"Blue Brain Project" Glossary

Glossary
 
Term | Description |
-omics | The study of the humane genome gave rise to the science and technology of genomics – the study of the genome.  Other –omics studies and technologies refer to other, higher levels of biological organization e.g. transcriptomics (the study of mRNA produced when genes are transcribed; proteomics (the study of the proteins produced when mRNA istranslated). When  “–omics” is used as a general term, it refers to the complete set of all such studies and technologies covering many levels of biological information. |
Atlas | A work of reference (e.g. the Allen Mouse Atlas) showing how one or more data sets (e.g. gene expression data) map to specific regions and subregions of the brain. |
BG/P | See Blue Gene/P. |
BlueGene/P | IBM supercomputer.The BlueGene/P used in the Blue Brain project is a massively parallel, tightly interconnect machine with 16384 processors, 56TeraFlops of peak performance, 16TeraByte of distributed memory and a 1 PetaByte file system. |
Bouton | An enlarged part of the axon of a nerve cells forming the presynaptic terminal of a synapse with another cell. |
Builder | A Blue Brain software application used tobuild models at a specific level of brain organization. |
c-code | Standardized Blue Brain characterization of the electrical behavior of a neural microcircuit, obtained through application of a benchmark stimulation protocol. |
Cable equation | A mathematical formulation, derived from classical electrodynamics, describing the propagation of current and voltage along a cable or (in the case ofneuroscience) a neural fiber. |
Capability job | A class of compute jobs that requires exclusive access to very large, tightly-coupled supercomputers. Simulation-based virtual experiments belong to this class. |
Capacity job | A class of compute jobs that requires medium size supercomputing resources. Numerous preparatory steps in the Blue Brain facility (e.g. builders) involve this kind ofjob. |
Channelome | The full set of ion channels expressed by a cell. |
Class hierarchy | Computer science term describing a hierarchy of classes at increasing levels of generality (e.g. individual, species, genus, family, etc.). Any “object” is an instance of a class in the hierarchy and of the superclasses to which the class belongs. |
Compartmentalized model | A spatially discretized modelof a neuron in which the neuron is represented by a set of digitized “compartments” each with its own individual attributes. Used for purposes of numerical approximation. |
Connectome | The complete connectivity map between neurons, including the locations of all synapses. |
Connectomics | The study of the connectome. |
Curation | Human processing (quality control, normalization ofterminology, annotation etc.) of data prior to use in modeling. |
Data Model | An abstract model of the different classes of data used by a computer application or system and the hierarchical relationships between these classes. |
Diffusion Tensor Imaging (DTI) | A magnetic resonance imaging (MRI) technique used to produce images of neural tracts. |
DTI | See Diffusion Tensor Imaging. |
e-code |Standardized Blue Brain characterization of the electrical behavior of a cell, obtained through application of a benchmark stimulation protocol. |
Electron Microscopy (EM) | Use of an Electron Microscope to obtain highly magnified images of biological tissues. |
EM | See Electron Microscopy. |
Endoplasmic Reticulum (ER). | An extensive system of parallel and folded membranes within a neuron. |Ephaptic effects | Effects due to current flow through the extracellular space. |
Field Potential | An electrical potential created by a set of current sources. |
Genetic Algorithm | An optimization technique based on a highly stylized version of Darwinian evolution. |
High Performance Computing (HPC) | The use of parallel processing to run advanced applications programs efficiently,...