Related papers: Design Patterns of Biological Cells
With the completion of human genome mapping, the focus of scientists seeking to explain the biological complexity of living systems is shifting from analyzing the individual components (such as a particular gene or biochemical reaction) to…
Metabolism is a fascinating cell machinery underlying life and disease and genome-scale reconstructions provide us with a captivating view of its complexity. However, deciphering the relationship between metabolic structure and function…
Here we introduce a new design framework for synthetic biology that exploits the advantages of Bayesian model selection. We will argue that the difference between inference and design is that in the former we try to reconstruct the system…
A theoretical study of cell evolution is presented here. By using a toolbox containing an intracellular catalytic reaction network model and a mutation-selection process, four distinct phases of self-organization were unveiled. First, the…
Biochemical networks are used in computational biology, to model the static and dynamical details of systems involved in cell signaling, metabolism, and regulation of gene expression. Parametric and structural uncertainty, as well as…
We explore a simplified class of models we call swarms, which are inspired by the collective behavior of social insects. We perform a mean-field stability analysis and perform numerical simulations of the model. Several interesting types of…
This paper describes a process for combining patterns and features, to guide a search process and make predictions. It is based on the functionality that a human brain might have, which is a highly distributed network of simple neuronal…
The protein folding problem has attracted an increasing attention from physicists. The problem has a flavor of statistical mechanics, but possesses the most common feature of most biological problems -- the profound effects of evolution. I…
Design patterns are distilled from many real systems to catalog common programming practice. However, some object-oriented design patterns are distorted or overly complicated because of the lack of supporting programming language constructs…
In data modelling, product information has most often been handled separately from process information. The integration of product and process models in a unified data model could provide the means by which information could be shared…
Proteins perform critical processes in all living systems: converting solar energy into chemical energy, replicating DNA, as the basis of highly performant materials, sensing and much more. While an incredible range of functionality has…
Data mining is the task of discovering interesting patterns from large amounts of data. There are many data mining tasks, such as classification, clustering, association rule mining, and sequential pattern mining. Sequential pattern mining…
Increasing reuse opportunities is a well-known problem for software designers as well as for hardware designers. Nonetheless, current software and hardware engineering practices have embraced different approaches to this problem. Software…
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…
A detailed algorithmic explanation is required for how a network of chemical reactions can generate the sophisticated behavior displayed by living cells. Though several previous works have shown that reaction networks are computationally…
The reaction-diffusion models have been extensively applied to explain the mechanism of pattern formations in early embryogenesis based on geometrically confined microtissues consisting of human pluripotent stem cells. Recently, mechanical…
The domain of analysis and conception of Decisional Information System (DIS) is, highly, applying new techniques and methods to succeed the process of the decision and minimizing the time of conception. Our objective in this paper is to…
Metabolic networks perform some of the most fundamental functions in living cells, including energy transduction and building block biosynthesis. While these are the best characterized networks in living systems, understanding their…
All aspects of our society, including the life sciences, need a mechanism for people working within them to represent the concepts they employ to carry out their research. For the information systems being designed and developed to support…
Biological networks provide insight into the complex organization of biological processes in a cell at the system level. They are an effective tool for understanding the comprehensive map of functional interactions, finding the functional…