Diego Jahn | Searcharxiv

arXiv2026

Morpheus.AI: agents autonomously generate, execute and refine virtual tissue models

Virtual tissue models link observations to mechanistic hypotheses, but building them demands expertise in biology, mathematics and programming. Here, large language model (LLM) agents paired with the simulator Morpheus (Morpheus.AI) autonomously built such models from fifteen benchmark studies, five without a published model. With a frontier LLM, agents that ran their simulations met 83-86% of study-specific criteria in under two hours and for under US\$4 per model. Such agents could make in silico modeling routine.

q-bio.QM↗

arXiv2022

BioSimulators: a central registry of simulation engines and services for recommending specific tools

Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, because the numerous formats and methods for simulating various subsystems and scales remain siloed by different software tools. For example, each tool must be executed through a distinct interface. To help investigators find and use simulation tools, we developed BioSimulators (https://biosimulators.org), a central registry of the capabilities of simulation tools and consistent Python, command-line, and containerized interfaces to each version of each tool. The foundation of BioSimulators is standards, such as CellML, SBML, SED-ML, and the COMBINE archive format, and validation tools for simulation projects and simulation tools that ensure these standards are used consistently. To help modelers find tools for particular projects, we have also used the registry to develop recommendation services. We anticipate that BioSimulators will help modelers exchange, reproduce, and combine simulations.

q-bio.QM↗