Related papers: PhysiBoSS-Models: A database for multiscale models
Simulation models are an absolute necessity in the human and social sciences, which can only very exceptionally use experimental science methods to construct their knowledge. Models enable the simulation of social processes by replacing the…
Background: Simulated nucleotide or amino acid sequences are frequently used to assess the performance of phylogenetic reconstruction methods. BEAST, a Bayesian statistical framework that focuses on reconstructing time-calibrated molecular…
With the growth of large language models, now incorporating billions of parameters, the hardware prerequisites for their training and deployment have seen a corresponding increase. Although existing tools facilitate model parallelization…
Systems Biology has emerged in the last years as a new holistic approach based on the global understanding of cells instead of only being focused on their individual parts (genes or proteins), to better understand the complexity of human…
Agent-based modeling is a powerful simulation technique to understand the collective behavior and microscopic interaction in complex financial systems. Recently, the concept for determining the key parameters of the agent-based models from…
PhysioZoo is a collaborative platform designed for the analysis of continuous physiological time series. The platform currently comprises four modules, each consisting of a library, a user interface, and a set of tutorials: (1) PhysioZoo…
Physiological whole-body models are valuable tools for the development of novel drugs where understanding the system aspects is important. This paper presents a generalized model that encapsulates the structure and flow of whole-body human…
The stochastic simulation of large-scale biochemical reaction networks is of great importance for systems biology since it enables the study of inherently stochastic biological mechanisms at the whole cell scale. Stochastic Simulation…
The rapid growth of scientific software has created practical barriers for bioinformatics research. Although powerful statistical, artificial intelligence (AI)-based methods are now widely available, their effective use is often hindered by…
We present a topology grounded, multiscale simulation platform for morphogenesis and biological active matter. Morphogenesis and biological active matter represent keystone problems in biology with additional, far-reaching implications…
The simulation of morphogenetic problems requires the simultaneous and coupled simulation of signalling and tissue dynamics. A cellular resolution of the tissue domain is important to adequately describe the impact of cell-based events,…
The proliferation of physiological sensors opens new opportunities to explore interactions, conduct experiments and evaluate the user experience with continuous monitoring of bodily functions. Commercial devices, however, can be costly or…
We introduce a model for describing the dynamics of large numbers of interacting cells. The fundamental dynamical variables in the model are sub-cellular elements, which interact with each other through phenomenological intra- and…
Computer models of humans are ubiquitous throughout computer animation and computer vision. However, these models rarely represent the dynamics of human motion, as this requires adding a complex layer that solves body motion in response to…
Biologists are increasingly using databases for storing and managing their data. Biological databases typically consist of a mixture of raw data, metadata, sequences, annotations, and related data obtained from various sources. Current…
We describe a framework that can integrate prior physical information, e.g., the presence of kinematic constraints, to support data-driven simulation in multi-body dynamics. Unlike other approaches, e.g., Fully-connected Neural Network…
Astronomy produces extremely large data sets from ground-based telescopes, space missions, and simulation. The volume and complexity of these rich data sets require new approaches and advanced tools to understand the information contained…
A formal but intuitive framework is introduced to bridge the gap between data obtained from empirical studies and that generated by agent-based models. This is based on three key tenets. Firstly, a simulation can be given multiple formal…
Boolean networks have long been used as models of molecular networks and play an increasingly important role in systems biology. This paper describes a software package, Polynome, offered as a web service, that helps users construct Boolean…
The genome-scale metabolic model with protein constraint (PC-model) has been increasingly popular for microbial metabolic simulations. We present PROSO Toolbox, a unified and simple-to-use PC-model toolbox that takes any high-quality…