Retinal development is a dynamic process both anatomically and functionally. High-resolution imaging and dynamic monitoring of photoreceptors and inner neurons can provide important information regarding the structure...
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Retinal development is a dynamic process both anatomically and functionally. High-resolution imaging and dynamic monitoring of photoreceptors and inner neurons can provide important information regarding the structure and function of the developing retina. In this chapter, we describe intrinsic optical signal (IOS) imaging as a high spatiotemporal resolution method for functional study of living retinal tissues. IOS imaging is based on near infrared (NIR) light detection of stimulus-evoked transient change of inherent optical characteristics of the cells. With no requirement for exogenous biomarkers, IOS imaging is totally noninvasive for functional mapping of stimulus-evoked spatiotemporal dynamics of the photoreceptors and inner retinal neurons. less
Dynamic clamp is a technique that combines computer modeling with experimental electrophysiology and is used to examine how specific ion channels modulate a variety of single-cell activities, by artificially emulating...
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Dynamic clamp is a technique that combines computer modeling with experimental electrophysiology and is used to examine how specific ion channels modulate a variety of single-cell activities, by artificially emulating the response properties of specific ionic conductances during an electrophysiological recording. This is accomplished by continuously and instantaneously varying the current that is injected into a recorded neuron as a function of a computer-generated conductance and of the difference between its apparent reversal potential and the actual fluctuations of the membrane potential of the recorded cell. Dynamic clamp is often used to model voltage-independent, voltage-dependent, and synaptic ion currents and is very useful to study how cortical neurons compute and integrate diverse synaptic currents or sequences of synaptic inputs into specific spike-train outputs. Cortical networks are composed of highly heterogeneous cell types, and it is often difficult to dissect individual aspects of signal propagation between neurons and how they contribute to shape network activities underlying several cortical functions. Here, we describe some implementations of the dynamic clamp technique useful to studying the contribution of different elements of cortical circuits to the generation of single cell spike outputs. less
Model-based analysis of ChIP-seq (MACS) is a computational algorithm that identifies genome-wide locations of transcription/chromatin factor binding or histone modification from ChIP-seq data. MACS consists of four st...
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Model-based analysis of ChIP-seq (MACS) is a computational algorithm that identifies genome-wide locations of transcription/chromatin factor binding or histone modification from ChIP-seq data. MACS consists of four steps: removing redundant reads, adjusting read position, calculating peak enrichment and estimating the empirical false discovery rate (FDR). In this protocol, we provide a detailed demonstration of how to install MACS and how to use it to analyze three common types of ChIP-seq data sets with different characteristics: the sequence-specific transcription factor FoxA1, the histone modification mark H3K4me3 with sharp enrichment and the H3K36me3 mark with broad enrichment. We also explain how to interpret and visualize the results of MACS analyses. The algorithm requires ∼3 GB of RAM and 1.5 h of computing time to analyze a ChIP-seq data set containing 30 million reads, an estimate that increases with sequence coverage. MACS is open source and is available from http://***/MACS/ . less
The concept of molecular shape has been considered in various forms in the context of drug design. The following chapter details the application of molecular shape to the design of compound libraries for assessment of...
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The concept of molecular shape has been considered in various forms in the context of drug design. The following chapter details the application of molecular shape to the design of compound libraries for assessment of potential biological activity. Whilst the utility of shape descriptors is well documented in the area of ligand similarity, the use of shape descriptors is equally applicable to protein structures. Indeed, work has been published using various descriptors to compare proteins but little published where protein shape descriptors have been used to investigate ligand selectivity. less
A number of proposals exist concerning how to support the concept of roles at the level of programming languages. While some of these proposals indeed exhibit very promising properties, the concept of roles has not fo...
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A number of proposals exist concerning how to support the concept of roles at the level of programming languages. While some of these proposals indeed exhibit very promising properties, the concept of roles has not found its way into mainstream programming languages. We argue that this is due to the richness of the concept of roles and the fact that each existing proposal focuses on some aspects of roles while neglecting others. We present the programming language ObjectTeams/Java and using the categories of Steimann (2000) we demonstrate that this language covers more aspects of roles than previous approaches. We suggest that a thoroughly defined programming language featuring roles may contribute to a better understanding also in other fields using roles.
Cython is a Python language extension that allows explicit type declarations and is compiled directly to C. As such, it addresses Python's large overhead for numerical loops and the difficulty of efficiently using...
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Cython is a Python language extension that allows explicit type declarations and is compiled directly to C. As such, it addresses Python's large overhead for numerical loops and the difficulty of efficiently using existing C and Fortran code, which Cython can interact with natively.
Semantic Computing is an emerging research field that has drawn much attention from both academia and industry. It addresses the derivation and matching of semantics of computational "content" where "co...
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Semantic Computing is an emerging research field that has drawn much attention from both academia and industry. It addresses the derivation and matching of semantics of computational "content" where "content" may be anything including text, multimedia, hardware, network, etc. which can be mapped to many areas in Computer Science that involve analyzing and processing the intentions of humans with computational content. This paper discusses some potential applications of Semantic Computing in Computer Science.
In 1975, Academician Glushkov proposed the concept of conveyor production of software from ready-made programs. This paper presents new theoretical results and analyzes the development of this concept on the basis of ...
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In 1975, Academician Glushkov proposed the concept of conveyor production of software from ready-made programs. This paper presents new theoretical results and analyzes the development of this concept on the basis of examples of earlier and current software factories. This makes it possible to testify to fact of emergence of the following two basic production concepts: interface as a stub in transmitting and transforming given software and as an integrated environment for assembling various ready-made products in some programming languages. Over the years, they were constantly being improved and become the basis for a modern software factory including an assembly infrastructure with the use of human, technological, and tool resources for assembling ready-made programs. Within the framework of a system, new interface tools will be developed for heterogeneous programs to convert standard data types to those available in many programming languages.
This paper proposes a simple high-level programming language, endowed with resources that help encoding self-modifying programs. With this purpose, a conventional imperative language syntax (not explicitly stated in t...
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This paper proposes a simple high-level programming language, endowed with resources that help encoding self-modifying programs. With this purpose, a conventional imperative language syntax (not explicitly stated in this paper) is incremented with special commands and statements forming an adaptive layer specially designed with focus on the dynamical changes to be applied to the code at run-time. The resulting language allows programmers to easily specify dynamic changes to their own program's code. Such a language succeeds to allow programmers to effortless describe the dynamic logic of their adaptive applications. In this paper, we describe the most important aspects of the design and implementation of such a language. A small example is finally presented for illustration purposes.
The process of comprehending a problem, strategically developing a solution and translating the solution into an algorithm is arguably the single most important series of skills acquired during the education of an und...
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The process of comprehending a problem, strategically developing a solution and translating the solution into an algorithm is arguably the single most important series of skills acquired during the education of an undergraduate computer science or information technology major. With this in mind, much care should be taken when choosing a programming language to deploy in the first University programming course. BLAKE, Beginners language for Acquiring Key programming Essentials, is designed specifically for use in a programming I class. BLAKE aids in enforcing fundamental object-oriented practices while simultaneously facilitating the transition to subsequent programming languages. BLAKE's major features include;consistent parameter passing, single inheritance, non-redundant control structures, a simple development environment, and hardware independent data types. The syntax remains relatively small while still facilitating a straightforward transition to industry standard programming languages.
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