Data-driven Neuroscience: Enabling Breakthroughs Via Innovative Data Management

Scientists in all disciplines increasingly rely on simulations to develop a better understanding of the subject they are studying. For example the neuroscientists we collaborate with in the Blue Brain project have started to simulate the brain on a supercomputer. The level of detail of their models is unprecedented as they model details on the subcellular level (e.g., the neurotransmitter). This level of detail, however, also leads to a true data deluge and the neuroscientists have only few tools to efficiently analyze the data.

This demonstration showcases three innovative spatial management solutions that have substantial impact on computational neuroscience and other disciplines in that they allow to build, analyze and simulate bigger and more detailed models. More particularly, we visualize the novel query execution strategy of FLAT, an index for the scalable and efficient execution of range queries on increasingly detailed spatial models. FLAT is used to build and analyze models of the brain. We furthermore demonstrate how SCOUT uses previous query results to prefetch spatial data with high accuracy and therefore speeds up the analysis of spatial models. We finally also demonstrate TOUCH, a novel in-memory spatial join, that speeds up the model building process.

Simple Neuron Models and Adaptation

Skander Mensi

Predicting activity of single neuron is an important part of the computational neuroscience and a great challenge. Several mathematical models exist, from the simple (one compartment and few parameters, like the SRM or the IF-type models), to the more complex (biophysical model like the Hodgkin-Huxley model). All these models have their own advantages and limitations, but no one is able to reproduce the exact behavior of real neurons. Multiple projects try to simulate complex neural networks, or even the whole brain (i.e. the blue brain project or other big network simulation). To achieve this goal it is very important that simple neuron models simulate, for a low computational cost, the precise activities of all neuron classes. It is well-known that neurons exhibit a lot of different activity patterns (from an electro-physiological point of view). Here we have focused on pyramidal neurons from the layer 5 of the neocortex. They are classified as regular spiking-cells. This cell type shows adaptation and like other neurons, refractoriness. Adaptation and refractoriness are very common neuronal activity in the brain, and so it is important to have a simple model which can reproduce this kind of activity. This project deals with two classical simple neuron models: the adaptive exponential integrate-and-fire model (AdEx) and the spike response model (SRM). We deter- mined the parameters of these two models using data generated with a detailed model, the Destexhe's model which is a HH-like model for cortical pyramidal cells, stimulated with different current injection scenarios. In a second time the model parameters have been set using data from in-vitro recordings of 4 layer 5 pyramidal rat neurons, stimulated with a sinusoid in vivo-like protocol, injected somatically in current-clamp configuration. Then we show that this type of model can capture adaptation and can reproduce the activity of neuron with a high reliability

2008

Hybrid Representation and Visualization Methods Applied to Neuronal Microcircuits

Sébastien Lasserre

For the past twenty years, scientific visualization has assisted simulation-based research to explore problems of organized complexity. Environmental research, social sciences, astronomy, and modern physics have exploited the increasing power of computer graphics to interactively visualize three-dimensional models. Of late, neuroscience has witnessed the use of large-scale simulation with biologically detailed neuron models, and aspires to benefit from scientific visualization too. This thesis is the result of a close collaboration with the Blue Brain Project, a neuroscience endeavor working on biologically detailed large-scale simulation of the brain, and tries to answer the following question: How can scientific visualization improve neuroscience insights in the context of simulation-based research? Scientific visualization of a model typically preserves its spatial layout. In continuity with this axiom, we identified in more depth the requirements for a scientific visualization solution in neuroscience. Thus, the preservation of the domain specificity, the hybrid visualization, the validation, and the adaptation to the limitations of the human-visual perception enhance the readability of the generated results. We applied these requirements to elaborate an hybrid representation of neuronal structures, and proposed a unified framework of visualization methods which preserves the domain specificities of neuroscience. This framework was finally assessed in case studies, where neuroscientific investigations about structure, composition, and dynamics of neuronal microcircuit challenge the developed visualization solutions to derive insight. We believe that these representations and visualization methods form a solid ground for the elaboration of virtual instruments dedicated to a new approach of neuroscience, where in silico landscapes of the brain are complementary to the classical in vitro and in vivo investigations.

EPFL2010

Simple Neuron Models and Adaptation

Skander Mensi

2008

Hybrid Representation and Visualization Methods Applied to Neuronal Microcircuits

Sébastien Lasserre

EPFL2010