Building the microcircuit

Neurons are not all alike - they come in a variety of complex shapes. The precise shape and structure of a neuron influences its electrical properties and connectivity with other neurons. A neuron's electrical properties are determined to a large extent by a variety of ion channels distributed in varying densities throughout the cell's membrane. Scientists have been collecting data on neuron morphology and electrical behavior of the juvenile rat in the laboratory for many years, and this data is used as the basis for a model that is run on the Blue Gene to recreate each of the 10,000 neurons in the NCC.

Modeling connections

To model the neocortical column, it is essential to understand the composition, density and distribution of the numerous cortical cell types. Each class of cells is present in specific layers of the column. The precise density of each cell type and the volume of the space it occupies provides essential information for cell positioning and constructing the foundation of the cortical circuit. Each neuron is connected to thousands of its neighbors at points where their dendrites or axons touch, known as synapses. In a column with 10,000 neurons, this translates into trillions of possible connections. The Blue Gene is used in this extremely computationally intensive calculation to fix the synapse locations, "jiggling" individual neurons in 3D space to find the optimal connection scenario.

Modeling the column

The result of all these calculations is a re-creation, at the cellular level, of the neocortical column, the basic microcircuit of the brain. In this case, it's the cortical column of a juvenile rat. This is the only biologically accurate replica to date of the NCC - the neurons are biologically realistic and their connectivity is optimized. This would be impossible without the huge computational capacity of the Blue Gene. A model of the NCC was completed at the end of 2006. 

In November, 2007, The Blue Brain Project officially announced the conclusion of Phase I of the project, with three specific acheivements:

1. A new modeling framework for automatic, on-demand construction of neural circuits built from biological data

2. A new simulation and calibration process that automatically and systematically analyzes the biological accuracy and consistency of each revision of the model

3. The first cellular-level neocortical column model built entirely from biological data that can now serve as a key tool for simulation-based research