Related papers: SIMMUNE, a tool for simulating and analyzing immun…
Enabling users to create their own simulations offers a powerful way to study team dynamics and performance. We introduce VirTLab, a system that allows researchers and practitioners to design interactive, customizable simulations of team…
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…
Artificial immune systems primarily mimic the adaptive nature of biological immune functions. Their ability to adapt to varying pathogens makes such systems a suitable choice for various robotic applications. Generally, AIS-based robotic…
Motivation: In a predictive modeling setting, if sufficient details of the system behavior are known, one can build and use a simulation for making predictions. When sufficient system details are not known, one typically turns to machine…
We present the MIM calculus, a modeling formalism with a strong biological basis, which provides biologically-meaningful operators for representing the interaction capabilities of molecular species. The operators of the calculus are…
The fundamental understanding of how cells physically interact with each other and their environment is key to understanding their organisation in living tissues. Over the past decades several computational methods have been developed to…
Agent-based simulations, especially those including communication, are complex to model and execute. To help researchers deal with this complexity and to encourage modular and maintainable research software, the Python-based framework mango…
Systems biology approaches to the integrative study of cells, organs and organisms offer the best means of understanding in a holistic manner the diversity of molecular assays that can be now be implemented in a high throughput manner. Such…
Agent-based modelling and simulation offers a new and exciting way of understanding the world of work. In this paper we describe the development of an agent-based simulation model, designed to help to understand the relationship between…
Distributed system as e.g. artificial immune systems, complex adaptive systems, or multi-agent systems are widely used in Computer Science, e.g. for network security, optimisations, or simulations. In these systems, small entities move…
We present DiSH-Sim, a simulator for large discrete models of biological signal transduction pathways, capable of simulating networks with multi-valued elements in both deterministic and stochastic manner. We focus on order of update and…
Recent advances in both theory and computational power have created opportunities to simulate biomolecular processes more efficiently using adaptive ensemble simulations. Ensemble simulations are now widely used to compute a number of…
This paper introduces two ongoing research projects which seek to apply computer modelling techniques in order to simulate human behaviour within organisations. Previous research in other disciplines has suggested that complex social…
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…
Critical infrastructures face demanding challenges due to natural and human-generated threats, such as pandemics, workforce shortages or cyber-attacks, which might severely compromise service quality. To improve system resilience,…
A growing body of research runs human subject evaluations to study whether providing users with explanations of machine learning models can help them with practical real-world use cases. However, running user studies is challenging and…
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…
Natural Immune system plays a vital role in the survival of the all living being. It provides a mechanism to defend itself from external predates making it consistent systems, capable of adapting itself for survival incase of changes. The…
Macrophages function as sentinel, cell-regulatory hubs capable of initiating, perpetuating and contributing to the resolution of an inflammatory response, following their activation from a resting state. Highly complex and varied gene…
In immune system simulation there are two competing simulation approaches: System Dynamics Simulation (SDS) and Agent-Based Simulation (ABS). In the literature there is little guidance on how to choose the best approach for a specific…