Glossary

Action potential: A short-lasting electrical event in which the membrane potential of a cell rapidly rises and falls, following a consistent trajectory of depolarization and hyperpolarization.

Axon: A long projection of a neuron that conducts electrical impulses that conducts electrical signals very efficiently, thanks to a special sheath surrounding it.

BlueGene: IBM supercomputer. The BlueGene/Q currently used in the EPFL Blue Brain Project is a massively parallel, tightly interconnect machine with 65,536 processors, 839 Teraflops of peak performance, 65 TeraBytes of RAM, 128 TeraBytes of BlueGene Active Storage (BIGAS) and more than 4 PetaBytes of hard disk.

Bouton: An enlarged part of a neuron or fibre, where it forms a synapse.

Brain atlas: A work of reference (e.g. the Allen Mouse Atlas), often available as an on-line public resource, showing how one or more data sets (e.g. gene expression data) map to specific regions and sub-regions of the brain.

Cable theory: A mathematical model that make it possible to calculate the flow of electric current (and accompanying voltage), assuming passive neuronal fibres such as axons and dendrites are cylindrical cable-like structures.

Cell type: Neurons can be into types according to their morphological, electrophysiological, and genetic properties. Current BBP digital reconstructions recognize 55 layer-specific morphological types (m-types) and 207 morpho-electrical subtypes. Neuron types play a fundamental role in the BBP digital reconstruction process.

Closed loop: The loop connecting the sensory organs of an animal (or a robot) to the brain, where the input signal is processed to produce motor behaviour.

Connection: a channel allowing two neurons to communicate – a connection always consists of multiple synapses.

Connectome: In BBP digital reconstructions, the complete connectivity map between neurons, including the locations of all synapses.

Connectomics: The study of the connectome.

Cortex: A region of the brain consisting of several areas associated with specific cognitive processes (auditory cortex, visual cortex etc.).

Cortical column: A densely interconnected column of neurons – about 10,000 in rats and 70,000 in humans – that transverses all six layers of the cortex, constituting a unit with a specific function.

Dendrite: The branched projections of a neuron that conduct electrochemical signals received from other neurons to the soma.

Digital reconstruction: A comprehensive digital model of a volume of neural tissue (a microcircuit, a brain region, the whole brain) representing multiple levels of anatomy and physiology (e.g. neuron morphologies, electrical behaviour, connectivity etc.).

Electron microscopy (EM): Use of an Electron Microscope to obtain highly magnified images of biological tissue.

Electrophysiology: The study of the electrical properties of excitable biological cells and tissues.

e-type: Electrical neuron type.

em-type: Electro-morphological neuron type.

Evoked activity: The activity of neural tissue when it is subject to physiological or experimental stimulation.

Exascale: Refers to a supercomputer with a performance of 1018 flops. Computers with this level of performance are expected to become available towards the end of this decade.

Flop: Floating Point Operations per Second. A measure of computer performance. The largest current supercomputers have a performance in the order of Petaflops (1015 flops). Exascale super-computers planned for the end of the decade would have a performance in the order of exaflops (1018 flops).

Gap junction: A synapse allowing molecules, ions and electrical impulses to pass directly between neurons.

Glia: Non-neuronal cells that maintain homeostasis, form myelin, and provide support and protection for neurons in the nervous system.

High Performance Computing (HPC): The use of parallel processing to run advanced applications programme efficiently, reliably and quickly. The term HPC is sometimes used as a synonym for supercomputing, although technically a supercomputer is a system that performs at or near the currently highest operational rate for computers.

In silico: A process or experiment performed on a computer. In the BBP a process or experiment that uses computer simulation.

In vitro: An experiment that uses components of an organism (e.g. a brain slice) that has been isolated from its usual biological context.

In vivo: Studies using a whole, living organism as opposed to a partial or dead organism.

Ion channel: A group of protein molecules located in the cell membrane. The molecules’ special properties allow or prevent the passage of specific substances between the inside and outside of the cell, a process that works in many different ways, depending on the molecules’ electrochemical properties. Ion channels are targets for neuromodulation and for drugs. The distribution of ion channels determines the electrical behaviour of the cell.

MCell: A widely used simulator from the Computational Neurobiology Lab, SALK Institute, USA. MCell is used in reaction diffusion simulations of molecular interactions.

Mechanistic: Refers to an explanation that identifies the causal chain of physical or chemical events leading from an initial cause (e.g. a gene defect) to its consequences (e.g. a change in behaviour). In clinical research, knowledge of such cascades is a precondition for rational drug design.

Microcircuit: A neural circuit that includes all the local arborisations of neurons lying at the centre of the circuit (typical radius 200–500 µm).

m-type: Morphological neuron type.

Molecular Dynamics: A form of computer simulation using approximations of known physics to estimate the motion of atoms and molecules.

Morphology: The 3-dimensional shape of a neuron. Neurons with different morphologies can be classified into morphological types (m-types).

mRNA: A molecule of RNA, transcribed from a template DNA, that acts as a blueprint for a final protein product.

Multi-Electrode Array (MEA): An array of electrodes allowing simultaneous stimulation of and recording from neural tissue.

Multi-level: A description of the brain or neural tissue that takes account of its different levels of organisation (molecules, cells, microcircuits, brain regions, the whole brain)

Multi-scale: A simulation technique that reproduces the different levels of organisation of a complex phenomenon (in the case of the BBP, the activity of the brain), switching dynamically between different levels of detail according to the needs of the simulation.

Multi-objective optimisation: An optimisation procedure that measures the “fitness” of alternative solutions in terms of more than one objective.

Neocortex: In evolutionary terms, the most recently evolved part of the cortex. The neocortex is made up of six layers, labelled from I to VI. In humans, the neocortex is the largest part of the cortex where it plays an important role in higher cognitive functions including perception, motor control, spatial reasoning, conscious thought, and language.

Neocortical column: A basic functional unit of the neocortex organised as a densely interconnected column of neurons traversing all 6 layers of the cortex.

Neural code(s): The code or codes used by the brain to transmit information within the brain.

Neuroinformatics: Discipline concerned with the use of computational tools to federate, organise and analyse neuroscience data. Not to be confused with neuromorphic computing, which seeks to reproduce cerebral mechanisms for technological purposes.

Neuro-Glia-Vascular System: The complex system of interactions between neurons, glia and blood vessels which is believed to play an important role in the regulation of neural activity and in generating the signals detected in neuroimaging (fMRI etc.).

Neuromodulation: The modulation of neural activity and plasticity by neuromodulators (neurotransmitters and other molecules).

Neuromorphic computing: An electronic or computing technology, which emulates or simulates the structure and function of neurons and neuronal circuits.

NEURON: A well-known environment for empirically based simulations of neurons and networks of neurons. Developed by Michael Hines, Yale University, USA.

Neurorobotic system: A robotic system comprised of a controller, a body, actuators and sensors, whose controller architecture is derived from a model of the brain.

Neurotransmitters: Chemical compounds released into the synapses by neurons, enabling communication between neurons. Neurotransmitters can also facilitate or inhibit signal transmission.

Optogenetics: The combination of genetic and optical methods to measure and control specific events in targeted cells of living tissue. Optogenetics provides the temporal precision (millisecond-timescale) needed to keep pace with functioning intact biological systems.

Organelles: Specialised subunits of cells which perform a specialised function within the cell.

Patch clamp: A widely used technique for simultaneously stimulating and recording from neurons. The Blue Brain Project has pioneered the use of patch clamp techniques with as many as 12 neurons.

Petascale: Refers to a supercomputer with a performance of 1015 flops. In November 2011, the Japanese K computer became the first machine to achieve a peak performance of more than 10 Petaflops.

Phenomenological model: A model that reproduces an observed behaviour without faithfully accounting for the underlying biophysics.

Plasticity: The ability of a synapse, a neuron or a neuronal circuit to change its properties in response to stimuli or the absence of stimuli.

Receptor: A protein molecule that receives and transmits chemical information across membranes.

Reconstruction: Technique used to trace and digitise the 3D morphology of a nerve cell from stained tissue through 2D microscopy.

Registration: The process whereby a concept (e.g. the name of a brain region) or a set of experimental data (e.g. data describing a brain region in an individual) is mapped to coordinates in a brain atlas.

Repair (of morphologies): Correction of 3D neuron morphologies to remove artefacts (typically slicing artefacts and artefacts due to tissue shrinkage).

Resting state: The state of the brain when not engaged in any specific cognitive activity.S

Simulation: In the BBP, a computation which predicts the time course of electro-physiological activity of a neuron or a neuronal circuit, given specified initial conditions. Simulations form the basis for a potentially unlimited range of in silico experiments, allowing stimulation and manipulation of digital reconstructions as well as systematic measurements that would be difficult or impossible in vitro or in vivo.

Soma: The cell body or compartment in a cell that houses the nucleus.

Somatosensory cortex: the area of the cortex that processes signals from the surface of the body (touch).

Spike-timing Dependent Plasticity: A process that adjusts the strength of connections between neurons based on relative timings of inputs and output signals.

Spontaneous activity: The activity of neural tissue (or digital reconstructions of the tissue) in the absence of physiological or experimental stimulation.

STDP: See Spike timing Dependent Plasticity.

STEPS: A simulator for stochastic reaction-diffusion systems in realistic morphologies from the Theoretical Neurobiology group, University of Antwerp, Belgium.

Supercomputer: A computer whose performance is close to the highest performance attainable at a given time.

Synapse: The area of contact between neurons that enables them to exchange electrical or chemical signals and permits communication between them.

Terascale: Refers to a supercomputer with a performance of 1012 flops.

Tract tracing: Using a labelling agent to detect long-range brain pathways.

Transcriptome: The set of information required to fully represent all cDNA expressed by a cell during translation of the genome.

Validation: In the BBP, testing of the structural and/or functional characteristics of a digital reconstruction or a simulation against results from laboratory experiments.

Workflow: A sequence of steps leading to a well-designed outcome. Term used both in management engineering and in computer science.