The CELLmicrocosmos tools: A small history of Java-based cell and membrane modelling open source software development

For more than one decade, CELLmicrocosmos tools are being developed. Here, we discus some of the technical and administrative hurdles to keep a software suite running so many years. The tools were being developed during a number of student projects and theses, whereas main developers refactored and maintained the code over the years. The focus of this publication is laid on two Java-based Open Source Software frameworks. Firstly, the CellExplorer with the PathwayIntegration combines the mesoscopic and the functional level by mapping biological networks onto cell components using database integration. Secondly, the MembraneEditor enables users to generate membranes of different lipid and protein compositions using the PDB format. Technicalities will be discussed as well as the historical development of these tools with a special focus on group-based development. In this way, university-associated developers of Integrative Bioinformatics applications should be inspired to go similar ways. All tools discussed in this publication can be downloaded and installed from https://www.CELLmicrocosmos.org

Hybrid stereoscopic photography - Analogue stereo photography meets the digital age with the StereoCompass app

Stereoscopic photography has a long history which started just a few years after the first known photo was taken: 1849 Sir David Brewster introduced the first binocular camera. Whereas mobile photography is omnipresent because of the wide distribution of smart phones, stereoscopic photography is only used by a very small set of enthusiasts or professional (stereo) photographers. One important aspect of professional stereoscopic photography is that the required technology is usually quite expensive. Here, we present an alternative approach, uniting easily affordable vintage analogue SLR cameras with smart phone technology to measure and predict the stereo base/camera separation as well as the focal distance to zero parallax. For this purpose, the StereoCompass app was developed which is utilizing a number of smart phone sensors, combined with a Google Maps-based distance measure- ment. Three application cases including red/cyan anaglyph stereo photographs are shown. More information and the app can be found at: http://stereocompass.i2d.u

Hybrid-Dimensional Visualization and Interaction - Integrating 2D and 3D Visualization with Semi-Immersive Navigation Techniques

The integration of 2D visualization and navigation techniques has reached a state where the potential for improvements is relatively low. With 3D-stereoscopy-compatible technology now commonplace not only in research but also in many households, the need for better 3D visualization and navigation techniques has increased. Nevertheless, for the representation of many abstract data such as networks, 2D visualization remains the primary choice. But often such abstract data is associated with spatial data, thereby increasing the need for combining both 2D and 3D visualization and navigation techniques. Here, we discuss a new hybrid-dimensional approach integrating 2D and 3D (stereoscopic) visualization as well as navigation into a semi-immersive virtual environment. This approach is compared to classical 6DOF navigation techniques. Three scientific as well as educational applications are presented: an educational car model, a plant simulation data exploration, and a cellular model with network exploration, each of these combining spatial with associated abstract data. The software is available at: http://Cm4.CELLmicrocosmos.org

IoT product pleasurability - Investigating the pleasurable user experiences between conventional products and IoT products through watches

The arrival of Internet of Things (IoT) overcomes limitations of time and space by providing ubiquitous accessibility of its products. Design and HCI research are challenged by an increasingly complex network of diverse types of interaction. To design pleasurable user experiences (UXs), new models need to be developed for emerging IoT products as previous models for conventional products might not be applicable anymore. From a human-centred perspective, this project investigates how the pleasurable UXs will change after a product develops into an IoT product. The project aims at understanding the attributes of IoT products that might contribute to understand the future relationship between users and IoT objects. The project applies UX theories by Jordan (a hierarchy of consumer needs, 2003) and Hassenzahl (top-ten psychological needs, 2010) as theoretical guidelines. These theories classified the contribution of human factors to design pleasurable products and agreed that the enjoyments from the psychological level are at the top of UX. The project uses two online questionnaires to collect data on 1) the UX of Smartwatches and 2) conventional Wristwatches (digital and analogue), in order to reflect on the influence of IoT products on the pleasurable UXs. The results show that the UXs of IoT Watches and conventional watches were not significantly different in terms of the four kinds of pleasure as proposed by Jordan; however, IoT products and conventional products did appear to influence some items in top-ten psychological needs differently

Bio-related design genres: A survey on familiarity and potential applications

Biophilia, biophilic design, bio-inspired and bio-design are design genres that adopted nature and biological elements as part of design processes. With the spread use of natural elements in design nowadays, from the analogical approach to the application of the biological materials in design brought up a different connotation towards the diverse use of nature in everyday life. This paper discusses the background knowledge of Biophilia, biophilic design, bio-inspired and bio-design and the application of biological materials in urban environments, especially for home. As part of a larger project on the application of biological materials in everyday products, this study investigates the emotional design and perception, while identifying the purposes of biological materials which incorporated into designs or systems. Data from 158 potential consumers were collected in an online survey specifically designed for this study, differentiating between design and non-design participants. Interesting findings are that more than 65% of non-design respondents are not aware of the terms biophilia and biophilic design, but they are familiar with the terms bio-inspired and bio-design. On the other hand, the potential consumers which are from non-design and design background as well agreed that having biological materials indoors, can a) help to release stress, b) create awareness of nature and ecological impact, c) can foster a sense of care, and d) can be educational

Using pleasurability to compare wristwatches and IoT smartwatches: Providing novel insights into UX design

The emergence of the Internet of Things (IoT) has brought more challenges for designers to fully understand networked objects and develop pleasurable user experiences (UXs). Due to the radical change of products when they are connected, traditional experience design theories may not be applicable in this new context. Based on two well-established UX design theories, this paper presents a survey study that investigated the pleasurability of IoT devices by comparing a representative IoT device (i.e., the smartwatch) and its conventional form (i.e., the wristwatch). An online questionnaire was deployed to gather feedback from parallel wristwatch and smartwatch users. Their experiences using both types of watches were quantitatively and qualitatively compared by data analysis. The results highlighted the differences in UXs between smartwatches and wristwatches in three types of pleasure and five psychological needs. The study revealed design opportunities to improve the pleasurability of smartwatches and provides novel design insights informing the development of pleasurable UXs for future IoT devices

Immersive design engineering

Design Engineering is an innovative field that usually combines a number of disciplines, such as material science, mechanics, electronics, and/or biochemistry, etc. New immersive technologies, such as Virtual Reality (VR) and Augmented Reality (AR), are currently in the process of being widely adapted in various engineering fields. It is a proven fact that the modeling of spatial structures is supported by immersive exploration. But the field of Design Engineering reaches beyond standard engineering tasks. With this review paper we want to achieve the following: define the term “Immersive Design Engineering”, discuss a number of recent immersive technologies in this context, and provide an inspiring overview of work that belongs to, or is related to the field of Immersive Design Engineering. Finally, the paper concludes with definitions of research questions as well as a number of suggestions for future developments

Identifying the purposes of biological materials in everyday designs

The exploration of new materials has provided new insights into the progressive use of living biological materials in everyday designs. Living biological materials are expected to have the potential to overcome the depletion of non-renewable resources. Through bio-design and biophilic design in the urban environment, designers apply living systems as appropriate solutions to everyday designs. This paper aims to classify the biological materials and the sense of ownership towards biological materials embedded in products in terms of a) Function, b) Aesthetic and Semantic, and c) Emotion and Experience. A survey was conducted from 173 respondents through an online questionnaire

JIB.tools 2.0 – A Bioinformatics Registry for Journal Published Tools with Interoperability to bio.tools

JIB.tools 2.0 is a new approach to more closely embed the curation process in the publication process. This website hosts the tools, software applications, databases and workflow systems published in the Journal of Integrative Bioinformatics (JIB). As soon as a new tool-related publication is published in JIB, the tool is posted to JIB.tools and can afterwards be easily transferred to bio.tools, a large information repository of software tools, databases and services for bioinformatics and the life sciences. In this way, an easily-accessible list of tools is provided which were published in JIB a well as status information regarding the underlying service. With newer registries like bio.tools providing these information on a bigger scale, JIB.tools 2.0 closes the gap between journal publications and registry publication. (Reference: https://jib.tools)

TEAMwISE: synchronised immersive environments for exploration and analysis of animal behaviour

The recent availability of affordable and lightweight tracking sensors allows researchers to collect large and complex movement data sets. To explore and analyse these data, applications are required that are capable of handling the data while providing an environment that enables the analyst(s) to focus on the task of investigating the movement in the context of the geographic environment it occurred in. We present an extensible, open-source framework for collaborative analysis of geospatial–temporal movement data with a use case in collective behaviour analysis. The framework TEAMwISE supports the concurrent usage of several program instances, allowing to have different perspectives on the same data in collocated or remote set-ups. The implementation can be deployed in a variety of immersive environments, for example, on a tiled display wall and mobile VR devices