10 simple rules to create a serious game, illustrated with examples from structural biology

Serious scientific games are games whose purpose is not only fun. In the field of science, the serious goals include crucial activities for scientists: outreach, teaching and research. The number of serious games is increasing rapidly, in particular citizen science games, games that allow people to produce and/or analyze scientific data. Interestingly, it is possible to build a set of rules providing a guideline to create or improve serious games. We present arguments gathered from our own experience ( Phylo , DocMolecules , HiRE-RNA contest and Pangu) as well as examples from the growing literature on scientific serious games

Molecular simulations and visualization: introduction and overview

Here we provide an introduction and overview of current progress in the field of molecular simulation and visualization, touching on the following topics: (1) virtual and augmented reality for immersive molecular simulations; (2) advanced visualization and visual analytic techniques; (3) new developments in high performance computing; and (4) applications and model building

A cognitive prosthesis for complex decision-making

While simple heuristics can be ecologically rational and effective in naturalistic decision making contexts, complex situations require analytical decision making strategies, hypothesis-testing and learning. Sub-optimal decision strategies – using simplified as opposed to analytic decision rules – have been reported in domains such as healthcare, military operational planning, and government policy making. We investigate the potential of a computational toolkit called “IMAGE” to improve decision-making by developing structural knowledge and increasing understanding of complex situations. IMAGE is tested within the context of a complex military convoy management task through (a) interactive simulations, and (b) visualization and knowledge representation capabilities. We assess the usefulness of two versions of IMAGE (desktop and immersive) compared to a baseline. Results suggest that the prosthesis helped analysts in making better decisions, but failed to increase their structural knowledge about the situation once the cognitive prosthesis is removed

Virtual reality computer program for biomolecule structure determination

Protein structures are complex 3-dimensional shapes that are experimentally determined using x-ray crystallography and cryogenic electron microscopy. Interpreting the data that these methods yield involves building simplified 3D models. Some portion of time spent creating these models must be spent manually modifying the model in order to make it line up with the data; this is difficult and time consuming, in part because the data is “blurry” in three dimensions. We have created a computer program for performing this task in virtual reality, which allows structural biologists to build models using their hands. Furthermore, we have evaluated the program and found that it speeds up model building, in certain circumstances

Multisensory VR interaction for protein-docking in the CoRSAIRe project

Proteins take on their function in the cell by interacting with other proteins or biomolecular complexes. To study this process, computational methods, collectively named protein docking, are used to predict the position and orientation of a protein ligand when it is bound to a protein receptor or enzyme, taking into account chemical or physical criteria. This process is intensively studied to discover new biological functions for proteins and to better understand how these macromolecules take on these functions at the molecular scale. Pharmaceutical research also employs docking techniques for a variety of purposes, most notably in the virtual screening of large databases of available chemicals to select likely molecular candidates for drug design. The basic hypothesis of our work is that Virtual Reality (VR) and multimodal interaction can increase efficiency in reaching and analysing docking solutions, in addition to fully a computational docking approach. To this end, we conducted an ergonomic analysis of the protein–protein current docking task as it is carried out today. Using these results, we designed an immersive and multimodal application where VR devices, such as the three-dimensional mouse and haptic devices, are used to interactively manipulate two proteins to explore possible docking solutions. During this exploration, visual, audio, and haptic feedbacks are combined to render and evaluate chemical or physical properties of the current docking configuration

Interactive molecular docking with haptics and advanced graphics

Biomolecular interactions underpin many of the processes that make up life. Molecular docking is the study of these interactions in silico. Interactive docking applications put the user in control of the docking process, allowing them to use their knowledge and intuition to determine how molecules bind together. Interactive molecular docking applications often use haptic devices as a method of controlling the docking process. These devices allow the user to easily manipulate the structures in 3D space, whilst feeling the forces that occur in response to their manipulations. As a result of the force refresh rate requirements of haptic devices, haptic assisted docking applications are often limited, in that they model the interacting proteins as rigid, use low fidelity visualisations or require expensive propriety equipment to use. The research in this thesis aims to address some of these limitations. Firstly, the development of a visualisation algorithm capable of rendering a depiction of a deforming protein at an interactive refresh rate, with per-pixel shadows and ambient occlusion, is discussed. Then, a novel approach to modelling molecular flexibility whilst maintaining a stable haptic refresh rate is developed. Together these algorithms are presented within Haptimol FlexiDock, the first haptic-assisted molecular docking application to support receptor flexibility with high fidelity graphics, whilst also maintaining interactive refresh rates on both the haptic device and visual display. Using Haptimol FlexiDock, docking experiments were performed between two protein-ligand pairs: Maltodextrin Binding Protein and Maltose, and glutamine Binding Protein and Glucose. When the ligand was placed in its approximate binding site, the direction of over 80% of the intra-molecular movement aligned with that seen in the experimental structures. Furthermore, over 50% of the expected backbone motion was present in the structures generated with FlexiDock. Calculating the deformation of a biomolecule in real time, whilst maintaining an interactive refresh rate on the haptic device (> 500Hz) is a breakthrough in the field of interactive molecular docking, as, previous approaches either model protein flexibility, but fail to achieve the required haptic refresh rate, or do not consider biomolecular flexibility at all

Assistance à l'interaction homme-molécule in virtuo (application au chromosome)

L'une des finalités de la Biologie Moléculaire est l'étude de l'architecture spatiale des molécules. Les expérimentations in silico permettant la modélisation 3D utilisent le plus souvent des approches automatiques. Or, ces approches présentent certains inconvénients: temps de traitement important, modélisation souvent partielle, modèle 3D généralement figé, etc.L'apport des connaissances des experts, de manière interactive, pendant le processus de modélisation automatique peut pallier certains défauts des méthodes calculatoires usuelles. Il s'agit de placer le biologiste au centre des essais virtuels plutôt qu'en observateur de résultats de simulations. C'est ce que nous appelons l'approche hybride, qui associe les avantages des expérimentations in silico (capacité de calcul) à ceux des Interactions Homme-Machine et de la Réalité Virtuelle: commande naturelle, immersion dans l'environnement virtuel (EV), multimodalité, etc. Le résultat de cette approche est la création d'analyses in virtuo, qui comportent trois phases fondamentales: la modélisation 3D, la visualisation et l'interaction 3D (I3D). Cependant, des domaines complexes tels que la Biologie sont régis par un ensemble de contraintes qui peuvent être locales (liées aux objets 3D ou aux tâches d'I3D) et globales (liées à l'espace des objets 3D ou au système d'I3D). Par conséquent, l'intervention des experts ne peut pas être réalisée efficacement par des techniques d'I3D classiques, indépendantes de la complexité et des contraintes du domaine. Plus généralement, nous sommes confrontés au problème innovant de l I3D sous contraintes qui intègre les règles de comportement imposées par l'EV. Pour y répondre, nous formalisons un modèle d'assistance qui associe les contraintes, les tâches d'interaction et des outils d'assistance que sont les guides virtuels. Nous avons appliqué ces deux concepts, d'approche hybride et d'assistance à l'I3D sous contraintes, au problème de la modélisation 3D du chromosome. Les contraintes identifiées sont ici architecturales (données physico-chimiques) et fonctionnelles (modèles biologiques). Ces contraintes issues des lois de la Biologie imposent l'ordonnancement spatial du chromosome. Le système d'interaction Hommme-Molécule in virtuo proposé peut être considéré plus crédible puisqu'il respecte les contraintes environnementales, tant au niveau de la structure 3D qu'au niveau de l'I3D.One of the aims of Molecular Biology (MB) is the study of the molecules' 3D structure. In silico experiments (ie. computing simulations) for 3D modeling usually use automatic approaches. However, these approaches have limits: important computing time, local modeling, 3D model generally fixed, etc. The contribution of expert knowledge, interactively during the automatic modeling process, can overcome some limits of the usual computational methods. It involves placing the biologist in the center of virtual experiments, rather than an observer of automatic simulation results. This is what we call hybrid approach, that combines the advantages of in silico experiments and those of Human-Computer Interaction (HCI) and Virtual Reality (VR): natural interaction, immersion in the virtual environment (VE), multimodality, etc. The result of this approach is the creation of in virtuo experiments which has three components: the 3D modeling, the visualization and the 3D interaction (3DI). However, complex domains such as MB are governed by several constraints that may be local (linked to 3D objects or 3DI techniques) or global (linked to virtual environment or to the 3DI system). Therefore, experts intervention can not be efficiently realized by conventional 3DI techniques, without taking into account the domain complexity (ie. constraints). More generally, we are confronted to the problem of constrained 3DI which includes behavior rules imposed by the VE.The solution we propose is an assistance model that associates constraints, interaction task and assistance tools. The assistance tools are Virtual Fixtures. We applied these two concepts, hybrid approach and assistance model, to the chromosome 3D modeling. The identified constraints are architectural (ie. physico-chemical data) and functional (ie. biological models). These biological constraints dictate the chromosome spatial organization. The in virtuo Human-Molecule interaction system can be considered more credible because it respects the environment constraints, both in the 3D structure and at the level of 3DI.EVRY-Bib. électronique (912289901) / SudocSudocFranceF