v2ecoli reports
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.
Architecture comparisons
- 4-way architecture comparison
— baseline, departitioned, reconciled, biological (pilot).
Mass trajectories, divergence tables, per-architecture state snapshots.
- Three-engine comparison
— vEcoli 1.0 (vivarium), vEcoli 2.0 (composite migration),
v2ecoli (pure process-bigraph). Overlay plots and wall-time benchmarks.
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.
Cell lifecycle
- Workflow report
— full single-cell lifecycle: mother grown to division, then
both daughters run for half a generation. Mass, growth, ppGpp,
chromosome state, and process-bigraph network view.
- Multigeneration report
— single-lineage simulation across a configurable number of
generations. Each cell runs to division, one daughter is kept, and
the process repeats. Mass trajectories plotted end-to-end with
generation boundaries.
Colony simulation
- Colony report
— one whole-cell E. coli embedded in a 2D colony of
adder-kinetics surrogates, with synced colony and chromosome animations.
Composition graphs
Reports are generated by scripts in the reports/
directory: compare_report.py, v1_v2_report.py,
colony_report.py, workflow_report.py,
multigeneration_report.py, network_report.py,
and benchmark_report.py.