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检索条件"主题词=Programming Language"

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Parameter Estimation in Mathematical Models of Viral Infections Using R

Parameter Estimation in Mathematical Models of Viral Infecti...

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作者： Van Kinh Nguyen Esteban A. Hernandez-Vargas

In recent years, mathematical modeling approaches have played a central role in understanding and quantifying mechanisms in different viral infectious diseases. In this approach, biology-based hypotheses are expressed via mathematical relations and then tested based on empirical data. The simulation results can be used to either identify underlying mechanisms and provide predictions of infection outcomes or to evaluate the efficacy of a treatment. Conducting parameter estimation for mathematical models is not an easy task. Here we detail an approach to conduct parameter estimation and to evaluate the results using the free software R. The method is applicable to influenza virus dynamics at different complexity levels, widening experimentalists’ capabilities in understanding their data. The parameter estimation approach presented here can be also applied to other viral infections or biological applications. less

关键词： Mathematical Modeling Statistical Calculation Cell And Tissue Culture programming language Influenzavirus A Viruses Viral infection Influenza virus Parameter estimation

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IgE and IgG4 Epitope Mapping of Food Allergens with a Peptide Microarray Immunoassay

IgE and IgG4 Epitope Mapping of Food Allergens with a Peptid...

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作者： Javier Martínez-Botas Carlos Fernández-Lozano Aida Vaquero-Rey Belén Hoz

Peptide microarrays are a powerful tool to identify linear epitopes of food allergens in a high-throughput manner. The main advantages of the microarray-based immunoassay are as follows: the possibility to assay thousands of targets simultaneously, the requirement of a low volume of serum, the more robust statistical analysis, and the possibility to test simultaneously several immunoglobulin subclasses. Among them, the last one has a special interest in the field of food allergy, because the development of tolerance to food allergens has been associated with a decrease in IgE and an increase in IgG4 levels against linear epitopes. However, the main limitation to the clinical use of microarray is the automated analysis of the data. Recent studies mapping the linear epitopes of food allergens with peptide microarray immunoassays have identified peptide biomarkers that can be used for early diagnosis of food allergies and to predict their severity or the self-development of tolerance. Using this approach, we have worked on epitope mapping of the two most important food allergens in the Spanish population, cow’s milk, and chicken eggs. The final aim of these studies is to define subsets of peptides that could be used as biomarkers to improve the diagnosis and prognosis of food allergies. This chapter describes the protocol to produce microarrays using a library of overlapping peptides corresponding to the primary sequences of food allergens and data acquisition and analysis of IgE and IgG4 binding epitopes. less

关键词： Peptide Microarray Epitope Mapping Immunoassay Microarray Microarray Immunoassay Statistical Calculation Protein Microarray Data analysis programming language Data Mining Machine Learning HPLC Mass Spectrometry Homo sapiens Bos taurus biomarkers food allergy linear epitope Anti-rat Anti-human IgE

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Identifying RNA Editing Sites in miRNAs by Deep Sequencing

Identifying RNA Editing Sites in miRNAs by Deep Sequencing

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作者： Shahar Alon Eli Eisenberg

Deep sequencing has many possible applications; one of them is the identification and quantification of RNA editing sites. The most common type of RNA editing is adenosine to inosine (A-to-I) editing. A prerequisite for this editing process is a double-stranded RNA (dsRNA) structure. Such dsRNAs are formed as part of the microRNA (miRNA) maturation process, and it is therefore expected that miRNAs are affected by A-to-I editing. Indeed, tens of editing sites were found in miRNAs, some of which change the miRNA binding specificity. Here, we describe a protocol for the identification of RNA editing sites in mature miRNAs using deep sequencing data. less

关键词： Deep Sequencing Genomics Statistical Calculation Bowtie Illumina Sequencing programming language Mus musculus Bioinformatics miRNA A-to-I editing

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Teaching programming technique with edutainment robot construction

Teaching programming technique with edutainment robot constr...

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2010 2nd International Conference on Education Technology and Computer(第二届IEEE教育技术与计算机国际会议 ICETC 2010)

作者： Hsien-Tang Lin Tzai-Hsing Kuo Department of Computer Science and Information Engineering Tahwa Institute of Technology ＃1 Tahwa Rd Department of Computer Science National Chiao Tung University 1001 Ta Hsueh Road Hsinchu300 Taiwan

ISBN: (纸本)9781424463671

recently,building robot has become the current trend for the teaching and learning the subject of science in elementary and secondary *** objective of this paper is to propose a teaching approach for programming language by the application of weblog on robot *** is hoped that such an approach may make learning more enjoyable as well as effective and may further motivate students in future experiments.A study of teaching computer program in high school with VPL-based tool to construct robots was *** formed in team to build robots and write program to perform the specified *** result shows that students have achieved good results in terms of learning motivation.

关键词： component Robot programming language blog

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Use of Dynamic-Clamp as a Tool to Reveal the Computational Properties of Single Neurons Embedded in Cortical Circuits

Use of Dynamic-Clamp as a Tool to Reveal the Computational P...

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作者： Alberto Bacci Antonio Pazienti Michele Giugliano

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

关键词： Electrophysiology MATLAB programming language Dynamic clamp Synaptic transmission Cortical networks

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Measurements of Rhodopsin Diffusion Within Signaling Membrane Microcompartments in Live Photoreceptors

Measurements of Rhodopsin Diffusion Within Signaling Membran...

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作者： Mehdi Najafi Peter D. Calvert

High-resolution multiphoton imaging of live cells has become an invaluable method to study protein dynamics in highly compartmentalized subcellular environments. Here we describe procedures that we recently developed to quantify rhodopsin mobility within and between retinal rod photoreceptor light signaling microcompartments, the disc membrane lobules, using multiphoton fluorescence relaxation after photoconversion. less

关键词： Live Cell Imaging FRAP Dissection Image Processing Decapitation Multiphoton Microscopy Transillumination MATLAB programming language Xenopus laevis Bos taurus Lens Xenopus G protein-coupled receptors Cell signaling Rhodopsin diffusion Microcompartments

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Computational Approaches for Mining GRO-Seq Data to Identify and Characterize Active Enhancers

Computational Approaches for Mining GRO-Seq Data to Identify...

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作者： Anusha Nagari Shino Murakami Venkat S. Malladi W. Lee Kraus

Transcriptional enhancers are DNA regulatory elements that are bound by transcription factors and act to positively regulate the expression of nearby or distally located target genes. Enhancers have many features that have been discovered using genomic analyses. Recent studies have shown that active enhancers recruit RNA polymerase II (Pol II) and are transcribed, producing enhancer RNAs (eRNAs). GRO-seq, a method for identifying the location and orientation of all actively transcribing RNA polymerases across the genome, is a powerful approach for monitoring nascent enhancer transcription. Furthermore, the unique pattern of enhancer transcription can be used to identify enhancers in the absence of any information about the underlying transcription factors. Here, we describe the computational approaches required to identify and analyze active enhancers using GRO-seq data, including data pre-processing, alignment, and transcript calling. In addition, we describe protocols and computational pipelines for mining GRO-seq data to identify active enhancers, as well as known transcription factor binding sites that are transcribed. Furthermore, we discuss approaches for integrating GRO-seq-based enhancer data with other genomic data, including target gene expression and function. Finally, we describe molecular biology assays that can be used to confirm and explore further the function of enhancers that have been identified using genomic assays. Together, these approaches should allow the user to identify and explore the features and biological functions of new cell type-specific enhancers. less

关键词： GRO-seq Statistical Calculation Genome Visualization DNase-Seq High-Throughput Sequencing Genomics Cutadapt Trimmomatic Data analysis SAMtools bedtools programming language Python Transcription Gene regulation Motif search Promoter Transcription factor Enhancer Motif Response element groHMM Enhancer RNAs (eRNAs) Enhancer prediction Looping Transcription unit

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Quality Control for Genome-Wide Association Studies

Quality Control for Genome-Wide Association Studies

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作者： Cedric Gondro Seung Hwan Lee Hak Kyo Lee Laercio R. Porto-Neto

This chapter overviews the quality control (QC) issues for SNP-based genotyping methods used in genome-wide association studies. The main metrics for evaluating the quality of the genotypes are discussed followed by a worked out example of QC pipeline starting with raw data and finishing with a fully filtered dataset ready for downstream analysis. The emphasis is on automation of data storage, filtering, and manipulation to ensure data integrity throughput the process and on how to extract a global summary from these high dimensional datasets to allow better-informed downstream analytical decisions. All examples will be run using the R statistical programming language followed by a practical example using a fully automated QC pipeline for the Illumina platform. less

关键词： Statistical Calculation Genotyping programming language Quality control Genome-wide association studies Illumina

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False Discovery Rate Estimation in Proteomics

False Discovery Rate Estimation in Proteomics

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作者： Suruchi Aggarwal Amit Kumar Yadav

With the advancement in proteomics separation techniques and improvements in mass analyzers, the data generated in a mass-spectrometry based proteomics experiment is rising exponentially. Such voluminous datasets necessitate automated computational tools for high-throughput data analysis and appropriate statistical control. The data is searched using one or more of the several popular database search algorithms. The matches assigned by these tools can have false positives and statistical validation of these false matches is necessary before making any biological interpretations. Without such procedures, the biological inferences do not hold true and may be outright misleading. There is a considerable overlap between true and false positives. To control the false positives amongst a set of accepted matches, there is a need for some statistical estimate that can reflect the amount of false positives present in the data processed. False discovery rate (FDR) is the metric for global confidence assessment of a large-scale proteomics dataset. This chapter covers the basics of FDR, its application in proteomics, and methods to estimate FDR. less

关键词： Shotgun Proteomics Proteomics Database Search Genomics Data analysis programming language False discovery rate Posterior error probability Target-decoy Peptide spectrum matches Statistical validation

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Freshwater Viromes: From Sampling to Evaluation

Freshwater Viromes: From Sampling to Evaluation

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作者： Catherine Putonti Zoë Diener Siobhan C. Watkins

There are a number of options available to researchers who wish to collect and analyze viral metagenomes (viromes) from environmental samples. Here we describe a laboratory procedure for generation of viromes from freshwater samples, specifically targeting dsDNA bacteriophages. We also discuss methods for bioinformatic analysis of the resulting data. less

关键词： Metagenomics Nucleic Acid Extraction Library Preparation Genomics Trimmomatic Data analysis Python programming language tangential flow filtration Viruses Bacteriophage Viromes Viral bioinformatics

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