Related papers: Computer algebra in systems biology
A primary motivation for our research in digital ecosystems is the desire to exploit the self-organising properties of biological ecosystems. Ecosystems are thought to be robust, scalable architectures that can automatically solve complex,…
Machine learning is a modern approach to problem-solving and task automation. In particular, machine learning is concerned with the development and applications of algorithms that can recognize patterns in data and use them for predictive…
Biological systems and processes are networks of complex nonlinear regulatory interactions between nucleic acids, proteins, and metabolites. A natural way in which to represent these interaction networks is through the use of a graph. In…
Many forms of programmable matter have been proposed for various tasks. We use an abstract model of self-organizing particle systems for programmable matter which could be used for a variety of applications, including smart paint and…
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…
In this paper, by way of three examples - a fourth order low pass active RC filter, a rudimentary BJT amplifier, and an LC ladder - we show, how the algebraic capabilities of modern computer algebra systems can, or in the last example,…
Understanding the behaviour of biological systems requires a complex setting of in vitro and in vivo experiments, which attracts high costs in terms of time and resources. The use of mathematical models allows researchers to perform…
This article is a review of analytical performance modeling for computer systems. It discusses the motivation for this area of research, examines key issues, introduces some ideas, illustrates how it is applied, and points out a role that…
The last decade has witnessed a surge of theoretical and computational models to describe the dynamics of complex gene regulatory networks, and how these interactions can give rise to multistable and heterogeneous cell populations. As the…
In most of the cases, the experimental study of Nanotechnology involves high cost for Laboratory set-up and the experimentation processes were also slow. So, one cannot rely on experimental nanotechnology alone. As such, the Computer-Based…
This paper aims at identifying emerging computational intelligence trends for the design and modeling of complex biometric-enabled infrastructure and systems. Biometric-enabled systems are evolving towards deep learning and deep inference…
The traditional methods of the biology, based on illustrative descriptions and linear logic explanations, are discussed. This work aims to improve this approach by introducing alternative tools to describe and represent complex biological…
This article is devoted to applications of projection operators to simulate phenomenological properties of the molecular-genetic code system. Oblique projection operators are under consideration, which are connected with matrix…
The genetic blueprint for the essential functions of life is encoded in DNA, which is translated into proteins -- the engines driving most of our metabolic processes. Recent advancements in genome sequencing have unveiled a vast diversity…
Computer algebra systems are a great help for mathematical research but sometimes unexpected errors in the software can also badly affect it. As an example, we show how we have detected an error of Mathematica computing determinants of…
An astonishingly diverse biomolecular circuitry orchestrates the functioning machinery underlying every living cell. These biomolecules and their circuits have been engineered not only for various industrial applications but also to perform…
Biological systems, from a cell to the human brain, are inherently complex. A powerful representation of such systems, described by an intricate web of relationships across multiple scales, is provided by complex networks. Recently, several…
A supervisory controller controls and coordinates the behavior of different components of a complex machine by observing their discrete behaviour. Supervisory control theory studies automated synthesis of controller models, known as…
Biological organisms are composed of numerous interconnected biochemical processes. Diseases occur when normal functionality of these processes is disrupted. Thus, understanding these biochemical processes and their interrelationships is a…
Recent tumor genome sequencing confirmed that one tumor often consists of multiple cell subpopulations (clones) which bear different, but related, genetic profiles such as mutation and copy number variation profiles. Thus far, one tumor has…