Interactive Modeling of Multi-scale Biological Systems

Funding Details
Natural Sciences and Engineering Research Council of Canada
  • Grant type: Discovery Grants Program - Individual
  • Years: 2014/15 to 2018/19
  • Total Funding: $160,000
Keywords
Principle Investigator(s)
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Project Summary

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.