cryo-EM at Sabalcore High Performance Cloud

Sabalcore provides pay-as-you-go High Performance Computing (HPC) systems in a private cloud for scientists and researchers. Discounts available for academics and nonprofits.

RELION (for REgularised LIkelihood OptimisatioN, pronounced “rely-on”) employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM). The cryo-electron microscopy (cryo-EM) technique produces highly detailed images of viruses, areas within cells, and single proteins. RELION’s compute requirements can be extreme. High performance computing is required to convert these images into three-dimensional models, or even videos. RELION is pre-installed and ready to use on all Sabalcore high performance clusters which feature the latest Intel® Xeon® Scalable Processors and nVidia Tesla GPUs.

Workflow

Transitioning to Sabalcore’s cloud is straight-forward. Direct access to the compute environment means more control and flexibility.

  1. Collect cryo-EM data.
  2. Prepare refinement.
  3. Log into Sabalcore.
  4. Download your data to your account at Sabalcore. This can be done manually or automated from your local PC or any cloud storage provider.
  5. Choose the number of CPUs or GPUs you need.
  6. Submit RELION ‘job’ for processing. Batch job automation scripts can help streamline the process.
  7. Visualize/Post-process results directly using our ssClient with visualization or download for local analysis.

Sabalcore vs. Amazon

Sabalcore provides High Performance Computing (HPC) systems in a private cloud for scientists and researchers. Built from the ground up, our compute systems are designed to run computationally intensive numerical applications with performance and efficiency similar to true “supercomputers” found at large universities and national labs. The Sabalcore platform was built specifically for high-performance while commodity clouds such as Amazon only provide a HPC-like experience upon their virtual platform.

  • True “bare-metal” processing – We sell core-hours on bare-metal CPU cores. Not virtual CPUs like Amazon.
  • True high performance network – We use non-virtual high performance network connectivity (known as Infiniband) between compute nodes and storage systems at speeds up to 100Gbps with ultra-low latency. Infiniband is most commonly used interconnect in supercomputers today and is important for MPI-enabled software like RELION. Amazon’s network is commonly 10G Ethernet which is much slower – ~50 times slower than Sabalcore’s 100Gbps Infiniband.
  • Tightly Coupled System – For data sensitive applications, it is important that the storage system is directly attached to the compute infrastructure. Sabalcore’s storage systems are directly attached to the compute nodes. Amazon block storage is not directly attached which causes significant latency and can be a substantial bottleneck.
  • Single Origin – It is important to know where and who is responsible for your HPC service. We own and operate all servers and networks so you know exactly where and who manages your data.
  • Fully Managed – Unlike Amazon, Azure, or Google where you must configure manage your own environment or rely on 3rd party tools, your environment at Sabalcore is fully managed and ready to go so you can focus on what is important to you.

Start Today

Run RELION today with 1,000 free core-hours.