From Virtual Reality to Immersive Analytics in Bioinformatics

ColocZStats: a z-stack signal colocalization extension tool for 3D slicer

Confocal microscopy has evolved to be a widely adopted imaging technique in molecular biology and is frequently utilized to achieve accurate subcellular localization of proteins. Applying colocalization analysis on image z-stacks obtained from confocal fluorescence microscopes is a dependable method of revealing the relationship between different molecules. In addition, despite the established advantages and growing adoption of 3D visualization software in various microscopy research domains, there have been few systems that can support colocalization analysis within a user-specified region of interest (ROI). In this context, several broadly employed biological image visualization platforms are meticulously explored in this study to understand the current landscape. It has been observed that while these applications can generate three-dimensional (3D) reconstructions for z-stacks, and in some cases transfer them into an immersive virtual reality (VR) scene, there is still little support for performing quantitative colocalization analysis on such images based on a user-defined ROI and thresholding levels. To address these issues, an extension called ColocZStats (pronounced Coloc-Zee-Stats) has been developed for 3D Slicer, a widely used free and open-source software package for image analysis and scientific visualization. With a custom-designed user-friendly interface, ColocZStats allows investigators to conduct intensity thresholding and ROI selection on imported 3D image stacks. It can deliver several essential colocalization metrics for structures of interest and produce reports in the form of diagrams and spreadsheets.

Aplicaciones del metaverso en medicina y atención sanitaria

El metaverso es un mundo virtual, aún en proceso de desarrollo, que permite a las personas interactuar entre ellas, así como con objetos digitales de una forma más inmersiva. Esta innovadora herramienta aúna las tres principales tendencias tecnológicas: la telepresencia, el gemelo digital y la cadena de bloques. La telepresencia permite a las personas “reunirse” de manera virtual, aunque se encuentren en distintos lugares. El gemelo digital es el equivalente virtual y digital de un paciente, dispositivo médico o incluso de un hospital. Por último, la cadena de bloques puede ser utilizada por los pacientes para almacenar sus informes médicos personales de forma segura. En medicina, el metaverso podría tener distintas aplicaciones: (1) consultas médicas virtuales; (2) educación y formación médica; (3) educación del paciente; (4) investigación médica; (5) desarrollo de medicamentos; (6) terapia y apoyo; (7) medicina de laboratorio. El metaverso permitiría una atención sanitaria más personalizada, eficiente y accesible, mejorando así los resultados clínicos y reduciendo los costes de atención médica. No obstante, la implementación del metaverso en medicina y atención sanitaria requerirá una cuidadosa evaluación de los aspectos éticos y de privacidad, así como técnicos, sociales y jurídicos. En términos generales, el futuro del metaverso en el campo de la medicina parece prometedor, aunque es necesario desarrollar nuevas leyes que regulen específicamente el metaverso, con el fin de superar sus posibles inconvenientes.

Applications of the metaverse in medicine and healthcare

The metaverse is a virtual world that is being developed to allow people to interact with each other and with digital objects in a more immersive way. It involves the convergence of three major technological trends: telepresence, the digital twin, and blockchain. Telepresence is the ability of people to "be together" in a virtual way while not being close to each other. The digital twin is a virtual, digital equivalent of a patient, a medical device or even a hospital. Blockchain can be used by patients to keep their personal medical records secure. In medicine and healthcare, the metaverse could be used in several ways: (1) virtual medical consultations; (2) medical education and training; (3) patient education; (4) medical research; (5) drug development; (6) therapy and support; (7) laboratory medicine. The metaverse has the potential to enable more personalized, efficient, and accessible healthcare, improving patient outcomes and reducing healthcare costs. However, the implementation of the metaverse in medicine and healthcare will require careful consideration of ethical and privacy concerns, as well as social, technical and regulatory challenges. Overall, the future of the metaverse in healthcare looks bright, but new metaverse-specific laws should be created to help overcome any potential downsides.

From complex data to clear insights: visualizing molecular dynamics trajectories

Advances in simulations, combined with technological developments in high-performance computing, have made it possible to produce a physically accurate dynamic representation of complex biological systems involving millions to billions of atoms over increasingly long simulation times. The analysis of these computed simulations is crucial, involving the interpretation of structural and dynamic data to gain insights into the underlying biological processes. However, this analysis becomes increasingly challenging due to the complexity of the generated systems with a large number of individual runs, ranging from hundreds to thousands of trajectories. This massive increase in raw simulation data creates additional processing and visualization challenges. Effective visualization techniques play a vital role in facilitating the analysis and interpretation of molecular dynamics simulations. In this paper, we focus mainly on the techniques and tools that can be used for visualization of molecular dynamics simulations, among which we highlight the few approaches used specifically for this purpose, discussing their advantages and limitations, and addressing the future challenges of molecular dynamics visualization.

Computational modeling of protein-carbohydrate interactions: Current trends and future challenges

The article leads the reader through an up-to-date presentation of the concepts, developments, and main applications of computational modeling to study protein-carbohydrate interactions. It follows with the presentation of some current issues and perspectives arising from the expected evolution of generic methodological developments in deep learning, immersive analytics, and virtual reality for molecular visualization and data management. Such methodological developments for macromolecular interactions would greatly benefit a wide range of scientific endeavors in the field of carbohydrate chemistry and biochemistry, including the following interrelated efforts dealing with highly crowded media, with examples concerning glycoside transferases, the extracellular matrix, and the exploration of interactions between complex carbohydrates and intrinsically disordered proteins.

Design X Bioinformatics: a community-driven initiative to connect bioinformatics and design

Bioinformatics applies computer science approaches to the analysis of biological data. It is widely known for its genomics-based analysis approaches that have supported, for example, the 1000 Genomes Project. In addition, bioinformatics relates to many other areas, such as analysis of microscopic images (e.g., organelle localization), molecular modelling (e.g., proteins, biological membranes), and visualization of biological networks (e.g., protein-protein interaction networks, metabolism). Design is a highly interdisciplinary field that incorporates aspects such as aesthetic, economic, functional, philosophical, and/or socio-political considerations into the creative process and is usually determined by context. While visualization plays a critical role in bioinformatics, as reflected in a number of conferences and workshops in the field, design in bioinformatics-related research contexts in particular is not as well studied. With this special issue in conjunction with an international workshop, we aim to bring together bioinformaticians from different fields with designers, design researchers, and medical and scientific illustrators to discuss future challenges in the context of bioinformatics and design.

Bioinformatics and the Metaverse: Are We Ready?

COVID-19 forced humanity to think about new ways of working globally without physically being present with other people, and eXtended Reality (XR) systems (defined as Virtual Reality, Augmented Reality and Mixed Reality) offer a potentially elegant solution. Previously seen as mainly for gaming, commercial and research institutions are investigating XR solutions to solve real world problems from training, simulation, mental health, data analysis, and studying disease progression. More recently large corporations such as Microsoft and Meta have announced they are developing the Metaverse as a new paradigm to interact with the digital world. This article will look at how visualization can leverage the Metaverse in bioinformatics research, the pros and cons of this technology, and what the future may hold.

Role-Aware Information Spread in Online Social Networks

Understanding the complex process of information spread in online social networks (OSNs) enables the efficient maximization/minimization of the spread of useful/harmful information. Users assume various roles based on their behaviors while engaging with information in these OSNs. Recent reviews on information spread in OSNs have focused on algorithms and challenges for modeling the local node-to-node cascading paths of viral information. However, they neglected to analyze non-viral information with low reach size that can also spread globally beyond OSN edges (links) via non-neighbors through, for example, pushed information via content recommendation algorithms. Previous reviews have also not fully considered user roles in the spread of information. To address these gaps, we: (i) provide a comprehensive survey of the latest studies on role-aware information spread in OSNs, also addressing the different temporal spreading patterns of viral and non-viral information; (ii) survey modeling approaches that consider structural, non-structural, and hybrid features, and provide a taxonomy of these approaches; (iii) review software platforms for the analysis and visualization of role-aware information spread in OSNs; and (iv) describe how information spread models enable useful applications in OSNs such as detecting influential users. We conclude by highlighting future research directions for studying information spread in OSNs, accounting for dynamic user roles.

VRmol: an integrative web-based virtual reality system to explore macromolecular structure

SUMMARY

Structural visualization and analysis are fundamental to explore macromolecular functions. Here, we present a novel integrative web-based virtual reality (VR) system-VRmol, to visualize and study molecular structures in an immersive virtual environment. Importantly, it is integrated with multiple online databases and is able to couple structure studies with associated genomic variations and drug information in a visual interface by cloud-based drug docking. VRmol thus can serve as an integrative platform to aid structure-based translational research and drug design.

AVAILABILITY AND IMPLEMENTATION

VRmol is freely available (https://VRmol.net), with detailed manual and tutorial (https://VRmol.net/docs). The code of VRmol is available as open source under the MIT license at http://github.com/kuixu/VRmol.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Visualizing protein structures - tools and trends

Molecular visualization is fundamental in the current scientific literature, textbooks and dissemination materials. It provides an essential support for presenting results, reasoning on and formulating hypotheses related to molecular structure. Tools for visual exploration of structural data have become easily accessible on a broad variety of platforms thanks to advanced software tools that render a great service to the scientific community. These tools are often developed across disciplines bridging computer science, biology and chemistry. This mini-review was written as a short and compact overview for scientists who need to visualize protein structures and want to make an informed decision which tool they should use. Here, we first describe a few 'Swiss Army knives' geared towards protein visualization for everyday use with an existing large user base, then focus on more specialized tools for peculiar needs that are not yet as broadly known. Our selection is by no means exhaustive, but reflects a diverse snapshot of scenarios that we consider informative for the reader. We end with an account of future trends and perspectives.

Building blocks for commodity augmented reality-based molecular visualization and modeling in web browsers

For years, immersive interfaces using virtual and augmented reality (AR) for molecular visualization and modeling have promised a revolution in the way how we teach, learn, communicate and work in chemistry, structural biology and related areas. However, most tools available today for immersive modeling require specialized hardware and software, and are costly and cumbersome to set up. These limitations prevent wide use of immersive technologies in education and research centers in a standardized form, which in turn prevents large-scale testing of the actual effects of such technologies on learning and thinking processes. Here, I discuss building blocks for creating marker-based AR applications that run as web pages on regular computers, and explore how they can be exploited to develop web content for handling virtual molecular systems in commodity AR with no more than a webcam- and internet-enabled computer. Examples span from displaying molecules, electron microscopy maps and molecular orbitals with minimal amounts of HTML code, to incorporation of molecular mechanics, real-time estimation of experimental observables and other interactive resources using JavaScript. These web apps provide virtual alternatives to physical, plastic-made molecular modeling kits, where the computer augments the experience with information about spatial interactions, reactivity, energetics, etc. The ideas and prototypes introduced here should serve as starting points for building active content that everybody can utilize online at minimal cost, providing novel interactive pedagogic material in such an open way that it could enable mass-testing of the effect of immersive technologies on chemistry education.

Network-Based Approaches for Multi-omics Integration

Network-based approach is rapidly emerging as a promising strategy to integrate and interpret different -omics datasets, including metabolomics. The first section of this chapter introduces the current progresses and main concepts in multi-omics integration. The second section provides an overview of the public resources available for creation of biological networks. The third section describes three common application scenarios including subnetwork identification, network-based enrichment analysis, and systems metabolomics. The section four introduces the concept of hierarchical community network analysis. The section five discusses different tools for network visualization. The chapter ends with a future perspective on multi-omics integration.

Visualizing biomolecular electrostatics in virtual reality with UnityMol-APBS

Virtual reality is a powerful tool with the ability to immerse a user within a completely external environment. This immersion is particularly useful when visualizing and analyzing interactions between small organic molecules, molecular inorganic complexes, and biomolecular systems such as redox proteins and enzymes. A common tool used in the biomedical community to analyze such interactions is the Adaptive Poisson-Boltzmann Solver (APBS) software, which was developed to solve the equations of continuum electrostatics for large biomolecular assemblages. Numerous applications exist for using APBS in the biomedical community including analysis of protein ligand interactions and APBS has enjoyed widespread adoption throughout the biomedical community. Currently, typical use of the full APBS toolset is completed via the command line followed by visualization using a variety of two-dimensional external molecular visualization software. This process has inherent limitations: visualization of three-dimensional objects using a two-dimensional interface masks important information within the depth component. Herein, we have developed a single application, UnityMol-APBS, that provides a dual experience where users can utilize the full range of the APBS toolset, without the use of a command line interface, by use of a simple graphical user interface (GUI) for either a standard desktop or immersive virtual reality experience.

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.