VCell Alert Notification
VCell 7.5 has been released!
Released 2023-February
New Features in VCell 7.5:
Quality Assurance
- Significantly expanded automated Unit testing
- Significantly expanded automated Integration testing
- Test equivalence of BioModel math generation with originally stored math for an extensive test suite of 1000 public models - identified and fixed several minor bugs.
- Test SBML/SEDML export and import against all public VCell models which are mappable to SBML with rigorous round-trip verification.
- Test SBML import from the official SBML test suite (1753 test cases), to identify and document unsupported SBML features (e.g. Delay, Algebraic Rules, XOR operator, 0D/1D compartments).
VCell Features
- Comprehensive support for SBML and SEDML import, export, and execution.
- Statistics displayed and exported for multiple trajectory stochastic simulations.
- Allow parameter scans on local client-side simulation runs.
- Parameter Estimation upgraded to the latest version of COPASI and improved feedback during execution (new plot of objective function vs iteration)
- Greatly expanded VCell CLI, including archive conversion and validation. (try docker run -it ghcr.io/virtualcell/biosimulators_vcell:latest help)
- Improved support for external access to a subset of VCell solvers (containerized version with command line execution e.g. docker run -it ghcr.io/virtualcell/vcell-solvers:latest FiniteVolume_x64 to run our standalone PDE solver - contact us for more information)
- Complete support for changing a BioModel’s unit system transformation
- Export to HDF5 file format for ODE simulations including parameter scans and for spatial applications from both the VCell client UI and the CLI.
Behind the scenes
- Complete support for changing a BioModel’s unit system
- Greatly improved algorithm for comparing mathematical equivalence of models.
- improved expression simplification for cleaner imported models.
Infrastructure
- Pre-release support for PostgreSQL database as an alternative to Oracle.
- VCell API authentication and RBAC ported to standard JWT bearer tokens in preparation for future OIDC and single sign-on.
- updated VCell API security (TLS)
- improved docker and multi-platform native builds for VCell solvers in GitHub actions.
- improved structured logging and server metrics integrated with Elastic Stack.
- improved administrative CLI tools
Thank you for using VCell.