Supercomputers, Clouds and Grids powered by BigPanDA for Brain studies

The PanDA WMS - Production and Distributed Analysis Workload Management System - has been developed and used by the ATLAS experiment at the LHC ( Large Hadron Collider) for all data processing and analysis challenges. BigPanDA is an extension of the PanDA WMS to run ATLAS and non-ATLAS applications on Leadership Class Facilities and supercomputers, as well as traditional grid and cloud resources. The success of the BigPanDA project has drawn attention from other compute intensive sciences such as biology. In 2017, a pilot project was started between BigPanDA and the Blue Brain Project ( BBP) of the Ecole Polytechnique Federal de Lausanne ( EPFL) located in Lausanne, Switzerland. This proof of concept project is aimed at demonstrating the efficient application of the BigPanDA system to support the complex scientific workflow of the BBP, which relies on using a mix of desktop, cluster and supercomputers to reconstruct and simulate accurate models of brain tissue.

Large Volume Imaging of Rodent Brain Anatomy with Emphasis on Selective Plane Illumination Microscopy

Jean Pierre Ghobril

Inside the human brain there are 86 Billion neurons exchanging electrical impulses to allow reaction, homoeostasis and intelligence. Their coarse organization has been described, leaving us with a fair understanding of macrocircuitry. The microcircuitry of the brain is also being explored with patch clamp recordings. But a more integrative view on mesoscale organization of the central nervous system is still lacking. Recent developments in microscopy methods have opened new windows to address this point. It is the goal of this thesis to analyze and compare anatomical features of the brain with current routine techniques as well as explore light sheet microscopy for large scale quantitative reconstructions of rodent brains. Integration efforts of the cortical column model of the Blue Brain project into more detailed cortical circuitry sparked the search of acute slice preparations suitable for long range electrophysiology. Serial section reconstruction of the rat S1 hindlimb anterograde projections was performed with special attention to the anatomical relationship between S1 hindlimb region and VPL nucleus of thalamus. It was found that a functional electrophysiological slice preparation between S1-HL and VPL is feasible. The subsequent experimental exploration proved the intact fiber path in acute slice preparations based on the morphometric measurements of the previous serial sectioning reconstruction. Another mesoscale trait investigated was the excitatory to inhibitory ratio of the juvenile rat cortex. The measured numbers for the cellular density are higher than previously published. Cellular density for S1-HL is 84535

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4400 neurons/mm

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high with an E-I ratio of 8.3. Like in other brains the cellular density is a continuously adapting function of the distance from pia and the current brain region. In the second part of this dissertation Selective Plane Illumination Microscopy(SPIM) and tissue clearing are evaluated as novel tools for whole mount rodent brain scanning, with emphasis on somata, fibers and vasculature as quantifiable brain features. Clearing methods are evaluated and a novel embedding medium for cleared tissues is presented: Thiodiethanol(TDE). Index matched brains with TDE show high degree of fluorescence conservation and transparency. Whole mount mouse and rat brains are imaged and reconstructed. The results show that whole mount microscopy is a potent tool that allows routine quantification of anatomic features on a whole brain level.

EPFL2015

The Human Brain Project: Creating a European Research Infrastructure to Decode the Human Brain

Martin Telefont

Decoding the human brain is perhaps the most fascinating scientific challenge in the 21st century. The Human Brain Project (HBP), a 10-year European Flagship, targets the reconstruction of the brain's multiscale organization. It uses productive loops of experiments, medical, data, data analytics, and simulation on all levels that will eventually bridge the scales. The HBP IT architecture is unique, utilizing cloud-based collaboration and development platforms with databases, workflow systems, petabyte storage, and supercomputers. The HBP is developing toward a European research infrastructure advancing brain research, medicine, and brain-inspired information technology.

Cell Press2016

Introducing the Human Brain Project

Richard Frackowiak, Henry Markram

The Human Brain Project (HBP) is a candidate project in the European Union's FET Flagship Program, funded by the ICT Program in the Seventh Framework Program. The project will develop a new integrated strategy for understanding the human brain and a novel research platform that will integrate all the data and knowledge we can acquire about the structure and function of the brain and use it to build unifying models that can be validated by simulations running on supercomputers. The project will drive the development of supercomputing for the life sciences, generate new neuroscientific data as a benchmark for modeling, develop radically new tools for informatics, modeling and simulation, and build virtual laboratories for collaborative basic and clinical studies, drug simulation and virtual prototyping of neuroprosthetic, neuromorphic, and robotic devices. (C) Selection and peer-review under responsibility of FET11 conference organizers and published by Elsevier B.V.

Elsevier Science, Reg Sales Off, Customer Support Dept, 655 Ave Of The Americas, New York, Ny 10010 Usa2011

Large Volume Imaging of Rodent Brain Anatomy with Emphasis on Selective Plane Illumination Microscopy

Jean Pierre Ghobril

\pm

4400 neurons/mm

^{3}

EPFL2015