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Statistical Computing Environment (SCE)


The Egnyte’s Platform supports a wide variety of use cases for Life Sciences organizations.  One key use case is to serve as a Statistical Computing Environment (SCE) for the analysis of clinical data by biostatisticians.  In an SCE, organizations provide an environment where raw clinical data can be imported and then analyzed with tools like SAS, R, and Python.  Biostatisticians write code to process and analyze data and then output results to reports which are used as part of regulatory submissions.

Key capabilities supporting this use are:

  • Ease of ingesting clinical data from multiple sources
  • Unified file system with fine grained permissions
  • Deployment in cloud and desktop environments
  • Support for a wide variety of applications and statistical tools
  • Rich auditing of all user actions
  • GxP compliant environment

This use case summary will detail each of these capabilities and provide you with the steps to deploy an SCE with the Egnyte Platform.

Ingesting Clinical Data from Multiple Sources

Raw data for analysis often comes from a variety of sources, including R&D lab data, ePRO, IRT, EDC, and other data from CROs and external teams.

While any of Egnyte’s applications, supported protocols, and integrations can be used to ingest raw clinical data, the following are typically used:

  • SFTP (SSH File Transfer Protocol): many clinical applications have mechanisms for transferring data to a secure FTP server. Egnyte’s file server supports SFTP as both an input and output mechanism.  You can create a service account with access to a folder that will allow those 3rd party systems to transfer data to Egnyte on a regular basis.
  • Standard User access: you can create a Standard User for an external user who needs to access your file system directly.  You control their access to folders with permissions and can grant them rights to upload files.
  • Upload Links: use an Upload Link to allow an external user to upload files to Egnyte without having to create an account for them.  They’ll be able to upload content without having access to see Egnyte folders or log in.
  • APIs: Egnyte’s Public APIs expose a set of REST APIs that can be used to automate the ingestion and manipulation of data in Egnyte.

Unified File System with Fine Grained Access

Regardless of how your content gets into Egnyte, the data follows the same audit and integrity protocols and is stored in a unified file system whose access is governed by folder permissions.  The Egnyte platform is a petabyte-scale globally distributed file system.

Egnyte’s folder permission model allows you to segment data access and visibility for different groups within your organization.  You can create separate folder hierarchies for each study, phase, or area of investigation.  Fine grained permissions allow you to override permission at any level of the hierarchy to provide a least privilege approach to minimize risk.

File and Folder Templates can be used to create common folder hierarchies that can be reused for new studies or analyses.  Egnyte’s Public API can also be used to automate folder permissions and 

Supporting a Wide Variety of Statistical Applications

Egnyte’s Platform is agnostic to both raw data format as well as the programming language used to analyze data.  Nearly any application or server that analyzes data directly on a user’s computer or on a file server can be used with Egnyte.  Popular analytical tools used in an Egnyte SCE include SAS, R/RStudio/Posit, and Python.

Deployment in Cloud and Local Environments

Egnyte’s Platform is cloud-based, but provides tools to cache large volumes of data in the public cloud and end-user computers for high-speed data analysis. A single deployment often combines both of these models to enable users to work in the environment that is best suited to their role.

The following diagram shows a representative SCE deployment that combines usage of Egnyte with AWS for large scale data processing.


Public Cloud Deployment

The public cloud (AWS, Azure, GCP) is an obvious choice for a high scale computing environment where you need to process large volumes of data and have shared computing resources.  Processing of data is done with either server software (e.g. a SAS server) or with desktop software or code (e.g. R or Python).  

One approach to deploying in the public cloud is to use Egnyte’s Storage Sync. Storage Sync is a virtual appliance that can synchronize data and expose it as a file share on the local network.  Applications can read directly from the file server, providing fast access to large volumes of data. Because Storage Sync exposes content as a file server, it can be accessed from a wide variety of clients including servers, Linux VMs, and Windows VMs. Any application that is capable of reading files from a file server will work with Storage Sync.

All file access and changes are audited and changes to files are automatically captured as file versions.

Desktop Access

Users who need to run analyses directly on their desktop can utilize the Egnyte Desktop App to mount the Egnyte file system on their desktop as a drive. By default, the Desktop App provides real-time access to your Egnyte files without having to store those files directly on your computer.  If your analysis requires the highest speed access to those files, you can sync the files to your computer to give you hard disk-speed access to raw data.

The Desktop App can be used in an office or at home without need for a VPN. 

Storing Source Code

While it is technically possible to store source code in Egnyte, most companies deploying an SCE store and manage their source code for data analysis in a dedicated source code management (SCM) tool such as GIT.  The code stored in the SCM is used to process the raw data in Egnyte and output the reports and completed analysis back to Egnyte.

Auditing and Compliance

All data ingestion, manipulation, sharing, and access is captured in Egnyte audit reports.  These audit reports track the file or folder being acted upon, the user performing the action, dates, IP addresses, and other key information that can provide a full picture of activity within Egnyte.

Egnyte’s Secure & Govern provides a host of capabilities that allow you to manage and govern your content within Egnyte:

  • Content lifecycle management - create retention, archival, and deletion policies.
  • Content classification - identify data with HIPAA, PII, GDPR, and other sensitive information with 500+ built-in patterns or your own custom lists.
  • Access control governance - monitor and manage permissions for internal and external users.  Set policies to limit sharing control based on the sensitivity of content.
  • Threat management - detect ransomware attacks, unusual behavior, and compromised accounts.

This comprehensive suite of tools helps you to ensure the integrity of your data, its access, and the output of your analysis.

GxP Compliant Environment

If you are analyzing clinical data, you likely need to run this analysis in a GxP compliant environment. Egnyte’s GxP Platform takes the power of Egnyte’s collaboration and governance platform and wraps it in a compliance envelope so that you can create, manage, and analyze regulated clinical content.

The platform includes a detailed validation package covering the product requirements and the tests that demonstrate the product’s adherence to those requirements. Customers can use these documents to validate their environment or rely on Egnyte’s GxP Quality team to create validation documentation. The GxP Compliance Portal provides easy access to those requirements along with results of daily automated tests for all core functionality.

21 CFR Part 11 and Annex 11 compliant workflows allow for the review and approval of documents and reports meeting regulatory requirements.

These tools combine to simplify and speed up the process of deploying a GxP compliant SCE environment.


Egnyte’s Platform provides all the building blocks needed to deploy a Statistical Compute Environment that meets regulatory and GxP requirements.  Engyte provides numerous ways to ingest data from a variety of sources, both manual and automated. The system is flexible to support a wide range of data formats and analytical tools. A range of deployment options allow you to run large scale analysis in the public cloud or smaller workloads directly on a user’s computer.  All activity in Egnyte is audited and Egnyte’s GxP platform provides the foundation for a secure and auditable platform to meet regulatory requirements.

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