Related papers: PhysiBoSS-Models: A database for multiscale models
Developing complex biomolecular workflows is not always straightforward. It requires tedious developments to enable the interoperability between the different biomolecular simulation and analysis tools. Moreover, the need to execute the…
Agent-based modeling plays an essential role in gaining insights into biology, sociology, economics, and other fields. However, many existing agent-based simulation platforms are not suitable for large-scale studies due to the low…
Many biological phenomena are inherently multiscale, i.e. they are characterized by interactions involving different spatial and temporal scales simultaneously. Though several approaches have been proposed to provide "multilayer" models,…
Biological regulatory networks can be represented by computational models, which allow the study and analysis of biological behaviours, therefore providing a better understanding of a given biological process. However, as new information is…
The practical utility of agent-based models in decision-making relies on their capacity to accurately replicate populations while seamlessly integrating real-world data streams. Yet, the incorporation of such data poses significant…
Multiscale models allow for the treatment of complex phenomena involving different scales, such as remodeling and growth of tissues, muscular activation, and cardiac electrophysiology. Numerous numerical approaches have been developed to…
Probabilistic Boolean networks (PBNs) is an important mathematical framework widely used for modelling and analysing biological systems. PBNs are suited for modelling large biological systems, which more and more often arise in systems…
Like other types of computational research, modeling and simulation of biological processes (biomodels) is still largely communicated without sufficient detail to allow independent reproduction of results. But reproducibility in this area…
Modelling and computational methods have been essential in advancing quantitative science, especially in the past two decades with the availability of vast amount of complex, voluminous, and heterogeneous data. In particular, there has been…
A complex system is made up of many components with many interactions. So the design of systems such as simulation systems, cooperative systems or assistance systems includes a very accurate modelling of interactional and communicational…
phyloDB is a modular and extensible framework for large-scale phylogenetic analyses, which are essential for understanding epidemics evolution. It relies on the Neo4j graph database for data storage and processing, providing a schema and an…
Physiologically Based Pharmacokinetic (PBPK) modeling is a cornerstone of model-informed drug development (MIDD), providing a mechanistic framework to predict drug absorption, distribution, metabolism, and excretion (ADME). Despite its…
This paper proposes a model which aim is providing a more coherent framework for agents design. We identify three closely related anthropo-centered domains working on separate functional levels. Abstracting from human physiology,…
Recent advances in large language models (LLMs) have opened new avenues for applying multi-agent systems in very large-scale simulations. However, there remain several challenges when conducting multi-agent simulations with existing…
Animal cells are both encapsulated and subdivided by lipid bilayer membranes. Beyond just acting as boundaries, these membranes' shapes influence the function of cells and their compartments. Physically, membranes are two-dimensional fluids…
Using a Multi-agent systems paradigm, the present project develops, validates and exploits a computational $\textit{testbed}$ that simulates micro-biological complex systems, namely the aggregation patterns of the social amoeba…
We present an approach of using AI to model and simulate biology and life. Why is it important? Because at the core of medicine, pharmacy, public health, longevity, agriculture and food security, environmental protection, and clean energy,…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…
We present RoboManipBaselines, an open-source software framework for imitation learning research in robotic manipulation. The framework supports the entire imitation learning pipeline, including data collection, policy training, and…
Reliable contact simulation plays a key role in the development of (semi-)autonomous robots, especially when dealing with contact-rich manipulation scenarios, an active robotics research topic. Besides simulation, components such as…