SCEs (2025)

David Thiriot, Phil Bowsher & James Black

Python for Clinical Study Reports and Submission

2025
SCE
Authors

David Thiriot

Phil Bowsher

James Black

Published

September 15, 2025

SCEs in 2025

Chairs: David Thiriot, Phil Bowsher and James Black

See also: 2023 Discussion, 2024 Discussion

SCE Components (5 Core Elements)

  1. IDE: Development environment interface
  2. File and Version Management: Source control and file handling
  3. Data and Access: Data storage and access management
  4. Governance: Policies and compliance frameworks
  5. Compute: Processing and computational resources

Scope and Architecture Challenges

  • Historical Separation: Legacy approach had separate SCEs for GXP work vs. everything else
  • Unified Direction: Most companies moving toward single SCE for all work
  • User Diversity: Modern SCEs serve PK, Biostatistics, Stats Programming, and other groups on same platform

Vendor Considerations

  • Ecosystem Promises: Vendors offer packaged solutions but create vendor lock-in concerns
  • Missing Integrations: Gaps in vendor offerings, sometimes strategically maintained
  • Cost Management: Total cost of ownership concerns when using multiple vendors
  • Integration Overlap: Redundancy between different vendor products increases costs

Validation Challenges

  • Timeline: Validation processes take months (up to 3 months reported)
  • Test Suite Maintenance: Significant burden maintaining test suites as platforms change
  • IDE Validation Debate: Whether to validate IDE as part of environment or keep separate
  • System vs. Process: Best practice is qualifying systems while validating processes

Technology Evolution

  • Python Integration: Coming into clinical reporting, mainly for transformations
  • Python Validation Gap: Lacks standardized documentation and testing frameworks compared to R
  • Data Format Shift: Parquet replacing SAS7bdat as standard data format
  • Package Governance: Some companies using opinionated lists of approved R packages

Environment Management

  • Update Cycles: 3-6 months common window for base environment updates
  • Package Coupling: Most companies couple R packages with environments (some decouple)
  • Environment Tracking: Tools to flag whether environments are managed/production-ready
  • Consistency Requirements: Containers must be accessible across SCE, Shiny apps, HPC, etc.

Version Control and Data Access

  • Git Adoption: Standard direction but significant change management challenges
  • Learning Curve: Git presents training challenges for traditional SAS users
  • Data Access Complexity: Challenges with data access in Shiny applications
  • Technology Solutions: Denodo and AWS Data Zone mentioned for data access management