Immersive Modeling and Analytics of Multi-scale Biological Systems

我的研究计划的一个关键动机是探索计算机作为“思考工具”。特别是，我对创建计算增强环境（物理或虚拟）感兴趣，我们可以在其中探索看似复杂的系统。在核心，我感兴趣的是研究涌现系统的属性，其中相互作用的子系统的净效应似乎大于其单个部分的集合。自从我早期接触信息学和计算机科学作为一个学生，我一直对生物系统，他们的内部工作，他们是如何构造，建造和维护，以及自然的进化机制，以创建这样的系统非常感兴趣。 我通过研究了解到的一件事是，计算机科学家和生物学家以类似的方式思考复杂系统。生物学家倾向于将他们的研究对象视为离散的实体（微分子，蛋白质，细胞器，细胞，组织，器官，系统等）。在计算上，这些“对象”可以被表示为“代理人”，即具有特定属性并遵循某些互动规则的实体，这些规则导致动态系统的行为和表现。 作为一名计算机科学家，我研究如何通过3D交互式计算机模型捕捉、说明并探索此类看似复杂的系统。我们在进化与群体设计研究实验室开发的基于代理的模型有助于传达复杂系统及其动力学的基本原理。交互式模型使复杂的3D世界能够以新的方式进行调查，其中一个人沉浸在实际的模拟系统中。因此，计算机作为一个合作的“思考工具”，促进虚拟头脑风暴以及详细的实验和探索。“看见就是开始理解”。通过交互式模型探索我们自己的学习路径确实加深了我们的理解。 最近，我的研究团队已经开始研究混合现实用户界面，用于跨时间和空间尺度的可视化，导航，演示和模型层次结构的探索。根据我们在虚拟现实和增强现实方面的经验，沉浸式显示技术已被证明是数据呈现和交互式探索的游戏规则改变者。在寻找传播我们研究的创新方式时，我们通过使模拟在一系列计算平台（移动的、台式机、平板电脑、游戏站、云计算）上无缝运行，使更广泛的用户群可以访问复杂的模型。我们已经开始使用计算机游戏引擎，使我们的模拟平台不可知。游戏引擎还提供了优秀的开发平台，不仅计算机科学家可以使用，艺术家，设计师，教育家，生物学家或医学研究人员也可以作为领域专家。“人群共享”将提供高水平的可访问性，并支持计算模型的集体进步。

A key motivation of my research program is to explore computers as "think tools". In particular, I am interested in creating computationally augmented environments (physical or virtual), in which we can explore seemingly complex systems. At the core, I am interested in studying emergent system properties, where the net effect of interacting subsystems seems to be greater than a collection of its individual parts. Since my early exposure to informatics and computer science as a student, I have been keenly interested in biological systems, their inner workings, how they are constructed, built, and maintained, and Nature's evolutionary mechanisms to create such systems. One thing that I have learnt through my research is that computer scientists and biologists think about complex systems in similar ways. Biologists tend to think about their objects of study as discrete entities (micro molecules, proteins, organelles, cells, tissues, organs, systems, etc). Computationally, these `objects' can be represented as `agents', entities that have specific properties and follow certain rules of interaction that result in dynamic system behaviours and manifestations. As a computer scientist I look at how to capture, illustrate and make such seemingly complex systems explorable through 3D, interactive computer models. The agent-based models, that we develop in my Evolutionary & Swarm Design research lab, help to communicate fundamental principles of complex systems and their dynamics. Interactive models make complex 3D worlds accessible to new ways of investigation, where one is immersed in the actual simulated systems. Thus the computer acts as a collaborative "think tool" that facilitates virtual brain storming as well as detailed experimentation and explorations. "To see is to begin to understand". And to explore our own learning paths through interactive models does deepen our understanding. More recently, my research team has started to investigate mixed reality user interfaces for visualization, navigation, presentation, and exploration of model hierarchies across temporal and spatial scales. From our experiences with virtual and augmented reality, immersive display technologies have proven to be game changers for data presentation and interactive exploration. In searching for innovative ways of disseminating our research, we make complex models accessible to a wider user base by making simulations run seamlessly across a range of computing platforms (mobile, desktop, tablet, game stations, cloud computing). We have started to use computer game engines to make our simulations platform agnostic. Game engines also provide excellent development platforms which are not only accessible to computer scientists, but also to artists, designers, educators, and biologists or medical researchers as domain experts. "Crowd sharing" will provide a high level of accessibility and support collective advancements of computational models.