ResearchPad - technology-and-code https://www.researchpad.co Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[FluentDNA: Nucleotide Visualization of Whole Genomes, Annotations, and Alignments]]> https://www.researchpad.co/article/elastic_article_7640 Researchers seldom look at naked genome assemblies: instead the attributes of DNA sequences are mediated through statistics, annotations and high level summaries. Here we present software that visualizes the bare sequences of whole genome assemblies in a zoomable interface. This can assist in detection of chromosome architecture and contamination by the naked eye through changes in color patterns, in the absence of any other annotation. When available, annotations can be visualized alongside or on top of the naked sequence. Genome alignments can also be visualized, laying two genomes side by side in an alignment and highlighting their differences at nucleotide resolution. FluentDNA gives researchers direct visualization of whole genome assemblies, annotations and alignments, for quality control, hypothesis generation, and communicating results.

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<![CDATA[Modular Current Stimulation System for Pre-clinical Studies]]> https://www.researchpad.co/article/elastic_article_7633 Electric stimulators with precise and reliable outputs are an indispensable part of electrophysiological research. From single cells to deep brain or neuromuscular tissue, there are diverse targets for electrical stimulation. Even though commercial systems are available, we state the need for a low-cost, high precision, functional, and modular (hardware, firmware, and software) current stimulation system with the capacity to generate stable and complex waveforms for pre-clinical research. The system presented in this study is a USB controlled 4-channel modular current stimulator that can be expanded and generate biphasic arbitrary waveforms with 16-bit resolution, high temporal precision (μs), and passive charge balancing: the NES STiM (Neuro Electronic Systems Stimulator). We present a detailed description of the system’s structural design, the controlling software, reliability test, and the pre-clinical studies [deep brain stimulation (DBS) in hemi-PD rat model] in which it was utilized. The NES STiM has been tested with MacOS and Windows operating systems. Interfaces to MATLAB source codes are provided. The system is inexpensive, relatively easy to build and can be assembled quickly. We hope that the NES STiM will be used in a wide variety of neurological applications such as Functional Electrical Stimulation (FES), DBS and closed loop neurophysiological research.

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<![CDATA[MasterOfPores: A Workflow for the Analysis of Oxford Nanopore Direct RNA Sequencing Datasets]]> https://www.researchpad.co/article/Ne463e5d3-c104-43de-8f51-a6a841abc2ba

The direct RNA sequencing platform offered by Oxford Nanopore Technologies allows for direct measurement of RNA molecules without the need of conversion to complementary DNA, fragmentation or amplification. As such, it is virtually capable of detecting any given RNA modification present in the molecule that is being sequenced, as well as provide polyA tail length estimations at the level of individual RNA molecules. Although this technology has been publicly available since 2017, the complexity of the raw Nanopore data, together with the lack of systematic and reproducible pipelines, have greatly hindered the access of this technology to the general user. Here we address this problem by providing a fully benchmarked workflow for the analysis of direct RNA sequencing reads, termed MasterOfPores. The pipeline starts with a pre-processing module, which converts raw current intensities into multiple types of processed data including FASTQ and BAM, providing metrics of the quality of the run, quality-filtering, demultiplexing, base-calling and mapping. In a second step, the pipeline performs downstream analyses of the mapped reads, including prediction of RNA modifications and estimation of polyA tail lengths. Four direct RNA MinION sequencing runs can be fully processed and analyzed in 10 h on 100 CPUs. The pipeline can also be executed in GPU locally or in the cloud, decreasing the run time fourfold. The software is written using the NextFlow framework for parallelization and portability, and relies on Linux containers such as Docker and Singularity for achieving better reproducibility. The MasterOfPores workflow can be executed on any Unix-compatible OS on a computer, cluster or cloud without the need of installing any additional software or dependencies, and is freely available in Github (https://github.com/biocorecrg/master_of_pores). This workflow simplifies direct RNA sequencing data analyses, facilitating the study of the (epi)transcriptome at single molecule resolution.

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<![CDATA[A Bayesian Approach to the Analysis of Local Average Treatment Effect for Missing and Non-normal Data in Causal Modeling: A Tutorial With the ALMOND Package in R]]> https://www.researchpad.co/article/Nfd8e5604-17ce-4f94-ae37-e439e32523c2

One practical challenge in observational studies and quasi-experimental designs is selection bias. The issue of selection bias becomes more concerning when data are non-normal and contain missing values. Recently, a Bayesian robust two-stage causal modeling with instrumental variables was developed and has the advantages of addressing selection bias and handle non-normal data and missing data simultaneously in one model. The method provides reliable parameter and standard error estimates when missing data and outliers exist. The modeling technique can be widely applied to empirical studies particularly in social, psychological and behavioral areas where any of the three issues (e.g., selection bias, data with outliers and missing data) is commonly seen. To implement this method, we developed an R package named ALMOND (Analysis of LATE (Local Average Treatment Effect) for Missing Or/and Nonnormal Data). Package users have the flexibility to directly apply the Bayesian robust two-stage causal models or write their own Bayesian models from scratch within the package. To facilitate the application of the Bayesian robust two-stage causal modeling technique, we provide a tutorial for the ALMOND package in this article, and illustrate the application with two examples from empirical research.

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<![CDATA[BarleyNet: A Network-Based Functional Omics Analysis Server for Cultivated Barley, Hordeum vulgare L.]]> https://www.researchpad.co/article/Na7fb7a8c-58cf-4727-b4e8-e1a22d6aadf4

Cultivated barley (Hordeum vulgare L.) is one of the most produced cereal crops worldwide after maize, bread wheat, and rice. Barley is an important crop species not only as a food source, but also in plant genetics because it harbors numerous stress response alleles in its genome that can be exploited for crop engineering. However, the functional annotation of its genome is relatively poor compared with other major crops. Moreover, bioinformatics tools for system-wide analyses of omics data from barley are not yet available. We have thus developed BarleyNet, a co-functional network of 26,145 barley genes, along with a web server for network-based predictions (http://www.inetbio.org/barleynet). We demonstrated that BarleyNet's prediction of biological processes is more accurate than that of an existing barley gene network. We implemented three complementary network-based algorithms for prioritizing genes or functional concepts to study genetic components of complex traits such as environmental stress responses: (i) a pathway-centric search for candidate genes of pathways or complex traits; (ii) a gene-centric search to infer novel functional concepts for genes; and (iii) a context-centric search for novel genes associated with stress response. We demonstrated the usefulness of these network analysis tools in the study of stress response using proteomics and transcriptomics data from barley leaves and roots upon drought or heat stresses. These results suggest that BarleyNet will facilitate our understanding of the underlying genetic components of complex traits in barley.

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<![CDATA[4See: A Flexible Browser to Explore 4C Data]]> https://www.researchpad.co/article/N0cb432c1-b335-4034-a6a7-58661e730a03

It is established that transcription of many metazoan genes is regulated by distal regulatory sequences beyond the promoter. Enhancers have been identified at up to megabase distances from their regulated genes, and/or proximal to or within the introns of unregulated genes. The unambiguous identification of the target genes of newly identified regulatory elements can thus be challenging. Well-studied enhancers have been found to come into direct physical proximity with regulated genes, presumably by the formation of chromatin loops. Chromosome conformation capture (3C) derivatives that assess the frequency of proximity between different genetic elements is thus a popular method for exploring gene regulation by distal regulatory elements. For studies of chromatin loops and promoter-enhancer communication, 4C (circular chromosome conformation capture) is one of the methods of choice, optimizing cost (required sequencing depth), throughput, and resolution. For ease of visual inspection of 4C data we present 4See, a versatile and user-friendly browser. 4See allows 4C profiles from the same bait to be flexibly plotted together, allowing biological replicates to either be compared, or pooled for comparisons between different cell types or experimental conditions. 4C profiles can be integrated with gene tracks, linear epigenomic profiles, and annotated regions of interest, such as called significant interactions, allowing rapid data exploration with limited computational resources or bioinformatics expertise.

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<![CDATA[DscoreApp: A Shiny Web Application for the Computation of the Implicit Association Test D-Score]]> https://www.researchpad.co/article/Nc600c33c-1c57-46af-90f9-fc3805616f42

Several options are available for computing the most common score for the Implicit Association Test, the so-called D-score. However, all these options come with some drawbacks, related to either the need for a license, for being tailored on a specific administration procedure, or for requiring a degree of familiarity with programming. By using the R shiny package, a user-friendly, interactive, and open source web application (DscoreApp) has been created for the D-score computation. This app provides different options for computing the D-score algorithms and for applying different cleaning criteria. Beyond making the D-score computation easier, DscoreApp offers the chance to have an immediate glimpse on the results and to see how they change according to different settings configurations. The resulting D-scores are immediately available and can be seen in easy-readable and interactive graphs, along with meaningful descriptive statistics. Graphical representations, data sets containing the D-scores, and other information on participants' performance are downloadable. In this work, the use of DscoreApp is illustrated on an empirical data set.

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<![CDATA[Sepia, Tarsier, and Chameleon: A Modular C++ Framework for Event-Based Computer Vision]]> https://www.researchpad.co/article/Nd57412ac-d0d3-4812-a6e8-532bc068a993

This paper introduces an new open-source, header-only and modular C++ framework to facilitate the implementation of event-driven algorithms. The framework relies on three independent components: sepia (file IO), tarsier (algorithms), and chameleon (display). Our benchmarks show that algorithms implemented with tarsier are faster and have a lower latency than identical implementations in other state-of-the-art frameworks, thanks to static polymorphism (compile-time pipeline assembly). The observer pattern used throughout the framework encourages implementations that better reflect the event-driven nature of the algorithms and the way they process events, easing future translation to neuromorphic hardware. The framework integrates drivers to communicate with the DVS, the DAVIS, the Opal Kelly ATIS, and the CCam ATIS.

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<![CDATA[Assaying Homodimers of NF-κB in Live Single Cells]]> https://www.researchpad.co/article/N57c2bd30-6c26-4f7d-8b83-97d2ae14dc93

NF-κB is a family of heterodimers and homodimers which are generated from subunits encoded by five genes. The predominant classical dimer RelA:p50 is presumed to operate as “NF-κB” in many contexts. However, there are several other dimer species which exist and may even be more functionally relevant in specific cell types. Accurate characterization of stimulus-specific and tissue-specific dimer repertoires is fundamentally important for understanding the downstream gene regulation by NF-κB proteins. In vitro assays such as immunoprecipitation have been widely used to analyze subunit composition, but these methods do not provide information about dimerization status within the natural intracellular environment of intact live cells. Here we apply a live single cell microscopy technique termed Number and Brightness to examine dimers translocating to the nucleus in fibroblasts after pro-inflammatory stimulation. This quantitative assay suggests that RelA:RelA homodimers are more prevalent than might be expected. We also found that the relative proportion of RelA:RelA homodimers can be perturbed by small molecule inhibitors known to disrupt the NF-κB pathway. Our findings show that Number and Brightness is a useful method for investigating NF-κB dimer species in live cells. This approach may help identify the relevant targets in pathophysiological contexts where the dimer specificity of NF-κB intervention is desired.

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