The EMBL de.NBI Cloud site provides a flexible and scalable cloud environment tailored for life scientists, with a focus on reproducible, containerized scientific computing. Our site specializes in modern cloud-native technologies such as Kubernetes and virtual desktop infrastructure (VDI) to support a wide range of scientific use cases, particularly in the life sciences and image analysis.
At the core of our services is ABCdesktop, a virtual desktop platform that allows researchers to access pre-installed, hardware-accelerated scientific applications, removing the need for complex local installations and ensuring consistent computing environments. Our platform is designed to support both interactive and automated workflows, enabling researchers to focus on their science rather than infrastructure management.
We offer services across three of the “classic” cloud layers:
- Infrastructure as a Service (IaaS):
Users are provided with Kubernetes namespaces as their isolated compute environments. These namespaces allow users to deploy their own services, run custom workloads, and manage containerized applications at scale. Resources are GPU-enabled and optimized for scientific computing, supporting a wide range of computational biology and imaging workloads. - Platform as a Service (PaaS):
Our Abcdesktop environment offers an intuitive virtual desktop interface where users can create and manage OCI-compliant containers. These containers are seamlessly integrated into our cloud infrastructure, allowing users to develop, test, and execute custom scientific software within a reproducible and shareable environment. The platform is especially suited for container-based workflows in imaging, data analysis, and simulation. - Software as a Service (SaaS):
We provide immediate access to a range of pre-installed, GPU-accelerated scientific software directly within the Abcdesktop environment. This includes widely used tools such as Fiji, Blender (for image analysis and visualization), Ilastik, Napari, Cellpose, and IMOD. These applications are maintained and optimized for performance, offering a ready-to-use solution for researchers working with microscopy data, 3D modeling, segmentation, and deep learning-based image analysis.
The EMBL de.NBI cloud site aims to lower the barrier to entry for life scientists seeking advanced computing resources, while promoting best practices in containerization and reproducibility. Our focus is on delivering a highly interactive, GPU-accelerated platform for image analysis and scientific computing, tailored to the specific needs of the bioimaging and computational biology communities.