merge-v2parca@f79637a [uncommitted changes] ·
eranagmon@LT-0919936 ·
Darwin 24.2.0 arm64 (16 cores) ·
Python 3.12.9
2026-04-16 08:08 ·
Simulation pipeline · process-bigraph Composite.run()
v2ecoli is a whole-cell E. coli model running natively on
process-bigraph.
This report covers the simulation phase: building the online
model from a pre-fitted sim_data, running a single cell to
division, and continuing into daughter simulations.
The upstream ParCa (Parameter Calculator) that produces
sim_data from the raw knowledge base is covered in the separate
ParCa Workflow Report.
out/workflow/simData.cPickle)
·
Cache: out/workflow/cache
(27 process configs,
16,321 bulk molecules)
·
ParCa Workflow Report →
| Metric | Value |
|---|---|
| Sim duration | 2200s |
| Wall time | 170s |
| Speed (sim/wall) | 13.0x |
| Final dry mass | 695.6 fg |
| Division reached | Yes |
| Snapshots | 45 |
The Division step uses process-bigraph's native _add/_remove structural
updates. When division is triggered (dry mass ≥ threshold with ≥ 2 chromosomes):
divide_cell() partitions the mother cell's state:
build_document_from_configs() builds complete
cell states with fresh process instances from the divided initial state + cached configsTests run on pre-division state (t=2150s, 2 chromosomes, dry mass 703 fg).
| Molecule | Mother (active) | Daughter 1 | Daughter 2 | Conserved |
|---|---|---|---|---|
| full_chromosome | 2 | 1 | 1 | Yes |
| oriC | 4 | 2 | 2 | Yes |
| chromosome_domain | 7 | 3 | 3 | No |
| active_replisome | 4 | 2 | 2 | Yes |
| promoter | 8364 | 4182 | 4182 | Yes |
| gene | 11622 | 5811 | 5811 | Yes |
| DnaA_box | 812 | 406 | 406 | Yes |
| active_RNAP | 1447 | 722 | 725 | Yes |
| RNA | 7692 | 3818 | 3874 | Yes |
| chromosomal_segment | 0 | 0 | 0 | Yes |
| active_ribosome | 25556 | 12631 | 12925 | Yes |
Two daughter cells from the pre-division state, each run for 1100s (approximately half a generation).
Interactive Cytoscape.js viewer of the composite — stores on the left, processes on the right,
sorted by execution layer. Click a node for math, ports, config; switch layouts from the dropdown.
Full-screen viewer: network.html.
Interactive Cytoscape.js view of the upstream ParCa 9-Step pipeline that
produces sim_data from the raw knowledge base. Stores on the left, Steps on the right;
click a node for ports, class, and docstring.
Full-screen viewer: parca_network.html
· details: ParCa Workflow Report →
| Step | Wall Time | Sim Time | Speed |
|---|---|---|---|
| Model build | 1.07s | — | — |
| Single cell (to division) | 169.7s | 2200s | 13.0x realtime |
| Division split | 0.012s | — | — |
| Daughter simulations | 151.3s | 2200s (2x1100s) | 14.5x realtime |
| Total | 322s | 4400s | — |