Related papers: Foundations of a Compositional Systems Biology
The applicability of computational models to the biological world is an active topic of debate. We argue that a useful path forward results from abandoning hard boundaries between categories and adopting an observer-dependent, pragmatic…
Nearly all cell models explicitly or implicitly deal with the biophysical constraints that must be respected for life to persist. Despite this, there is almost no systematicity in how these constraints are implemented, and we lack a…
A main challenge of data-driven sciences is how to make maximal use of the progressively expanding databases of experimental datasets in order to keep research cumulative. We introduce the idea of a modeling-based dataset retrieval engine…
Significant advances have been made in artificial systems by using biological systems as a guide. However, there is often little interaction between computational models for emergent communication and biological models of the emergence of…
The standard assumptions that underlie many conceptual and quantitative frameworks do not hold for many complex physical, biological, and social systems. Complex systems science clarifies when and why such assumptions fail and provides…
A notion of biologic system or just a system implies a functional wholeness of comprising system components. Positive and negative feedback are the examples of how the idea to unite anatomical elements in the whole functional structure was…
Mathematical models are increasingly used in both academia and the pharmaceutical industry to understand how phenotypes emerge from systems of molecular interactions. However, their current construction as monolithic sets of equations…
In a multi-modeling based approach, the system under development is described by several models that represent various perspectives and concerns. Obviously, these partial representations are less complex than the global model, but they need…
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…
Throughout the evolution of biological species on Earth, cells and organs have developed many complex structures and processes to ensure their interactions with individual chemical molecules (small and macromolecular) and nanoscale objects…
A vast array of transformative technologies developed over the past decade has enabled measurement and perturbation at ever increasing scale, yet our understanding of many systems remains limited by experimental capacity. Overcoming this…
Assuring the correct behavior of cyber-physical systems requires significant modeling effort, particularly during early stages of the engineering and design process when a system is not yet available for testing or verification of proper…
Synthetic biologists have made great progress over the past decade in developing methods for modular assembly of genetic sequences and in engineering biological systems with a wide variety of functions in various contexts and organisms.…
A modeling formalism is proposed for the description and study of living and life-like systems. It provides an abstract conceptual model framework for real life and evolution of biological organisms. It is proposed, that this model…
Compositionality supports the manipulation of large systems by working on their components. For model-based testing, this means that large systems can be tested by modelling and testing their components: passing tests for all components…
Integrative biological simulations have a varied and controversial history in the biological sciences. From computational models of organelles, cells, and simple organisms, to physiological models of tissues, organ systems, and ecosystems,…
As the frontiers of biology become increasingly interdisciplinary, the physics education community has engaged in ongoing efforts to make physics classes more relevant to life sciences majors. These efforts are complicated by the many…
We are entering a new era in which software systems are becoming more and more complex and larger. So, the composition of such systems is becoming infeasible by manual means. To address this challenge, self-organising software models…
In its broadest definition, systems biology is the application of a `systems' way of thinking about and doing cell biology. By implication, this also invites us to consider a systems approach in the context of medicine and the treatment of…
Building multiscale biological models requires integrating independently developed submodels, which involves sharing variables and coordinating execution. Most existing tools focus on isolated mechanisms and numerical methods, but rarely…