Publications de Judit Planas Carbonell

Modeling and Simulation of Neocortical Micro- and Mesocircuitry. Part I: Anatomy

Henry Markram, Kathryn Hess Bellwald, Eilif Benjamin Muller, Srikanth Ramaswamy, Michael Reimann, James Gonzalo King, Lida Kanari, Ying Shi, Armando Romani, Adrien Michel Achille Devresse

The function of the neocortex is fundamentally determined by its repeating microcircuit motif, but also by its rich, hierarchical, interregional structure with a highly specific laminar architecture. The last decade has seen the emergence of extensive new ...

2024

Modeling and simulation of neocortical micro- and mesocircuitry. Part II: Physiology and experimentation

Henry Markram, Eilif Benjamin Muller, Srikanth Ramaswamy, Michael Reimann, James Gonzalo King, Rajnish Ranjan, Armando Romani, Mustafa Anil Tuncel, Aleksandra Zuzanna Teska, Polina Litvak

Cortical dynamics underlie many cognitive processes and emerge from complex multi-scale interactions, which are challenging to study in vivo. Large-scale, biophysically detailed models offer a tool which can complement laboratory approaches. We present a m ...

2024

Community-based reconstruction and simulation of a full-scale model of region CA1 of rat hippocampus

Henry Markram, Eilif Benjamin Muller, Srikanth Ramaswamy, Michael Reimann, James Gonzalo King, Lida Kanari, Ying Shi, Armando Romani, Davide Bella, Felix Schürmann

The CA1 region of the hippocampus is one of the most studied regions of the rodent brain, thought to play an important role in cognitive functions such as memory and spatial navigation. Despite a wealth of experimental data on its structure and function, i ...

2024

Synthesis of geometrically realistic and watertight neuronal ultrastructure manifolds for in silico modeling

Daniel Keller, Marwan Muhammad Ahmed Abdellah, Jean-Denis Georges Emile Courcol, Jay Coggan, Georges Khazen, Judit Planas Carbonell, Elvis Boci, Nadir Roman Guerrero, Juan José García Cantero, Alessandro Enrico Foni

Understanding the intracellular dynamics of brain cells entails performing three-dimensional molecular simulations incorporating ultrastructural models that can capture cellular membrane geometries at nanometer scales. While there is an abundance of neuron ...

Oxford University Press (OUP)2024

The SONATA data format for efficient description of large-scale network models

Eilif Benjamin Muller, James Gonzalo King, Adrien Michel Achille Devresse, Werner Alfons Hilda Van Geit, Jean-Denis Georges Emile Courcol, Juan Bautista Hernando Vieites, Michael Emiel Gevaert, Judit Planas Carbonell

Increasing availability of comprehensive experimental datasets and of high-performance computing resources are driving rapid growth in scale, complexity, and biological realism of computational models in neuroscience. To support construction and simulation ...

2020

Exploring the interoperability of remote GPGPU virtualization using rCUDA and directive-based programming models

Judit Planas Carbonell

Directive-based programming models, such as OpenMP, OpenACC, and OmpSs, enable users to accelerate applications by using coprocessors with little effort. These devices offer significant computing power, but their use can introduce two problems: an increase ...

SPRINGER2018

Accelerating Data Analysis in Simulation Neuroscience with Big Data Technologies

Felix Schürmann, Judit Planas Carbonell, Fabien Jonathan Delalondre

Important progress in computational sciences has been made possible recently thanks to the increasing computing power of high performance systems. Following this trend, larger scientific studies, like brain tissue simulations, will continue to grow in the ...

Springer International Publishing2018

Neuromapp: A Mini-application Framework to Improve Neural Simulators

Felix Schürmann, Francesco Cremonesi, Judit Planas Carbonell, Timothée Ewart, Fabien Jonathan Delalondre

The increasing complexity and heterogeneity of extreme scale systems makes the optimization of large scale scientific applications particularly challenging. Efficiently leveraging these complex systems requires a great deal of technical expertise and a con ...

Springer International Publishing2017