Related papers: Foundations of a Compositional Systems Biology
Engineering methodologies predominantly revolve around established principles of decomposition and recomposition. These principles involve partitioning inputs and outputs at the component level, ensuring that the properties of individual…
Cellular Agent-Based Models are commonly employed to describe a variety biological systems. Over the course of the past years, many modeling tools have emerged which solve particular research questions. In this short opinion piece, we argue…
The implications of large-scale coherence in biological systems and possible links to quantum theory are only beginning to be explored. Whether quantum-like coherent phenomena are relevant, or even possible at all, at the high temperatures…
Experience in the physical sciences suggests that the only realistic means of understanding complex systems is through the use of mathematical models. Typically, this has come to mean the identification of quantitative models expressed as…
Metabolism displays striking and robust regularities in the forms of modularity and hierarchy, whose composition may be compactly described. This renders metabolic architecture comprehensible as a system, and suggests the order in which…
The discipline of `theoretical biology' has been developing from its inception several decades ago almost in parallel with the advances in biology, so much so that the latter is often considered to be almost exclusively an empirical…
Modular structure is pervasive in many complex networks of interactions observed in natural, social and technological sciences. Its study sheds light on the relation between the structure and function of complex systems. Generally speaking,…
Self-organisation of individuals within large collectives occurs throughout biology. Mathematical models can help elucidate the individual-level mechanisms behind these dynamics, but analytical tractability often comes at the cost of…
In bacterial populations, cells are able to cooperate in order to yield complex collective functionalities. Interest in population-level cellular behaviour is increasing, due to both our expanding knowledge of the underlying biological…
Using bioimaging technology, biologists have attempted to identify and document analytical interpretations that underlie biological phenomena in biological cells. Theoretical biology aims at distilling those interpretations into knowledge…
We argue for a convergence of crystallography, materials science and biology, that will come about through asking materials questions about biology and biological questions about materials, illuminated by considerations of information. The…
Exchange of biochemical substances is essential way in establishing communication between bacterial cells. It is noticeable that all phases of the process are heavily influenced by perturbations of either internal or external parameters.…
Networked systems are systems of interconnected components, in which the dynamics of each component are influenced by the behavior of neighboring components. Examples of networked systems include biological networks, critical…
Complementarity among species with different traits is one of the basic processes affecting biodiversity, defined as the number of species in the ecosystem. We present here a soluble model ecosystem in which the species are characterized by…
The compositionality and sparsity of high-throughput sequencing data poses a challenge for regression and classification. However, in microbiome research in particular, conditional modeling is an essential tool to investigate relationships…
The physiological tradition of biological research analyzes biological systems using reduced descriptions much as an engineer uses a 'black box' description of an amplifier. Simple models have been used by physiologists for a very long…
Cellular heterogeneity is an immanent property of biological systems that covers very different aspects of life ranging from genetic diversity to cell-to-cell variability driven by stochastic molecular interactions, and noise induced cell…
Many of life's most fascinating phenomena emerge from interactions among many elements--many amino acids determine the structure of a single protein, many genes determine the fate of a cell, many neurons are involved in shaping our thoughts…
Complex systems are fascinating because their rich macroscopic properties emerge from the interaction of many simple parts. Understanding the building principles of these emergent phenomena in nature requires assessing natural complex…
Software production research is quickly evolving on two parallel approaches: conventional and bio-inspired. The bio-inspired approaches are generally developed and presented as enhancements of the conventional ones. However the conventional…