Related papers: Computer algebra in systems biology
This paper proposes a new method to reverse engineer gene regulatory networks from experimental data. The modeling framework used is time-discrete deterministic dynamical systems, with a finite set of states for each of the variables. The…
Symmetry principles play an important role in geometry, and physics, allowing for the reduction of complicated systems to simpler, more comprehensible models that preserve the system's features of interest. Biological systems are often…
A disconcerting ramification of water pollution caused by burgeoning populations, rapid industrialization and modernization of agriculture, has been the exponential increase in the incidence of algal growth across the globe. Harmful algal…
Ever increasing computational power will require methods for automatic programming. We present an alternative to genetic programming, based on a general model of thinking and learning. The advantage is that evolution takes place in the…
Modern biological tools have made it possible to unequivocally demonstrate the deep relationship among species in terms of genes and basic molecular mechanisms. In addition, results from genetic, physical and physiological approaches…
Microbes are essentially yet convolutedly linked with human lives on the earth. They critically interfere in different physiological processes and thus influence overall health status. Studying microbial species is used to be constrained to…
We explore the commonalities between methods for assuring the security of computer systems (cybersecurity) and the mechanisms that have evolved through natural selection to protect vertebrates against pathogens, and how insights derived…
With increased access to data and the advent of computers, the use of statistical tools and numerical simulations is becoming commonplace for ecologists. These approaches help improve our understanding of ecological phenomena and their…
Organic Computing is an initiative in the field of systems engineering that proposed to make use of concepts such as self-adaptation and self-organisation to increase the robustness of technical systems. Based on the observation that…
Biomolecular computers, along with quantum computers, may be a future alternative for traditional, silicon-based computers. Main advantages of biomolecular computers are massive parallel processing of data, expanded capacity of storing…
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…
Biological systems are generally complicated and/or complex. In the former approach, one sets up a model with a large number of parameters to describe the system in detail. The latter approach focuses on understanding the universal aspects…
Innovation in synthetic biology often still depends on large-scale experimental trial-and-error, domain expertise, and ingenuity. The application of rational design engineering methods promise to make this more efficient, faster, cheaper…
Characterizing structural and dynamic properties of proteins and large macromolecular assemblies is crucial to understand the molecular mechanisms underlying biological functions. In the field of Structural Biology, no single method…
We demonstrate how methods in Functional Programming can be used to implement a computer algebra system. As a proof-of-concept, we present the computational-algebra package. It is a computer algebra system implemented as an embedded…
It has been a long time that computer architecture and systems are optimized for efficient execution of machine learning (ML) models. Now, it is time to reconsider the relationship between ML and systems, and let ML transform the way that…
The BIOSCAN project, led by the International Barcode of Life Consortium, seeks to study changes in biodiversity on a global scale. One component of the project is focused on studying the species interaction and dynamics of all insects. In…
We describe several techniques for using bulk matter for special purpose computation. In each case it is necessary to use an evolutionary algorithm to program the substrate on which the computation is to take place. In addition, the…
Biological processes underlying the basic functions of a cell involve complex interactions between genes. From a technical point of view, these interactions can be represented through a graph where genes and their connections are,…
Whole-cell computational models aim to predict cellular phenotypes from genotype by representing the entire genome, the structure and concentration of each molecular species, each molecular interaction, and the extracellular environment.…