offer 8.3% end-of-year bonus and 8% holiday allowance. Calculate your net salary here.
• Free and unlimited access to our online learning environment GoodHabitz.
• Pension accrual with the ABP, of which we pay 70% of the premium.
• A (partial) reimbursement of your public transport expenses. Do you prefer to come by bike? Then we have a good bicycle scheme.
• An active staff association and Jong Amsterdam UMC association, both of which organize fun (sports) activities and events.

Amsterdam UMC

The imaging, flow cytometry, and & omics (genomics, proteomics, metabolomics) Core Facilities of the Amsterdam UMC are working together to expand their team of data & compute experts to facilitate the storage, processing, integration and sharing of scientific research data to enable data integration for multi omics and AI based research. FAIR and AVG compliant data services and High-Performance Computing (HPC) resources are provided to allow integration of CF data, enabling pipelines and developing harmonized FAIR data policies for the Amsterdam UMC life scientists. Our services and resources serve as a solid foundation to provide well defined and connected imaging, flow cytometry and omics data sets for research and to provide access to vast amounts of data for AI-driven research.

The goals of this project include the 1) Harmonized FAIR data management of the CFs for data integration, standardization, and annotation; 2) Creation of a data sharing infrastructure and pipelines to enable controlled access to data generated by the Amsterdam UMC CFs; 3) Enable the combination of datasets from different CFs for data analysis and AI modelling; and 4) Provide an integrated data management and computing resource to all CF users to establish & secure the knowledge including scripts, software, and data analysis pipelines. Integrating data from imaging, flow cytometry, and omics core facilities will catalyze innovations with cost efficient services for researchers and enhance the visibility of Amsterdam UMC in the Dutch and European research infrastructure landscape.

More information on our CFs can be found here: https://www.amsterdamumc.org/en/research/core-facility.htm.