Immersive Modeling and Analytics of Multi-scale Biological Systems

我的研究项目的一个主要动机是将计算机作为“思考工具”进行探索。特别是，我对创建计算增强的环境(物理或虚拟)感兴趣，在其中我们可以探索看似复杂的系统。在核心方面，我对研究新出现的系统属性感兴趣，在这些属性中，相互作用的子系统的净影响似乎大于其单个部分的集合。自从我在学生时代接触到信息学和计算机科学以来，我就对生物系统、它们的内部工作方式、它们是如何构建、构建和维护的，以及大自然创建这些系统的进化机制一直非常感兴趣。我从我的研究中学到的一件事是，计算机科学家和生物学家对复杂系统的思考方式相似。生物学家倾向于认为他们的研究对象是离散的实体(小分子、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，这些交互规则导致动态的系统行为和表现。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捉、说明并使这些看似复杂的系统变得可探索。我们在我的进化和群体设计研究实验室开发的基于代理的模型，有助于交流复杂系统的基本原理及其动力学。交互式模型使复杂的3D世界可以通过新的调查方式进入，其中一个人沉浸在实际的模拟系统中。因此，计算机充当了一个协作性的“思考工具”，促进了虚拟头脑风暴以及详细的实验和探索。“看到就是开始理解”。而通过互动模式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，用于可视化、导航、演示和探索跨时间和空间尺度的模型层次结构。从我们使用虚拟现实和增强现实的经验来看，沉浸式显示技术已被证明是数据呈现和互动探索的游戏规则改变者。在寻找传播我们的研究的创新方法时，我们通过使模拟在一系列计算平台(移动、台式机、平板电脑、游戏站、云计算)上无缝运行，使更多的用户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访问，艺术家、设计师、教育工作者、生物学家或医学研究人员也可以作为领域专家访问这些平台。“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.