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检索条件"主题词=Programming language"

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Characterization of the Rat Gut Microbiota via 16S rRNA Amplicon Library Sequencing

Characterization of the Rat Gut Microbiota via 16S rRNA Ampl...

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作者： Aaron C. Ericsson Susheel B. Busi James M. Amos-Landgraf

It is becoming increasingly apparent that microbiota have measurable effects on numerous phenotypes in laboratory animals. This “second genome” has often been disregarded or ignored due to its commensal nonpathogenic nature, and the difficulty, expense, and analysis of sequence. Recent advances in sequencing methods and analyses of large datasets have made characterization of microbiota populations routine and have uncovered previously unknown relationships of microbial communities and host biological systems. The largest and most diverse microbial community in the laboratory rat is in the gut, and has been shown to affect the physiology of the whole animal, and genetic disease penetrance. We present here a cost-effective method for the characterization of the rat fecal microbiota through multiplexed 16S ribosomal sequencing and freely available software. less

关键词： DNA Extraction Library Preparation PCR Statistical Calculation 16s rRNA Sequencing Principal Component Analysis Shotgun Sequencing Data analysis programming language Rattus norvegicus Sequencing Microbiota 16S rRNA gene Operational taxonomic unit (OTU)

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Post-processing of Large Bioactivity Data

Post-processing of Large Bioactivity Data

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作者： Jason Bret Harris

Bioactivity data is a valuable scientific data type that needs to be findable, accessible, interoperable, and reusable (FAIR) (Wilkinson et al. Sci Data 3:160018, 2016). However, results from bioassay experiments often exist in formats that are difficult to interoperate across and reuse in follow-up research, especially when attempting to combine experimental records from many different sources. This chapter details common issues associated with the processing of large bioactivity data and methods for handling these issues in a post-processing scenario. Specifically described are observations from a recent effort (Harris, http://*** , 2017) to post-process massive amounts of bioactivity data from the NIH’s PubChem Bioassay repository (Wang et al., Nucleic Acids Res 42:1075–1082, 2014). less

关键词： GenBank programming language Bioassay PubChem Data integration Big data Bioactivity ScrubChem Hit-calls

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Information-Theoretic Inference of an Optimal Dictionary of Protein Supersecondary Structures

Information-Theoretic Inference of an Optimal Dictionary of ...

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作者： Arun S. Konagurthu Ramanan Subramanian Lloyd Allison David Abramson Maria Garcia Banda Peter J. Stuckey Arthur M. Lesk

We recently developed an unsupervised Bayesian inference methodology to automatically infer a dictionary of protein supersecondary structures (Subramanian et al., IEEE data compression conference proceedings (DCC), 340–349, 2017). Specifically, this methodology uses the information-theoretic framework of minimum message length (MML) criterion for hypothesis selection (Wallace, Statistical and inductive inference by minimum message length, Springer Science & Business Media, New York, 2005). The best dictionary of supersecondary structures is the one that yields the most (lossless) compression on the source collection of folding patterns represented as tableaux (matrix representations that capture the essence of protein folding patterns (Lesk, J Mol Graph. 13:159–164, 1995). This book chapter outlines our MML methodology for inferring the supersecondary structure dictionary. The inferred dictionary is available at http://***/proteinConcepts/scop100/*** . less

关键词： Protein Structure Analysis Dissection Simulated Annealing programming language Supersecondary structure Minimum message length MML Tableau representation Protein folding pattern

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Guidelines for using sigQC for systematic evaluation of gene signatures

Guidelines for using sigQC for systematic evaluation of gene...

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作者： Andrew Dhawan Alessandro Barberis Wei-Chen Cheng Enric Domingo Catharine West Tim Maughan Jacob G. Scott Adrian L. Harris Francesca M. Buffa

With the increased use of next-generation sequencing generating large amounts of genomic data, gene expression signatures are becoming critically important tools for the interpretation of these data, and are poised to have a substantial effect on diagnosis, management, and prognosis for a number of diseases. It is becoming crucial to establish whether the expression patterns and statistical properties of sets of genes, or gene signatures, are conserved across independent datasets. Conversely, it is necessary to compare established signatures on the same dataset to better understand how they capture different clinical or biological characteristics. Here we describe how to use sigQC, a tool that enables a streamlined, systematic approach for the evaluation of previously obtained gene signatures across multiple gene expression datasets. We implemented sigQC in an R package, making it accessible to users who have knowledge of file input/output and matrix manipulation in R and a moderate grasp of core statistical principles. SigQC has been adopted in basic biology and translational studies, including, but not limited to, the evaluation of multiple gene signatures for potential clinical use as cancer biomarkers. This protocol uses a previously obtained signature for breast cancer metastasis as an example to illustrate the critical quality control steps involved in evaluating its expression, variability, and structure in breast tumor RNA-sequencing data, a different dataset from that in which the signature was originally derived. We demonstrate how the outputs created from sigQC can be used for the evaluation of gene signatures on large-scale gene expression datasets. less

关键词： Transcriptomics RNA-seq Data analysis programming language Data processing Gene expression Biomarkers

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Selection Strategy of a Linguistic Base for Software Development, Functioned in Engineering CAD-Systems

Selection Strategy of a Linguistic Base for Software Develop...

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IEEE International Conference on Quality Management, Transport and Information Security, Information Technologies (IT and QM and IS)

作者： Nesterov, Ivan V. Smirnova, Olga V. Merzliakova, Aleksandra D. Naumov, Vladimir S. Russian Univ Transport MIIT Comp Aided Design Dept Moscow Russia Moscow State Univ Civil Engn MGSU Moscow Russia

ISBN: (纸本)9781538667576

The modern software market provides application programmers a diverse selection of tools for program development. It is necessary to choose the right software envelope in which the software product will be created when developing complex science-intensive software, which is connected in a large number of mathematical calculations and functioning in engineering CAD systems. The article is devoted to the problems of software selection strategy for the development of structures' engineering analysis.

关键词： programming language software graphic editor complex automation

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Using RuleBuilder to Graphically Define and Visualize BioNetGen-language Patterns and Reaction Rules

Using RuleBuilder to Graphically Define and Visualize BioNet...

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作者： Ryan Suderman G. Matthew Fricke William S. Hlavacek

RuleBuilder is a tool for drawing graphs that can be represented by the BioNetGen language (BNGL), which is used to formulate mathematical, rule-based models of biochemical systems. BNGL provides an intuitive plain text, or string, representation of such systems, which is based on a graphical formalism. Reactions are defined in terms of graph-rewriting rules that specify the necessary intrinsic properties of the reactants, a transformation, and a rate law. Rules also contain contextual constraints that restrict application of the rule. In some cases, the specification of contextual constraints can be verbose, making a rule difficult to read. RuleBuilder is designed to ease the task of reading and writing individual reaction rules or other BNGL patterns required for model formulation. The software assists in the reading of existing models by converting BNGL strings of interest into a graph-based representation composed of nodes and edges. RuleBuilder also enables the user to construct de novo a visual representation of BNGL strings using drawing tools available in its interface. As objects are added to the drawing canvas, the corresponding BNGL string is generated on the fly, and objects are similarly drawn on the fly as BNGL strings are entered into the application. RuleBuilder thus facilitates construction and interpretation of rule-based models. less

关键词： Mathematical Modeling Rearrangement programming language Visualization Software Systems biology Dynamical systems Rule-based modeling Chemical kinetics Graph rewriting Drawing tool

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Imaging Single mRNA Molecules in Mammalian Cells Using an Optimized MS2-MCP System

Imaging Single mRNA Molecules in Mammalian Cells Using an Op...

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作者： Maria Vera Evelina Tutucci Robert H. Singer

Visualization of single mRNAs in their native cellular environment provides key information to study gene expression regulation. This fundamental biological question triggered the development of the MS2-MCP (MS2-Capsid Protein) system to tag mRNAs and image their life cycle using widefield fluorescence microscopy. The last two decades have evolved toward improving the qualitative and quantitative characteristics of the MS2-MCP system. Here, we provide a protocol to use the latest versions, MS2V6 and MS2V7, to tag and visualize mRNAs in mammalian cells in culture. The motivation behind engineering MS2V6 and MS2V7 was to overcome a degradation caveat observed in S. cerevisiae with the previous MS2-MCP systems. While for yeast we recommend the use of MS2V6, we found that for live-cell imaging experiments in mammalian cells, the MS2V7 has improved reporter properties. less

关键词： Lentivirus Production Live Cell Imaging Fluorescence Microscopy Wide-field Microscopy FISH PCR DNA Extraction Cell And Tissue Culture Transient Transfection CRISPR-Cas9 Genome Editing Imaging Techniques MetaMorph Recombinant Protein Expression Fiji Single-molecule FISH MATLAB CellProfiler DNA Purification Cell Separation And Isolation Transfection Microscopy Image Analysis DNA Ligation programming language Data analysis Mus musculus Escherichia coli Lentivirus HEK293T Single-molecule imaging Single cell MS2 system MS2V6 MS2V7 Short-lived mRNAs

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CRISPR/Cas9-Based Chemogenomic Profiling in Mammalian Cells

CRISPR/Cas9-Based Chemogenomic Profiling in Mammalian Cells

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作者： Dominic Hoepfner Gregory McAllister Gregory R. Hoffman

Chemogenomic profiling is a powerful and unbiased approach to elucidate pharmacological targets and the mechanism of bioactive compounds. It is based on identifying cellular hypersensitivity and resistance caused by individual gene modulations with genome-wide coverage. Due to the requirement of bar-coded, genome-wide deletion collections, high-resolution experiments of this nature have historically been limited to fungal systems. Pooled RNAi reagents have enabled similar attempts in mammalian cells but efforts have been hampered by significant off-target effects and experimental noise. The CRISPR/Cas9 system for the first time enables precise DNA editing at defined loci in a genome-wide fashion. Here we present the detailed protocol that leverages the CRISPR/Cas9 system for chemogenomic profiling and target identification of diverse chemical probes. less

关键词： CRISPR Genomics DNA Extraction Next Generation Sequencing RNA Interference CRISPR-Cas9 Genome Editing Liquid Handling Cell And Tissue Culture Regression Analysis Transfection Virus Production Real-time PCR Immunofluorescence Western Blot Flow Cytometry FACS Illumina Sequencing Bowtie Statistical Calculation Principal Component Analysis Data analysis programming language Python HCT 116 HEK293T Target identification Genetics Resistance Cas9 Gene editing Haploinsufficiency Chemogenomic profiling NAMPT Signal peptidase

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Gene Regulatory Networks from Single Cell Data for Exploring Cell Fate Decisions

Gene Regulatory Networks from Single Cell Data for Exploring...

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作者： Thalia E. Chan Michael P. Stumpf Ann C. Babtie

Single cell experimental techniques now allow us to quantify gene expression in up to thousands of individual cells. These data reveal the changes in transcriptional state that occur as cells progress through development and adopt specialized cell fates. In this chapter we describe in detail how to use our network inference algorithm (PIDC)—and the associated software package ***—to infer functional interactions between genes from the observed gene expression patterns. We exploit the large sample sizes and inherent variability of single cell data to detect statistical dependencies between genes that indicate putative (co-)regulatory relationships, using multivariate information measures that can capture complex statistical relationships. We provide guidelines on how best to combine this analysis with other complementary methods designed to explore single cell data, and how to interpret the resulting gene regulatory network models to gain insight into the processes regulating cell differentiation. less

关键词： Real-time PCR RNA-seq MATLAB Neuronal Differentiation Statistical Calculation programming language Python Gene regulation Network inference Single cell Information theory Cell development

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Mastering High Performance with Kotlin 1

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丛书名： []

2018年

作者： Igor Kucherenko

ISBN: (数字)9781788998352

ISBN: (纸本)9781788996648

Find out how to write Kotlin code without overhead and how to use different profiling tools and bytecode viewer to inspect expressions of Kotlin language. Key Features Apply modern Kotlin features to speed up processing and implement highly efficient and reliable codes. Learn memory optimization, concurrency, multi-threading, scaling, and caching techniques to achieve high performance. Learn how to prevent unnecessary overhead and use profiling tools to detect performance issues. Book Description The ease with which we write applications has been increasing, but with it comes the need to address their performance. A balancing act between easily implementing complex applications and keeping their performance optimal is a present-day requirement In this book, we explore how to achieve this crucial balance, while developing and deploying applications with Kotlin. The book starts by analyzing various Kotlin specifcations to identify those that have a potentially adverse effect on performance. Then, we move on to monitor techniques that enable us to identify performance bottlenecks and optimize performance metrics. Next, we look at techniques that help to us achieve high performance: memory optimization, concurrency, multi threading, scaling, and caching. We also look at fault tolerance solutions and the importance of logging. We'll also cover best practices of Kotlin programming that will help you to improve the quality of your code base. By the end of the book, you will have gained some insight into various techniques and solutions that will help to create high-performance applications in the Kotlin environment What you will learn Understand the importance of high performance Learn performance metrics Learn popular design patterns currently being used in Kotlin Understand how to apply modern Kotlin features to data processing Learn how to use profling tools Discover how to read bytecode Learn to perform memory optimizations Uncover approaches to the multithreading envi

关键词： Kotlin Android app development programming language Kotlin language High performance

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