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Biocomplexity Software Available For Download:

Our goal is to develop techniques and tools of broad utility to bioscientists and to distribute these freely to the community at large:


Our initial target software corresponds to our research projects:

  • Software for the analysis of complex networks.
  • Software to model cytoskeletal activity, including mitosis and cell motility, using a combined continuum/molecular dynamics approach.
  • Software to model organogenesis at the cell level, based on Potts model and reaction diffusion techniques.
  • Database management tools.
  • Hybrid finite element software to predict tissue properties from component properties.
  • Improved software for cell tracking using confocal microscopy and for image reconstruction from MRI and CT data.


Software will employ standardized input and output schemes to allow it to interact with programs simulating other levels or systems from our own and other institutions. Similarly, we will present all quantitative data from our experimental program in standardized web-based databases. Planned databases include measured cell and tissue properties and indices of network connections in genetic, metabolic, and proteomic networks. Our collaboration with the Beckman Institute's Bioimaging Laboratory at the California Institute of Technology should lead to image analysis and processing software for medical and research applications. We will also interact closely with the Nanotechnology Center at the University of Notre Dame, which will assist with the design and manufacture of devices for cell level and subcellular stimulation and measurement. In turn, the experiments and simulations developed by the Center will assist directly in current biotechnology and nanotechnology applications. Longer term, we are interested in developing packages for modeling differentiation pathways using reaction-kinetics and the response of bone and the circulatory system to stress.

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Last Updated: Monday, June 10, 2013
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