While feminist and critical data theories have long critiqued the use of data to uphold a positivist-informed view about science, few examples offer alternative methods to display scientific constructs. In response, we present Data and Me: an exhibit informed by feminist and critical data theories, which we designed and launched at a local science museum. Data and Me introduces museum visitors to data using a [AT]:hugging_face: vibe -- a vibe that signals that data can be [hashtag]slow, [hashtag]handmade, and [hashtag]personal. We designed this vibe to be noticeably different than the [AT]Science vibe in the rest of the museum. Throughout our design process, we adapted visualization vibes as an analytic and generative tool in the context of a science museum. We present four design choices that enable the design of a vibe: visual, topical, material, and crediting. We discuss how our exhibit aligns with ongoing discussions about alternative research outcomes and calls for plurality in HCI.

Visualization has matured into an established research field, producing widely adopted tools, design frameworks, and empirical foundations. As the field has grown, ideas from outside computer science have increasingly entered visualization discourse, questioning the fundamental values and assumptions on which visualization research stands. In this short position paper, we examine a set of values that we see underlying the seminal works of Jacques Bertin, John Tukey, Leland Wilkinson, Colin Ware, and Tamara Munzner. We articulate three prominent values in these texts — universality, objectivity, and efficiency — and examine how these values permeate visualization tools, curricula, and research practices. We situate these values within a broader set of critiques that call for more diverse priorities and viewpoints. By articulating these tensions, we call for our community to embrace a more pluralistic range of values to shape our future visualization tools and guidelines.

Abstract Visualization researchers utilize workshops both for applied research and to engage different populations with visualization‐based activities. While there are many benefits to running visualization workshops, their utility and impact rely on the presence of a researcher who has deep knowledge about visualization theory and practice. In this work, we introduce workshop‐in‐a‐box as a design concept intended to challenge the researcher‐centric approach to data physicalization workshops. Through a design study with a socially innovative organization, we deployed several data physicalization workshops that our collaborator ran instead of us. Based on this experience, along with two accompanying case studies that validate the concept, we present material and procedural considerations for how to put data physicalization workshops into a box and the implications it has for extending visualization research outside the bounds of academia.

Abstract 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.

Data-driven decision making has become a popular practice in science, industry, and public policy. Yet data alone, as an imperfect and partial representation of reality, is often insufficient to make good analysis decisions. Knowledge about the context of a dataset, its strengths and weaknesses, and its applicability for certain tasks is essential. Analysts are often not only familiar with the data itself, but also have data hunches about their analysis subject. In this work, we present an interview study with analysts from a wide range of domains and with varied expertise and experience, inquiring about the role of contextual knowledge. We provide insights into how data is insufficient in analysts' workflows and how they incorporate other sources of knowledge into their analysis. We analyzed how knowledge of data shaped their analysis outcome. Based on the results, we suggest design opportunities to better and more robustly consider both knowledge and data in analysis processes.

A growing body of work draws on feminist thinking to challenge assumptions about how people engage with and use visualizations. This work draws on feminist values, driving design and research guidelines that account for the influences of power and neglect. This prior work is largely prescriptive, however, forgoing articulation of how feminist theories of knowledge - or feminist epistemology - can alter research design and outcomes. At the core of our work is an engagement with feminist epistemology, drawing attention to how a new framework for how we know what we know enabled us to overcome intellectual tensions in our research. Specifically, we focus on the theoretical concept of entanglement, central to recent feminist scholarship, and contribute: a history of entanglement in the broader scope of feminist theory; an articulation of the main points of entanglement theory for a visualization context; and a case study of research outcomes as evidence of the potential of feminist epistemology to impact visualization research. This work answers a call in the community to embrace a broader set of theoretical and epistemic foundations and provides a starting point for bringing feminist theories into visualization research.

Many long-established, traditional manufacturing businesses are becoming more digital and data-driven to improve their production. These companies are embracing visual analytics in these transitions through their adoption of commercial dashboarding systems. Although a number of studies have looked at the technical challenges of adopting these systems, very few have focused on the socio-technical issues that arise. In this paper, we report on the results of an interview study with 17 participants working in a range of roles at a long-established, traditional manufacturing company as they adopted Microsoft Power BI. The results highlight a number of socio-technical challenges the employees faced, including difficulties in training, using and creating dashboards, and transitioning to a modern digital company. Based on these results, we propose a number of opportunities for both companies and visualization researchers to improve these difficult transitions, as well as opportunities for rethinking how we design dashboarding systems for real-world use.

A common research process in visualization is for visualization researchers to collaborate with domain experts to solve particular applied data problems. While there is existing guidance and expertise around how to structure collaborations to strengthen research contributions, there is comparatively little guidance on how to navigate the implications of, and power produced through the socio-technical entanglements of collaborations. In this paper, we qualitatively analyze reflective interviews of past participants of collaborations from multiple perspectives: visualization graduate students, visualization professors, and domain collaborators. We juxtapose the perspectives of these individuals, revealing tensions about the tools that are built and the relationships that are formed — a complex web of competing motivations. Through the lens of matters of care, we interpret this web, concluding with considerations that both trouble and necessitate reformation of current patterns around collaborative work in visualization design studies to promote more equitable, useful, and care-ful outcomes.

The trouble with data is that it frequently provides only an imperfect representation of a phenomenon of interest. Experts who are familiar with their datasets will often make implicit, mental corrections when analyzing a dataset, or will be cautious not to be overly confident about their findings if caveats are present. However, personal knowledge about the caveats of a dataset is typically not incorporated in a structured way, which is problematic if others who lack that knowledge interpret the data. In this work, we define such analysts' knowledge about datasets as data hunches. We differentiate data hunches from uncertainty and discuss types of hunches. We then explore ways of recording data hunches, and, based on a prototypical design, develop recommendations for designing visualizations that support data hunches. We conclude by discussing various challenges associated with data hunches, including the potential for harm and challenges for trust and privacy. We envision that data hunches will empower analysts to externalize their knowledge, facilitate collaboration and communication, and support the ability to learn from others' data hunches.

Personal informatics research helps people track personal data for the purposes of self-reflection and gaining self-knowledge. This field, however, has predominantly focused on the data collection and insight-generation elements of self-tracking, with less attention paid to flexible data analysis. As a result, this inattention has led to inflexible analytic pipelines that do not reflect or support the diverse ways people want to engage with their data. This paper contributes a review of personal informatics and visualization research literature to expose a gap in our knowledge for designing flexible tools that assist people engaging with and analyzing personal data in personal contexts, what we call the personal informatics analysis gap. We explore this gap through a multistage longitudinal study on how asthmatics engage with personal air quality data, and we report how participants: were motivated by broad and diverse goals; exhibited patterns in the way they explored their data; engaged with their data in playful ways; discovered new insights through serendipitous exploration; and were reluctant to use analysis tools on their own. These results present new opportunities for visual analysis research and suggest the need for fundamental shifts in how and what we design when supporting personal data analysis.

This February 2021 issue of the IEEE Transactions on Visualization and Computer Graphics (TVCG) contains the proceedings of IEEE VIS 2020, held online between 25-30 October 2020, hosted by General Chairs from the University of Utah. With IEEE VIS 2020, the conference series is in its 31st year. IEEE VIS consists of three conferences, held concurrently: the IEEE Visual Analytics Science and Technology Conference (VAST), the IEEE Information Visualization Conference (InfoVis), and the IEEE Scientific Visualization Conference (SciVis). These three conferences are the premier venues for the visualization community to exchange the latest ideas and developments, attracting researchers and practitioners alike.

We present a method for the browsing of hierarchical 3D models in which we combine the typical navigation of hierarchical structures in a 2D environment-using clicks on nodes, links, or icons-with a 3D spatial data visualization. Our approach is motivated by large molecular models, for which the traditional single-scale navigational metaphors are not suitable. Multi-scale phenomena, e. g., in astronomy or geography, are complex to navigate due to their large data spaces and multi-level organization. Models from structural biology are in addition also densely crowded in space and scale. Cutaways are needed to show individual model subparts. The camera has to support exploration on the level of a whole virus, as well as on the level of a small molecule. We address these challenges by employing HyperLabels: active labels that-in addition to their annotational role-also support user interaction. Clicks on HyperLabels select the next structure to be explored. Then, we adjust the visualization to showcase the inner composition of the selected subpart and enable further exploration. Finally, we use a breadcrumbs panel for orientation and as a mechanism to traverse upwards in the model hierarchy. We demonstrate our concept of hierarchical 3D model browsing using two exemplary models from meso-scale biology.

Design study is an established approach of conducting problem-driven visualization research. The academic visualization community has produced a large body of work for reporting on design studies, informed by a handful of theoretical frameworks, and applied to a broad range of application areas. The result is an abundance of reported insights into visualization design, with an emphasis on novel visualization techniques and systems as the primary contribution of these studies. In recent work we proposed a new, interpretivist perspective on design study and six companion criteria for rigor that highlight the opportunities for researchers to contribute knowledge that extends beyond visualization idioms and software. In this work we conducted a year-long collaboration with evolutionary biologists to develop an interactive tool for visual exploration of multivariate datasets and phylogenetic trees. During this design study we experimented with methods to support three of the rigor criteria: ABUNDANT, REFLEXIVE, and TRANSPARENT. As a result we contribute two novel visualization techniques for the analysis of multivariate phylogenetic datasets, three methodological recommendations for conducting design studies drawn from reflections over our process of experimentation, and two writing devices for reporting interpretivist design study. We offer this work as an example for implementing the rigor criteria to produce a diverse range of knowledge contributions.

We develop a new perspective on research conducted through visualization design study that emphasizes design as a method of inquiry and the broad range of knowledge-contributions achieved through it as multiple, subjective, and socially constructed. From this interpretivist position we explore the nature of visualization design study and develop six criteria for rigor. We propose that rigor is established and judged according to the extent to which visualization design study research and its reporting are INFORMED, REFLEXIVE, ABUNDANT, PLAUSIBLE, RESONANT, and TRANSPARENT. This perspective and the criteria were constructed through a four-year engagement with the discourse around rigor and the nature of knowledge in social science, information systems, and design. We suggest methods from cognate disciplines that can support visualization researchers in meeting these criteria during the planning, execution, and reporting of design study. Through a series of deliberately provocative questions, we explore implications of this new perspective for design study research in visualization, concluding that as a discipline, visualization is not yet well positioned to embrace, nurture, and fully benefit from a rigorous, interpretivist approach to design study. The perspective and criteria we present are intended to stimulate dialogue and debate around the nature of visualization design study and the broader underpinnings of the discipline.

Abstract Multivariate networks are made up of nodes and their relationships (links), but also data about those nodes and links as attributes. Most real‐world networks are associated with several attributes, and many analysis tasks depend on analyzing both, relationships and attributes. Visualization of multivariate networks, however, is challenging, especially when both the topology of the network and the attributes need to be considered concurrently. In this state‐of‐the‐art report, we analyze current practices and classify techniques along four axes: layouts, view operations, layout operations, and data operations. We also provide an analysis of tasks specific to multivariate networks and give recommendations for which technique to use in which scenario. Finally, we survey application areas and evaluation methodologies.

Abstract Two of the primary reasons rainbow color maps are considered ineffective trace back to the idea that they implicitly discretize encoded data into hue‐based bands, yet no research addresses what this discretization looks like or how consistent it is across individuals. This paper presents an exploratory study designed to empirically investigate the implicit discretization of common spectral schemes and explore whether the phenomenon can be modeled by variations in lightness, chroma, and hue. Our results suggest that three commonly used rainbow color maps are implicitly discretized with consistency across individuals. The results also indicate, however, that this implicit discretization varies across different datasets, in a way that suggests the visualization community's understanding of both rainbow color maps, and more generally effective color usage, remains incomplete.

Applied visualization researchers often work closely with domain collaborators to explore new and useful applications of visualization. The early stages of collaborations are typically time consuming for all stakeholders as researchers piece together an understanding of domain challenges from disparate discussions and meetings. A number of recent projects, however, report on the use of creative visualization-opportunities (CVO) workshops to accelerate the early stages of applied work, eliciting a wealth of requirements in a few days of focused work. Yet, there is no established guidance for how to use such workshops effectively. In this paper, we present the results of a 2-year collaboration in which we analyzed the use of 17 workshops in 10 visualization contexts. Its primary contribution is a framework for CVO workshops that: 1) identifies a process model for using workshops; 2) describes a structure of what happens within effective workshops; 3) recommends 25 actionable guidelines for future workshops; and 4) presents an example workshop and workshop methods. The creation of this framework exemplifies the use of critical reflection to learn about visualization in practice from diverse studies and experience.

This paper presents a framework for externalizing and analyzing expert knowledge about discrepancies in data through the use of visualization. Grounded in an 18-month design study with global health experts, the framework formalizes the notion of data discrepancies as implicit error, both in global health data and more broadly. We use the term implicit error to describe measurement error that is inherent to and pervasive throughout a dataset, but that isn't explicitly accounted for or defined. Instead, implicit error exists in the minds of experts, is mainly qualitative, and is accounted for subjectively during expert interpretation of the data. Externalizing knowledge surrounding implicit error can assist in synchronizing, validating, and enhancing interpretation, and can inform error analysis and mitigation. The framework consists of a description of implicit error components that are important for downstream analysis, along with a process model for externalizing and analyzing implicit error using visualization. As a second contribution, we provide a rich, reflective, and verifiable description of our research process as an exemplar summary toward the ongoing inquiry into ways of increasing the validity and transferability of design study research.

Multivariate graphs are prolific across many fields, including transportation and neuroscience. A key task in graph analysis is the exploration of connectivity, to, for example, analyze how signals flow through neurons, or to explore how well different cities are connected by flights. While standard node-link diagrams are helpful in judging connectivity, they do not scale to large networks. Adjacency matrices also do not scale to large networks and are only suitable to judge connectivity of adjacent nodes. A key approach to realize scalable graph visualization are queries: instead of displaying the whole network, only a relevant subset is shown. Query-based techniques for analyzing connectivity in graphs, however, can also easily suffer from cluttering if the query result is big enough. To remedy this, we introduce techniques that provide an overview of the connectivity and reveal details on demand. We have two main contributions: (1) two novel visualization techniques that work in concert for summarizing graph connectivity; and (2) Graffinity, an open-source implementation of these visualizations supplemented by detail views to enable a complete analysis workflow. Graffinity was designed in a close collaboration with neuroscientists and is optimized for connectomics data analysis, yet the technique is applicable across domains. We validate the connectivity overview and our open-source tool with illustrative examples using flight and connectomics data.

Abstract Many factors can shape the flow of visual data‐driven stories, and thereby the way readers experience those stories. Through the analysis of 80 existing stories found on popular websites, we systematically investigate and identify seven characteristics of these stories, which we name “flow‐factors,” and we illustrate how they feed into the broader concept of “visual narrative flow.” These flow‐factors are navigation input, level of control, navigation progress, story layout, role of visualization, story progression, and navigation feedback. We also describe a series of studies we conducted, which shed initial light on how different visual narrative flows impact the reading experience. We report on two exploratory studies, in which we gathered reactions and preferences of readers for stepper‐ vs. scroller‐driven flows. We then report on a crowdsourced study with 240 participants, in which we explore the effect of the combination of different flow‐factors on readers’ engagement. Our results indicate that visuals and navigation feedback (e.g., static vs. animated transitions) have an impact on readers’ engagement, while level of control (e.g., discrete vs. continuous) may not.

A common workflow for visualization designers begins with a generative tool, like D3 or Processing, to create the initial visualization; and proceeds to a drawing tool, like Adobe Illustrator or Inkscape, for editing and cleaning. Unfortunately, this is typically a one-way process: once a visualization is exported from the generative tool into a drawing tool, it is difficult to make further, data-driven changes. In this paper, we propose a bridge model to allow designers to bring their work back from the drawing tool to re-edit in the generative tool. Our key insight is to recast this iteration challenge as a merge problem - similar to when two people are editing a document and changes between them need to reconciled. We also present a specific instantiation of this model, a tool called Hanpuku, which bridges between D3 scripts and Illustrator. We show several examples of visualizations that are iteratively created using Hanpuku in order to illustrate the flexibility of the approach. We further describe several hypothetical tools that bridge between other visualization tools to emphasize the generality of the model.

The expressiveness principle for visualization design asserts that a visualization should encode all of the available data, and only the available data, implying that continuous data types should be visualized with a continuous encoding channel. And yet, in many domains binning continuous data is not only pervasive, but it is accepted as standard practice. Prior work provides no clear guidance for when encoding continuous data continuously is preferable to employing binning techniques or how this choice affects data interpretation and decision making. In this paper, we present a study aimed at better understanding the conditions in which the expressiveness principle can or should be violated for visualizing continuous data. We provided participants with visualizations employing either continuous or binned greyscale encodings of geospatial elevation data and compared participants' ability to complete a wide variety of tasks. For various tasks, the results indicate significant differences in decision making, confidence in responses, and task completion time between continuous and binned encodings of the data. In general, participants with continuous encodings were faster to complete many of the tasks, but never outperformed those with binned encodings, while performance accuracy with binned encodings was superior to continuous encodings in some tasks. These findings suggest that strict adherence to the expressiveness principle is not always advisable. We discuss both the implications and limitations of our results and outline various avenues for potential work needed to further improve guidelines for using continuous versus binned encodings for continuous data types.

Abstract The field of cyber security is faced with ever‐expanding amounts of data and a constant barrage of cyber attacks. Within this space, we have designed BubbleNet as a cyber security dashboard to help network analysts identify and summarize patterns within the data. This design study faced a range of interesting constraints from limited time with various expert users and working with users beyond the network analyst, such as network managers. To overcome these constraints, the design study employed a user‐centered design process and a variety of methods to incorporate user feedback throughout the design of BubbleNet. This approach resulted in a successfully evaluated dashboard with users and further deployments of these ideas in both research and operational environments. By explaining these methods and the process, it can benefit future visualization designers to help overcome similar challenges in cyber security or alternative domains.

The digital humanities have experienced tremendous growth within the last decade, mostly in the context of developing computational tools that support what is called distant reading - collecting and analyzing huge amounts of textual data for synoptic evaluation. On the other end of the spectrum is a practice at the heart of the traditional humanities, close reading - the careful, in-depth analysis of a single text in order to extract, engage, and even generate as much productive meaning as possible. The true value of computation to close reading is still very much an open question. During a two-year design study, we explored this question with several poetry scholars, focusing on an investigation of sound and linguistic devices in poetry. The contributions of our design study include a problem characterization and data abstraction of the use of sound in poetry as well as Poemage, a visualization tool for interactively exploring the sonic topology of a poem. The design of Poemage is grounded in the evaluation of a series of technology probes we deployed to our poetry collaborators, and we validate the final design with several case studies that illustrate the disruptive impact technology can have on poetry scholarship. Finally, we also contribute a reflection on the challenges we faced conducting visualization research in literary studies.

Meteorologists process and analyze weather forecasts using visualization in order to examine the behaviors of and relationships among weather features. In this design study conducted with meteorologists in decision support roles, we identified and attempted to address two significant common challenges in weather visualization: the employment of inconsistent and often ineffective visual encoding practices across a wide range of visualizations, and a lack of support for directly visualizing how different weather features relate across an ensemble of possible forecast outcomes. In this work, we present a characterization of the problems and data associated with meteorological forecasting, we propose a set of informed default encoding choices that integrate existing meteorological conventions with effective visualization practice, and we extend a set of techniques as an initial step toward directly visualizing the interactions of multiple features over an ensemble forecast. We discuss the integration of these contributions into a functional prototype tool, and also reflect on the many practical challenges that arise when working with weather data.

User-centered design can aid visualization designers to build better, more practical tools that meet the needs of cyber security users. The cyber security visualization research community can adopt a variety of design methods to more efficiently and effectively build tools. We demonstrate how previous cyber visualization research has omitted a discussion of effectiveness and process in the explanation of design methods. In this paper, we discuss three design methods and illustrate how each method informed two real-world cyber security visualization projects which resulted in successful deployments to users.

Abstract Increasing the safety of vehicles is an important goal for vehicle manufacturers. These manufacturers often turn to simulations to understand how to improve a vehicle's design as real‐world safety tests are expensive and time consuming. Understanding the results of these simulations, however, is challenging due to the complexity of the data, which often includes both spatial and nonspatial data types. In this design study we collaborated with analysts who are trying to understand the vulnerability of military vehicles. From this design study we contribute a problem characterization, data abstraction, and task analysis for vehicle vulnerability analysis, as well as a validated and deployed tool called Shotviewer. Shotviewer links 3D spatial views with abstract 2D views to support a broad range of analysis needs. Furthermore, reflection on our design study process elucidates a strategy of view‐design parallelism for creating multiview visualizations, as well as four recommendations for conducting design studies in large organizations with sensitive data.

In recent years many popular data visualizations have emerged that are created largely by designers whose main area of expertise is not computer science. Designers generate these visualizations using a handful of design tools and environments. To better inform the development of tools intended for designers working with data, we set out to understand designers' challenges and perspectives. We interviewed professional designers, conducted observations of designers working with data in the lab, and observed designers working with data in team settings in the wild. A set of patterns emerged from these observations from which we extract a number of themes that provide a new perspective on design considerations for visualization tool creators, as well as on known engineering problems.

An important aspect in visualization design is the connection between what a designer does and the decisions the designer makes. Existing design process models, however, do not explicitly link back to models for visualization design decisions. We bridge this gap by introducing the design activity framework, a process model that explicitly connects to the nested model, a well-known visualization design decision model. The framework includes four overlapping activities that characterize the design process, with each activity explicating outcomes related to the nested model. Additionally, we describe and characterize a list of exemplar methods and how they overlap among these activities. The design activity framework is the result of reflective discussions from a collaboration on a visualization redesign project, the details of which we describe to ground the framework in a real-world design process. Lastly, from this redesign project we provide several research outcomes in the domain of cybersecurity, including an extended data abstraction and rich opportunities for future visualization research.

Abstract In this paper, we present a user‐centered design study on poetry visualization. We develop a rule‐based solution to address the conflicting needs for maintaining the flexibility of visualizing a large set of poetic variables and for reducing the tedium and cognitive load in interacting with the visual mapping control panel. We adopt Munzner's nested design model to maintain high‐level interactions with the end users in a closed loop. In addition, we examine three design options for alleviating the difficulty in visualizing poems latitudinally. We present several example uses of poetry visualization in scholarly research on poetry.

A GPU implementation is given for real-time visualization of aggregate eye movements (gaze) via heatmaps. Parallelization of the algorithm leads to substantial speedup over its CPU-based implementation and, for the first time, allows real-time rendering of heatmaps atop video. GLSL shader colorization allows the choice of color ramps. Several luminance-based color maps are advocated as alternatives to the popular rainbow color map, considered inappropriate (harmful) for depiction of (relative) gaze distributions.

Design studies are an increasingly popular form of problem-driven visualization research, yet there is little guidance available about how to do them effectively. In this paper we reflect on our combined experience of conducting twenty-one design studies, as well as reading and reviewing many more, and on an extensive literature review of other field work methods and methodologies. Based on this foundation we provide definitions, propose a methodological framework, and provide practical guidance for conducting design studies. We define a design study as a project in which visualization researchers analyze a specific real-world problem faced by domain experts, design a visualization system that supports solving this problem, validate the design, and reflect about lessons learned in order to refine visualization design guidelines. We characterize two axes - a task clarity axis from fuzzy to crisp and an information location axis from the domain expert's head to the computer - and use these axes to reason about design study contributions, their suitability, and uniqueness from other approaches. The proposed methodological framework consists of 9 stages: learn, winnow, cast, discover, design, implement, deploy, reflect, and write. For each stage we provide practical guidance and outline potential pitfalls. We also conducted an extensive literature survey of related methodological approaches that involve a significant amount of qualitative field work, and compare design study methodology to that of ethnography, grounded theory, and action research.

MOTIVATION: Comparative genomics heavily relies on alignments of large and often complex DNA sequences. From an engineering perspective, the problem here is to provide maximum sensitivity (to find all there is to find), specificity (to only find real homology) and speed (to accommodate the billions of base pairs of vertebrate genomes). RESULTS: Satsuma addresses all three issues through novel strategies: (i) cross-correlation, implemented via fast Fourier transform; (ii) a match scoring scheme that eliminates almost all false hits; and (iii) an asynchronous 'battleship'-like search that allows for aligning two entire fish genomes (470 and 217 Mb) in 120 CPU hours using 15 processors on a single machine. AVAILABILITY: Satsuma is part of the Spines software package, implemented in C++ on Linux. The latest version of Spines can be freely downloaded under the LGPL license from http://www.broadinstitute.org/science/programs/genome-biology/spines/.

Abstract Biologists pioneering the new field of comparative functional genomics attempt to infer the mechanisms of gene regulation by looking for similarities and differences of gene activity over time across multiple species. They use three kinds of data: functional data such as gene activity measurements, pathway data that represent a series of reactions within a cellular process, and phylogenetic relationship data that describe the relatedness of species. No existing visualization tool can visually encode the biologically interesting relationships between multiple pathways, multiple genes, and multiple species. We tackle the challenge of visualizing all aspects of this comparative functional genomics dataset with a new interactive tool called Pathline. In addition to the overall characterization of the problem and design of Pathline, our contributions include two new visual encoding techniques. One is a new method for linearizing metabolic pathways that provides appropriate topological information and supports the comparison of quantitative data along the pathway. The second is the curvemap view, a depiction of time series data for comparison of gene activity and metabolite levels across multiple species. Pathline was developed in close collaboration with a team of genomic scientists. We validate our approach with case studies of the biologists’ use of Pathline and report on how they use the tool to confirm existing findings and to discover new scientific insights.

Cells in an organism share the same genetic information in their DNA, but have very different forms and behavior because of the selective expression of subsets of their genes. The widely used approach of measuring gene expression over time from a tissue sample using techniques such as microarrays or sequencing do not provide information about the spatial position within the tissue where these genes are expressed. In contrast, we are working with biologists who use techniques that measure gene expression in every individual cell of entire fruitfly embryos over an hour of their development, and do so for multiple closely-related subspecies of Drosophila. These scientists are faced with the challenge of integrating temporal gene expression data with the spatial location of cells and, moreover, comparing this data across multiple related species. We have worked with these biologists over the past two years to develop MulteeSum, a visualization system that supports inspection and curation of data sets showing gene expression over time, in conjunction with the spatial location of the cells where the genes are expressed--it is the first tool to support comparisons across multiple such data sets. MulteeSum is part of a general and flexible framework we developed with our collaborators that is built around multiple summaries for each cell, allowing the biologists to explore the results of computations that mix spatial information, gene expression measurements over time, and data from multiple related species or organisms. We justify our design decisions based on specific descriptions of the analysis needs of our collaborators, and provide anecdotal evidence of the efficacy of MulteeSum through a series of case studies.

In the field of comparative genomics, scientists seek to answer questions about evolution and genomic function by comparing the genomes of species to find regions of shared sequences. Conserved syntenic blocks are an important biological data abstraction for indicating regions of shared sequences. The goal of this work is to show multiple types of relationships at multiple scales in a way that is visually comprehensible in accordance with known perceptual principles. We present a task analysis for this domain where the fundamental questions asked by biologists can be understood by a characterization of relationships into the four types of proximity/location, size, orientation, and similarity/strength, and the four scales of genome, chromosome, block, and genomic feature. We also propose a new taxonomy of the design space for visually encoding conservation data. We present MizBee, a multiscale synteny browser with the unique property of providing interactive side-by-side views of the data across the range of scales supporting exploration of all of these relationship types. We conclude with case studies from two biologists who used MizBee to augment their previous automatic analysis work flow, providing anecdotal evidence about the efficacy oft he system for the visualization of syntenic data, the analysis of conservation relationships, and the communication of scientific insights.

The method of Moving Least Squares (MLS) is a popular framework for reconstructing continuous functions from scattered data due to its rich mathematical properties and well-understood theoretical foundations. This paper applies MLS to volume rendering, providing a unified mathematical framework for ray casting of scalar data stored over regular as well as irregular grids. We use the MLS reconstruction to render smooth isosurfaces and to compute accurate derivatives for high-quality shading effects. We also present a novel, adaptive preintegration scheme to improve the efficiency of the ray casting algorithm by reducing the overall number of function evaluations, and an efficient implementation of our framework exploiting modern graphics hardware. The resulting system enables high-quality volume integration and shaded isosurface rendering for regular and irregular volume data.

Methods that faithfully and robustly capture the geometry of complex material interfaces in labeled volume data are important for generating realistic and accurate visualizations and simulations of real-world objects. The generation of such multimaterial models from measured data poses two unique challenges: first, the surfaces must be well-sampled with regular, efficient tessellations that are consistent across material boundaries; and second, the resulting meshes must respect the nonmanifold geometry of the multimaterial interfaces. This paper proposes a strategy for sampling and meshing multimaterial volumes using dynamic particle systems, including a novel, differentiable representation of the material junctions that allows the particle system to explicitly sample corners, edges, and surfaces of material intersections. The distributions of particles are controlled by fundamental sampling constraints, allowing Delaunay-based meshing algorithms to reliably extract watertight meshes of consistently high-quality.

This paper describes a method for constructing isosurface triangulations of sampled, volumetric, three-dimensional scalar fields. The resulting meshes consist of triangles that are of consistently high quality, making them well suited for accurate interpolation of scalar and vector-valued quantities, as required for numerous applications in visualization and numerical simulation. The proposed method does not rely on a local construction or adjustment of triangles as is done, for instance, in advancing wavefront or adaptive refinement methods. Instead, a system of dynamic particles optimally samples an implicit function such that the particles' relative positions can produce a topologically correct Delaunay triangulation. Thus, the proposed method relies on a global placement of triangle vertices. The main contributions of the paper are the integration of dynamic particles systems with surface sampling theory and PDE-based methods for controlling the local variability of particle densities, as well as detailing a practical method that accommodates Delaunay sampling requirements to generate sparse sets of points for the production of high-quality tessellations.

Visualization has become an important component of the simulation pipeline, providing scientists and engineers a visual intuition of their models. Simulations that make use of the high-order finite element method for spatial subdivision, however, present a challenge to conventional isosurface visualization techniques. High-order finite element isosurfaces are often defined by basis functions in reference space, which give rise to a world-space solution through a coordinate transformation, which does not necessarily have a closed-form inverse. Therefore, world-space isosurface rendering methods such as marching cubes and ray tracing must perform a nested root finding, which is computationally expensive. We thus propose visualizing these isosurfaces with a particle system. We present a framework that allows particles to sample an isosurface in reference space, avoiding the costly inverse mapping of positions from world space when evaluating the basis functions. The distribution of particles across the reference space isosurface is controlled by geometric information from the world-space isosurface such as the surface gradient and curvature. The resulting particle distributions can be distributed evenly or adapted to accommodate world-space surface features. This provides compact, efficient, and accurate isosurface representations of these challenging data sets.

Recent research on point-based surface representations suggests that point sets may be a viable alternative to parametric surface representations in applications where the topological constraints of a parameterization are unwieldy or inefficient. Particle systems offer a mechanism for controlling point samples and distributing them according to needs of the application. Furthermore, particle systems can serve as a surface representation in their own right, or to augment implicit functions, allowing for both efficient rendering and control of implicit function parameters. The state of the art in surface sampling particle systems, however, presents some shortcomings. First, most of these systems have many parameters that interact with some complexity, making it difficult for users to tune the system to meet specific requirements. Furthermore, these systems do not lend themselves to spatially adaptive sampling schemes, which are essential for efficient, accurate representations of complex surfaces. In this paper we present a new class of energy functions for distributing particles on implicit surfaces and a corresponding set of numerical techniques. These techniques provide stable, scalable, efficient, and controllable mechanisms for distributing particles that sample implicit surfaces within a locally adaptive framework.