v2ecoli Workflow Report

v2ecoli is a whole-cell E. coli model running natively on process-bigraph. It migrates all 55 biological steps from vEcoli to run through the standard Composite.run() pipeline with custom bigraph-schema types for bulk molecules, unique molecules, and listener stores.

This report runs a 7-step pipeline, caching intermediate results for fast re-runs.

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How Division Works

The Division step uses process-bigraph's native _add/_remove structural updates. When division is triggered (dry mass ≥ threshold with ≥ 2 chromosomes):

1. State splitting — divide_cell() partitions the mother cell's state:
   • Bulk molecules: binomial distribution (p=0.5) on each molecule's count
   • Chromosomes: alternating assignment (even→D1, odd→D2) with descendant domain tracking
   • Chromosome-attached molecules: follow their domain
   • RNAs: full transcripts binomial, partial transcripts follow RNAP domain
   • Ribosomes: follow their mRNA
2. Daughter cell construction — build_document_from_configs() builds complete cell states with fresh process instances from the divided initial state + cached configs

Tests run on pre-division state (t=2500s, 2 chromosomes, dry mass 703 fg).

Two daughter cells from the pre-division state, each run for 1275s (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.