There is, I think, something ethereal about i —the square root of minus one. I remember first hearing about it at school. It seemed an odd beast at that time—an intruder hovering on the edge of reality.

Usually familiarity dulls this sense of the bizarre, but in the case of i it was the reverse: over the years the sense of its surreal nature intensified. It seemed that it was impossible to write mathematics that described the real world in …

I and i

Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape's software Core provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link the network to databases of functional annotations. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features. Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.

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Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks

Publisher Summary This chapter provides an account of different neural network architectures for pattern recognition. A neural network consists of several simple processing elements called neurons. Each neuron is connected to some other neurons and possibly to the input nodes. Neural networks provide a simple computing paradigm to perform complex recognition tasks in real time. The chapter categorizes neural networks into three types: single-layer networks, multilayer feedforward networks, and feedback networks. It discusses the gradient descent and the relaxation method as the two underlying mathematical themes for deriving learning algorithms. A lot of research activity is centered on learning algorithms because of their fundamental importance in neural networks. The chapter discusses two important directions of research to improve learning algorithms: the dynamic node generation, which is used by the cascade correlation algorithm; and designing learning algorithms where the choice of parameters is not an issue. It closes with the discussion of performance and implementation issues.

Neural Networks for Pattern Recognition

Graphene is a wonder material with many superlatives to its name. It is the thinnest known material in the universe and the strongest ever measured. Its charge carriers exhibit giant intrinsic mobility, have zero effective mass, and can travel for micrometers without scattering at room temperature. Graphene can sustain current densities six orders of magnitude higher than that of copper, shows record thermal conductivity and stiffness, is impermeable to gases, and reconciles such conflicting qualities as brittleness and ductility. Electron transport in graphene is described by a Dirac-like equation, which allows the investigation of relativistic quantum phenomena in a benchtop experiment. This review analyzes recent trends in graphene research and applications, and attempts to identify future directions in which the field is likely to develop.

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Graphene: Status and Prospects

Cell signaling by receptor-tyrosine kinases

There are two fundamental ways to view coupled systems of chemical equations:  as continuous, represented by differential equations whose variables are concentrations, or as discrete, represented by stochastic processes whose variables are numbers of molecules. Although the former is by far more common, systems with very small numbers of molecules are important in some applications (e.g., in small biological cells or in surface processes). In both views, most complicated systems with multiple reaction channels and multiple chemical species cannot be solved analytically. There are exact numerical simulation methods to simulate trajectories of discrete, stochastic systems, (methods that are rigorously equivalent to the Master Equation approach) but these do not scale well to systems with many reaction pathways. This paper presents the Next Reaction Method, an exact algorithm to simulate coupled chemical reactions that is also efficient:  it (a) uses only a single random number per simulation event, and (b) ...

Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels

A system which uses redundant storage and redundant communication to provide a robust distributed server system.

A reliable array of distributed computing nodes

The impressive capabilities of the mammalian brain—ranging from perception, pattern recognition and memory formation to decision making and motor activity control—have inspired their re-creation in a wide range of artificial intelligence systems for applications such as face recognition, anomaly detection, medical diagnosis and robotic vehicle control Yet before neuron-based brains evolved, complex biomolecular circuits provided individual cells with the ‘intelligent’ behaviour required for survival However, the study of how molecules can ‘think’ has not produced an equal variety of computational models and applications of artificial chemical systems Although biomolecular systems have been hypothesized to carry out neural-network-like computations in vivo and the synthesis of artificial chemical analogues has been proposed theoretically, experimental work has so far fallen short of fully implementing even a single neuron Here, building on the richness of DNA computing and strand displacement circuitry, we show how molecular systems can exhibit autonomous brain-like behaviours Using a simple DNA gate architecture that allows experimental scale-up of multilayer digital circuits, we systematically transform arbitrary linear threshold circuits (an artificial neural network model) into DNA strand displacement cascades that function as small neural networks Our approach even allows us to implement a Hopfield associative memory with four fully connected artificial neurons that, after training in silico, remembers four single-stranded DNA patterns and recalls the most similar one when presented with an incomplete pattern Our results suggest that DNA strand displacement cascades could be used to endow autonomous chemical systems with the capability of recognizing patterns of molecular events, making decisions and responding to the environment

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Neural network computation with DNA strand displacement cascades

We present a novel method, that we call EVENODD, for tolerating up to two disk failures in RAID architectures. EVENODD employs the addition of only two redundant disks and consists of simple exclusive-OR computations. This redundant storage is optimal, in the sense that two failed disks cannot be retrieved with less than two redundant disks. A major advantage of EVENODD is that it only requires parity hardware, which is typically present in standard RAID-5 controllers. Hence, EVENODD can be implemented on standard RAID-5 controllers without any hardware changes. The most commonly used scheme that employes optimal redundant storage (i.e., two extra disks) is based on Reed-Solomon (RS) error-correcting codes. This scheme requires computation over finite fields and results in a more complex implementation. For example, we show that the complexity of implementing EVENODD in a disk array with 15 disks is about 50% of the one required when using the RS scheme. The new scheme is not limited to RAID architectures: it can be used in any system requiring large symbols and relatively short codes, for instance, in multitrack magnetic recording. To this end, we also present a decoding algorithm for one column (track) in error. >

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EVENODD: an efficient scheme for tolerating double disk failures in RAID architectures

In addition to preventing crosstalk among related signaling pathways, scaffold proteins might facilitate signal transduction by preforming multimolecular complexes that can be rapidly activated by incoming signal. In many cases, such as mitogen-activated protein kinase (MAPK) cascades, scaffold proteins are necessary for full activation of a signaling pathway. To date, however, no detailed biochemical model of scaffold action has been suggested. Here we describe a quantitative computer model of MAPK cascade with a generic scaffold protein. Analysis of this model reveals that formation of scaffold-kinase complexes can be used effectively to regulate the specificity, efficiency, and amplitude of signal propagation. In particular, for any generic scaffold there exists a concentration value optimal for signal amplitude. The location of the optimum is determined by the concentrations of the kinases rather than their binding constants and in this way is scaffold independent. This effect and the alteration of threshold properties of the signal propagation at high scaffold concentrations might alter local signaling properties at different subcellular compartments. Different scaffold levels and types might then confer specialized properties to tune evolutionarily conserved signaling modules to specific cellular contexts.

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Jehoshua Bruck

Papers

Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels

A reliable array of distributed computing nodes

Neural network computation with DNA strand displacement cascades

EVENODD: an efficient scheme for tolerating double disk failures in RAID architectures

Scaffold proteins may biphasically affect the levels of mitogen-activated protein kinase signaling and reduce its threshold properties.