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”。我特别对创建计算增强环境（物理或虚拟）感兴趣，在其中我们可以探索看似复杂的系统。从本质上讲，我对研究新兴系统属性感兴趣，其中相互作用的子系统的净效应似乎大于其各个部分的集合。自从我作为一名学生早期接触信息学和计算机科学以来，我一直对生物系统、它们的内部工作原理、它们是如何构建、建造和维护的，以及创建此类系统的自然进化机制非常感兴趣。 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，这些对象可以表示为代理，即具有特定属性并遵循某些交互规则的实体，从而导致动态系统行为和表现。 作为一名计算机科学家，我研究如何通过 3D 交互式计算机模型来捕获、说明和探索这些看似复杂的系统。我们在进化和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态的基本原理。交互式模型使复杂的 3D 世界能够以新的方式进行研究，使人们沉浸在实际的模拟系统中。因此，计算机充当协作“思考工具”，促进虚拟头脑风暴以及详细的实验和探索。 “看到就是开始理解”。而通过交互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，我的研究团队开始研究混合现实用户界面，用于跨时间和空间尺度的模型层次结构的可视化、导航、演示和探索。根据我们在虚拟和增强现实方面的经验，沉浸式显示技术已被证明可以改变数据呈现和交互式探索的游戏规则。 在寻找传播我们研究的创新方法时，我们通过在一系列计算平台（移动、桌面、平板电脑、游戏站、云计算）上无缝运行模拟，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来使我们的模拟平台变得不可知。游戏引擎还提供了出色的开发平台，不仅可供计算机科学家使用，而且也可供作为领域专家的艺术家、设计师、教育工作者、生物学家或医学研究人员使用。 “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.