Interactive Modeling of Multi-scale Biological Systems

多尺度生物系统的交互建模

• 批准号: RGPIN-2014-06094
• 负责人: Jacob, Christian
• 金额: $ 2.33万
• 依托单位: University of Calgary
• 依托单位国家: 加拿大
• 项目类别: Discovery Grants Program - Individual
• 财政年份: 2015
• 资助国家: 加拿大
• 起止时间: 2015-01-01 至 2016-12-31
• 项目状态: 已结题
• 来源: https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=588806
• 关键词: Interactive; Modeling; Multi; scale; Biological

I am interested in understanding in emergent properties of seemingly complex systems, where “the sum is greater than its parts”. For more than a decade, I have been collaborating with biologists, medical researchers, and medical educators to design and test computational models of biological systems. Biologists tend to think about their objects of study as discrete entities. Computationally, these entities can be represented by ‘agents’, whose interaction rules are known or can be identified, and ultimately represented by ‘simple programs’ with concise algorithmic descriptions. Once such interacting elements are arranged within compartments, which are organized into interconnected larger units (‘universes’), complex behaviors emerge. As a computer scientist I look at how to capture, illustrate and make seemingly complex systems explorable through 3-dimensional, interactive computer models. The agent-based models, that we develop in my Evolutionary & Swarm Design research lab, help to communicate our fundamental understanding of complex systems. Going beyond carefully crafted animations, the development of new algorithms and methodologies to build such models does not only enhance research in “systems” sciences but creates new computational approaches for generating, visualizing, and exploring complex models in simulated 3D spaces. “To see is to begin to understand”. And to explore our own learning paths through interactive models deepens our understanding. The next steps in my research focus on how to integrate multi-scale models across different levels of resolution in space and time. My current research focus is on how to combine continuous mathematical models with agent-based approaches. The mathematical models capture concentration changes averaged over a large number of particles (such as molecules), whereas agent methods are a better fit for representing entities that appear in small quantities, and where specific interactions among these entities (such as proteins or cells) can be modeled to a high level of detail in 3D. As many complex systems are composed of a hierarchy of subsystems across a range of scales (e.g., from systems and organs to tissues, cells, and proteins), multi-scale computational models need to incorporate and integrate processes that occur at different spatial scales and at different resolutions in time. Making multi-scale models accessible is another important aspect in my research. I investigate user interfaces for visualization, navigation, presentation, and exploration of model hierarchies across temporal and spatial scales. At the same time, I want our models to be run in real time while maintaining interactivity at any point. I strive to make complex models accessible to a wider user base, by exploring solutions for running simulations on mobile computing platforms.

我对理解看似复杂的系统的涌现特性很感兴趣，在这些系统中，“总和大于部分”。十多年来，我一直与生物学家、医学研究人员和医学教育工作者合作，设计和测试生物系统的计算模型。生物学家倾向于认为他们的研究对象是离散的实体。在计算上，这些实体可以用“代理”来表示，这些代理的交互规则是已知的或可以识别的，最终用带有简明算法描述的“简单程序”来表示。一旦这些相互作用的元素被安排在隔间内，这些隔间又被组织成相互连接的更大的单位（“宇宙”），复杂的行为就出现了。