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Last modified: Tuesday, August 10, 2010

Cell simulation workshop draws international cast of researchers to IU Bloomington

Editor's Note: A computer simulation produced by IU graduate student Abbas Shirinifard using the open source modeling tool CompuCell3D and showing vascular tumor growth can be seen in this downloadable video clip.

Aug. 10, 2010

BLOOMINGTON, Ind. -- Researchers from around the world searching for the most accurate ways to capture how cells behave -- from adhesion and clustering to growth, division and death -- are at Indiana University Bloomington this summer to perfect their use of two of the most widely accepted tools for simulating cellular interactions.

Glazier Team

Researchers from Switzerland, United Kingdom, Netherlands, Canada, Brazil, Ireland, Argentina, France, the U.S.'s Environmental Protection Agency and National Aeronautics and Space Administration, and numerous U.S. universities are gathered at Indiana University for two weeks to learn how to implement cellular simulations into their work.

Print-Quality Photo

James Osborne and Sophie Kershaw arrived from the United Kingdom's Oxford University to IU's Biocomplexity Institute in hopes of improving efforts at modeling types of cancer progression.

Willy Supatto of the Institut Jacques Monod in Paris is interested in using the modeling tool Compucell3D (CC3D), developed in part by IU Biocomplexity Institute director James Glazier, to investigate mechanisms involved in early embryonic morphogenesis.

U.S. National Aeronautics and Space Administration scientists are evaluating long-term interactions between human tissue and space radiation in efforts to advance a human presence in space, and one of the scientists, Natalia Alexandrov, is at IU hoping to use the modeling tool in that research.

Scientists also have come from universities in Switzerland, Netherlands, Ireland, Canada, Brazil, Argentina, from a number of other top U.S. research universities and from the U.S. Environmental Protection Agency, which is represented by four researchers looking at modeling tissue toxicity and also vertebrae development.

"The genomic revolution has yet to realize its promise to transform medicine, biology and bioengineering because of the many complex layers of interactions that intervene between genome and organism," Glazier said as the workshop on developing multi-scale, multi-cell developmental and biomedical simulations began its second and final week yesterday (Aug. 9). "Even focusing on the behaviors of the networks of biochemical interactions within a cell or within an organism is a great oversimplification, because it neglects the complex interactions between cells, and between cells and their extracellular environment, which can either amplify or damp down disturbances."

Abbas Movie

This image produced by CompuCell3D shows a vascular tumor (green) which is growing in a tissue (transparent) with blood vessels (red). The tumor grows and the cells in its core begin to starve (colored region inside tumor), they send out a signal (Vascular Endothelial Growth Factor), which causes some of the red vascular cells to become activated. They start dividing and moving towards the source of the growth factor. The extra blood vessels supply extra nutrients to the tumor, which then grows and spreads. In real life, the activity would occur in a 3 millimeter square space over about one month.

Because of these complex chains of interconnection, manipulating single factors cleanly in experiments is almost impossible, Glazier noted, but simulations based on modeling tools that represent and understand the host of complex interactions inside and outside of cells can indeed provide that needed ability to study effects individually.

Using a lattice-based computation model called the Glazier-Graner-Hogeweg model that simulates the collective behavior of cell structures and that has been implemented into the open source CC3D tool, workshop participants are given the opportunity while at IU to implement a basic simulation of their particular biological problem. Once back in their own labs, the scientists can also receive post-course, collaborative support to continue developing those simulations.

"CC3D is unique because it is totally free, and it allows researchers to develop their simulations using high-level scripting, thus simulations which might take months to years to develop using traditional approaches can be developed in days to weeks," Glazier said. "In addition, unlike other methods, it allows the publishing and reuse of models and model components for validation, extension and redeployment. The result is that we have a huge demand from scientists wishing to apply CC3D to their particular systems."

This year, for the first time, students also learn to use Systems Biology Workbench (SBW), the most popular tool for modeling the biochemical reaction networks that control cell behaviors. Teaching these two tools together allows students to build much more complex and biomedically significant models than they could with either tool by itself.

Courses taught during the two-week workshop are a crucial part of the outreach effort scientists at the IU Biocomplexity Institute make to help others learn their approaches and to then begin to build their own simulations, Glazier added.

Organizing the workshop with Glazier and also from IU are research scientist Maciej Swat, research scientist Randy Heiland and graduate student Abbas Shirinfard. University of Washington faculty members Herbert Sauro and Frank Bergmann, developers of the SBW, a tool for developing simulations at the sub-cellular scale of biochemical reaction networks that regulate cell division, differentiation and metabolism, are co-organizers also teaching at the workshop.

"Combining CompuCell3D and SBW simulations allows construction of comprehensive multiscale models to explore normal and disease states at a level of detail previously unachievable," Glazier said.

The workshop is funded by the EPA, the National Institutes of Health and the IU Biocomplexity Institute, with conference space for the workshop provided by the IU Department of Physics, where Glazier is a professor.

To speak with Glazier or other workshop organizers or participants, please contact Steve Chaplin, IU Communications, at 812-856-1896 or