Interactive Graphical Tool Research Articles

EDARA: An ERA5-based Dataset for Atmospheric River Analysis

Atmospheric Rivers (ARs) are long and narrow bands of strong horizontal water vapour transport concentrated in the lower troposphere. ARs play an important role in producing some high-impact weather events such as extreme precipitation and flooding, damaging winds, and temperature anomalies. To facilitate various studies on the short- and long-term variability of ARs and their impacts, I compiled a multi-decade global dataset containing 12 relevant meteorological variables for AR analysis. These variables were derived from the European Centre for Medium-Range Weather Forecasts atmospheric reanalysis version 5 (ERA5). They are available at 6-hour intervals from 1940 to present. Also included in the dataset is an interactive web browser-based graphical tool for visualising the AR evolution on regional (North America) and global scales. This ERA5-based Dataset for Atmospheric River Analysis (EDARA) may serve as a valuable resource for many AR-related research and applications.

Analysing the SEDs of protoplanetary disks with machine learning

Context. The analysis of spectral energy distributions (SEDs) of protoplanetary disks to determine their physical properties is known to be highly degenerate. Hence, a full Bayesian analysis is required to obtain parameter uncertainties and degeneracies. The main challenge here is computational speed, as one proper full radiative transfer model requires at least a couple of CPU minutes to compute. Aims. We performed a full Bayesian analysis for 30 well-known protoplanetary disks to determine their physical disk properties, including uncertainties and degeneracies. To circumvent the computational cost problem, we created neural networks (NNs) to emulate the SED generation process. Methods. We created two sets of MCFOST Monte Carlo radiative transfer disk models to train and test two NNs that predict SEDs for continuous and discontinuous disks, with 18 and 26 free model parameters, respectively. A Bayesian analysis was then performed on 30 protoplanetary disks with SED data collected by the FP7-Space DIANA project to determine the posterior distributions of all parameters. We ran this analysis twice, (i) with old distances and additional parameter constraints as used in a previous study, to compare results, and (ii) with updated distances and free choice of parameters to obtain homogeneous and unbiased model parameters. We evaluated the uncertainties in the determination of physical disk parameters from SED analysis, and detected and quantified the strongest degeneracies. Results. The NNs are able to predict SEDs within ~1 ms with uncertainties of about 5% compared to the true SEDs obtained by the radiative transfer code. We find parameter values and uncertainties that are significantly different from previous values obtained by χ2 fitting. Comparing the global evidence for continuous and discontinuous disks, we find that 26 out of 30 objects are better described by disks that have two distinct radial zones. The analysed sample shows a significant trend for massive disks to have small scale heights, which is consistent with lower midplane temperatures in massive disks. We find that the frequently used analytic relationship between disk dust mass and millimetre-flux systematically underestimates the dust mass for high-mass disks (dust mass ≥10−4 M⊙). We determine how well the dust mass can be determined with our method for different numbers of flux measurements. As a byproduct, we created an interactive graphical tool that instantly returns the SED predicted by our NNs for any parameter combination.

An interactive graphical interface tool for parameter calibration, sensitivity analysis, uncertainty analysis, and visualization for the Soil and Water Assessment Tool

The Soil and Water Assessment Tool (SWAT) is one of the most widely used and well-tested eco-hydrological models. However, parameter calibration, sensitivity analysis and uncertainty analysis remain among the most challenging tasks. Existing SWAT parameter calibration, sensitivity analysis, and uncertainty analysis tools are either commercial products or free tools with limited options. This study demonstrates an interactive graphical user interface tool in the R environment for SWAT parameter calibration, sensitivity and uncertainty analyses, and visualization, called R-SWAT. Different R functions/packages for parameter calibration, sensitivity analysis, and uncertainty analysis have been incorporated into R-SWAT. Third-party packages can be integrated into R-SWAT with minimum effort. The application of R-SWAT for a test case study demonstrates its functionalities. In general, R-SWAT (1) is a potential platform for developing and testing new sensitivity or optimization packages, and (2) promotes the understanding of hydrological processes with open-source SWAT and R.

Visualization of a curated Oryza sativa L. CDPKs Protein-Protein Interaction Network (CDPK-OsPPIN).

Calcium-Dependent Protein Kinases (CDPKs) translate calcium ion (Ca2+) signals into direct phosphorylation of proteins involved in stress response and plant growth. To get a clear picture of CDPKs functions, we must identify and explore the CDPKs targets and their respective roles in plant physiology. Here, we present a manually curated Oryza sativa L. CDPK Protein-Protein Interaction Network (CDPK-OsPPIN). The CDPK-OsPPIN provides an interactive graphical tool to assist hypothesis generation by researchers investigating CDPK roles and functional diversity.

Microbial Phylogenetic Context Using Phylogenetic Outlines.

Microbial studies typically involve the sequencing and assembly of draft genomes for individual microbes or whole microbiomes. Given a draft genome, one first task is to determine its phylogenetic context, that is, to place it relative to the set of related reference genomes. We provide a new interactive graphical tool that addresses this task using Mash sketches to compare against all bacterial and archaeal representative genomes in the Genome Taxonomy Database taxonomy, all within the framework of SplitsTree5. The phylogenetic context of the query sequences is then displayed as a phylogenetic outline, a new type of phylogenetic network that is more general than a phylogenetic tree, but significantly less complex than other types of phylogenetic networks. We propose to use such networks, rather than trees, to represent phylogenetic context, because they can express uncertainty in the placement of taxa, whereas a tree must always commit to a specific branching pattern. We illustrate the new method using a number of draft genomes of different assembly quality.

Introducing a Real-time Interactive GUI Tool for Visualization of Galaxy Spectra

Abstract To aid the understanding of the nonlinear relationship between galaxy properties and predicted spectral energy distributions (SED), we present a new interactive graphical user interface tool pipes_vis based on Bagpipes. It allows for real-time manipulation of a model galaxy’s star formation history, dust and other relevant properties through sliders and text boxes, with each change’s effect on the predicted SED reflected instantaneously. We hope the tool will assist in building intuition about what affects the SED of galaxies, potentially helping to speed up fitting stages such as prior construction, and aid in undergraduate and graduate teaching. pipes_vis is available online (pipes_vis is maintained and documented online at https://github.com/HinLeung622/pipes_vis, or version 0.4.1 is archived in Zenodo (Leung 2021) and also available for installation through pip install pipes_vis).

A Fast GUI-Based Tool for Group-Velocity Analysis of Surface Waves

AbstractWe present an interactive graphical tool for extraction of group-velocity dispersion curves of seismic traces for rapid manual picking of large amounts of data: a task commonly encountered in ambient-noise tomography. The program can be used for group-velocity analysis of surface waves from earthquakes and controlled source data as well as of Green’s functions from cross-correlated ambient-noise data. The presented tool is especially suited to datasets in which automatic picking algorithms fail and so dispersion analysis is only possible by visual inspection. Such situations can occur in highly heterogeneous regions with complex surface-wave dispersion or where surface-wave arrivals are poorly emerged (as can often be the case with ambient-noise-derived Green’s functions from temporary seismic deployments). In these datasets, the poor signal-to-noise ratio, spectral holes, or limited bandwidth may therefore mean that manual analysis is the only choice. However, without an efficient workflow the feasibility of this can be seriously constrained by the analysis time for the potentially vast number of traces to be analyzed. We tackled this problem by implementing well-known techniques of dispersion curve analysis (traditional frequency–time analysis) in a fast and interactive graphical environment. It is specifically developed for high user processing speed, prioritizing fast computation, and high display responsiveness. This solution retains the benefits of manual dispersion picking for complex datasets, while maintaining good user processing efficiency. An experienced analyst can measure upward of 200 traces per hour. xdcpick stands for an X-window-based picking of dispersion curves.

Normalized Mass Maps in Three-Dimensional Space Combining Kendrick-like Values with Chromatographic Separation for Enhanced Data Deconvolution.

The incorporation of retention-time information into a fully rotatable and interactive three-dimensional (3D), "Kendrick-like" normalized mass map (NMM) using a single software platform is reported. Surprising discoveries were made about the elution pattern of block ethoxylate-propoxylate oligomers (ca. 2800 Da) in the supercritical fluid after combined SFC-Orbitrap FTMS analysis. The 3D NMM also facilitated identification of impurities using interactive graphics tools within the map. By selecting map glyphs, associated reconstructed ion chromatograms were automatically generated. Last, since Kendrick and Kendrick-like mapping (NMM) are chemical-formula-based, incorporating retention time in 3D space allows the possibility of resolving isomers in the map.

Robust Control of Wireless Power Transfer Despite Load and Data Communications Uncertainties

This article focuses on the robust control of wireless power transfer (WPT) systems, to work satisfactorily around the desired resonant frequency in the presence of load and data communications uncertainties. The proposed robust control system is based on the quantitative feedback theory (QFT), consisting of a feedback compensator and a prefilter, which are designed by shaping the system's frequency responses, to satisfy the design constraints defined in terms of stability, tracking, and other desired requirements. A feature of QFT is to provide the designer with interactive graphical tools for the design and tuning of the feedback compensator and prefilter. Without loss of generality, this article elaborates the design of the QFT-based robust control for a WPT system with a full-bridge inverter and series-series capacitor-based compensation circuits and uncertain direct-current (dc) load. The data communications uncertainties are also addressed in the design. The effectiveness of the proposed QFT-based robust control methodology is evaluated through simulations and practical experiments and compared with H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">∞</sub> and Skogestad internal model control (SIMC) design methods. Since QFT is a model-based approach, this article also elaborates on small-signal transfer function modeling of WPT systems.

SNPnexus: a web server for functional annotation of human genome sequence variation (2020 update).

SNPnexus is a web-based annotation tool for the analysis and interpretation of both known and novel sequencing variations. Since its last release, SNPnexus has received continual updates to expand the range and depth of annotations provided. SNPnexus has undergone a complete overhaul of the underlying infrastructure to accommodate faster computational times. The scope for data annotation has been substantially expanded to enhance biological interpretations of queried variants. This includes the addition of pathway analysis for the identification of enriched biological pathways and molecular processes. We have further expanded the range of user directed annotation fields available for the study of cancer sequencing data. These new additions facilitate investigations into cancer driver variants and targetable molecular alterations within input datasets. New user directed filtering options have been coupled with the addition of interactive graphical and visualization tools. These improvements streamline the analysis of variants derived from large sequencing datasets for the identification of biologically and clinically significant subsets in the data. SNPnexus is the most comprehensible web-based application currently available and these new set of updates ensures that it remains a state-of-the-art tool for researchers. SNPnexus is freely available at https://www.snp-nexus.org.

Elicitation of prior probability distributions for a proposed Bayesian randomized clinical trial of whole blood for trauma resuscitation

BACKGROUNDWhole blood trauma resuscitation is conceptually appealing and increasingly used but lacks evidence. A randomized controlled trial is needed but challenging to design. A Bayesian approach might be more efficient and more interpretable than a conventional frequentist design. We report the results on an elicitation meeting to create prior probability distributions to help develop such a trial.METHODSIn‐person expert elicitation meeting, based on Sheffield Elicitation Framework methodology. We used an interactive graphical tool to elicit the quantities of interest (24‐hour mortality and certainty required). Two rounds were conducted, with an intervening discussion of deidentified responses. Individual responses were aggregated into probability distributions.RESULTSFifteen experts participated. The pooled belief was that the median 24‐hour mortality of trauma patients with hemorrhagic shock treated with component therapy (the current standard of care) was 19% (95% credible interval [CrI], 6%‐45%), and the median 24‐hour mortality of those treated with whole blood, 16% (95% CrI, 5%‐39%). The pooled prior distribution for the relative risk had a median of 0.84 (95% CrI, 0.26‐3.1), indicating that the expert group had a 64% prior belief that whole blood decreases 24‐hour mortality compared to component therapy.CONCLUSIONSExperts had moderately strong beliefs that whole blood reduces the 24‐hour mortality of trauma patients with hemorrhagic shock. These data will assist with the design and planning of a Bayesian trial of whole blood resuscitation, which will help to answer a key question in contemporary transfusion practice.

Py_convrot: rotation conventions, to understand and to apply

Rotation is a core crystallographic operation. Two sets of Cartesian coordinates of each point of a rotated object, those before and after rotation, are linearly related, and the coefficients of these linear combinations can be represented in matrix form. This 3 × 3 matrix is unique for all points and thus describes unambiguously a particular rotation. However, its nine elements are mutually dependent and are not interpretable in a straightforward way. To describe rotations by independent and comprehensible parameters, crystallographic software usually refers to Euler or to polar angles. In crystallography and cryo-electron microscopy, there exists a large choice of conventions, making direct comparison of rotation parameters difficult and sometimes confusing. The program py_convrot, written in Python, is a converter of parameters describing rotations. In particular, it deals with all possible choices of polar angles and with all kinds of Euler angles, including all choices of rotation axes and rotation directions. Using a menu, a user can build their own rotation parameterization; its action can be viewed with an interactive graphical tool, Demo. The tables in this article and the extended help pages of the program describe details of these parameterizations and the decomposition of rotation matrices into all types of parameters. The program allows orthogonalization conventions and symmetry operations to be taken into account. This makes the program and its supporting materials both an illustrative teaching material, especially for non-specialists in mathematics and computing, and a tool for practical use.

SWITCH workbench: A novel approach for the development and deployment of time-critical microservice-based cloud-native applications

Time-critical applications, such as early warning systems or live event broadcasting, present particular challenges. They have hard limits on Quality of Service constraints that must be maintained, despite network fluctuations and varying peaks of load. Consequently, such applications must adapt elastically on-demand, and so must be capable of reconfiguring themselves, along with the underlying cloud infrastructure, to satisfy their constraints. Software engineering tools and methodologies currently do not support such a paradigm. In this paper, we describe a framework that has been designed to meet these objectives, as part of the EU SWITCH project. SWITCH offers a flexible co-programming architecture that provides an abstraction layer and an underlying infrastructure environment, which can help to both specify and support the life cycle of time-critical cloud native applications. We describe the architecture, design and implementation of the SWITCH components and describe how such tools are applied to three time-critical real-world use cases. • The main objective is to address entire life cycle of time-critical cloud applications • SWITCH offers middleware services for infrastructure planning and provisioning • Interactive graphical modelling tools for specification of time-critical requirements • Self-adaptation of on-demand resources and reconfigurability of infrastructure • The concept of co-programming model to support programmability and controllability

Simple high-resolution NMR spectroscopy as a tool in molecular biology.

NMR is one of the major techniques for investigating the structure, dynamics and interactions between biomolecules. However, non‐experts often experience NMR experimentation and data analysis as intimidating. We discuss a simple yet powerful NMR technique, the so‐called chemical shift perturbation (CSP) analysis, as a tool to elucidate macromolecular interactions in small‐ and medium‐sized complexes, including protein‐protein, protein‐drug, and protein‐DNA/RNA interactions. We discuss current software packages for NMR data analysis and present a new interactive graphical tool implemented in CcpNmr AnalysisAssign version‐3, which can drastically reduce the time required for the CSP analysis. Lastly, we illustrate the usefulness of a protein three‐dimensional structure for interpretation of the CSP data.

GfaViz: flexible and interactive visualization of GFA sequence graphs.

The graphical fragment assembly (GFA) formats are emerging standard formats for the representation of sequence graphs. Although GFA 1 was primarily targeting assembly graphs, the newer GFA 2 format introduces several features, which makes it suitable for representing other kinds of information, such as scaffolding graphs, variation graphs, alignment graphs and colored metagenomic graphs. Here, we present GfaViz, an interactive graphical tool for the visualization of sequence graphs in GFA format. The software supports all new features of GFA 2 and introduces conventions for their visualization. The user can choose between two different layouts and multiple styles for representing single elements or groups. All customizations can be stored in custom tags of the GFA format itself, without requiring external configuration files. Stylesheets are supported for storing standard configuration options for groups of files. The visualizations can be exported to raster and vector graphics formats. A command line interface allows for batch generation of images. GfaViz is available at https://github.com/ggonnella/gfaviz. Supplementary data are available at Bioinformatics online.

Integrating design thinking with sustainability science: a Research through Design approach

Design disciplines have a long history of creating well-integrated solutions to challenges which are complex, uncertain and contested by multiple stakeholders. Society faces similar challenges in implementing the Sustainable Development Goals, so design methods hold much potential. While principles of good design are well established, there has been limited integration of design thinking with sustainability science. To advance this integration, we examine the process of designing MetaMAP: an interactive graphic tool for collaborating to understand social–ecological systems and design well-integrated solutions. MetaMAP was created using Research through Design methods which integrate creative and scientific thinking. By applying design thinking, researchers and practitioners from different backgrounds undertook multiple cycles of problem framing, solution development, testing and reflection. The testing was highly collaborative involving over 150 people from diverse disciplines in workshops, case studies, interviews and critique. Reflecting on this process, we discuss design principles and opportunities for integrating design thinking with sustainability science to help achieve Sustainable Development Goals.

Probabilistic Prognostic Estimates of Survival in Metastatic Cancer Patients (PPES-Met) Utilizing Free-Text Clinical Narratives

We propose a deep learning model - Probabilistic Prognostic Estimates of Survival in Metastatic Cancer Patients (PPES-Met) for estimating short-term life expectancy (>3 months) of the patients by analyzing free-text clinical notes in the electronic medical record, while maintaining the temporal visit sequence. In a single framework, we integrated semantic data mapping and neural embedding technique to produce a text processing method that extracts relevant information from heterogeneous types of clinical notes in an unsupervised manner, and we designed a recurrent neural network to model the temporal dependency of the patient visits. The model was trained on a large dataset (10,293 patients) and validated on a separated dataset (1818 patients). Our method achieved an area under the ROC curve (AUC) of 0.89. To provide explain-ability, we developed an interactive graphical tool that may improve physician understanding of the basis for the model’s predictions. The high accuracy and explain-ability of the PPES-Met model may enable our model to be used as a decision support tool to personalize metastatic cancer treatment and provide valuable assistance to the physicians.

Use of Interactive Graphical Tools to Demonstrate Changes in Time-Resolved Fluorescence Intensity Decays

Use of Interactive Graphical Tools to Demonstrate Changes in Time-Resolved Fluorescence Intensity Decays

PP75 Genetic Testing For Bladder And Kidney Cancer: An Interactive Evidence Map

Introduction:Recently, voluminous research and commentary have touted genetic and molecular testing to improve the management of urologic cancer. The purposes of such testing include screening, risk assessment, diagnosis, prognosis, pharmacogenetics, and monitoring (for example, recurrence, predicting treatment response). An interactive graphical tool (“evidence map”) would help policy makers examine the current state of research, identify prevailing trends, and prioritize research efforts.Methods:A professional information specialist searched MEDLINE/EMBASE for articles published in 2010 or later that primarily focused on genetic/molecular testing and either kidney or bladder/urothelial cancer. Two research analysts classified all relevant abstracts regarding to cancer type, genetic marker(s), clinical purpose(s), assay methods, publication type, and author country/region. We created an interactive map using HTML5 and JavaScript.Results:We identified 4,731 articles, 828 (18 percent) of which met our inclusion criteria. Our map has interactive filters which allow flexible selection of articles and automatic updating of the counts. For example, one can quickly redraw the map to focus only on U.S./European systematic reviews and meta-analyses. Research on bladder/urothelial cancer focuses on both diagnosis and prognosis, with some interest in monitoring. In kidney cancer, research on prognosis outweighs research on diagnosis. Overall, research on genetic/molecular markers is in an exploratory phase, e.g. for kidney cancer prognosis alone, 173 empirical studies considered hundreds of different markers.Conclusions:Assessing prognosis is a common purpose of genetic tests for both bladder/urothelial and kidney cancer. Increased research on the monitoring of bladder/urothelial cancer may be due to its high recurrence rates, whereas lower interest in genetic tests to diagnose kidney cancer may be due to effective imaging tests. For policy makers, evidence maps can inform decisions about the scope of commissioned systematic reviews as well as the targets for recommendation statements. Interactive features allow maps to be redrawn to align with users’ specific interests.

Support and Expectations for Biochemistry and Molecular Biology Faculty Promotion and Tenure at PUI Institutions

Biochemistry and Molecular Biology (BMB) faculty at Primarily Undergraduate Institutions (PUI) work in very diverse environments. PUI institutions are those defined by the NSF as U.S. four‐year, masters‐level, and small doctoral colleges and universities, that award on average no more than 2 Ph.D. or D.Sc. degrees per year in a department. BMB faculty work at private and public universities, in chemistry and biology departments, and with a varied ratio of teaching, research and service expectations. Within these parameters characterizing, comparing and developing expectations for promotion and/or tenure is challenging, with limited data to assist in important decision making. In order to assist faculty and administrators with strategic planning, goal setting, measuring productivity, and to provide guidance for internal and external program/departmental reviewers, we have initiated a survey to collect a broad set of data from PUIs. After writing and testing sample survey questions and responses, a final survey was developed to query participants about parameters such as teaching load, research support, and output. Initial survey results and plans to disseminate the results including using interactive graphical tools will be presented.