scholarly journals PinAPL-Py: A comprehensive web-application for the analysis of CRISPR/Cas9 screens

2017 ◽  
Author(s):  
Philipp N. Spahn ◽  
Tyler Bath ◽  
Ryan J. Weiss ◽  
Jihoon Kim ◽  
Jeffrey D. Esko ◽  
...  
Keyword(s):  
Web Application ◽  
Large Scale ◽  
Sequencing Data ◽  
Bioinformatic Tools ◽  
Link Type ◽  
Screening Experiments ◽  
Independent Analysis ◽  
Wide Range ◽  
Set Up ◽  
Sequence Quality

AbstractBackgroundLarge-scale genetic screens using CRISPR/Cas9 technology have emerged as a major tool for functional genomics. With its increased popularity, experimental biologists frequently acquire large sequencing datasets for which they often do not have an easy analysis option. While a few bioinformatic tools have been developed for this purpose, their utility is still hindered either due to limited functionality or the requirement of bioinformatic expertise.ResultsTo make sequencing data analysis of CRISPR/Cas9 screens more accessible to a wide range of scientists, we developed a Platform-independent Analysis of Pooled Screens using Python (PinAPL-Py), which is operated as an intuitive web-service. PinAPL-Py implements state-of-the-art tools and statistical models, assembled in a comprehensive workflow covering sequence quality control, automated sgRNA sequence extraction, alignment, sgRNA enrichment/depletion analysis and gene ranking. The workflow is set up to use a variety of popular sgRNA libraries as well as custom libraries that can be easily uploaded. Various analysis options are offered, suitable to analyze a large variety of CRISPR/Cas9 screening experiments. Analysis output includes ranked lists of sgRNAs and genes, and publication-ready plots.ConclusionsPinAPL-Py helps to advance genome-wide screening efforts by combining comprehensive functionality with user-friendly implementation. PinAPL-Py is freely accessible at http://pinapl-py.ucsd.edu with instructions, documentation and test datasets. The source code is available at https://github.com/LewisLabUCSD/PinAPL-Py

scholarly journals RiboA: a web application to identify ribosome A-site locations in ribosome profiling data

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Danying Shao ◽  
Nabeel Ahmed ◽  
Nishant Soni ◽  
Edward P. O’Brien
Keyword(s):  
Integer Programming ◽  
Web Application ◽  
Stop Codon ◽  
Ribosome Profiling ◽  
Programming Method ◽  
Analysis Tool ◽  
Site Location ◽  
Link Type ◽  
Wide Range ◽  
A Site

Abstract Background Translation is a fundamental process in gene expression. Ribosome profiling is a method that enables the study of transcriptome-wide translation. A fundamental, technical challenge in analyzing Ribo-Seq data is identifying the A-site location on ribosome-protected mRNA fragments. Identification of the A-site is essential as it is at this location on the ribosome where a codon is translated into an amino acid. Incorrect assignment of a read to the A-site can lead to lower signal-to-noise ratio and loss of correlations necessary to understand the molecular factors influencing translation. Therefore, an easy-to-use and accurate analysis tool is needed to accurately identify the A-site locations. Results We present RiboA, a web application that identifies the most accurate A-site location on a ribosome-protected mRNA fragment and generates the A-site read density profiles. It uses an Integer Programming method that reflects the biological fact that the A-site of actively translating ribosomes is generally located between the second codon and stop codon of a transcript, and utilizes a wide range of mRNA fragment sizes in and around the coding sequence (CDS). The web application is containerized with Docker, and it can be easily ported across platforms. Conclusions The Integer Programming method that RiboA utilizes is the most accurate in identifying the A-site on Ribo-Seq mRNA fragments compared to other methods. RiboA makes it easier for the community to use this method via a user-friendly and portable web application. In addition, RiboA supports reproducible analyses by tracking all the input datasets and parameters, and it provides enhanced visualization to facilitate scientific exploration. RiboA is available as a web service at https://a-site.vmhost.psu.edu/. The code is publicly available at https://github.com/obrien-lab/aip_web_docker under the MIT license.

The structure of weakly compressible grid-generated turbulence

2001 ◽  
Vol 432 ◽  
pp. 219-283 ◽  
Author(s):  
G. BRIASSULIS ◽  
J. H. AGUI ◽  
Y. ANDREOPOULOS
Keyword(s):  
Mach Number ◽  
Large Scale ◽  
Isotropic Turbulence ◽  
Three Dimensional ◽  
High Amplitude ◽  
Time Dependent ◽  
Wide Range ◽  
Dynamical Flow ◽  
Set Up ◽  
Decay Exponent

A decaying compressible nearly homogeneous and nearly isotropic grid-generated turbulent flow has been set up in a large scale shock tube research facility. Experiments have been performed using instrumentation with spatial resolution of the order of 7 to 26 Kolmogorov viscous length scales. A variety of turbulence-generating grids provided a wide range of turbulence scales with bulk flow Mach numbers ranging from 0.3 to 0.6 and turbulent Reynolds numbers up to 700. The decay of Mach number fluctuations was found to follow a power law similar to that describing the decay of incompressible isotropic turbulence. It was also found that the decay coefficient and the decay exponent decrease with increasing Mach number while the virtual origin increases with increasing Mach number. A possible mechanism responsible for these effects appears to be the inherently low growth rate of compressible shear layers emanating from the cylindrical rods of the grid. Measurements of the time-dependent, three dimensional vorticity vectors were attempted for the first time with a 12-wire miniature probe. This also allowed estimates of dilatation, compressible dissipation and dilatational stretching to be obtained. It was found that the fluctuations of these quantities increase with increasing mean Mach number of the flow. The time-dependent signals of enstrophy, vortex stretching/tilting vector and dilatational stretching vector were found to exhibit a rather strong intermittent behaviour which is characterized by high-amplitude bursts with values up to 8 times their r.m.s. within periods of less violent and longer lived events. Several of these bursts are evident in all the signals, suggesting the existence of a dynamical flow phenomenon as a common cause.

scholarly journals A curated transcriptome dataset collection to investigate inborn errors of immunity

2019 ◽  
Author(s):  
Salim Bougarn ◽  
Sabri Boughorbel ◽  
Damien Chaussabel ◽  
Nico Marr
Keyword(s):  
Web Application ◽  
Large Scale ◽  
Mononuclear Cells ◽  
Ex Vivo ◽  
Clinical Manifestations ◽  
Inherited Disorders ◽  
Transcriptional Responses ◽  
Control Subjects ◽  
A Genome ◽  
Wide Range

ABSTRACTPrimary immunodeficiencies (PIDs) are a heterogeneous group of inherited disorders, frequently caused by loss-of-function and less commonly by gain-of-function mutations, which can result in susceptibility to a broad or a very narrow range of infections but also in inflammatory, allergic or malignant diseases. Owing to the wide range in clinical manifestations and variability in penetrance and expressivity, there is an urgent need to better understand the underlying molecular, cellular and immunological phenotypes in PID patients in order to improve clinical diagnosis and management. Here we have compiled a manually curated collection of public transcriptome datasets mainly obtained from human whole blood, peripheral blood mononuclear cells (PBMCs) or fibroblasts of patients with PIDs and of control subjects for subsequent meta-analysis, query and interpretation. A total of nineteen (19) datasets derived from studies of PID patients were identified and retrieved from the NCBI Gene Expression Omnibus (GEO) database and loaded in GXB, a custom web application designed for interactive query and visualization of integrated large-scale data. The dataset collection includes samples from well characterized PID patients that were stimulated ex vivo under a variety of conditions to assess the molecular consequences of the underlying, naturally occurring gene defects on a genome-wide scale. Multiple sample groupings and rank lists were generated to facilitate comparisons of the transcriptional responses between different PID patients and control subjects. The GXB tool enables browsing of a single transcript across studies, thereby providing new perspectives on the role of a given molecule across biological systems and PID patients. This dataset collection is available at: http://pid.gxbsidra.org/dm3/geneBrowser/list.

scholarly journals re-Searcher: GUI-based bioinformatics tool for simplified genomics data mining of VCF files

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11333
Author(s):  
Daniyar Karabayev ◽  
Askhat Molkenov ◽  
Kaiyrgali Yerulanuly ◽  
Ilyas Kabimoldayev ◽  
Asset Daniyarov ◽  
...  
Keyword(s):  
Web Application ◽  
High Throughput Sequencing ◽  
Sequencing Data ◽  
Data Types ◽  
Standard Format ◽  
Standard Data ◽  
Additional Information ◽  
Link Type ◽  
Sequencing Platforms ◽  
User Friendly

Background High-throughput sequencing platforms generate a massive amount of high-dimensional genomic datasets that are available for analysis. Modern and user-friendly bioinformatics tools for analysis and interpretation of genomics data becomes essential during the analysis of sequencing data. Different standard data types and file formats have been developed to store and analyze sequence and genomics data. Variant Call Format (VCF) is the most widespread genomics file type and standard format containing genomic information and variants of sequenced samples. Results Existing tools for processing VCF files don’t usually have an intuitive graphical interface, but instead have just a command-line interface that may be challenging to use for the broader biomedical community interested in genomics data analysis. re-Searcher solves this problem by pre-processing VCF files by chunks to not load RAM of computer. The tool can be used as standalone user-friendly multiplatform GUI application as well as web application (https://nla-lbsb.nu.edu.kz). The software including source code as well as tested VCF files and additional information are publicly available on the GitHub repository (https://github.com/LabBandSB/re-Searcher).

scholarly journals Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex

2020 ◽  
Author(s):  
Kristen R. Maynard ◽  
Leonardo Collado-Torres ◽  
Lukas M. Weber ◽  
Cedric Uytingco ◽  
Brianna K. Barry ◽  
...  
Keyword(s):  
Gene Expression ◽  
Prefrontal Cortex ◽  
Web Application ◽  
Dorsolateral Prefrontal Cortex ◽  
Large Scale ◽  
Brain Regions ◽  
Autism Spectrum ◽  
Sequencing Data ◽  
Dorsolateral Prefrontal ◽  
Transcriptomics Data

AbstractWe used the 10x Genomics Visium platform to define the spatial topography of gene expression in the six-layered human dorsolateral prefrontal cortex (DLPFC). We identified extensive layer-enriched expression signatures, and refined associations to previous laminar markers. We overlaid our laminar expression signatures onto large-scale single nuclei RNA sequencing data, enhancing spatial annotation of expression-driven clusters. By integrating neuropsychiatric disorder gene sets, we showed differential layer-enriched expression of genes associated with schizophrenia and autism spectrum disorder, highlighting the clinical relevance of spatially-defined expression. We then developed a data-driven framework to define unsupervised clusters in spatial transcriptomics data, which can be applied to other tissues or brain regions where morphological architecture is not as well-defined as cortical laminae. We lastly created a web application for the scientific community to explore these raw and summarized data to augment ongoing neuroscience and spatial transcriptomics research (http://research.libd.org/spatialLIBD).

scholarly journals CRISPR-RT: A web service for designing CRISPR-C2c2 crRNA with improved target specificity

2017 ◽  
Author(s):  
Houxiang Zhu ◽  
Emily Richmond ◽  
Chun Liang
Keyword(s):  
Web Service ◽  
Genome Editing ◽  
Rna Editing ◽  
Model Organisms ◽  
Future Research ◽  
Target Specificity ◽  
Link Type ◽  
Wide Range ◽  
Set Up

AbstractCRISPR-Cas systems have been successfully applied in genome editing. Recently, the CRISPR-C2c2 system has been reported as a tool for RNA editing. Here we describe CRISPR-RT (CRISPR RNA-Targeting), the first web service to help biologists design the crRNA with improved target specificity for the CRISPR-C2c2 system. CRISPR-RT allows users to set up a wide range of parameters, making it highly flexible for current and future research in CRISPR-based RNA editing. CRISPR-RT covers major model organisms and can be easily extended to cover other species. CRISPR-RT will empower researchers in RNA editing. It is available at http://bioinfolab.miamioh.edu/CRISPR-RT.

scholarly journals sangeranalyseR: simple and interactive analysis of Sanger sequencing data in R

2020 ◽  
Author(s):  
Kuan-Hao Chao ◽  
Kirston Barton ◽  
Sarah Palmer ◽  
Robert Lanfear
Keyword(s):  
Sanger Sequencing ◽  
Reference Sequence ◽  
Supplementary Information ◽  
File Format ◽  
Bioconductor Package ◽  
Sequencing Data ◽  
Interactive Analysis ◽  
Link Type ◽  
Online Documentation ◽  
Wide Range

AbstractSummarysangeranalyseR is an interactive R/Bioconductor package and two associated Shiny applications designed for analysing Sanger sequencing from data from the ABIF file format in R. It allows users to go from loading reads to saving aligned contigs in a few lines of R code. sangeranalyseR provides a wide range of options for a number of commonly-performed actions including read trimming, detecting secondary peaks, viewing chromatograms, and detecting indels using a reference sequence. All parameters can be adjusted interactively either in R or in the associated Shiny applications. sangeranalyseR comes with extensive online documentation, and outputs detailed interactive HTML reports.Availability and implementationsangeranalyseR is implemented in R and released under an MIT license. It is available for all platforms on Bioconductor (https://bioconductor.org/packages/sangeranalyseR) and on Github (https://github.com/roblanf/sangeranalyseR)[email protected] informationDocumentation at https://sangeranalyser.readthedocs.io/.

scholarly journals Sustainable Hospitality Management and Dimensions of Environmental Regulations: A Qualitative Study on the Puducherry Perspective

2012 ◽  
Vol 7 (2) ◽  
pp. 23-40
Author(s):  
Anu Chandran R C ◽  
Sherry Abraham
Keyword(s):  
Land Use Planning ◽  
Large Scale ◽  
Hospitality Industry ◽  
Hospitality Management ◽  
Business Practices ◽  
Environmental Laws ◽  
Wide Range ◽  
Set Up ◽  
Traditional Patterns ◽  
Tourism And Hospitality

Tourism  and  hospitality,  globally,  is  experiencing  a paradigm shift. The modern day tourists and clients of hospitality are very discerning and opt for higher quality and value based products and services. To cater to their needs, a wide range of properties at various scales are being introduced in  the  sector. At the same time, it is increasingly recognised that unplanned and uncontrolled hospitality ventures are causing certain adverse impacts on  the  environment.  These  necessitate thorough supervision of the hospitality  projects, both existing as well as upcoming, and positively check whether they are abiding by the prescribed guidelines as prevailing under the environmental notifications. That is, the set up and operations  must  be  actively  monitored  as  per the Environmental Laws and Rules. The accelerated growth of  international  and  domestic  tourists  to  Puducherry resulted in the spurt of hospitality establishments across the destination. This growth can be sustained only if the hotels, resorts, restaurants and other hospitality outlets operate by showing profound consideration towards the environment. The  business  practices  in  the  hospitality sector  of  Puducherry  are  undergoing  great transformations,  imbibing  the  latest  and  the  best  of things. Technological  advancements  have  also  altered traditional  patterns  and  many  innovative  trends  are emerging  in  the  hospitality  trade.  With  the  increased impact on  the  environment  owing  to  large  scale establishment  and  expansion  of  hospitality  projects  in Puducherry, comes the need for informed planning and sustainable  management  as  well  as  education  and training for  developers,  investors,  planners,  managers and  local  communities.  Owing  to  this  reason, the management  of  hospitality  firms  in  Puducherry  must abide by the Environmental Laws and Rules to prevent haphazard,  uncontrolled  growth,  spatial  and  land  use planning;  conforming  to  strict  architectural  controls, sewerage facilities and water treatment plants. This paper brings  to  light  the  challenges  faced  by the hospitality industry of Puducherry with regards to consumption and conservation  of  natural  resources, by  gathering  and analysing the opinion  of  experts  from the hospitality trade  and the environmental  pollution  control organisations.  This  study elucidates  the  Environmental Laws and Rules which are necessary, as in the case of the hospitality  industry  of  Puducherry, to  curtail  adverse effects  on  the  environment.  It  is  for  sure  that, in the future, quality  practices  and  management  styles  as guided and enforced by the environmental laws would contribute to  resolve  many  shortcomings  faced  by the hospitality enterprises in Puducherry.

scholarly journals From the Ocean to the Lab—Assessing Iron Limitation in Cyanobacteria: An Interface Paper

2020 ◽  
Vol 8 (12) ◽  
pp. 1889
Author(s):  
Annie Vera Hunnestad ◽  
Anne Ilse Maria Vogel ◽  
Evelyn Armstrong ◽  
Maria Guadalupe Digernes ◽  
Murat Van Ardelan ◽  
...  
Keyword(s):  
Inductively Coupled Plasma ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Fluorescence Emission ◽  
Cellular Level ◽  
Iron Limitation ◽  
Inductively Coupled ◽  
Wide Range ◽  
Plasma Mass Spectrometry ◽  
Set Up

Iron is an essential, yet scarce, nutrient in marine environments. Phytoplankton, and especially cyanobacteria, have developed a wide range of mechanisms to acquire iron and maintain their iron-rich photosynthetic machinery. Iron limitation studies often utilize either oceanographic methods to understand large scale processes, or laboratory-based, molecular experiments to identify underlying molecular mechanisms on a cellular level. Here, we aim to highlight the benefits of both approaches to encourage interdisciplinary understanding of the effects of iron limitation on cyanobacteria with a focus on avoiding pitfalls in the initial phases of collaboration. In particular, we discuss the use of trace metal clean methods in combination with sterile techniques, and the challenges faced when a new collaboration is set up to combine interdisciplinary techniques. Methods necessary for producing reliable data, such as High Resolution Inductively Coupled Plasma Mass Spectrometry (HR-ICP-MS), Flow Injection Analysis Chemiluminescence (FIA-CL), and 77K fluorescence emission spectroscopy are discussed and evaluated and a technical manual, including the preparation of the artificial seawater medium Aquil, cleaning procedures, and a sampling scheme for an iron limitation experiment is included. This paper provides a reference point for researchers to implement different techniques into interdisciplinary iron studies that span cyanobacteria physiology, molecular biology, and biogeochemistry.

Preparation of Metal-Gr Composite Coatings via Electro-Plating for High Performances: A Review

MRS Advances ◽  
2019 ◽  
Vol 4 (35) ◽  
pp. 1913-1928
Author(s):  
Sishi Li ◽  
Yanpeng Yang ◽  
Gongsheng Song ◽  
Qiang Fu ◽  
Chunxu Pan
Keyword(s):  
Mechanical Properties ◽  
Corrosion Resistance ◽  
Large Scale ◽  
Low Cost ◽  
Composite Coatings ◽  
Scale Production ◽  
Electro Deposition ◽  
Wide Range ◽  
Set Up ◽  
Wear And Corrosion Resistance

ABSTRACTDeveloping metal-based composite coatings with improved mechanical properties and good corrosion resistance has been an attractive research topic in recent years. Graphene (Gr), as a new type of two-dimensional (2D) carbon nanomaterial with excellent physical, chemical and mechanical properties, can be used as a reinforcement to improve hardness, tensile strength, wear and corrosion resistance of metal-based composites. There have been substantial efforts focused on the fabrication of metal-Gr composite coatings via various approaches. Electro-deposition is an effective electrochemical method with wide range of advantages, such as a fast deposition rate, simple set-up with large scale production and relatively low cost. This overview covers the previous research and development studies on metal-Gr composite coatings using electro-deposition method and the resulting properties. In addition, recent work in this area which provides a developed process with industrial production perspective, is discussed.

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