Gene ontology (GO) enrichment analysis is frequently undertaken during exploration of various -omics data sets. Despite the wide array of tools available to biologists to perform this analysis, ...meaningful visualisation of the overrepresented GO in a manner which is easy to interpret is still lacking.
Monash Gene Ontology (MonaGO) is a novel web-based visualisation system that provides an intuitive, interactive and responsive interface for performing GO enrichment analysis and visualising the results. MonaGO supports gene lists as well as GO terms as inputs. Visualisation results can be exported as high-resolution images or restored in new sessions, allowing reproducibility of the analysis. An extensive comparison between MonaGO and 11 state-of-the-art GO enrichment visualisation tools based on 9 features revealed that MonaGO is a unique platform that simultaneously allows interactive visualisation within one single output page, directly accessible through a web browser with customisable display options.
MonaGO combines dynamic clustering and interactive visualisation as well as customisation options to assist biologists in obtaining meaningful representation of overrepresented GO terms, producing simplified outputs in an unbiased manner. MonaGO will facilitate the interpretation of GO analysis and will assist the biologists into the representation of the results.
Since the COVID-19 pandemic started in 2019, the virus responsible for the outbreak-SARS-CoV-2-has continued to evolve. Mutations of the virus' spike protein, the main protein driving infectivity and ...transmissibility, are especially concerning as they may allow the virus to improve its infectivity, transmissibility, and ability to evade the immune system. Understanding how specific molecular changes can alter the behaviour of a virus is challenging for non-experts, but this information helps us to understand the pandemic we are living through and the public health measures and interventions needed to bring it under control. In response to communication challenges arising from the COVID-19 pandemic, we recently developed an online educational application to explain the molecular biology of SARS-CoV-2 spike protein mutations to the general public. We used visualisation techniques such as 3D modelling and animation, which have been shown to be highly effective teaching tools in molecular biology, allowing the viewer to better understand protein structure, function, and dynamics. We also included interactive elements for users to learn actively by engaging with the digital content, and consequently improve information retention.This chapter presents the methodological and technological framework which we used to create this resource, the 'SARS-CoV-2 Spike Protein Mutation Explorer' (SSPME). It explains how molecular visualisation and 3D modelling software were used to develop accurate models of relevant proteins; how 3D animation software was used to accurately visualise the dynamic molecular processes of SARS-CoV-2 infection, transmission, and antibody evasion; and how game development software was used to compile the 3D models and animations into a comprehensive, informative interactive application on SARS-CoV-2 spike protein mutations. This chapter indicates how cutting-edge visualisation techniques and technologies can be used to improve science communication about complex topics in molecular biology and infection biology to the general public, something that is critical to gaining control of the continuing COVID-19 pandemic.
In this paper we present the interactive Reservoir Operations Notebooks and Software (iRONS) toolbox for reservoir modelling and optimisation. The toolbox is meant to serve the research and ...professional community in hydrology and water resource management and contribute to bridge the gaps between them. iRONS is composed of a package of Python core functions and a set of interactive Jupyter Notebooks. Core functions implement typical reservoir modelling tasks and the interactive Jupyter Notebooks illustrate, with practical examples, the key functionalities of iRONS. We describe our development philosophy, the key features of iRONS, and report some results of evaluating the effectiveness of interactive Jupyter Notebooks for training and knowledge transfer. The paper may be of interest also beyond the water resources management field, as an example of how Jupyter Notebooks and interactive visualisation help improving the documentation and sharing of open-source code and the communication of underpinning methodologies.
•We present a Python package, iRONS, for reservoir operations simulation and optimisation.•We discuss our development philosophy of modularity, minimalism, openness and accessibility.•We evaluate the use of interactive Jupyter Notebooks for documentation and training.
Instructional guidance, provided using worked examples, helps the inexperienced learner cope with complex information, that may be difficult to process in limited capacity working memory. For ...students of chemistry, such complex information can pertain to the visualisation of structural changes in molecules throughout chemical reactions. This can be alleviated through the affordances of augmented reality (AR) technology. 3D structures are important as they have a crucial impact on the chemical and physical properties of molecules. Within a framework of Cognitive Load Theory, this study illustrates how AR-supported worked examples may enhance learning of electrophilic aromatic substitution. The participant cohort were FHEQ level 5 undergraduate students studying a module of organic chemistry. In addition, the achievement motivation of learner's was also explored, and how this may be impacted by the provision of AR technology and worked examples. The control group was provided with a copy of our worked examples that contained 2D reaction mechanism drawings. Data was collected using a combination of quantitative instruments and qualitative surveys/interviews. For this cohort of students, significant intragroup improvements, and greater normalised change values, in conceptual understanding were observed in the AR group. This was not observed in the control group. No significant intergroup differences in reported cognitive load or achievement motivation of students were found. This was unaffected when introducing prior relevant chemistry experience as a covariate. Student feedback and subsequent thematic analysis show not only the positive impacts on student engagement, but also how students convey their understanding of electrophilic aromatic substitution principles.
Interactive visualisation and analysis of time series data is a critical part of many data-driven optimisation processes, particularly in Industry 4.0 and Smart Manufacturing. Time series ...visualisation enables data analysts or domain experts to visually identify problems such as missing values, sensor drift, precision degradation, or faulty data, before or after algorithmic analysis. A common technique to support the visual exploration of large time series is the overview+detail (O+D) technique. O+D provides both detail and context information by displaying a detailed view showing the actual data and a thumbnail overview for showing its context. User studies have shown that users analyse and navigate data sets more efficently and effectively with than without O+D, but that this strongly depends on the task and the nature and amount of the data to be displayed.
We present results of a quantitative user study that was performed on Amazon Mechanical Turk with 95 participants to identify scenarios in which O+D could not effectively solve the challenge of visualising large time series. By this, we identify potential usability issues of O+D for typical time series analysis tasks and discuss their origins. For each of these usability issues, we also propose alternative interaction and visualisation designs or other strategies to maintain good usability, even for challenging task types and data densities.
We propose a framework for the 3D exploration of heterogeneous environmental data within a geographical region of interest. Based on Unity, the system can be built for a variety of platforms and ...works both on regular machines as well as in virtual reality environments, where it can be considered a basis for a virtual geographic environment. Focussing on the catchment of the Müglitz River in south-eastern Germany, a large collection of observation data acquired via a wide range of measurement devices has been integrated in a geographical reference frame for the region. Results of area-wide numerical simulations for both groundwater and soil moisture have been added to the scene and allow for the exploration of the delayed consequences of transient phenomena such as heavy rainfall events and their impact on the catchment scale. This study focusses on the concurrent visualisation and synchronised animation of multiple area wide datasets from different environmental compartments. The resulting application allows to explore the region of interest during specific hydrological events for an assessment of the interrelation of processes. As such, it offers the opportunity for knowledge transfer between researchers of different domains as well as for outreach to an interested public.
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•Visualisation of a large heterogeneous data collection in a unified geographical context•Concurrent visualisation of time-dependent observation and simulation data•Visual demonstration of multi-compartment analysis from basic input data•Interactive framework for outreach activities and stakeholder information•General framework for creating similar applications for other regions of interest.
Augmented reality (AR) has the capacity to afford a virtual experience that obviates the reliance on using two-dimensional representations of 3D molecules for teaching stereochemistry to ...undergraduate students. Using a combination of quantitative instruments and qualitative surveys/interviews, this study explored the relationships between students’ attitudes, perceived cognitive load, spatial ability, and academic performance when engaging in an asynchronous online stereochemistry activity. Our activity was designed using elements of game-based learning, and integrated AR technologies. The control group was provided with a copy of our activity that used two-dimensional drawings, whereas the AR group completed an activity using the AR technologies. For this cohort of students, results indicated significant improvement in academic performance in both the control and AR groups. The introduction of AR technologies did not result in the AR group outperforming the control group. Participants from both groups displayed significant improvements in spatial ability throughout the research period. Further, a moderate correlation (
r
s
= 0.416) between students’ spatial ability and academic performance was found. No significant intergroup differences in the perceived cognitive loads of students were observed. A significant difference was observed on one item of the Intellectual Accessibility subscale of the ASCI (V2), Complicated–Simple. We found no correlation for student attitude or cognitive load with academic performance. The findings of this study provide insights for future AR-related studies to explore the role of spatial ability, student attitude, and cognitive load in learning performance.
Despite the importance of emotions in science education, research on affect remains sparse. A promising direction is to explore the role of immersive visualisation in evoking affective responses. We ...investigate whether touch-based zooming interaction with a tabletop visualisation of the tree of life evokes various affective responses, particularly, the epistemic affective responses of awe, curiosity, surprise, and confusion. Ten students participated in semi-structured interviews while interacting with the visualisation. Verbal utterances and interactions with the visual interface were videorecorded. Students' verbal and non-verbal affective responses in relation to five evolutionary themes were analysed. Results revealed that students expressed all four affective responses while engaging the zooming feature, with awe and surprise most frequently uttered. Most affective responses were associated with the themes of biological relationships and evolutionary time. Awe was highly associated with evolutionary time, surprise with biological relationships, and confusion with both these conceptual themes. For eight participants, awe was the initial affective response generated after exposure to the dynamic tree of life. The study demonstrates that interacting with an immersive visualisation through zooming can induce affective responses in relation to multiple conceptual themes in evolution. The findings provide insight into multidirectional interconnections between affect, dynamic visualisation, and biology concepts.
The use of digital models of cultural heritage objects obtained from 3D scanning or photogrammetry requires the development of strategies in order to optimise computational resources and enhance the ...user experience when they are used in interactive applications or virtual museums. Through a case study, this work compares an original photogrammetric model with its optimised version using traditional remeshing techniques and an improved version using Nanite technology, developed by Epic Games. A self-contained executable is created in Unreal® 5.1 game engine to test the performance of the three models measured in frames per second (FPS). As a result, it was demonstrated that, although there is no substantial difference in the FPS rate, the Nanite technology avoids the need to perform the mesh and texture editing processes that lead to the construction of the optimised model. This saves considerable time and specialised effort, as the photogrammetric model can be converted to a Nanite object automatically. This would be a great advantage in the case of virtualisations of large collections of heritage objects, which is a common case in virtual museums.
We introduce a method to calculate and store approximately 1.2 million surname distributions calculated for surnames found in Great Britain for six years of historic population data and 20 years of ...contemporary population registers compiled from various consumer sources. We subsequently show how this database can be incorporated into an interactive web-environment specifically designed for the public dissemination of detailed surname statistics. Additionally, we argue that the database can be used in the quantitative analysis of surnames in Great Britain and potentially offer valuable insights into processes of contagious and hierarchical diffusion of populations as well as the regional distinctiveness of demographic change and stasis.
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