Browsing by Subject "visualization"

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  • He, Chen; Micallef, Luana; He, Liye; Peddinti, Gopal; Aittokallio, Tero; Jacucci, Giulio (2021)
    Understanding the quality of insight has become increasingly important with the trend of allowing users to post comments during visual exploration, yet approaches for qualifying insight are rare. This article presents a case study to investigate the possibility of characterizing the quality of insight via the interactions performed. To do this, we devised the interaction of a visualization tool—MediSyn—for insight generation. MediSyn supports five types of interactions: selecting, connecting, elaborating, exploring, and sharing. We evaluated MediSyn with 14 participants by allowing them to freely explore the data and generate insights. We then extracted seven interaction patterns from their interaction logs and correlated the patterns to four aspects of insight quality. The results show the possibility of qualifying insights via interactions. Among other findings, exploration actions can lead to unexpected insights; the drill-down pattern tends to increase the domain values of insights. A qualitative analysis shows that using domain knowledge to guide exploration can positively affect the domain value of derived insights. We discuss the study’s implications, lessons learned, and future research opportunities.
  • Zheng, Shuyu; Poczai, Peter; Hyvönen, Jaakko; Tang, Jing; Amiryousefi, Ali (2020)
    Understanding the complexity of genomic structures and their unique architecture is linked with the power of visualization tools used to represent these features. Such tools should be able to provide a realistic and scalable version of genomic content. Here, we present an online organelle plotting tool focused on chloroplasts, which were developed to visualize the exclusive structure of these genomes. The distinguished unique features of this program include its ability to represent the Single Short Copy (SSC) regions in reverse complement, which allows the depiction of the codon usage bias index for each gene, along with the possibility of the minor mismatches between inverted repeat (IR) regions and user-specified plotting layers. The versatile color schemes and diverse functionalities of the program are specifically designed to reflect the accurate scalable representation of the plastid genomes. We introduce a Shiny app website for easy use of the program; a more advanced application of the tool is possible by further development and modification of the downloadable source codes provided online. The software and its libraries are completely coded in R, available at
  • Leskinen, Petri; Miyakita, Goki; Koho, Mikko; Hyvönen, Eero (2018)
    This paper discusses practical experiences on creating data-analytic visualizations in a browser, on top of a SPARQL endpoint based on the results of faceted search. Four use cases related to Digital Humanities research in proposography are discussed where the SPARQL Faceter tool was used and extended in different ways. The Faceter tool allows the user to select a group of people with shared properties, e.g., people with the same place of birth, gender, profession, or employer. The filtered data can then be visualized, e.g., as column charts, with business graphics, sankey diagrams, or on a map. The use cases examine the potential of visualization as well as automated knowledge discovery in Digital Humanities research.
  • Mäkinen, Ville; Oksanen, Juha; Sarjakoski, Tapani (Stichting AGILE, 2019)
    The digital elevation model (DEM) is an invaluable product in numerous geospatial applications from orthorectification of aerial photographs to hydrological modelling and advanced 3D visualisation. With the current aerial laser scanning methods, superior quality digital elevation models can be produced over land areas, but surfaces over water bodies are visually problematic, especially for streams in 3D. We present a method to generate smooth, monotonically decreasing elevation surfaces over water bodies in DEMs. The method requires the point cloud data and the polygons delineating the water bodies as input data. We show how DEM visualisations improve by applying the presented method.
  • Hosseini, Morteza; Pratas, Diogo; Morgenstern, Burkhard; Pinho, Armando J. (2020)
    Background: The development of high-throughput sequencing technologies and, as its result, the production of huge volumes of genomic data, has accelerated biological and medical research and discovery. Study on genomic rearrangements is crucial owing to their role in chromosomal evolution, genetic disorders, and cancer. Results: We present Smash++, an alignment-free and memory-efficient tool to find and visualize small- and large-scale genomic rearrangements between 2 DNA sequences. This computational solution extracts information contents of the 2 sequences, exploiting a data compression technique to find rearrangements. We also present Smash++ visualizer, a tool that allows the visualization of the detected rearrangements along with their self- and relative complexity, by generating an SVG (Scalable Vector Graphics) image. Conclusions: Tested on several synthetic and real DNA sequences from bacteria, fungi, Aves, and Mammalia, the proposed tool was able to accurately find genomic rearrangements. The detected regions were in accordance with previous studies, which took alignment-based approaches or performed FISH (fluorescence in situ hybridization) analysis. The maximum peak memory usage among all experiments was similar to 1 GB, which makes Smash++ feasible to run on present-day standard computers.
  • Jussila, Anssi (Helsingfors universitet, 2017)
    Studies of the last ice age have been made in Finland since the early 20th century. The result is a wealth of information on activities related to the continental ice sheet and the location of the ice margins. The purpose of this thesis was to find out the usefulness of animations when visualizing research results. Animations have the advantage of sharing a large amount of information in a short time and they often are easier to comprehend compared to texts and images. In addition to this the aim was to visualize dynamics of the ice sheet and its ice margin positions. The materials from different studies that were used in visualization contain visual materials from ice sheet in northern Europe and more precisely from Finland. The animations were created by using ArcGis program and Blender 3D graphics software. In ArcGis the GIS-database was modified for suitable format to be used in Blender. Based on the visual materials, objects were formed in Blender from polygons that reflect the geometry of the ice sheet and its environment. The movements and other events were modelled by animating them and their visual look was formed by assigning different materials for different objects. Lastly, the animation was post-processed through composite and then rendered out of the program in the desired format. The results of the study were two animations about the activities related to the continental ice sheet in Northern Europe and Finland. The animation of Northern Europe is a general overview of growth and retreat of the ice sheet between 34–10 ka. The main result of the study is an animation of retreat of the ice sheet during deglaciation in Finland between 14–10 ka. The animation of the Finnish area visualizes ice lobes and stagnant ice areas between them. In addition to the ice sheet the animation also visualizes ice lakes, terminal moraines and calving of the ice sheet, as well as the sub-aquatic and supra-aquatic regions in Finland. The study can be further refined by adding all existing research data of ice margin positions and ice sheet dynamics. The animation regarding the ice sheet dynamics of Finland could be further expanded and refined towards areas in Norway, Sweden and Russia. In addition to that, one could add an elevation model and the development model of Baltic Sea and other water bodies to create a more diverse work. Based on the study, the usability of the animation in glacial geologic studies is significant when it is based on extensive research data and up-to-date glacial geological knowledge. The applications of animations are numerous and they can be used to generalize geological events.
  • Virtanen, Pirjo Kristiina; Saunaluoma, Sanna (2017)
    Producing geometric designs and images on materials, such as pottery, basketry, and bead artwork, as well as the human body, is elemental and widespread among Amazonian Indigenous peoples. In this article, we examine the different geometric forms identified in the precolonial geoglyph architecture of southwestern Amazonia in the context of geometric design making and relational ontologies. Our aim is to explore earthwork iconography through the lens of Amerindian visual arts and movement. Combining ethnographic and archaeological data from the Upper Purus, Brazil, the article shows how ancient history and socio-cosmology are deeply "written" onto the landscape in the form of geometric earthworks carved out of the soil, which materialize interactions between nonhuman and human actors. We underline skills in visualization, imaginative practices, and movement as ways to promote well-balanced engagements with animated life forms. Here, iconography inserted in the landscape is both a form of writing and also emerges as an agent, affecting people through visual and corporal practices.