The abundance of both taxonomic groups and gene categories in microbiome samples can now be easily assayed via various sequencing technologies, and visualized using a variety of software tools. ...However, the assemblage of taxa in the microbiome and its gene content are clearly linked, and tools for visualizing the relationship between these two facets of microbiome composition and for facilitating exploratory analysis of their co-variation are lacking. Here we introduce
, a web tool for interactive visualization of microbiome multi-omic data with paired taxonomic and functional information. BURRITO simultaneously visualizes the taxonomic and functional compositions of multiple samples and dynamically highlights relationships between taxa and functions to capture the underlying structure of these data. Users can browse for taxa and functions of interest and interactively explore the share of each function attributed to each taxon across samples. BURRITO supports multiple input formats for taxonomic and metagenomic data, allows adjustment of data granularity, and can export generated visualizations as static publication-ready formatted figures. In this paper, we describe the functionality of BURRITO, and provide illustrative examples of its utility for visualizing various trends in the relationship between the composition of taxa and functions in complex microbiomes.
POPTREE software, including the command line (POPTREE) and the Windows (POPTREE2) versions, is available to perform evolutionary analyses of allele frequency data, computing distance measures for ...constructing population trees and average heterozygosity (H) (measure of genetic diversity within populations) and G(ST) (measure of genetic differentiation among subdivided populations). We have now developed a web version POPTREEW (http://www.med.kagawa-u.ac.jp/∼genomelb/takezaki/poptreew/) to provide cross-platform access to all POPTREE functions including interactive tree editing. Furthermore, new POPTREE software (POPTREE, POPTREE2, and POPTREEW) computes standardized G(ST) and Jost's D, which may be appropriate for data with high variability, and accepts genotype data in GENEPOP format as an input.
Plant microbial fuel cells (PMFCs) are electrochemical systems capable of producing electrical energy from plant growth. Despite their limited power density, PMFCs hold pomise as power source for ...wireless sensor, without using embedded battery, especially in isolated locations. In this study, a complete wireless system was presented, with Cyperus papyrus-based microbial fuel cell. The Cyperus papyrus system was studied over 900 days. Although there was a slight decrease in power output attributed to anodic decreasing performance, the reduction at the cathode remained stable. This stability is likely due to biocatalyst activity, supported by the oxygen transport from the plant to the roots. Although performance of Cyperus papyrus microbial fuel cell were lower than those found in literature, these plants were stacked to power a microcontroller equipped with a temperature/humidity sensor. This microcontroller transmitted measurements wirelessly to a web server every 2 h. The web server, accessible via a web interface, provided real-time data to users on the local network. Finally, the intervals between measurements could serve as indicators of environmental stress, such as variations in soil moisture content.
Abstract
Large-scale selection analyses of protein-coding sequences and phylogenetic tree reconstructions require suitable trees in Newick format. We developed the NewickTreeModifier (NTM), a simple ...web-based tool to trim and modify Newick trees for such analyses. The users can choose provided master trees or upload a tree to prune it to selected species available in FASTA, NEXUS, or PHYLIP sequence format with an internal converter, a simple species list, or directly determined from a checklist interface of the master trees. Plant, insect, and vertebrate master trees comprise the maximum number of species in an up-to-date phylogenetic order directly transferable to the pruned Newick outfile. NTM is available at https://retrogenomics.uni-muenster.de/tools/ntm.
In an organisation with multiple departments and division of labour, email management becomes a daunting task, and choosing the right email allocation system significantly impacts the success of ...business communication. Although various webmail services and email client are available, mSPECTRA was developed at Journal of Clinical and Diagnostic Research (JCDR) to meet the key requirements of the company. mSPECTRA is an easy-to-use web-based email management system integrated in manuscript database portal and database resources that helps to effectively manage, track and respond to the large influx of emails.
Genome assemblies are foundational for understanding the biology of a species. They provide a physical framework for mapping additional sequences, thereby enabling characterization of, for example, ...genomic diversity and differences in gene expression across individuals and tissue types. Quality metrics for genome assemblies gauge both the completeness and contiguity of an assembly and help provide confidence in downstream biological insights. To compare quality across multiple assemblies, a set of common metrics are typically calculated and then compared to one or more gold standard reference genomes. While several tools exist for calculating individual metrics, applications providing comprehensive evaluations of multiple assembly features are, perhaps surprisingly, lacking. Here, we describe a new toolkit that integrates multiple metrics to characterize both assembly and gene annotation quality in a way that enables comparison across multiple assemblies and assembly types.
Our application, named GenomeQC, is an easy-to-use and interactive web framework that integrates various quantitative measures to characterize genome assemblies and annotations. GenomeQC provides researchers with a comprehensive summary of these statistics and allows for benchmarking against gold standard reference assemblies.
The GenomeQC web application is implemented in R/Shiny version 1.5.9 and Python 3.6 and is freely available at https://genomeqc.maizegdb.org/ under the GPL license. All source code and a containerized version of the GenomeQC pipeline is available in the GitHub repository https://github.com/HuffordLab/GenomeQC.
Precision agriculture allows farmers to manage their crops and agriculture field remotely by making use of IoT sensor. Present research has focused on enhancement of security services in precision ...agriculture. In previous research limited work has been made to improve security services in case of IoT based precision agriculture. Considering issues of cluster key management and problems in web interface configuration proposed work has introduced novel approach that is allowing cluster key management to enhance security. Moreover, web interface has been developed to capture the feedback from IoT sensor nodes. The web interface allows notification management after detecting signal from IoT sensor.
Nowadays the software market is increasingly looking to optimize in its processes and to achieve higher quality in its products. Among the processes under improvement, there is the Software Testing ...one, which contributes considerably to systems quality. Among them is the Interface Test, which is based on the definition of a sequence of events in the components of a graphical interface in order to search for faults.It is common to use automation tools with the ability to manage and control tests to assist this process. Among the main tools in the market there is Selenium WebDriver, which has limitations in its application. Therefore, the objective of this work is to carry out a comparative analysis between Cypress and Playwright, two tools whose architectures are different from Selenium, in order to assist professionals to choose automation frameworks related to the graphical interface. Based on this analysis, it was possible to verify a balance between the tools, with Cypress obtaining an advantage in relation to the efficiency of the tests and Playwright ensuring an advantage in the criteria of execution time and coverage of the tests.
Quantifying the response of cell lines to drugs or other perturbagens is the cornerstone of pre-clinical drug development and pharmacogenomics as well as a means to study factors that contribute to ...sensitivity and resistance. In dividing cells, traditional metrics derived from dose-response curves such as IC
, AUC, and E
, are confounded by the number of cell divisions taking place during the assay, which varies widely for biological and experimental reasons. Hafner et al. (Nat Meth 13:521-627, 2016) recently proposed an alternative way to quantify drug response, normalized growth rate (GR) inhibition, that is robust to such confounders. Adoption of the GR method is expected to improve the reproducibility of dose-response assays and the reliability of pharmacogenomic associations (Hafner et al. 500-502, 2017).
We describe here an interactive website ( www.grcalculator.org ) for calculation, analysis, and visualization of dose-response data using the GR approach and for comparison of GR and traditional metrics. Data can be user-supplied or derived from published datasets. The web tools are implemented in the form of three integrated Shiny applications (grcalculator, grbrowser, and grtutorial) deployed through a Shiny server. Intuitive graphical user interfaces (GUIs) allow for interactive analysis and visualization of data. The Shiny applications make use of two R packages (shinyLi and GRmetrics) specifically developed for this purpose. The GRmetrics R package is also available via Bioconductor and can be used for offline data analysis and visualization. Source code for the Shiny applications and associated packages (shinyLi and GRmetrics) can be accessed at www.github.com/uc-bd2k/grcalculator and www.github.com/datarail/gr_metrics .
GRcalculator is a powerful, user-friendly, and free tool to facilitate analysis of dose-response data. It generates publication-ready figures and provides a unified platform for investigators to analyze dose-response data across diverse cell types and perturbagens (including drugs, biological ligands, RNAi, etc.). GRcalculator also provides access to data collected by the NIH LINCS Program ( http://www.lincsproject.org /) and other public domain datasets. The GRmetrics Bioconductor package provides computationally trained users with a platform for offline analysis of dose-response data and facilitates inclusion of GR metrics calculations within existing R analysis pipelines. These tools are therefore well suited to users in academia as well as industry.
The language history questionnaire (LHQ) is an important tool for assessing the linguistic background of bilinguals or second language learners and for generating self-reported proficiency in ...multiple languages. Previously we developed a generic LHQ based on the most commonly asked questions in published studies (Li, Sepanski & Zhao, 2006). Here we report a new web-based interface (LHQ 2.0) that has more flexibility in functionality, more accuracy in data recording, and more privacy for users and data. LHQ 2.0 achieves flexibility, accuracy, and privacy by using dynamic web-design features for enhanced data collection. It allows investigators to dynamically construct individualized LHQs on the fly and allows participants to complete the LHQ online in multiple languages. Investigators can download and delete the LHQ results and update their user and experiment information on the web. Privacy issues are handled through the online assignment of a unique ID number for each study and password-protected access to data.
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