Related papers: Computer algebra in systems biology
Systems are growing into more complex ones for developing and maintaining. Existing systems which do not have much in common on the first look are connected, due to the technical progress, even if it was never intended that way. It is an…
Computer experiments refer to the study of real systems using complex simulation models. They have been widely used as alternatives to physical experiments. Design and analysis of computer experiments have attracted great attention in past…
Compositionality is a key property for dealing with complexity, which has been studied from many points of view in diverse fields. Particularly, the composition of individual computations (or programs) has been widely studied almost since…
Synthetic Biology is an interdisciplinary field that utilizes well-established engineering principles, ranging from electrical, control and computer systems, for analyzing the biological systems, such as biological circuits, enzymes,…
Researchers in the field of biocomputing have, for many years, successfully "harvested and exploited" the natural world for inspiration in developing systems that are robust, adaptable and capable of generating novel and even "creative"…
Biology is data-rich, and it is equally rich in concepts and hypotheses. Part of trying to understand biological processes and systems is therefore to confront our ideas and hypotheses with data using statistical methods to determine the…
The fields of computing and biology have begun to cross paths in new ways. In this paper a review of the current research in biological computing is presented. Fundamental concepts are introduced and these foundational elements are explored…
Multicellular self-organization drives development in biological organisms, yet a comprehensive theory is lacking as basic properties of cells can complicate common approaches. Framing such properties by dynamic graphs led to new…
Recently, the place of the main programming language for scientific and engineering computations has been little by little taken by Julia. Some users want to work completely within the Julia framework as they work within the Python…
Background: Many biological systems are modeled qualitatively with discrete models, such as probabilistic Boolean networks, logical models, Petri nets, and agent-based models, with the goal to gain a better understanding of the system. The…
One of the most compelling problems in science consists in understanding how living systems process information. After all, the way they process information defines their capacities to learning and adaptation. There is an increasing…
Mathematical modelling is a cornerstone of computational biology. While mechanistic models might describe the interactions of interest of a system, they are often difficult to study. On the other hand, abstract models might capture key…
In the context of superintelligent AI systems, the term "oracle" has two meanings. One refers to modular systems queried for domain-specific tasks. Another usage, referring to a class of systems which may be useful for addressing the value…
In this work, a machine learning approach for identifying the multi-omics metabolic regulatory control circuits inside the pathways is described. Therefore, the identification of bacterial metabolic pathways that are more regulated than…
We survey the notion and history of error-correcting codes and the algorithms needed to make them effective in information transmission. We then give some basic as well as more modern constructions of, and algorithms for, error-correcting…
Composition is a powerful principle for systems biology, focused on the interfaces, interconnections, and orchestration of distributed processes to enable integrative multiscale simulations. Whereas traditional models focus on the structure…
Living systems self-organize in ways that conventional physical frameworks-based on forces, energies, and continuous fields-cannot fully capture. Processes like gene regulation and cellular decision-making involve rule-based logic and…
Just as in eukaryotes, high-throughput chromosome conformation capture (Hi-C) data have revealed nested organizations of bacterial chromosomes into overlapping interaction domains. In this chapter, we present a multiscale analysis framework…
A brief characteristic of the specialized computer algebra system GRG_EC intended for symbolic computations in the field of general relativity is given.
Microorganisms are found in almost every environment, including the soil, water, air, and inside other organisms, like animals and plants. While some microorganisms cause diseases, most of them help in biological processes such as…