Related papers: Foundations of a Compositional Systems Biology
Currently, biological signaling is envisaged as a combination of activation and movement, triggered by local molecular interactions and molecular diffusion, respectively. However, we here suggest, that other fundamental physical mechanisms…
Here we introduce a new design framework for synthetic biology that exploits the advantages of Bayesian model selection. We will argue that the difference between inference and design is that in the former we try to reconstruct the system…
Modeling and simulation are recognized as important aspects of the scientific method for more than 70 years but its adoption in biology has been slow. Debates on its representativeness, usefulness, and whether the effort spent on such…
We consider the basic features of complex dynamic and control systems, including systems having hierarchical structure. Special attention is paid to the problems of design and synthesis of complex systems and control models, and to the…
Nowadays, multiscale modelling is recognized as the most suitable way to study biological processes. Indeed, almost every phenomenon in nature exhibits a multiscale behaviour, i.e., it is the outcome of interactions that occur at different…
In computer science, we can theoretically neatly separate transmission and processing of information, hardware and software, and programs and their inputs. This is much more intricate in biology, Nevertheless, I argue that Shannon's concept…
Context-dependent nature of biological phenomena are well documented in every branch of biology. While there have been few previous attempts to (implicitly) model various facets of biological context-dependence, a formal and general…
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,…
Cellular bioelectricity describes the biological phenomenon in which cells in living tissue generate and maintain patterns of voltage gradients induced by differing concentrations of charged ions. A growing body of research suggests that…
The dynamic interplay between collective cell movement and the various molecules involved in the accompanying cell signalling mechanisms plays a crucial role in many biological processes including normal tissue development and pathological…
Compositionality is a key feature of process algebras which is often cited as one of their advantages as a modelling technique. It is certainly true that in biochemical systems, as in many other systems, model construction is made easier in…
In a complex system, the individual components are neither so tightly coupled or correlated that they can all be treated as a single unit, nor so uncorrelated that they can be approximated as independent entities. Instead, patterns of…
Living systems, from single cells to higher vertebrates, receive a continuous stream of non-stationary inputs that they sense, e.g., via cell surface receptors or sensory organs. Integrating these time-varying, multi-sensory, and often…
Synthetic Biology is the new engineering-based approach to biology that includes applications of designing complex biological devices. At present, it is not yet clear what will emerge as the defining principles of Synthetic Biology. One…
A clear definition of system dynamics modeling can provide shared understanding and clarify the impact of the field. We introduce a set of characteristics that define quantitative system dynamics, selected to capture core philosophy,…
How can we build recommender systems to take into account fairness? Real-world recommender systems are often composed of multiple models, built by multiple teams. However, most research on fairness focuses on improving fairness in a single…
The modelling and analysis of biological systems has deep roots in Mathematics, specifically in the field of Ordinary Differential Equations. Alternative approaches based on formal calculi, often derived from process algebras or term…
Composition is an important feature of a specification language, as it enables the design of a complex system in terms of a product of its parts. Decomposition is equally important in order to reason about structural properties of a system.…
We discuss the relevance of studying ecology within the framework of Complexity Science from a statistical mechanics approach. Ecology is concerned with understanding how systems level properties emerge out of the multitude of interactions…
Information flow provides a natural measure for the causal interaction between dynamical events. This study extends our previous rigorous formalism of componentwise information flow to the bulk information flow between two complex…