VEARD: Visual Exploration environment for Analyzing gene Regulation in Developmental processes

Understanding the development of complex-shaped biological structures in space and time is a major visualization problem. Investigating these structures requires an interactive visualization environment which can be used for quantitative research on complex shaped and variable biological objects and model-based research on these objects.

Understanding the development of complex-shaped biological structures in space and time is a major visualization problem. Investigating these structures requires an interactive visualization environment which can be used for quantitative research on complex shaped and variable biological objects and model-based research on these objects. An important characteristic of model-based studies on biological objects is that the models are usually characterized by a relatively large number of (usually unknown) parameters. An important visualization issue here is the exploration of these parameter spaces, investigation of these parameter spaces can provide crucial information about the structure of these spaces. In many model-based studies on biological objects these parameter spaces are investigated using optimization methods to extract model parameters, frequently this optimization is very expensive, a visual exploration of parameter spaces may be used here to guide the optimization process. In this project we develop visualization techniques for quantitative research on complex shaped and variable biological and simulated objects and techniques for the visualization of abstract n-dimensional parameter spaces in models of gene regulatory networks. The project aims to develop methods and tools to extract and present geometrical information from spatial measurements and simulation, to develop visualization methods to compare simulation models and measured data, and techniques for the navigation of morphometric parameter spaces (morphospaces) and model parameter spaces. We focus on a prototypical case study: gene regulation of development in metazoans with a relatively simple body plan (sponges and scleractinian corals).

Project members

  • Prof. Dr. Robert van Liere
  • Dr. Chris Kruszynski

Partners

  • Universiteit van Amsterdam