Multiscale modeling with GENESIS 3, using the G-shell and Python
© Rodriguez et al; licensee BioMed Central Ltd. 2012
Published: 16 July 2012
The CBI architecture  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 , 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 (https://www.gradschool.uni-luebeck.de/index.php?id=366).
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.
Armando L. Rodriguez and David Beeman are partially supported by NIH grant 3 R01 NS049288-06S1 to James M. Bower.
- 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.0028956View ArticleGoogle Scholar
- 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.0029018View ArticleGoogle Scholar
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 (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.