arXiv subjects
Publications and source records attributed to Katy Borner.
Iterative Bleaching Extends multipleXity (IBEX) is a versatile method for highly multiplexed imaging of diverse tissues. Based on open science principles, we created the IBEX Knowledge-Base, a resource for reagents, protocols and more, to empower innovation.
Virtual reality (VR) has seen increased use for training and instruction. Designers can enable VR users to gain insights into their own performance by visualizing telemetry data from their actions in VR. Our ability to detect patterns and trends visually suggests the use of data visualization as a tool for users to identify strategies for improved performance. Typical tasks in VR training scenarios are manipulation of 3D objects (e.g., for learning how to maintain a jet engine) and navigation (e.g., to learn the geography of a building or landscape before traveling on-site). In this paper, we present the results of the RUI VR (84 subjects) and Luddy VR studies (68 subjects), where participants were divided into experiment and control cohorts. All subjects performed a series of tasks: 44 cube-matching tasks in RUI VR and 48 navigation tasks through a virtual building in Luddy VR (all divided into two sets). All Luddy VR subjects used VR gear; RUI VR subjects were divided across three setups: 2D Desktop (with laptop and mouse), VR Tabletop (in VR, sitting at a table), and VR Standup (in VR, standing). In an intervention called "Reflective phase," the experiment cohorts were presented with data visualizations, designed with the Data Visualization Literacy Framework (DVL-FW), of the data they generated during the first set of tasks before continuing to the second part of the study. For Luddy VR, we found that experiment users had significantly faster completion times in their second trial (p = 0.014) while scoring higher in a mid-questionnaire about the virtual building (p = 0.009). For RUI VR, we found no significant differences for completion time and accuracy between the two cohorts in the VR setups; however, 2D Desktop subjects in the experiment cohort had significantly higher rotation accuracy as well as satisfaction (p(rotation) = 0.031, p(satisfaction) = 0.040).
Working with organs and extracted tissue blocks is an essential task in surgery and anatomy environments. To prepare specimens from human donors for analysis, wet-bench workers must dissect human tissue and collect metadata for downstream analysis, including information about the spatial origin of tissue. The Registration User Interface (RUI) was developed to allow stakeholders in the Human Biomolecular Atlas Program (HuBMAP) to register tissue blocks, i.e., to record the size, position, and orientation of human tissue data with regard to reference organs. In this paper, we compare three setups for registering one 3D tissue block object to another 3D reference organ (target) object. The first setup is a 2D Desktop implementation featuring a traditional screen, mouse, and keyboard interface. The remaining setups are both virtual reality (VR) versions of the RUI: VR Tabletop, where users sit at a physical desk which is replicated in virtual space; VR Standup, where users stand upright while performing their tasks. We then ran a user study for these three setups involving 42 human subjects completing 14 increasingly difficult and then 30 identical tasks in sequence and reporting position accuracy, rotation accuracy, completion time, and satisfaction. While VR Tabletop and VR Standup users are about three times as fast and about a third more accurate in terms of rotation than 2D Desktop users (for the sequence of 30 identical tasks), there are no significant differences between the three setups for position accuracy when normalized by the height of the virtual kidney across setups.
This paper analyzes the impact of air transport connectivity and accessibility on scientific collaboration.
It appears paradoxical that science is producing outstanding new results and theories at a rapid rate at the same time that researchers are identifying serious problems in the practice of science that cause many reports to be irreproducible and invalid. Certainly the practice of science needs to be improved and scientists are now pursuing this goal. However, in this perspective we argue that this seeming paradox is not new, has always been part of the way science works, and likely will remain so. We first introduce the paradox. We then review a wide range of challenges that appear to make scientific success difficult. Next, we describe the factors that make science work-in the past, present, and presumably also in the future. We then suggest that remedies for the present practice of science need to be applied selectively so as not to slow progress, and illustrate with a few examples. We conclude with arguments that communication of science needs to emphasize not just problems but the enormous successes and benefits that science has brought and is now bringing to all elements of modern society.
Scientific research is a major driving force in a knowledge based economy. Income, health and wellbeing depend on scientific progress. The better we understand the inner workings of the scientific enterprise, the better we can prompt, manage, steer, and utilize scientific progress. Diverse indicators and approaches exist to evaluate and monitor research activities, from calculating the reputation of a researcher, institution, or country to analyzing and visualizing global brain circulation. However, there are very few predictive models of science that are used by key decision makers in academia, industry, or government interested to improve the quality and impact of scholarly efforts. We present a novel 'bibliographic bibliometric' analysis which we apply to a large collection of books relevant for the modelling of science. We explain the data collection together with the results of the data analyses and visualizations. In the final section we discuss how the analysis of books that describe different modelling approaches can inform the design of new models of science.
Effectively showing the relationships between objects in a dataset is one of the main tasks in information visualization. Typically there is a well-defined notion of distance between pairs of objects, and traditional approaches such as principal component analysis or multi-dimensional scaling are used to place the objects as points in 2D space, so that similar objects are close to each other. In another typical setting, the dataset is visualized as a network graph, where related nodes are connected by links. More recently, datasets are also visualized as maps, where in addition to nodes and links, there is an explicit representation of groups and clusters. We consider these three Techniques, characterized by a progressive increase of the amount of encoded information: node diagrams, node-link diagrams and node-link-group diagrams. We assess these three types of diagrams with a controlled experiment that covers nine different tasks falling broadly in three categories: node-based tasks, network-based tasks and group-based tasks. Our findings indicate that adding links, or links and group representations, does not negatively impact performance (time and accuracy) of node-based tasks. Similarly, adding group representations does not negatively impact the performance of network-based tasks. Node-link-group diagrams outperform the others on group-based tasks. These conclusions contradict results in other studies, in similar but subtly different settings. Taken together, however, such results can have significant implications for the design of standard and domain specific visualizations tools.
The scientific system that we use today was devised centuries ago and is inadequate for our current ICT-based society: the peer review system encourages conservatism, journal publications are monolithic and slow, data is often not available to other scientists, and the independent validation of results is limited. Building on the Innovation Accelerator paper by Helbing and Balietti (2011) this paper takes the initial global vision and reviews the theoretical and technological building blocks that can be used for implementing an innovation (in first place: science) accelerator platform driven by re-imagining the science system. The envisioned platform would rest on four pillars: (i) Redesign the incentive scheme to reduce behavior such as conservatism, herding and hyping; (ii) Advance scientific publications by breaking up the monolithic paper unit and introducing other building blocks such as data, tools, experiment workflows, resources; (iii) Use machine readable semantics for publications, debate structures, provenance etc. in order to include the computer as a partner in the scientific process, and (iv) Build an online platform for collaboration, including a network of trust and reputation among the different types of stakeholders in the scientific system: scientists, educators, funding agencies, policy makers, students and industrial innovators among others. Any such improvements to the scientific system must support the entire scientific process (unlike current tools that chop up the scientific process into disconnected pieces), must facilitate and encourage collaboration and interdisciplinarity (again unlike current tools), must facilitate the inclusion of intelligent computing in the scientific process, must facilitate not only the core scientific process, but also accommodate other stakeholders such science policy makers, industrial innovators, and the general public.