Dataset Information

Genome Dashboards: Framework and Examples.

ABSTRACT: Genomics is a sequence-based informatics science and a three-dimensional-structure-based material science. However, in practice, most genomics researchers utilize sequence-based informatics approaches or three-dimensional-structure-based material science techniques, not both. This division is, at least in part, the result of historical developments rather than a fundamental necessity. The underlying computational tools, experimental techniques, and theoretical models were developed independently. The primary result presented here is a framework for the unification of informatics- and physics-based data associated with DNA, nucleosomes, and chromatin. The framework is based on the mathematical representation of geometrically exact rods and the generalization of DNA basepair step parameters. Data unification enables researchers to integrate computational, experimental, and theoretical approaches for the study of chromatin biology. The framework can be implemented using model-view-controller design principles, existing genome browsers, and existing molecular visualization tools. We developed a minimal, web-based genome dashboard, G-Dash-min, and applied it to two simple examples to demonstrate the usefulness of data unification and proof of concept. Genome dashboards developed using the framework and design principles presented here are extensible and customizable and are therefore more broadly applicable than the examples presented. We expect a number of purpose-specific genome dashboards to emerge as a novel means of investigating structure-function relationships for genomes that range from basepairs to entire chromosomes and for generating, validating, and testing mechanistic hypotheses.

SUBMITTER: Li Z

PROVIDER: S-EPMC7203004 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundSince the outbreak of COVID-19, the development of dashboards as dynamic, visual tools for communicating COVID-19 data has surged worldwide. Dashboards can inform decision-making and support behavior change. To do so, they must be actionable. The features that constitute an actionable dashboard in the context of the COVID-19 pandemic have not been rigorously assessed.ObjectiveThe aim of this study is to explore the characteristics of public web-based COVID-19 dashboards by assessing their purpose and users ("why"), content and data ("what"), and analyses and displays ("how" they communicate COVID-19 data), and ultimately to appraise the common features of highly actionable dashboards.MethodsWe conducted a descriptive assessment and scoring using nominal group technique with an international panel of experts (n=17) on a global sample of COVID-19 dashboards in July 2020. The sequence of steps included multimethod sampling of dashboards; development and piloting of an assessment tool; data extraction and an initial round of actionability scoring; a workshop based on a preliminary analysis of the results; and reconsideration of actionability scores followed by joint determination of common features of highly actionable dashboards. We used descriptive statistics and thematic analysis to explore the findings by research question.ResultsA total of 158 dashboards from 53 countries were assessed. Dashboards were predominately developed by government authorities (100/158, 63.0%) and were national (93/158, 58.9%) in scope. We found that only 20 of the 158 dashboards (12.7%) stated both their primary purpose and intended audience. Nearly all dashboards reported epidemiological indicators (155/158, 98.1%), followed by health system management indicators (85/158, 53.8%), whereas indicators on social and economic impact and behavioral insights were the least reported (7/158, 4.4% and 2/158, 1.3%, respectively). Approximately a quarter of the dashboards (39/158, 24.7%) did not report their data sources. The dashboards predominately reported time trends and disaggregated data by two geographic levels and by age and sex. The dashboards used an average of 2.2 types of displays (SD 0.86); these were mostly graphs and maps, followed by tables. To support data interpretation, color-coding was common (93/158, 89.4%), although only one-fifth of the dashboards (31/158, 19.6%) included text explaining the quality and meaning of the data. In total, 20/158 dashboards (12.7%) were appraised as highly actionable, and seven common features were identified between them. Actionable COVID-19 dashboards (1) know their audience and information needs; (2) manage the type, volume, and flow of displayed information; (3) report data sources and methods clearly; (4) link time trends to policy decisions; (5) provide data that are "close to home"; (6) break down the population into relevant subgroups; and (7) use storytelling and visual cues.ConclusionsCOVID-19 dashboards are diverse in the why, what, and how by which they communicate insights on the pandemic and support data-driven decision-making. To leverage their full potential, dashboard developers should consider adopting the seven actionability features identified.

Project description:BackgroundToday, the use of data in administrative and clinical processes is quite challenging due to the large volume of data, data collection from various sources, and lack of data structure. As a data management tool, dashboards play an important role in timely visual display of critical information on key performances.ObjectivesThis systematic review aimed to identify functional and non-functional requirements, as well as challenges of using dashboards in hospitals.MethodsIn this systematic review, four databases, including the Web of Science, PubMed, EMBASE, and Scopus, were searched to find relevant articles from 2000 until May 30, 2020. The final search was conducted on May 30, 2020. Data collection was performed using a data extraction form and reviewing the content of relevant studies on the potentials and challenges of dashboard implementation.ResultsFifty-four out of 1254 retrieved articles were selected for this study based on the inclusion and exclusion criteria. The functional requirements for dashboards included reporting, reminders, customization, tracking, alert creation, and assessment of performance indicators. On the other hand, the non-functional requirements included the dashboard speed, security, ease of use, installation on different devices (e.g., PCs and laptops), integration with other systems, web-based design, inclusion of a data warehouse, being up-to-data, and use of data visualization elements based on the user's needs. Moreover, the identified challenges were categorized into four groups: data sources, dashboard content, dashboard design, implementation, and integration in other systems at the hospital level.ConclusionDashboards, by providing information in an appropriate manner, can lead to the proper use of information by users. In order for a dashboard to be effective in clinical and managerial processes, particular attention must be paid to its capabilities, and the challenges of its implementation need to be addressed.

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Genome Dashboards: Framework and Examples.

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