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Biocharts : A Viusal Formalism for Complex Biological Systems 

Unify biological hypotheses with models and experiments

For any assistance regarding downloading and using the tool and questions about the methodology please email Hillel Kugler at (

New Beta Site for the Tool : New Site

Download prototype modeling tool:

Web-based version: Biocharts 0.9.1 (Silverlight) download

Desktop version: SBT 1.0.0 download

Documentation: Tutorial, Examples

Related Publications:

A model of stem cell population dynamics: in-silico analysis and in-vivo validation

Y. Setty, D. Dalfo, D.Z. Korta, E.J. A. Hubbard, and H. Kugler (2012) Development 139: 47-56.

Synthesizing Biological Theories

H. Kugler, C. Plock, A. Roberts (CAV, 2011)

Biocharts: A Visual Formalism for Complex Biological Systems

Hillel Kugler, Antti Larjo, David Harel (Interface, 2010)

Movies Description: A simulation combining chemotactic and metabolic models. The set-up is a tube filled with aspartate and bacteria placed randomly on the other end of the tube. The box in the top portion of the figure represents the tube; the diamonds are bacteria in their running state and the 'x's are bacteria in their tumble state. The diameter of the tube is 200um. Bacteria shown in red were born as the result of divisions taking place within the last 1.5 seconds. Aspartate concentration inside the tube is shown by the curve beneath the box.

Movie1    Simulation time ~ 60 seconds

Movie2    Simulation time ~ 1000 seconds