Cx3Dp: A Parallel Framework for Modeling the Growth and Development of Neural Tissue

Abstract

Event Abstract Back to Event Cx3Dp: A Parallel Framework for Modeling the Growth and Development of Neural Tissue Andreas Hauri1* and Rodney Douglas1 1 UZH / ETHZ, Institute of Neuroinformatics, Switzerland The development of neural tissues such as the neocortex unfolds from a limited number of stem cells by successive mitosis, migration, differentiation and adaptation of cells that finally come to take up specific functional roles. Unlike self-assembly in which the necessary components are given, and assembly depends largely on complementary structure and forces of interaction. The self-construction of development makes explicit use of structural and organizational information encoded in the genome. We have been exploring this complex process by modeling and simulation. In a previous publication, we described a software framework (Cx3D), that enables the simulation of development in physical 3D environment that respects the physical of interaction of objects as well as diffusion of morphogens. (Zubler and Douglas, 2009). However, the success of that system in simulating development soon brought us to the limits of single-threaded, single-computer applications. To open the route to simulating larger cortical areas and their inter-areal connections, we require a more general version of Cx3D that can exploit multiprocessor/multicomputer systems. To this end we have designed a parallel version of Cx3D (Cx3Dp) that addresses these improvements and can also be run cross-platform. The system scales well with addition of processors and computers. Computers can be dynamically added to the simulation if the need for more computational power or more memory arises. The load balancing will acquire the new resources and balance the system in a way that each computer takes the same amount of time to complete one time step. The simulation can be saved after any time step, over multiple computers, and can be reloaded and continued again if necessary. The diffusion framework has also been redesigned. The diffusion is now implemented on an octree grid system that can be adapted to a desired resolution, according to the resolution necessary for the diffusion. Compared to the previous version of Cx3D. This improvement allows higher flexibility in assigning the computational resources to the diffusion. Currently we are running simulations of up to 200’000 cells and 400’000 cell compartments on 3 machines with 64 GB of memory and 24 cores each, using only 25% of the memory available. The system scales well in speed when adding cores, and in speed and memory on adding machines. The new Cx3Dp thus opens the way to very large scale simulation of developing systems on simple networks of consumer computers. Keywords: Large scale modeling Conference: 4th INCF Congress of Neuroinformatics, Boston, United States, 4 Sep - 6 Sep, 2011. Presentation Type: Demo Presentation Topic: Large scale modeling Citation: Hauri A and Douglas R (2011). Cx3Dp: A Parallel Framework for Modeling the Growth and Development of Neural Tissue. Front. Neuroinform. Conference Abstract: 4th INCF Congress of Neuroinformatics. doi: 10.3389/conf.fninf.2011.08.00106 Copyright: The abstracts in this collection have not been subject to any Frontiers peer review or checks, and are not endorsed by Frontiers. They are made available through the Frontiers publishing platform as a service to conference organizers and presenters. The copyright in the individual abstracts is owned by the author of each abstract or his/her employer unless otherwise stated. Each abstract, as well as the collection of abstracts, are published under a Creative Commons CC-BY 4.0 (attribution) licence (https://creativecommons.org/licenses/by/4.0/) and may thus be reproduced, translated, adapted and be the subject of derivative works provided the authors and Frontiers are attributed. For Frontiers’ terms and conditions please see https://www.frontiersin.org/legal/terms-and-conditions. Received: 17 Oct 2011; Published Online: 19 Oct 2011. * Correspondence: Dr. Andreas Hauri, UZH / ETHZ, Institute of Neuroinformatics, Zurich, Switzerland, haurian@ini.ch Login Required This action requires you to be registered with Frontiers and logged in. To register or login click here. Abstract Info Abstract The Authors in Frontiers Andreas Hauri Rodney Douglas Google Andreas Hauri Rodney Douglas Google Scholar Andreas Hauri Rodney Douglas PubMed Andreas Hauri Rodney Douglas Related Article in Frontiers Google Scholar PubMed Abstract Close Back to top Javascript is disabled. Please enable Javascript in your browser settings in order to see all the content on this page.