v2ecoli reports

vEcoli, reimagined as a composable process-bigraph whole-cell model and research workspace.

Each report opens with a Run provenance banner showing the date (Eastern time), git commit, host, and Python version at the time of generation. Checked-in copies reflect the run whose output is live on this page.

📑 Investigation reports

Self-contained, reviewable write-ups of each research question (build → simulate → evaluate → decide), with embedded charts and an inline GitHub-issue feedback widget.

Colony & Microfluidic Phenotype Quantification in progress

Does whole-cell E. coli phenotype survive colony embedding, and match microfluidic-device data, across a cost/fidelity ladder of cell models? Runs N whole-cell (or cheaper) agents in one pymunk 2D device geometry and measures a shared phenotype panel (growth rate, size-at-division, added length,…

8 studies

Multiscale Complexity in a Whole-Cell E. coli planning

A biology-forward discovery showcase across three scales of the v2ecoli whole-cell model, framed around a single question a modeler actually faces: when the model disagrees with biology, is the gap already-correct, structural, or fixable — and how do you tell without fooling yourself? Each arc ru…

11 studies

v2ecoli Baseline Showcase: from ecoli-sources to a calibrated whole cell active

A demonstration walkthrough of the v2ecoli pipeline: ecoli-sources to ParCa to a calibrated baseline to a perturbation to a next-direction decision. Six studies rebuild the ParCa in full, run the wild-type baseline ensemble (multiseed/multigen, checked against doubling time, mass fractions, Toya…

6 studies

v2ecoli → PDMP Whole-Cell Model Reformulation in progress

Incrementally transforms v2ecoli from a hybrid algorithmic whole-cell model into a piecewise-deterministic Markov process. Six phases each swap one WCM component -- characterization, a metabolism ODE, jump processes, an inference layer, a compiled runtime, and causal discovery -- while leaving th…

6 studies

Whole-Cell Model Comparison —

Does v2ecoli reproduce vEcoli across nutrient conditions when both engines swap FBA Metabolism for MetabolismRedux? Five studies (basal, with_aa, succinate, no_oxygen, acetate) run both engines from matched ParCa initial states, single generation, 6 seeds requested per condition (5 effective vEco…

12 studies

🔬 Interactive model viewer

Composite viewers hub — every curated composite (baseline, biological, Millard FBA bridge, colony, reactor–bird coupling) as an interactive bigraph: open each in bigraph-loom (pan/zoom, expand store chips, inspect port schemas with units and formal process descriptions), bigraph-viz2 (lightweight interactive), or a static bigraph-viz diagram.
Mathematical structure — the formal mathematical structure of each process (state variables and update rules), e.g. chromosome replication initiate/elongate/terminate.

Engine comparison

Composite comparison — the default engine comparison. Thorough multi-engine run of vEcoli, the v2ecoli baseline, and the millard_fba_bridge_harness over a full division cycle: per-step runtime (mean/median/p95 + peak RSS), divergence-verdict badges and shared-axis behavioral overlays for every observable, FBA-bridge flux-pin diagnostics, and a per-reaction flux divergence deep-dive (which metabolic pathways carry different flux between engines).
vEcoli vs v2ecoli (legacy 2-way) — the older fixed two-engine report: wall-time benchmarks and mass/growth trajectories. Superseded by the Composite comparison above.

ParCa

ParCa workflow report — merged nine-Step ParCa pipeline run. Per-step runtimes, port manifests, raw-data (flat TSV) stats, and distribution overlays vs vEcoli reference where intermediates are available.
ecoli-sources bundle — ParCa input data sources pulled from the ecoli-sources package (reconstruction flat files); real ParCa output plus a multi-ParCa demo (operons on/off).

Composition graphs

Baseline (partitioned) — the current single-cell baseline model.
ParCa pipeline — upstream 9-Step ParCa composite that produces sim_data.

Reports are generated by scripts in the reports/ directory: v1_v2_report.py, colony_report.py, workflow_report.py, multigeneration_report.py, and network_report.py. Source: vivarium-collective/v2ecoli.