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Published April 18, 2026 | Version 7.7.0.73
Software Open

virtualcell/vcell: 7.7.0.73

Authors/Creators

  • 1. UConn Health @virtualcell
  • 2. CCAM
  • 3. UConn Health
  • 4. @TheClimateCorporation
  • 5. Stealth
  • 6. Eliceiri/LOCI lab, UW-Madison
  • 7. @deeporiginbio
  • 8. Gitter

Description

First master release with pre-built Apptainer SIF support and parameter estimation migration.

Pre-built Apptainer SIF for SLURM containers

  • Container image properties renamed from *_docker_name to *_apptainer_image with ORAS URL values
  • SlurmProxy derives local SIF filenames from ORAS URLs; fail-fast on missing SIF
  • CI build-and-publish-sif job publishes vcell-opt + vcell-batch SIFs to GHCR via ORAS
  • See docs/apptainer-image-build.md for operational reference

Parameter estimation migration (parest-bug branch)

  • Database-backed job tracking (vc_optjob table)
  • REST endpoints: POST/GET /api/v1/optimization
  • Cross-protocol Artemis messaging (AMQP 1.0 ↔ OpenWire JMS)
  • Desktop client rewritten to use generated OptimizationResourceApi
  • Legacy /api/v0/optimization endpoints and socket server removed
  • COPASI upgraded (basico 0.40→0.86, python-copasi 4.37→4.46)

Other fixes

  • Fix CodeQL partial path traversal alert #226
  • Restore executable permission on langevin_x64 in batch container
  • Fail fast when notarytool submit fails
  • Increase optimization polling timeout to 10 minutes

Companion changes required

  • vcell-fluxcd: rename properties in submit.env, add htc_singularity_imagedir, add vcell-sif-prepull k8s Job
  • One-time: bootstrap vcell-solvers + vcell-fvsolver SIFs to GHCR via ORAS

UI improvements (PR #1666)

  • New renderers, extra options, dimming on mouse over, crosshair snap node highlight

Files

virtualcell/vcell-7.7.0.73.zip

Files (137.4 MB)

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md5:07e091049b610cd2d12d374b657004d9
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Additional details

Related works

Is supplement to
Software: https://github.com/virtualcell/vcell/tree/7.7.0.73 (URL)

Software

Repository URL
https://github.com/virtualcell/vcell