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检索条件"主题词=Programming Language"

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High-speed fixed-target serial virus crystallography

High-speed fixed-target serial virus crystallography

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作者： Philip Roedig Helen M Ginn Tim Pakendorf Geoff Sutton Karl Harlos Thomas S Walter Jan Meyer Pontus Fischer Ramona Duman Ismo Vartiainen Bernd Reime Martin Warmer Aaron S Brewster Iris D Young Tara Michels-Clark Nicholas K Sauter Abhay Kotecha James Kelly David J Rowlands Marcin Sikorsky Silke Nelson Daniel S Damiani Roberto Alonso-Mori Jingshan Ren Elizabeth E Fry Christian David David I Stuart Armin Wagner Alke Meents

We report a method for serial X-ray crystallography at X-ray free-electron lasers (XFELs), which allows for full use of the current 120-Hz repetition rate of the Linear Coherent Light Source (LCLS). Using a micropatterned silicon chip in combination with the high-speed Roadrunner goniometer for sample delivery, we were able to determine the crystal structures of the picornavirus bovine enterovirus 2 (BEV2) and the cytoplasmic polyhedrosis virus type 18 polyhedrin, with total data collection times of less than 14 and 10 min, respectively. Our method requires only micrograms of sample and should therefore broaden the applicability of serial femtosecond crystallography to challenging projects for which only limited sample amounts are available. By synchronizing the sample exchange to the XFEL repetition rate, our method allows for most efficient use of the limited beam time available at XFELs and should enable a substantial increase in sample throughput at these facilities. less

关键词： Nanocrystallography Statistical Calculation X-ray Crystallography Ultracentrifugation Lithography Macromolecular Crystallography serial femtosecond crystallography Python programming language Virology Proteins

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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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Identifying ChIP-seq enrichment using MACS

Identifying ChIP-seq enrichment using MACS

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作者： Jianxing Feng Tao Liu Bo Qin Yong Zhang Xiaole Shirley Liu

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

关键词： ChIP Assay Histone Analysis ChIP-seq Bowtie Peak Calling Library Preparation Genomics Genome Visualization Python SAMtools programming language Homo sapiens T-47D K-562 GM12878 Computational biology and bioinformatics Next-generation sequencing

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A Study on Atomics-based Integer Sum Reduction in HIP on AMD GPU 22

A Study on Atomics-based Integer Sum Reduction in HIP on AMD...

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Workshop Proceedings of the 51st International Conference on Parallel Processing

作者： Zheming Jin Jeffrey Vetter Oak Ridge National Laboratory United States of America Oak Ridge National Laboratory USA

ISBN: (纸本)9781450394451

Integer sum reduction is a primitive operation commonly used in scientific computing. Implementing a parallel reduction on a GPU often involves concurrent memory accesses using atomic operations and synchronization of work-items in a work-group. For a better understanding of these operations, we redesigned micro-kernels in the HIP programming language to measure the time of atomic operations over global memory, the cost of barrier synchronization, and reduction within a work-group to shared local memory using one atomic addition per work-item on a compute unit in an AMD MI100 GPU. Then, we describe the implementations of the reduction kernels with vectorized memory accesses, parameterized workload sizes, and vendor's library APIs. Our experimental results show that 1) there is a performance tradeoff between the cost of barrier synchronization and the amount of parallelism from atomic operations over shared local memory when we increase the size of a work-group. 2) a reduction kernel with vectorized memory accesses and vector data types is approximately 3% faster for the large problem size than the kernels written with the vendor's library APIs. 3) the compiler needs to assist the hardware processor with data dependency resolution at the level of instruction set architecture. 4) the power consumption of the kernel execution on the GPU fluctuates between 277 Watts and 301 Watts and the dynamic power of other GPU activities is at most 31 Watts.

关键词： programming language Parallel reduction GPU

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Computational Systems Biology of Morphogenesis

Computational Systems Biology of Morphogenesis

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作者： Jason M. Ko Reza Mousavi Daniel Lobo

Extracting mechanistic knowledge from the spatial and temporal phenotypes of morphogenesis is a current challenge due to the complexity of biological regulation and their feedback loops. Furthermore, these regulatory interactions are also linked to the biophysical forces that shape a developing tissue, creating complex interactions responsible for emergent patterns and forms. Here we show how a computational systems biology approach can aid in the understanding of morphogenesis from a mechanistic perspective. This methodology integrates the modeling of tissues and whole-embryos with dynamical systems, the reverse engineering of parameters or even whole equations with machine learning, and the generation of precise computational predictions that can be tested at the bench. To implement and perform the computational steps in the methodology, we present user-friendly tools, computer code, and guidelines. The principles of this methodology are general and can be adapted to other model organisms to extract mechanistic knowledge of their morphogenesis. less

关键词： Machine Learning Mathematical Modeling MATLAB Python Recombinant Protein Expression Cell And Tissue Culture STRING programming language Morphogenesis Systems Biology Computational Biology

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Ensembl Plants: Integrating Tools for Visualizing, Mining, and Analyzing Plant Genomic Data

Ensembl Plants: Integrating Tools for Visualizing, Mining, a...

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作者： Dan M. Bolser Daniel M. Staines Emily Perry Paul J. Kersey

Ensembl Plants (http://*** ) is an integrative resource presenting genome-scale information for 39 sequenced plant species. Available data includes genome sequence, gene models, functional annotation, and polymorphic loci; for the latter, additional information including population structure, individual genotypes, linkage, and phenotype data is available for some species. Comparative data is also available, including genomic alignments and “gene trees,” which show the inferred evolutionary history of each gene family represented in the resource. Access to the data is provided through a genome browser, which incorporates many specialist interfaces for different data types, through a variety of programmatic interfaces, and via a specialist data mining tool supporting rapid filtering and retrieval of bulk data. Genomic data from many non-plant species, including those of plant pathogens, pests, and pollinators, is also available via the same interfaces through other divisions of Ensembl. Ensembl Plants is updated 4–6 times a year and is developed in collaboration with our international partners in the Gramene (http://*** ) and transPLANT projects (http://*** ). less

关键词： Genome Visualization Transcriptomics Functional Genomics Data Mining RNA-seq Multiple Sequence Alignment Genome Assembly Genomics Genome Alignment Ensembl Gramene Database Management System programming language Arabidopsis lyrata Arabidopsis thaliana Homo sapiens Chlamydomonas reinhardtii Medicago truncatula Oryza barthii Oryza brachyantha Oryza glaberrima Oryza glumipatula Oryza longistaminata Oryza meridionalis Oryza nivara Oryza punctata Oryza rufipogon Physcomitrella patens Populus trichocarpa Populus (cottonwood) Selaginella moellendorffii Setaria italica Solanum lycopersicum Zea mays Oryza sativa Indica Group Oryza sativa Japonica Group Brassica oleracea Brassica rapa Glycine max Prunus Rosaceae Solanum tuberosum Theobroma Triticum aestivum Genetic variation Databases Cereals Phenotype Crops

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Characterizing Auxin Response Circuits in

Characterizing Auxin Response Circuits in

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作者： Edith Pierre-Jerome R. Clay Wright Jennifer L. Nemhauser

Recapitulation of the nuclear auxin response pathway in Saccharomyces cerevisiae (yeast) provides a means to functionally assay the contribution of individual signaling components to response dynamics. Here, we describe a time course assay for characterizing auxin response circuits using flow cytometry. This method allows for quantitative measurements of the dynamic response of up to 12 circuits (strains) at once. We also describe a steady-state assay and how to utilize an R package we developed to facilitate data analysis. less

关键词： Flow Cytometry Statistical Calculation PCR Cytometry Assay Data analysis programming language Saccharomyces cerevisiae Synthetic biology Fluorescent reporters Signaling dynamics

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Mathematical Linear programming to Model MicroRNAs-Mediated Gene Regulation Using Gurobi Optimizer

Mathematical Linear Programming to Model MicroRNAs-Mediated ...

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作者： Vijaykumar Yogesh Muley

Genes are transcribed into various RNA molecules, and a portion of them called messenger RNA (mRNA) is then translated into proteins in the process known as gene expression. Gene expression is a high-energy demanding process, and aberrant expression changes often manifest into pathophysiology. Therefore, gene expression is tightly regulated by several factors at different levels. MicroRNAs (miRNAs) are one of the powerful post-transcriptional regulators involved in key biological processes and diseases. They inhibit the translation of their mRNA targets or degrade them in a sequence-specific manner, and hence control the rate of protein synthesis. In recent years, in response to experimental limitations, several computational methods have been proposed to predict miRNA target genes based on sequence complementarity and structural features. However, these predictions yield a large number of false positives. Integration of gene and miRNA expression data drastically alleviates this problem. Here, I describe a mathematical linear modeling approach to identify miRNA targets at the genome scale using gene and miRNA expression data. Mathematical modeling is faster and more scalable to genome-level compared to conventional statistical modeling approaches. less

关键词： RNA Interference Mathematical Modeling Statistical Modeling Gene Expression Profiling Python programming language Gene expression Gene regulation miRNA MicroRNA Post-transcriptional gene regulation Linear programming Linear modeling Gurobi Mathematical optimization

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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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Confined activation and subdiffractive localization enables whole-cell PALM with genetically expressed probes

Confined activation and subdiffractive localization enables ...

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作者： Andrew G York Alireza Ghitani Alipasha Vaziri Michael W Davidson Hari Shroff

We demonstrate three-dimensional (3D) super-resolution microscopy in whole fixed cells using photoactivated localization microscopy (PALM). The use of the bright, genetically expressed fluorescent marker photoactivatable monomeric (m)Cherry (PA-mCherry1) in combination with near diffraction-limited confinement of photoactivation using two-photon illumination and 3D localization methods allowed us to investigate a variety of cellular structures at <50 nm lateral and <100 nm axial resolution. Compared to existing methods, we have substantially reduced excitation and bleaching of unlocalized markers, which allows us to use 3D PALM imaging with high localization density in thick structures. Our 3D localization algorithms, which are based on cross-correlation, do not rely on idealized noise models or specific optical configurations. This allows instrument design to be flexible. By generating appropriate fusion constructs and expressing them in Cos7 cells, we could image invaginations of the nuclear membrane, vimentin fibrils, the mitochondrial network and the endoplasmic reticulum at depths of greater than 8 μm. less

关键词： Super-resolution Microscopy Photoactivated Localization Microscopy Transfection PCR Capillary Electrophoresis (CE) DNA Sequencing Atomic Force Microscopy (AFM) Python programming language Cell biology Fluorescent proteins

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