ArticleBMC bioinformatics2025
Start & Stop: a PhysiCell and PhysiBoSS 2.0 add-on for interactive simulation control.
Article in BMC bioinformatics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
1 citing paper in PubMed.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
In computational biology, in silico simulators are vital for exploring and understanding the behavior of complex biological systems. Hybrid multi-level simulators, such as PhysiCell and PhysiBoSS 2.0, integrate multiple layers of biological complexity, providing deeper insights into emergent patterns. However, one key limitation of these simulators is the inability to adjust simulation parameters once the simulation has started, which hinders the interactive exploration and adaptation of dynamic protocols ranging from biofabrication to in vitro pharmacological testing. To address this challenge, we introduce the Start & Stop add-on for PhysiCell and PhysiBoSS 2.0. This add-on offers multi-level state preservation and multi-modal stop control, triggered by simulation time or cell conditions, enabling users to pause a simulation, adjust parameters, and then resume from the exact halted state. We validate Start & Stop using two well-established PhysiBoSS 2.0 use cases, a tumor spheroid 3T3 mouse fibroblasts use case under tumor necrosis factor (TNF) stimulation, and a lung cancer cell line invasion simulation, demonstrating that it preserves the simulator's original behavior while enabling interactive configuration changes that facilitate the exploration of diverse and adaptive treatment strategies. By enhancing flexibility and user interaction, Start & Stop makes PhysiCell and PhysiBoSS 2.0 more akin to real in vitro scenarios, thus expanding the range of potential simulations and advancing more effective protocol development in a variety of applications.
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Identifiers
What Socratic holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.