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。在核心上，我对研究紧急系统的特性很感兴趣，其中交互子系统的净效应似乎比单个部分的集合更大。自从我作为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，它们是如何构建，建造和维护的，以及创造这些系统的自然进化机制非常感兴趣。******我从研究中学到的一件事是，计算机科学家和生物学家思考复杂系统的方式相似。生物学家倾向于认为他们的研究对象是离散的实体（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”，即具有特定属性并遵循某些交互规则的实体，这些规则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交互式计算机模型捕获，说明并使这些看似复杂的系统可探索。我们在进化与群体设计研究实验室开发的基于主体的模型，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调查，其中一个沉浸在实际的模拟系统中。因此，计算机作为一个协作的“思考工具”，促进了虚拟的头脑风暴以及详细的实验和探索。“看到了才开始明白”。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、表示和跨时间和空间尺度的模型层次探索。从我们在虚拟现实和增强现实方面的经验来看，沉浸式显示技术已经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。我们已经开始使用电脑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，这不仅适用于计算机科学家，也适用于美术师、设计师、教育家、生物学家或医学研究人员。“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.**