Related papers: Computer algebra in systems biology
As dynamic and control systems become more complex, relying purely on numerical computations for systems analysis and design might become extremely expensive or totally infeasible. Computer algebra can act as an enabler for analysis and…
These lectures given to graduate students in theoretical particle physics, provide an introduction to the ``inner workings'' of computer algebra systems. Computer algebra has become an indispensable tool for precision calculations in…
We use the lac operon in Escherichia coli as a prototype system to illustrate the current state, applicability, and limitations of modeling the dynamics of cellular networks. We integrate three different levels of description -molecular,…
This article is intended to an introductory lecture in material physics, in which the modern computational group theory and the electronic structure calculation are in collaboration. The effort of mathematicians in field of the group…
Understanding large molecular networks consisting of entities such as genes, proteins or RNAs that interact in complex ways to drive the cellular machinery has been an active focus of systems biology. Computational approaches have played a…
In the present paper, we describe some experiences in using programming, commands and graphical interfaces based on computer algebra systems, as tools for learning Physics and Mathematics.
Advances in molecular technologies underlie an enormous growth in the size of data sets pertaining to biology and biomedicine. These advances parallel those in the deep learning subfield of machine learning. Components in the differentiable…
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…
Information technologies for studying physical-mathematical disciplines on base of mathematical modeling in the computer algebra system Maple are described.
This dissertation explores the application of machine learning in molecular biology, focusing on gene expression regulation and cellular behavior at the single-cell level. Using modern neural networks, the research addresses key challenges…
Rearrangements of bacterial chromosomes can be studied mathematically at several levels, most prominently at a local, or sequence level, as well as at a topological level. The biological changes involved locally are inversions, deletions,…
We propose a variant of the CCS process algebra with new features aiming at allowing multiscale modelling of biological systems. In the usual semantics of process algebras for modelling biological systems actions are instantaneous. When…
Provided that there is no theoretical frame for complex engineered systems (CES) as yet, this paper claims that bio-inspired engineering can help provide such a frame. Within CES bio-inspired systems play a key role. The disclosure from…
In this survey I should like to introduce some concepts of algebraic geometry and try to demonstrate the fruitful interaction between algebraic geometry and computer algebra and, more generally, between mathematics and computer science. One…
In the past decade computational biology has grown from a cottage industry with a handful of researchers to an attractive interdisciplinary field, catching the attention and imagination of many quantitatively-minded scientists. Of interest…
Single-cell analysis is currently one of the most high-resolution techniques to study biology. The large complex datasets that have been generated have spurred numerous developments in computational biology, in particular the use of…
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…
In this article we highlight chemotaxis (cellular movement) as a rich source of potential engineering applications and computational models, highlighting current research and possible future work. We first give a brief description of the…
In the modern world, technology is at its peak. Different avenues in programming and technology have been explored for data analysis, automation, and robotics. Machine learning is key to optimize data analysis, make accurate predictions,…
Computer algebra systems are complex software systems that cover a wide range of scientific and practical problems. However, the absolute coverage cannot be achieved. Often, it is required to create a user extension for an existing computer…