Related papers: Design Patterns of Biological Cells
The two basic equations satisfied by the parameters of a block design define a three-dimensional affine variety $\mathcal{D}$ in $\mathbb{R}^{5}$. A point of $\mathcal{D}$ that is not in some sense trivial lies on four lines lying in…
We propose a set of compositional design patterns to describe a large variety of systems that combine statistical techniques from machine learning with symbolic techniques from knowledge representation. As in other areas of computer science…
Generic Ontology Design Patterns, GODPs, are defined in Generic DOL, an extension of DOL, the Distributed Ontology, Model and Specification Language, and implemented using Heterogeneous Tool Set. Parameters such as classes, properties,…
In this thesis, we have studied the large scale structure and system level dynamics of certain biological networks using tools from graph theory, computational biology and dynamical systems. We study the structure and dynamics of large…
Cellular bioelectricity describes the biological phenomenon in which cells in living tissue generate and maintain patterns of voltage gradients induced by differing concentrations of charged ions. A growing body of research suggests that…
We review the recent progress in computational approaches to protein design which builds on advances in statistical-mechanical protein folding theory. In particular, we evaluate the degeneracy of the protein code (i.e. how many sequences…
In the article a transition from pattern evolution equation of reaction-diffusion type to a cellular automaton (CA) is described. The applicability of CA is demonstrated by generating patterns of complex irregular structure on a hexagonal…
This paper provides a survey of the industry perspective on System Resiliency and Resiliency design approaches and briefly touches on Organizational Resiliency topics. Beginning with a composite definition of Resiliency, System…
There is a concerted effort to build domain-general artificial intelligence in the form of universal neural network models with sufficient computational flexibility to solve a wide variety of cognitive tasks but without requiring…
Design of experiments is a branch of statistics that aims to identify efficient procedures for planning experiments in order to optimize knowledge discovery. Network inference is a subfield of systems biology devoted to the identification…
The causal assumptions, the study design and the data are the elements required for scientific inference in empirical research. The research is adequately communicated only if all of these elements and their relations are described…
Many creativity methods follow similar structures and principles. Design Patterns capture such invariants of proven good practices and discuss why, when and how creative thinking methods match various situations of collaboration. Moreover…
Many developmental processes in biology utilize Notch-Delta signaling to construct an ordered pattern of cellular differentiation. This signaling modality is based on nearest-neighbor contact, as opposed to the more familiar mechanism…
This paper proposes a control theoretic framework to model and analyze the self-organized pattern formation of molecular concentrations in biomolecular communication networks, emerging applications in synthetic biology. In biomolecular…
Multipotent stem or progenitor cells undergo a sequential series of binary fate decisions, which ultimately generate the diversity of differentiated cells. Efforts to understand cell fate control have focused on simple gene regulatory…
Recent technological advancements in data acquisition tools allowed life scientists to acquire multimodal data from different biological application domains. Broadly categorized in three types (i.e., sequences, images, and signals), these…
Patterns are words with terminals and variables. The language of a pattern is the set of words obtained by uniformly substituting all variables with words that contain only terminals. In their original definition, patterns only allow for…
In the web age systems must be flexible, reconfigurable and adaptable in addition to being quick to develop. As a consequence, designing systems to cater for change is becoming not only desirable but required by industry. Allowing systems…
There are diverse mechanisms driving the evolution of social networks. A key open question dealing with understanding their evolution is: How various preferential linking mechanisms produce networks with different features? In this paper we…
This paper describes a new technique, called "knowledge patterns", for helping construct axiom-rich, formal ontologies, based on identifying and explicitly representing recurring patterns of knowledge (theory schemata) in the ontology, and…