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Multiscale modeling with GENESIS 3, using the G-shell and Python

The CBI architecture [1] being used as the basis of GENESIS 3 (G-3) allows a single model-container to be used to describe a model spanning many levels of scale. This feature allows a user to transparently run multi-scale simulations. As will be described in further detail during the workshop “Multi-Scale Modeling in Computational Neuroscience II: Challenges and Opportunities", the CBI architecture contains a communication component to upscale and downscale numerical variables when moving across different levels of scale. These new capabilities and advances in G-3 usability also allow interfacing with many Python graphical tools (e.g. wxPython, matplotlib), potential web interfaces (e.g. Django), and other independent modules (e.g. Chemesis-3) for use in simulations that cover multiple levels of scale. Progress in developing Python interfaces to G-3 [2], combined with recent implementation of network and biochemical modeling capabilities in G-3 have allowed us to construct a new series of self-guided hands-on modeling tutorials. These are being introduced at the Introduction to Genesis 3 Workshop held in Luebeck, Germany 30 April – 5 May 2012 (

This poster provides an introduction to these new modeling capabilities, and to the new instructional material. Additions to the existing G-3 tutorials on use of the G-shell cover network creation commands and the use of the Chemesis-3 module. The rewritten version of the tutorial "Creating large networks with GENESIS" demonstrates the use of Python scripting to create cortical network models in G-3. The tutorial "Adding a GUI to G-3 simulations" shows users how to leverage the Python programming interface to construct visual tools.

As an example, Figure 1 illustrates the use of the new G-3 Netview visualization application to display and replay an animation of the spreading excitation in the RSnet2 simulation that is the basis of the GENESIS network modeling tutorial.

Figure 1
figure 1

A short injection pulse applied to a 32 x 32 cell network of coupled excitatory cells starts a wave of excitation that can be replayed and examined in detail during any time window, using the G-3 Network Viewer.


  1. Cornelis H, Coop AD, Bower JM: A Federated Design for a Neurobiological Simulation Engine: The CBI Federated Software Architecture. PLoS ONE. 2005, 7 (1): e28956-doi:10.1371/journal.pone.0028956

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  2. Cornelis H, Rodriguez AL, Coop AD, Bower JM: Python as a Federation Tool for GENESIS 3.0. PLoS ONE. 2005, 7 (1): e29018-doi:10.1371/journal.pone.0029018

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Armando L. Rodriguez and David Beeman are partially supported by NIH grant 3 R01 NS049288-06S1 to James M. Bower.

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Correspondence to Armando L Rodriguez.

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This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Rodriguez, A.L., Cornelis, H., Beeman, D. et al. Multiscale modeling with GENESIS 3, using the G-shell and Python. BMC Neurosci 13 (Suppl 1), P176 (2012).

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