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"Meyer, Miriah"
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A new tool for annotating scientific animations and supporting scientific dialogue
A new interactive annotation interface supports a detailed molecular animation of the SARS-CoV-2 life cycle. With this tool, users can interactively explore the data used to create the animation and engage in scientific discourse through comments and questions.
Journal Article
A Conserved Developmental Patterning Network Produces Quantitatively Different Output in Multiple Species of Drosophila
Differences in the level, timing, or location of gene expression can contribute to alternative phenotypes at the molecular and organismal level. Understanding the origins of expression differences is complicated by the fact that organismal morphology and gene regulatory networks could potentially vary even between closely related species. To assess the scope of such changes, we used high-resolution imaging methods to measure mRNA expression in blastoderm embryos of Drosophila yakuba and Drosophila pseudoobscura and assembled these data into cellular resolution atlases, where expression levels for 13 genes in the segmentation network are averaged into species-specific, cellular resolution morphological frameworks. We demonstrate that the blastoderm embryos of these species differ in their morphology in terms of size, shape, and number of nuclei. We present an approach to compare cellular gene expression patterns between species, while accounting for varying embryo morphology, and apply it to our data and an equivalent dataset for Drosophila melanogaster. Our analysis reveals that all individual genes differ quantitatively in their spatio-temporal expression patterns between these species, primarily in terms of their relative position and dynamics. Despite many small quantitative differences, cellular gene expression profiles for the whole set of genes examined are largely similar. This suggests that cell types at this stage of development are conserved, though they can differ in their relative position by up to 3-4 cell widths and in their relative proportion between species by as much as 5-fold. Quantitative differences in the dynamics and relative level of a subset of genes between corresponding cell types may reflect altered regulatory functions between species. Our results emphasize that transcriptional networks can diverge over short evolutionary timescales and that even small changes can lead to distinct output in terms of the placement and number of equivalent cells.
Journal Article
s-CorrPlot: An Interactive Scatterplot for Exploring Correlation
The degree of correlation between variables is used in many data analysis applications as a key measure of interdependence. The most common techniques for exploratory analysis of pairwise correlation in multivariate datasets, like scatterplot matrices and clustered heatmaps, however, do not scale well to large datasets, either computationally or visually. We present a new visualization that is capable of encoding pairwise correlation between hundreds of thousands variables, called the s-CorrPlot. The s-CorrPlot encodes correlation spatially between variables as points on scatterplot using the geometric structure underlying Pearson's correlation. Furthermore, we extend the s-CorrPlot with interactive techniques that enable animation of the scatterplot to new projections of the correlation space, as illustrated in the companion video in supplementary materials. We provide the s-CorrPlot as an open-source R package and validate its effectiveness through a variety of methods including a case study with a biology collaborator. Supplementary materials for this article are available online.
Journal Article
A new tool for annotating scientific animations and supporting scientific dialogue
A new interactive annotation interface supports a detailed molecular animation of the SARS-CoV-2 life cycle. With this tool, users can interactively explore the data used to create the animation and engage in scientific discourse through comments and questions.
Journal Article
Designing Visualizations For Biological Data
Visualization is now a vital component of the biological discovery process. This article presents visualization design studies as a promising approach for creating effective, visualization tools for biological data.
Journal Article
Outcomes of an electronic social network intervention with neuro-oncology patient family caregivers
IntroductionInformal family caregivers (FCG) are an integral and crucial human component in the cancer care continuum. However, research and interventions to help alleviate documented anxiety and burden on this group is lacking. To address the absence of effective interventions, we developed the electronic Support Network Assessment Program (eSNAP) which aims to automate the capture and visualization of social support, an important target for overall FCG support. This study seeks to describe the preliminary efficacy and outcomes of the eSNAP intervention.MethodsForty FCGs were enrolled into a longitudinal, two-group randomized design to compare the eSNAP intervention in caregivers of patients with primary brain tumors against controls who did not receive the intervention. Participants were followed for six weeks with questionnaires to assess demographics, caregiver burden, anxiety, depression, and social support. Questionnaires given at baseline (T1) and then 3-weeks (T2), and 6-weeks (T3) post baseline questionnaire.ResultsFCGs reported high caregiver burden and distress at baseline, with burden remaining stable over the course of the study. The intervention group was significantly less depressed, but anxiety remained stable across groups.ConclusionsWith the lessons learned and feedback obtained from FCGs, this study is the first step to developing an effective social support intervention to support FCGs and healthcare providers in improving cancer care.
Journal Article
Feasibility of implementing an electronic social support and resource visualization tool for caregivers in a neuro-oncology clinic
PurposeThe goals of this study were to assess the feasibility of a web-based application—electronic Social Network Assessment Program (eSNAP)—to automate the capture and visualization of family caregiver social network data of neuro-oncology patients.MethodsCaregivers were recruited from a neuro-oncology clinic at an NCI-designated comprehensive cancer center. Participants completed baseline questionnaires on a laptop in clinic assessing demographic characteristics. After baseline, participants were randomly assigned to either create a social network visualization using eSNAP (intervention) or to usual care (control) condition. Those who used eSNAP provided likeability/usability data. All participants were asked to complete follow-up questionnaires at 3 and 6 weeks after baseline to determine feasibility of longitudinal study.ResultsWe recruited 40 caregivers of patients with primary malignant brain tumor to participate in this study. Participants rated eSNAP usability and likeability highly, indicating that eSNAP would help them consider their available social support. At 3 weeks, 90% of participants completed questionnaires and 82.5% completed questionnaires at 6 weeks.ConclusionsThere is a need to encourage family caregivers of patients with primary malignant brain tumor to engage their existing social network resources to help alleviate caregiver burden. Our findings suggest that our web-based application to address this issue is feasible to implement with high usability and likeability. This pilot study identified minor changes to the intervention to improve effectiveness and has implications for future research in this understudied population.Trial registrationclinicaltrials.gov, protocol number NCT03026699
Journal Article
Development of the Electronic Social Network Assessment Program Using the Center for eHealth and Wellbeing Research Roadmap
The number of Web-based psychological and behavioral interventions is growing. Beyond their theoretical underpinnings, a key factor to the success of these interventions is how they are designed and developed to ensure usability over a new method of delivery. Our team has adapted ecomapping, a tool for visualizing family caregiver social network resources, for the Web. Here, we describe how we designed and developed the electronic Social Network Assessment Program (eSNAP) Web-based tool using a framework of the Center for eHealth and Wellbeing Research (CeHRes) Roadmap for Web-based intervention development. The CeHRes Roadmap is still new in terms of tool development and we showcase an example of its application.
The aim of our study was to provide an example of the application of the Web-based intervention development process using the CeHRes Roadmap for other research teams to follow. In doing so, we are also sharing our pilot work to enhance eSNAP's acceptance and usability for users and the feasibility of its implementation.
We describe the development of the eSNAP app to support family caregivers of neuro-oncology patients. This development is based on the 5 iterative stages of the CeHRes Roadmap: contextual inquiry, value specification, design, operationalization, and summative evaluation. Research activities to support eSNAP development prior to implementation included literature review, focus groups, and iterative rounds of interviews.
Key lessons learned in developing the eSNAP app broadly fell under a theme of translating theoretical needs and ideas to the real world. This included how to prioritize needs to be addressed at one time, how the modality of delivery may change design requirements, and how to develop a tool to fit within the context it will be used.
Using the CeHRes Roadmap to develop Web-based interventions such as eSNAP helps to address potential issues by outlining important intervention development milestones. In addition, by encouraging inclusion of users and other stakeholders in the process, Web-based intervention developers using the Roadmap can identify what will work in the real world and increase feasibility and effectiveness.
Journal Article
Reflections on Traceability for Visualization Research
Decades of advocacy for reproducibility and replication have advanced open, transparent practices in the sciences. However, traditional notions of reproducibility fit poorly with design-oriented visualization research, where insights emerge through subjective, situated, and iterative work. So how can we ensure rigor and transparency in processes that are inherently unreproducible? To introduce transparency in design-oriented research, we propose to focus on traceability: surfacing the origin and development of research contributions based on rich sets of artifacts documenting the design process. We investigated traceability through a collaborative autoethnographic reflection that builds on several years of work exploring ways to make design-oriented research transparent. This exploration includes an experiment to build a tool to support traceability, which we called tRRRacer. The tRRRacer tool provided a testbed for us to operationalize the three tenets of a traceable process: (1) Record abundant, annotated artifacts representative of research activities; (2) Report curated research threads that articulate rationale and evolution of the process, allowing others to (3) Read via interfaces that help retrace claims and assess plausibility. Reflecting on our experiences, we contribute a theorization of traceability and reflections on how we might support it.
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