Related papers: Simulation in Biology
Biology-derived algorithms are an important part of computational sciences, which are essential to many scientific disciplines and engineering applications. Many computational methods are derived from or based on the analogy to natural…
This series presents an approach to mathematical biology which makes precise the function of biological molecules. Because biological systems compute, the theory is a general purpose computer language. I build a language for efficiently…
Dynamics of biological-ecological systems is strongly depending on spatial dimensions. Most of powerful simulators in ecology take into account for system spatiality thus embedding stochastic processes. Due to the difficulty of researching…
The article describes the method of using computer-learning tools during the modeling of biological processes in the high school. The author developed web pages for online processing of the results of simulation of the genetic structure of…
Computational reproducibility of scientific results, that is, the execution of a computational experiment (e.g., a script) using its original settings (data, code, etc.), should always be possible. However, reproducibility has become a…
As computer scientists working in bioinformatics/computational biology, we often face the challenge of coming up with an algorithm to answer a biological question. This occurs in many areas, such as variant calling, alignment, and assembly.…
Computer modelling for evolutionary systems consists in: 1) to store in the memory the individual features of each member of a large population; and 2) to update the whole system repeatedly, as time goes by, according to some prescribed…
Those seeking to reproduce a computational experiment often need to manually look at the code to see how to build necessary libraries, configure parameters, find data, and invoke the experiment; it is not automatic. Automatic…
Like other types of computational research, modeling and simulation of biological processes (biomodels) is still largely communicated without sufficient detail to allow independent reproduction of results. But reproducibility in this area…
Recent research has extended methods from the fields of thermodynamics and statistical mechanics into other disciplines. Most notably, one recent work creates a unified theoretical framework to understand evolutionary biology, machine…
At the frontier of most areas in science, computer simulations play a central role. The traditional division of natural science into experimental and theoretical investigations is now completely outdated. Instead, theory, simulation, and…
Simulation especially real-time simulation have been widely used for the design and testing of real-time systems. The advancement of simulation tools has largely attributed to the evolution of computing technologies. With the reduced cost…
We present an XML-based simulation authoring environment. The proposed description language allows to describe mathematical objects such as systems of ordinary differential equations, partial differential equations in two dimensions, or…
Unlike computation or the numerical analysis of differential equations, simulation does not have a well established conceptual and mathematical foundation. Simulation is an arguable unique union of modeling and computation. However,…
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…
Computational modeling plays an essential role in the study of language emergence. It aims to simulate the conditions and learning processes that could trigger the emergence of a structured language within a simulated controlled…
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…
Computation, the use of a computer to solve, simulate, or visualize a physical problem, has revolutionized how physics research is done. Computation is used widely to model systems, to simulate experiments, and to analyze data. Yet, in most…
The drive for reproducibility in the computational sciences has provoked discussion and effort across a broad range of perspectives: technological, legislative/policy, education, and publishing. Discussion on these topics is not new, but…
Programming languages are engineered languages that allow to instruct a machine and share algorithmic information; they have a great influence on the society since they underlie almost every information technology artefact, and they are at…