Colonization history: stochastic model, mechanism recovery and re-analysis of tandem flow-cell experiments
Year: 2026
Type: software
Abstract: Code, simulation outputs and derived observables for a study of how bacterial colonization history can be attributed to cells or surfaces. A stochastic attachment-division-detachment simulator implements six hypotheses (heterogeneous passive dynamics, residual-cell carryover, adhesive selection, cell history, surface history and both histories) calibrated to a common fresh-cell baseline. The package contains the calibrated factorial comparison, a random-forest mechanism-recovery study over experimental designs, observable extraction and residence-time analyses of the Pseudomonas aeruginosa tandem flow-cell image series of Lee et al. (2018), a pre-specified analysis plan with its deviations log, prospective power calculations, unit tests and an executed reproduction notebook. Derived observables are released under CC BY 4.0 with attribution to the original deposit (doi:10.6084/m9.figshare.5969335); code is released under the MIT licence.
Author: Pereira, Antonio
Institution: Universidade Federal do Pará
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7225327172