Documentation for VCell 7.8

RELEASE_NOTES_DRAFT.md

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+# VCell Release Notes: 7.7.0.15 → 7.8.0
+
+**Release Date:** December 2025
+**Previous Release:** 7.7.0.15 (February 5, 2025)
+**Commits:** 466 | **PRs Merged:** 55+
+
+---
+
+## Highlights
+
+This release represents approximately 10 months of development with major infrastructure improvements, a rewritten export system, enhanced SpringSaLaD/Langevin solver capabilities, and significant progress migrating the VCell API to modern Quarkus REST endpoints.
+
+---
+
+## New Features
+
+### Export System Overhaul
+- **Complete rewrite of the export system** using Quarkus REST API
+- Replaced ApacheMQ with ArtemisMQ for export job queuing
+- Created separate Docker image for export service for better scalability
+- Exports now use exclusively N5 format for improved reliability
+- Added asynchronous export processing with proper error handling and user notifications
+- New endpoints for tracking export job status
+
+### SpringSaLaD/Langevin Solver Enhancements
+- **Upgraded Langevin solver** through multiple versions (1.4.0 → 1.4.2 → 1.4.4)
+- **SLURM array job support** for running multiple trial simulations in parallel with dynamic job allocation
+- **Post-processing statistics** for multiple runs including:
+  - Averages, standard deviation, min/max calculations
+  - Cluster analysis for advanced statistics
+- Physical limit validation for site sizes, diffusion rates, and partition sizes
+- Improved sanity checks for reaction-limited restrictions and reaction radius calculations
+- Particle displacement calculations for given diffusion rates and time intervals
+- New UI for Steady State options in Simulation Options dialog (CVODE only)
+
+### Field Data System Improvements
+- **Moved field data processing to the server** (previously client-side), reducing network overhead
+- New REST endpoints for field data operations:
+  - Create field data from files
+  - Create field data from simulation results
+  - Copy field data between BioModels
+- Improved memory management for large field data operations
+- Algorithm optimization with reduced memory usage (up to 68% reduction)
+- Removed complex FieldDataOpSpec system in favor of simpler, atomic operations
+
+### Quarkus REST API Expansion
+New endpoints added for modern API access:
+- **BioModel endpoints**: save, delete, get, and info retrieval
+- **MathModel endpoints**: full CRUD operations
+- **Geometry endpoints**: creation and retrieval
+- **VCImage resource**: image handling through REST API
+- Improved error handling architecture with proper HTTP status codes
+- OpenAPI specification testing in CI to prevent breaking API changes
+- Generated clients for Java and Python updated automatically
+
+### User Access Control
+- **VCell Support role** added - support staff can now view models shared with VCell Support
+- Improved user role management in database and API
+
+---
+
+## Bug Fixes
+
+### Critical Fixes
+- **Fixed VCell reconnection/token refresh failure** - clients no longer lose connection after extended periods (#1471)
+- **Fixed Google login issues** - proper handling of Google account selection and logout (#1520)
+- **Fixed OutputFunctions being ignored** in spatial CLI data processing (#1595)
+- **Fixed Math Model export error** - type casting issue resolved (#1594)
+- **Fixed field data creation from simulations** - previously broken functionality restored (#1457)
+
+### Model & Simulation Fixes
+- Fixed PubMed links in Annotations tab (#1576)
+- Fixed NPE when inserting compartment (#1541)
+- Fixed concurrent modification exception in simulation results display (TreeMap replaced with ConcurrentSkipListMap) (#1465)
+- Fixed geometry viewer cropping bug (#1437)
+- Fixed parameter estimation requiring constant re-authentication (#1498)
+- Typo fix: "Constructed" → "Constructive" solid geometry (#1561)
+
+### Infrastructure & Security
+- **XML security hardening** - prevention of XXE (XML External Entity) attacks in XML parsing (#1531)
+- Fixed SSH command configuration for SLURM cluster migration (#1467)
+- Fixed duplicate SSH login issues (#1562)
+- Database connection improvements for Oracle and PostgreSQL
+
+---
+
+## Infrastructure Improvements
+
+### Server & Deployment
+- Configurable SSH options for SLURM via Kubernetes config
+- New HAProxy pod for SSH request proxying to SLURM submit nodes
+- Improved Terraform documentation for Kubernetes deployment
+- Apple code signing certificate renewal for macOS installers
+- Oracle database account restructuring:
+  - New `vcell_service` account for production
+  - New `vcell_dev` account for developers
+  - Deprecated shared `vcell` account for improved security
+
+### Native Library Compilation (libvcell)
+- **New GraalVM native compilation** of VCell Java code for use with pyvcell
+- Published libvcell package to PyPI with multi-platform support
+- Custom manylinux Docker image with bundled GraalVM, Maven, and Poetry
+- Endpoints for generating Finite Volume solver input from VCML and SBML
+
+### Build & CI/CD
+- OpenAPI specification CI testing to prevent breaking changes
+- Improved GitHub Actions workflows for native library builds
+- JSBML fork with custom resource bundle handling for native compilation
+- Updated JAI Core repository configuration
+
+---
+
+## External Integrations
+
+### Pathway Commons
+- Upgraded to BioPAX Level 3 support (#1574, #1586)
+- Improved pathway import using new pathwaycommons.org URLs
+- Better handling of pathway entities and reactions
+
+### BioSimulations Compatibility
+- Plots now reported as Reports for BioSimulations compatibility (#1444)
+- Updated CLI data handling for improved interoperability
+- Small mesh option for faster spatial simulations
+
+### BioModels Database
+- Updated list of supported/failed models for BMDB importing
+- Fixed import issues with models having variable compartment sizes (#1496)
+
+---
+
+## Developer Notes
+
+### API Migration Status
+The migration from legacy Jersey/RPC API to Quarkus REST continues. The following resources now use the new API:
+- BioModel (info, save, delete, get)
+- MathModel (full CRUD)
+- Geometry
+- VCImage
+- Field Data
+- Export (with new queue system)
+- User/Authentication
+
+### Breaking Changes
+- Export format now exclusively N5 (legacy formats deprecated)
+- KeyValue objects now serialize as strings in API responses
+- Some legacy RPC calls removed from client
+
+### Deprecated Features
+- Legacy ApacheMQ export queue (replaced by ArtemisMQ)
+- FieldDataOpSpec system (replaced by simpler endpoint model)
+- Direct Oracle 'vcell' account access (use vcell_dev or vcell_service)
+
+---
+
+## Known Issues
+
+- SpringSaLaD is disabled by default (enable via property `enableSpringSaLaD=true`)
+- Windows native library builds for pyvcell still in progress
+
+---
+
+## Contributors
+
+- **Ezequiel Valencia** - REST API development, Field Data system, Export system overhaul
+- **Dan Vasilescu** - SpringSaLaD/Langevin solver improvements, SLURM integration, post-processing statistics
+- **Logan Drescher** - CLI improvements, BioSimulations compatibility, Smoldyn performance optimizations
+- **Jim Schaff** - Infrastructure, pyvcell/libvcell, native compilation, system architecture
+
+---
+
+## Acknowledgments
+
+Special thanks to the VCell user community for bug reports and feedback. For questions or issues, contact vcell_support@uchc.edu.

RELEASE_NOTES_USER.md

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+# VCell 7.8.0 Release Notes
+
+**Release Date:** December 2025
+
+---
+
+## What's New
+
+### Faster, More Reliable Exports
+We've completely rebuilt the export system from the ground up. Exports are now more reliable, faster, and you can track their progress in real-time. All exports now use the N5 format, which provides better performance and compatibility with modern visualization tools.
+
+### Improved SpringSaLaD Simulations
+- **Run multiple trials in parallel** - SpringSaLaD simulations can now run many trials simultaneously on our computing cluster, dramatically reducing wait times for statistical analysis
+- **Built-in statistics** - Automatically calculate averages, standard deviations, and min/max values across multiple simulation runs
+- **Better validation** - The system now checks your model parameters before running to catch common issues early
+
+### Enhanced Field Data Management
+- Create field data directly from simulation results without downloading files first
+- Copy field data between your BioModels more easily
+- Significantly faster processing for large datasets
+
+### Better Connection Stability
+- Fixed issues where VCell would lose connection after extended periods
+- Improved Google login - switching between accounts now works correctly
+- More reliable reconnection when network issues occur
+
+### VCell Support Access
+Support staff can now view models you've shared with "VCell Support" to help troubleshoot issues more effectively.
+
+---
+
+## Bug Fixes
+
+- Fixed PubMed links in the Annotations tab
+- Fixed geometry viewer cropping issues
+- Fixed errors when inserting compartments in some models
+- Fixed Math Model export errors
+- Fixed parameter estimation requiring repeated logins
+- Fixed "Constructed Solid Geometry" typo (now correctly shows "Constructive Solid Geometry")
+- Fixed issues with spatial simulation output functions being ignored
+
+---
+
+## Pathway Commons Integration
+
+Importing pathways from Pathway Commons has been upgraded to support the latest BioPAX Level 3 format, providing access to more comprehensive pathway data.
+
+---
+
+## System Requirements
+
+No changes to system requirements from the previous version. VCell 7.8.0 is available for:
+- Windows 10/11
+- macOS 11 (Big Sur) and later
+- Linux (Ubuntu 20.04+ recommended)
+
+---
+
+## Getting Help
+
+- **Email:** vcell_support@uchc.edu
+- **Discussion Forum:** https://groups.google.com/group/vcell-discuss
+- **Documentation:** https://vcell.org
+
+---
+
+## Thank You
+
+Thank you to all users who reported bugs and provided feedback. Your input helps make VCell better for the entire computational biology community.