8.0.0.06

Highlights

• Langevin (SpringSaLaD) solver updated to 1.4.7 — fixes a NullPointerException that crashed the solver when a bound site transitioned to a state with no defined binding reaction (#1711, cam-center/LangevinNoVis01#36). The bond now keeps its existing reaction identity/length and stops spontaneously dissociating in that state instead of crashing.

What's Changed

• Patch BMDB nightly testing unicode handling in #1705
• Bump langevin solver to 1.4.7 by @jcschaff in #1711

Full Changelog: 8.0.0.05...8.0.0.06

8.0.0.05

What's Changed

• Update installer splash screen from "VCell 7" to "VCell 8" by @jcschaff in #1702
• SpringSaLaD bubble histogram by @danv61 in #1703

Full Changelog: 8.0.0.04...8.0.0.05

8.0.0.04

What's Changed

• Cluster mass distribution by @danv61 in #1699

Full Changelog: 8.0.0.03...8.0.0.04

VCell 8.0.0 — SpringSaLaD GA (build 8.0.0.03)

VCell 8.0.0 — SpringSaLaD GA

Build 8.0.0.03 is the production rollout of the VCell 8.0.0
public release: SpringSaLaD modeling is now a first-class VCell
modality.

Headline

VCell 8.0.0 introduces SpringSaLaD (Michalski & Loew, 2016) as a fully
supported VCell modality. SpringSaLaD enables spatial, stochastic,
particle-based simulation of biochemical reaction-diffusion systems,
representing biomolecules as collections of linked spherical sites with
explicit excluded-volume interactions in three-dimensional space —
bridging detailed molecular-dynamics approaches and cellular-level
reaction-network modeling. Available throughout the 7.7 line under a
beta-test feature flag, SpringSaLaD is now enabled across all VCell
deployments and appears in the standard application workflow alongside
ODE, stochastic, and PDE modalities — with a complete authoring
environment, multi-run simulation on the compute cluster via SLURM
array submission, and batch-results visualization.

Citation. Michalski PJ, Loew LM. SpringSaLaD: A Spatial,
Particle-Based Biochemical Simulation Platform with Excluded Volume.
Biophys J. 2016;110(3):523–529.
doi:10.1016/j.bpj.2015.12.026
· PMID: 26840718

What's in this build (8.0.0.03)

Patch release on the 8.0.0 line accompanying the SpringSaLaD GA
public release event:

• BioNetGen BNGL preprocessor — rewrites tilde-prefixed bare
  digits to the ~s<digit> form during preprocessing
  (e.g. ~0 → ~s0), resolving a parser ambiguity with state
  labels. (#1698)

What's in the 8.0.0 line so far

Aggregated across builds 8.0.0.01 / 8.0.0.02 / 8.0.0.03:

SpringSaLaD modeling — generally available

• Structural Sites. Anchor points within a molecule with
  positions in space, distinct from molecular components — useful
  for representing rigid scaffolds, junction points, and other
  geometric features that constrain molecular geometry without
  participating in reactions.
• Multi-run simulations. Specify number of trials and random
  seed for a Langevin simulation. Concurrent runs dispatched as
  SLURM array jobs on the compute cluster; batch results transfer
  back to the desktop client automatically. Default 20 trials,
  max 200; concurrent jobs capped at 20.
• Batch results visualization. Plots and tables for general
  statistics (average, min/max, standard deviation) and cluster
  analysis (ACS, SD, ACO) across multi-run results.
• Redesigned SpringSaLaD interface. Molecular-structure
  properties panel with editable links, tables for site attributes
  and links, large-shape site representation. (Most of this UI
  work rolled in during the 7.7 line and is now visible to all
  users.)
• Result filtering and physical-limit checks. Trivial-data
  result sets highlighted; site size, diffusion rate, and partition
  size validated before submission.
• Stricter integrator filtering — solver-choice dropdowns hide
  integrators unsuitable for SpringSaLaD applications.

Other 8.0.0 line additions

• Plot Options dialog for finer control over plot appearance
  across visualization panels (line colors, marker styles, axes,
  legends).
• Quick Run guardrails for Langevin — the "Quick Run" workflow
  now refuses multi-job Langevin configurations with an explicit
  error message rather than letting them launch and fail later in
  a non-obvious place.
• admincli report subcommand kit producing period-bounded
  NIH-RPPR-style usage reports — counts of new users, simulation
  jobs in the database, cumulative metrics as-of a given date, and
  CSV export of active users.

Improvements

• Langevin simulation-options dialog enforces the invariant that
  concurrent jobs cannot exceed total jobs, and clamps both to
  sensible maximum values.

API and integration

• REST API surface in 8.0.0 is unchanged from the final 7.7
  builds. No client migration is required for 8.0.0.
• /api/v1/ (Quarkus) endpoints coexist with legacy /api/v0/.
  New client work should target /api/v1/.
• OIDC authentication via Auth0 is required for /api/v1/.
• OpenAPI spec at tools/openapi.yaml.

Bug fixes inherited from late-7.7

The 8.0.0 line inherits the stability work shipped at the end of
the 7.7 line — JMS failover watchdog, OOM exit handler, DNS
negative-cache fix, charset-aware Oracle CLOB reads, and a
thread-safety fix in unit-of-measurement formatting.

Full release notes

• End-user narrative: release-notes/major/8.0.0.md
• Per-build engineer-track log: CHANGELOG.md
• Versioning and release conventions: docs/RELEASING.md
• Bridge from VCell 7.6 → 8.0.0 (three named 7.7 release events): release-notes/major/7.7.md

Known issues

None at release time. Please report issues at
https://github.com/virtualcell/vcell/issues.

---

Full Changelog: 8.0.0.02...8.0.0.03

8.0.0.02

What's Changed

• Simulation Options by @danv61 in #1695

Full Changelog: 8.0.0.01...8.0.0.02

8.0.0.01

What's Changed

• Add Structural Sites to SpringSaLaD
• Add admincli report toolkit for period-bounded usage reports by @jcschaff in #1690
• Plot Options Dialog by @danv61 in #1691
• SpringSaLaD is enabled by default by @danv61 in #1693

Full Changelog: 7.7.0.78...8.0.0.01

7.7.0.78

What's Changed

• Dan ss structural sites by @danv61 in #1685

Full Changelog: 7.7.0.77...7.7.0.78

7.7.0.77

What's Changed

• Don't cache failed DNS lookups in the desktop client by @jcschaff in #1684

Full Changelog: 7.7.0.76...7.7.0.77

7.7.0.76

What's Changed

• Add /loki-query slash command for VCell log access by @jcschaff in #1680
• Exit JVM and dump heap on OutOfMemoryError for server containers by @jcschaff in #1683
• Document direct kubectl logs as fallback for /loki-query by @jcschaff in #1682
• Add JmsFailoverWatchdog and bound failover reconnect by @jcschaff in #1681

Full Changelog: 7.7.0.75...7.7.0.76

7.7.0.75

What's Changed

• Tooling for support-email log processing and triage by @jcschaff in #1670
• Fix Oracle CLOB read: charset-aware character stream by @jcschaff in #1679
• Use UTF-8 explicitly when reading SBML/SED-ML XML by @jcschaff in #1676
• Validate XML chars in name and sbmlName setters by @jcschaff in #1677
• Add scan-xml-control-chars admin CLI by @jcschaff in #1678

Full Changelog: 7.7.0.74...7.7.0.75