Intuitive visualization of surface properties of biomolecules

In living cells, proteins are in continuous motion and interaction with the surrounding medium and/or other proteins and ligands. These interactions are mediated by protein features such as Electrostatic Potential (EP) and hydropathy expressed as Molecular Lipophilic Potential (MLP). The availability of protein structures enables the study of their surfaces and surface characteristics, based on atomic contribution. Traditionally, these properties are calculated by phisicochemical programs and visualized as range of colours that vary according to the tool used and imposes the necessity of a legend to decrypt it. The use of colour to encode both characteristics makes the simultaneous visualization almost impossible. This is why most of the times EP and MLP are presented in two different images. In this thesis, we describe a novel and intuitive code for the simultaneous visualization of these properties. For our purpose we use Blender, an open-source, free, cross-platform 3D application used for modelling, animation, gaming and rendering. On the basis of Blender, we developed BioBlender, a package dedicated to biological work: elaboration of proteins motion with the simultaneous visualization of their chemical and physical features. Blender's Game Engine, equipped with specific physico-chemical rules is used to elaborate the motion of proteins, interpolating between different conformations (NMR collections or different X-rays of the same protein). We obtain a physically plausible sequence of intermediate conformations which are the basis for the subsequent visual elaboration. A new visual code is introduced for MLP visualization: a range of optical features that goes from dull-rough surfaces for the most hydrophilic areas to shiny-smooth surfaces for the most lipophilic ones. This kind of representation permits a photorealistic rendering of the smooth spatial distribution of the values of MLP on the surface of the protein. EP is represented as animated line particles that flow along field lines, from positive to negative, proportional to the total charge of the protein. Our system permits EP and MLP simultaneous visualization of molecules and, in the case of moving proteins, the continuous perception of these features, calculated for each intermediate conformation. Moreover, this representation contributes to gain insight into the molecules function by drawing viewer's attention to the most active regions of the protein

Finding the Grammar of Generative Craft

Art and craft design is challenging even with the assistance of computer-aided design tools. Despite the increasing availability and intelligence of software and hardware, artists continue to find gaps between their practices and tools when designing physical craft artifacts. In many craft domains, artists need to acquire domain knowledge and develop skills in design-aid tools separately. Despite their power and versatility, generic design tools pose various challenges, such as requiring workarounds for specific crafts and having steep learning curves. Compared to generic design-aid tools, craft-specific systems can offer reasonable solutions to specific design tasks because they can offer domain-specific support. Nevertheless, craft-specific tools often have limited flexibility. In this dissertation, I introduce Grammar-driven Craft Design Tools (GCDTs), which explicitly embed and utilize craft domain knowledge (i.e., ``grammar" of the craft) as their primary mechanisms and interfaces. Like other types of information, craft knowledge is processable and organizable data. In this dissertation, I develop and examine a framework to document, process, preserve, and utilize craft domain knowledge. GCDTs are craft-specific tools. By explicitly embedding and utilizing craft domain knowledge, GCDTs bridge the gap between design-aid tools and craft domain knowledge. GCDTs also have additional benefits such as supporting generative design, facilitating learning, and preserving domain knowledge. This dissertation gives an overview of how the next generation of design-aid tools can help artists find their creative expressions. It presents the GCDT framework and introduces three GCDTs developed for distinct domains. InfiniteLayer assists the design of multilayer sculpture, which is a form of sculpture made with layers of material. Then, MarkMakerSquare helps designers to invent unconventional and creative mark-making tools using various fabrication strategies. Lastly, ThreadPlotter supports the design and fabrication of plotter-based delicate punch needle embroidery.PHDInformationUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/169800/1/heslicia_1.pd

Exploring the potential of physical visualizations

The goal of an external representation of abstract data is to provide insights and convey information about the structure of the underlying data, therefore helping people execute tasks and solve problems more effectively. Apart from the popular and well-studied digital visualization of abstract data there are other scarcely studied perceptual channels to represent data such as taste, sound or haptic. My thesis focuses on the latter and explores in which ways human knowledge and ability to sense and interact with the physical non-digital world can be used to enhance the way in which people analyze and explore abstract data. Emerging technological progress in digital fabrication allow an easy, fast and inexpensive production of physical objects. Machines such as laser cutters and 3D printers enable an accurate fabrication of physical visualizations with different form factors as well as materials. This creates, for the first time, the opportunity to study the potential of physical visualizations in a broad range. The thesis starts with the description of six prototypes of physical visualizations from static examples to digitally augmented variations to interactive artifacts. Based on these explorations, three promising areas of potential for physical visualizations were identified and investigated in more detail: perception & memorability, communication & collaboration, and motivation & self-reflection. The results of two studies in the area of information recall showed that participants who used a physical bar chart retained more information compared to the digital counterpart. Particularly facts about maximum and minimum values were be remembered more efficiently, when they were perceived from a physical visualization. Two explorative studies dealt with the potential of physical visualizations regarding communication and collaboration. The observations revealed the importance on the design and aesthetic of physical visualizations and indicated a great potential for their utilization by audiences with less interest in technology. The results also exposed the current limitations of physical visualizations, especially in contrast to their well-researched digital counterparts. In the area of motivation we present the design and evaluation of the Activity Sculptures project. We conducted a field study, in which we investigated physical visualizations of personal running activity. It was discovered that these sculptures generated curiosity and experimentation regarding the personal running behavior as well as evoked social dynamics such as discussions and competition. Based on the findings of the aforementioned studies this thesis concludes with two theoretical contributions on the design and potential of physical visualizations. On the one hand, it proposes a conceptual framework for material representations of personal data by describing a production and consumption lens. The goal is to encourage artists and designers working in the field of personal informatics to harness the interactive capabilities afforded by digital fabrication and the potential of material representations. On the other hand we give a first classification and performance rating of physical variables including 14 dimensions grouped into four categories. This complements the undertaking of providing researchers and designers with guidance and inspiration to uncover alternative strategies for representing data physically and building effective physical visualizations.Um aus abstrakten Daten konkrete Aussagen, komplexe Zusammenhänge oder überraschende Einsichten gewinnen zu können, müssen diese oftmals in eine, für den Menschen, anschauliche Form gebracht werden. Eine weitverbreitete und gut erforschte Möglichkeiten ist die Darstellung von Daten in visueller Form. Weniger erforschte Varianten sind das Verkörpern von Daten durch Geräusche, Gerüche oder physisch ertastbare Objekte und Formen. Diese Arbeit konzentriert sich auf die letztgenannte Variante und untersucht wie die menschlichen Fähigkeiten mit der physischenWelt zu interagieren dafür genutzt werden können, das Analysieren und Explorieren von Daten zu unterstützen. Der technische Fortschritt in der digitalen Fertigung vereinfacht und beschleunigt die Produktion von physischen Objekten und reduziert dabei deren Kosten. Lasercutter und 3D Drucker ermöglichen beispielsweise eine maßgerechte Fertigung physischer Visualisierungen verschiedenster Ausprägungen hinsichtlich Größe und Material. Dadurch ergibt sich zum ersten Mal die Gelegenheit, das Potenzial von physischen Visualisierungen in größerem Umfang zu erforschen. Der erste Teil der Arbeit skizziert insgesamt sechs Prototypen physischer Visualisierungen, wobei sowohl statische Beispiele beschrieben werden, als auch Exemplare die durch digital Inhalte erweitert werden oder dynamisch auf Interaktionen reagieren können. Basierend auf den Untersuchungen dieser Prototypen wurden drei vielversprechende Bereiche für das Potenzial physischer Visualisierungen ermittelt und genauer untersucht: Wahrnehmung & Einprägsamkeit, Kommunikation & Zusammenarbeit sowie Motivation & Selbstreflexion. Die Ergebnisse zweier Studien zur Wahrnehmung und Einprägsamkeit von Informationen zeigten, dass sich Teilnehmer mit einem physischen Balkendiagramm an deutlich mehr Informationen erinnern konnten, als Teilnehmer, die eine digitale Visualisierung nutzten. Insbesondere Fakten über Maximal- und Minimalwerte konnten besser im Gedächtnis behalten werden, wenn diese mit Hilfe einer physischen Visualisierung wahrgenommen wurden. Zwei explorative Studien untersuchten das Potenzial von physischen Visualisierungen im Bereich der Kommunikation mit Informationen sowie der Zusammenarbeit. Die Ergebnisse legten einerseits offen wie wichtig ein ausgereiftes Design und die Ästhetik von physischen Visualisierungen ist, deuteten anderseits aber auch darauf hin, dass Menschen mit geringem Interesse an neuen Technologien eine interessante Zielgruppe darstellen. Die Studien offenbarten allerdings auch die derzeitigen Grenzen von physischen Visualisierungen, insbesondere im Vergleich zu ihren gut erforschten digitalen Pendants. Im Bereich der Motivation und Selbstreflexion präsentieren wir die Entwicklung und Auswertung des Projekts Activity Sculptures. In einer Feldstudie über drei Wochen erforschten wir physische Visualisierungen, die persönliche Laufdaten repräsentieren. Unsere Beobachtungen und die Aussagen der Teilnehmer ließen darauf schließen, dass die Skulpturen Neugierde weckten und zum Experimentieren mit dem eigenen Laufverhalten einluden. Zudem konnten soziale Dynamiken entdeckt werden, die beispielsweise durch Diskussion aber auch Wettbewerbsgedanken zum Ausdruck kamen. Basierend auf den gewonnen Erkenntnissen durch die erwähnten Studien schließt diese Arbeit mit zwei theoretischen Beiträgen, hinsichtlich des Designs und des Potenzials von physischen Visualisierungen, ab. Zuerst wird ein konzeptionelles Framework vorgestellt, welches die Möglichkeiten und den Nutzen physischer Visualisierungen von persönlichen Daten veranschaulicht. Für Designer und Künstler kann dies zudem als Inspirationsquelle dienen, wie das Potenzial neuer Technologien, wie der digitalen Fabrikation, zur Darstellung persönlicher Daten in physischer Form genutzt werden kann. Des Weiteren wird eine initiale Klassifizierung von physischen Variablen vorgeschlagen mit insgesamt 14 Dimensionen, welche in vier Kategorien gruppiert sind. Damit vervollständigen wir unser Ziel, Forschern und Designern Inspiration und Orientierung zu bieten, um neuartige und effektvolle physische Visualisierungen zu erschaffen

Software Usability

This volume delivers a collection of high-quality contributions to help broaden developers’ and non-developers’ minds alike when it comes to considering software usability. It presents novel research and experiences and disseminates new ideas accessible to people who might not be software makers but who are undoubtedly software users

Investigating the use of 3D digitisation for public facing applications in cultural heritage institutions

This thesis contains research into the use of 3D digitisation technologies by cultural heritage institutions in public facing applications. It is particularly interested in those technologies that can be adopted by institutions with limited budget and no previous experience in 3D digitisation. Whilst there has been research in the area of 3D imaging by museums and cultural heritage institutions, the majority is concerned with the use of the technology for academic or professional, curatorial purposes and on technical comparisons of the various technologies used for capture. Similarly, research conducted on the use of 3D models for public facing and public engagement applications has tended to focus on the various capture technologies, while little has been published on processing raw data for public facing applications – a time-consuming and potentially costly procedure. This research will investigate the issues encountered through the entire 3D digitisation workflow, from capture through processing to dissemination, focusing on the specific problems inherent in public facing projects and the heterogeneous and often problematic nature of museum objects. There has been little research published on the efficacy of 3D models both as providers of informational content and as public engagement tools used to fulfil a cultural heritage institution’s public facing remit. This research assesses the utility of interactive 3D models, as well as rendered animations of 3D content used as in-gallery exhibits and disseminated online. It finds that there is a prima facie case for believing that 3D models may be used to further a museum’s engagement and educational aims, and that there is an appetite among the general public for the use of this type of content in cultural heritage applications. The research will also compare a variety of methods for assessing the success of models

Workshop, Long and Short Paper, and Poster Proceedings from the Fourth Immersive Learning Research Network Conference (iLRN 2018 Montana), 2018.

ILRN 2018 - Conferência internacional realizada em Montana de 24-29 de june de 2018.Workshop, short paper, and long paper proceedingsinfo:eu-repo/semantics/publishedVersio

Immersive analytics for oncology patient cohorts

This thesis proposes a novel interactive immersive analytics tool and methods to interrogate the cancer patient cohort in an immersive virtual environment, namely Virtual Reality to Observe Oncology data Models (VROOM). The overall objective is to develop an immersive analytics platform, which includes a data analytics pipeline from raw gene expression data to immersive visualisation on virtual and augmented reality platforms utilising a game engine. Unity3D has been used to implement the visualisation. Work in this thesis could provide oncologists and clinicians with an interactive visualisation and visual analytics platform that helps them to drive their analysis in treatment efficacy and achieve the goal of evidence-based personalised medicine. The thesis integrates the latest discovery and development in cancer patients’ prognoses, immersive technologies, machine learning, decision support system and interactive visualisation to form an immersive analytics platform of complex genomic data. For this thesis, the experimental paradigm that will be followed is in understanding transcriptomics in cancer samples. This thesis specifically investigates gene expression data to determine the biological similarity revealed by the patient's tumour samples' transcriptomic profiles revealing the active genes in different patients. In summary, the thesis contributes to i) a novel immersive analytics platform for patient cohort data interrogation in similarity space where the similarity space is based on the patient's biological and genomic similarity; ii) an effective immersive environment optimisation design based on the usability study of exocentric and egocentric visualisation, audio and sound design optimisation; iii) an integration of trusted and familiar 2D biomedical visual analytics methods into the immersive environment; iv) novel use of the game theory as the decision-making system engine to help the analytics process, and application of the optimal transport theory in missing data imputation to ensure the preservation of data distribution; and v) case studies to showcase the real-world application of the visualisation and its effectiveness