BioOS: A Gene-Driven Digital Twin Runtime for Emergent Plant Development

Predicting plant mutant phenotypes requires models that connect gene regulation to organ-scale morphogenesis without collapsing mechanism into phenomenological rules. We present BioOS, a curated mechanistic runtime built around the Formal Cell, a minimal signal-processing abstraction in which promoter evaluation, transcription, translation, and protein state drive cell division, differentiation, and elongation. A multi-scale architecture combining TissueUnits and FormalCells enables real-time simulation of bounded Arabidopsis thaliana developmental programs while keeping the primary claim anchored in primary-root auxin transport. On the official five-case root-auxin benchmark, BioOS achieves a 75.4% mean score, 5/5 qualitative matches, 5/5 quantitative passes, and Spearman severity correlation {rho} = 0.70. The deployed auxin slice uses a curated 35-gene registry; for readability, this manuscript details an 18-gene core subnetwork. Beyond the primary auxin claim, the same runtime closes official cytokinin (5/5), flowering (5/5), and photosynthesis (7/7) gates, while a candidate root-patterning panel passes 8/8. BioOS should therefore be read as a benchmark-validated runtime for bounded developmental prediction rather than as a single-slice demonstration. O_TEXTBOXKey Resulty ResultsThe following results summarize the current validation status of BioOS on the primary-root auxin slice and its surrounding benchmark framework: O_LI35-gene root-auxin runtime, with an 18-gene core GRN illustrated here C_LIO_LIEmergent division, differentiation, elongation from gene expression C_LIO_LIOfficial auxin panel closed: 5/5 qualitative matches, 5/5 full passes, 75.4% mean score, {rho} = 0.70 severity ranking C_LIO_LIFour official gates closed in one runtime: root_auxin 5/5, cytokinin 5/5, flowering 5/5, photosyn-thesis 7/7 C_LIO_LIBroader benchmark corpus: 6 suites / 63 cases; the 8-case candidate root-patterning panel currently passes 8/8 C_LIO_LIReal-time capable: 175 TissueUnits + 200 cells = 8 ms/tick C_LI C_TEXTBOX