Computational Infrastructure

NIS has developed a proprietary system to catalog, track, and design experiments for all of the samples, buffers and EM grids used in our cryo-EM workflows.  Each sample or grid receives a unique identifier that allows complete tracing of the chain of custody, related experiments, and analyses performed from sample intake through final report.

We have implemented and optimized advanced data collection pipelines on each of our microscopes utilizing modified versions of the Leginon and Appion applications. The pipelines are capable of rapid, fully automated image collection and pre-processing while also maintaining the experimental flexibility necessary to achieve the most efficient and effective imaging strategies for cryo-EM and microED. All experimental parameters for each image taken are tracked and recorded in our database systems.

Clients can view and evaluate images being collected through our secure, web-based system.  Depending on the type of experiment, viewing can be done in real-time, including the results of motion correction, and distortion and resolution estimates. Enabling contemporaneous feedback on data quality, this viewer allows NIS scientists and clients to collaborate remotely on the optimal data collection strategies to achieve the best outcome for each study.

NIS’s networking infrastructure enables fast, near real-time image uploads as they are collected on our microscopes, including support for end-to-end data encryption during the transfer. We support concurrent uploads to Amazon’s Simple Storage Service (AWS S3), Google’s Cloud Storage Service (GCS). We can also provide images on client-supplied encrypted hard drives.

We have engineered high performance computational and storage systems dedicated to running a complete pipeline for single particle data processing. These systems provide both real-time feedback on imaging experiments and rapid structure determination. We deploy a combination of cryoSPARC, cryoSPARC Live and Relion, along with internal procedures developed over our years of data processing experience, to obtain high resolution results in actionable time frames.

‍

‍

‍

‍

In addition to the Client Viewer, NIS offers a separate, secure, web-based portal with a dashboard for report and data delivery. Results of your study can be quickly downloaded within minutes of notification of a completed report. The Client Portal also supports small data transfers over our high bandwidth external internet connections.

NIS supports both on-site and co-localized high speed computing resources linked via high bandwidth fiber optic internet connections.  The hardware systems consist of over 500 processing cores, 50 GPUs, and six petabytes of storage space, all located within secure facilities behind multiple high availability firewalls following NIST security guidelines.

‍