Blue Brain Project

Reply Wed 13 Sep, 2017 06:02 am
Neocortical column modelling[edit]
The initial goal of the project, completed in December 2006,[4] was the simulation of a rat neocortical column, which is considered by some researchers to be the smallest functional unit of the neocortex[5][6] (the part of the brain thought to be responsible for higher functions such as conscious thought). In humans, each column is about 2 mm in length, has a diameter of 0.5 mm and contains about 60,000[contradictory] neurons; rat neocortical columns are very similar in structure but contain only 10,000 neurons (and 108 synapses). Between 1995 and 2005, Markram mapped the types of neurons and their connections in such a column.

In November 2007,[7] the project reported the end of the first phase, delivering a data-driven process for creating, validating, and researching the neocortical column.

By 2005, the first single cellular model was completed. The first artificial cellular neocortical column of 10,000 cells was built by 2008. By July 2011, a cellular mesocircuit of 100 neocortical columns with a million cells in total was built. A cellular rat brain is planned[needs update] for 2014 with 100 mesocircuits totalling a hundred million cells. Finally a cellular human brain is predicted possible by 2023 equivalent to 1000 rat brains with a total of a hundred billion cells.[8][9]

Now that the column is finished, the project is currently busying itself with the publishing of initial results in scientific literature, and pursuing two separate goals:

construction of a simulation on the molecular level,[1] which is desirable since it allows studying the effects of gene expression;
simplification of the column simulation to allow for parallel simulation of large numbers of connected columns, with the ultimate goal of simulating a whole neocortex (which in humans consists of about 1 million cortical columns).[contradictory]
In 2015, scientists at École Polytechnique Fédérale de Lausanne (EPFL) developed a quantitative model of the previously unknown relationship between the glial cell astrocytes and neurons. This model describes the energy management of the brain through the function of the neuro-glial vascular unit (NGV). The additional layer of neuron-glial cells is being added to Blue Brain Project models to improve functionality of the system.[10]

The project is funded primarily by the Swiss government and the Future and Emerging Technologies (FET) Flagship grant from the European Commission,[11] and secondarily by grants and some donations from private individuals. The EPFL bought the Blue Gene computer at a reduced cost because at that stage it was still a prototype and IBM was interested in exploring how different applications would perform on the machine. BBP was viewed a validation of the Blue Gene supercomputer concept.[12]

A 10-part documentary is being made by film director Noah Hutton, with each installment detailing the year-long workings of the project at the EPFL. Having started filming in 2009, the documentary is planned to be released in 2020, after the years of filming and editing have finished. Regular contributions from Henry Markram and the rest of the team provide an insight into the Blue Brain Project, while similar research tasks across the world are touched on.[13]

Cajal Blue Brain (Spain)[edit]

Cajal Blue Brain used the Magerit supercomputer (CeSViMa)
The Cajal Blue Brain[14] is coordinated by the Technical University of Madrid and uses the facilities of the Supercomputing and Visualization Center of Madrid and its supercomputer Magerit. The Cajal Institute also participates in this collaboration. The main lines of research currently being pursued at Cajal Blue Brain include neurological experimentation and computer simulations. Nanotechnology, in the form of a newly designed brain microscope, plays an important role in its research plans.[15]
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Reply Wed 13 Sep, 2017 08:25 am
The goal of the Blue Brain Project is to build biologically detailed digital reconstructions and simulations of the rodent, and ultimately the human brain.

The supercomputer-based reconstructions and simulations built by the project offer a radically new approach for understanding the multilevel structure and function of the brain.

The project's novel research strategy exploits interdependencies in the experimental data to obtain dense maps of the brain, without measuring every detail of its multiple levels of organization (molecules, cells, micro-circuits, brain regions, the whole brain).

This strategy allows the project to build digital reconstructions (computer models) of the brain at an unprecedented level of biological detail.

Supercomputer-based simulation of their behavior turns understanding the brain into a tractable problem, providing a new tool to study the complex interactions within different levels of brain organization and to investigate the cross-level links leading from genes to cognition.
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Reply Wed 13 Sep, 2017 12:11 pm
Will it know right from wrong? (Morally)
Reply Wed 13 Sep, 2017 12:26 pm
There is a new article about them going around. I plan to post about it later.
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Reply Wed 13 Sep, 2017 02:19 pm
Blue Brain Team Discovers a Multi-Dimensional Universe in Brain Networks

Using mathematics in a novel way in neuroscience, the Blue Brain Project shows that the brain operates on many dimensions, not just the three dimensions that we are accustomed to.

For most people, it is a stretch of the imagination to understand the world in four dimensions but a new study has discovered structures in the brain with up to eleven dimensions – ground-breaking work that is beginning to reveal the brain’s deepest architectural secrets.

Using algebraic topology in a way that it has never been used before in neuroscience, a team from the Blue Brain Project has uncovered a universe of multi-dimensional geometrical structures and spaces within the networks of the brain.

The research, published today in Frontiers in Computational Neuroscience, shows that these structures arise when a group of neurons forms a clique: each neuron connects to every other neuron in the group in a very specific way that generates a precise geometric object. The more neurons there are in a clique, the higher the dimension of the geometric object.

PR neuroscience news topology blue brain project markramTopology in neuroscience: The image attempts to illustrate something that can not be imaged – a universe of multi-dimensional structures and spaces. On the left is a digital copy of a part of the neocortex, the most evolved part of the brain. On the right are shapes of different sizes and geometries in an attempt to represent structures ranging from 1D to 7D and beyond. The “black-hole” in the middle is used to symbolise a complex x of multi-dimensional spaces, or cavities. Courtesy of the Blue Brain Project
“We found a world that we had never imagined,” says neuroscientist Henry Markram, director of Blue Brain Project and professor at the EPFL in Lausanne, Switzerland, “there are tens of millions of these objects even in a small speck of the brain, up through seven dimensions. In some networks, we even found structures with up to eleven dimensions.”

Markram suggests this may explain why it has been so hard to understand the brain. “The mathematics usually applied to study networks cannot detect the high-dimensional structures and spaces that we now see clearly.”

If 4D worlds stretch our imagination, worlds with 5, 6 or more dimensions are too complex for most of us to comprehend. This is where algebraic topology comes in: a branch of mathematics that can describe systems with any number of dimensions. The mathematicians who brought algebraic topology to the study of brain networks in the Blue Brain Project were Kathryn Hess from EPFL and Ran Levi from Aberdeen University.

“Algebraic topology is like a telescope and microscope at the same time. It can zoom into networks to find hidden structures – the trees in the forest – and see the empty spaces – the clearings – all at the same time,” explains Hess.

In 2015, Blue Brain published the first digital copy of a piece of the neocortex – the most evolved part of the brain and the seat of our sensations, actions, and consciousness. In this latest research, using algebraic topology, multiple tests were performed on the virtual brain tissue to show that the multi-dimensional brain structures discovered could never be produced by chance. Experiments were then performed on real brain tissue in the Blue Brain’s wet lab in Lausanne confirming that the earlier discoveries in the virtual tissue are biologically relevant and also suggesting that the brain constantly rewires during development to build a network with as many high-dimensional structures as possible.

When the researchers presented the virtual brain tissue with a stimulus, cliques of progressively higher dimensions assembled momentarily to enclose high-dimensional holes, that the researchers refer to as cavities. “The appearance of high-dimensional cavities when the brain is processing information means that the neurons in the network react to stimuli in an extremely organized manner,” says Levi. “It is as if the brain reacts to a stimulus by building then razing a tower of multi-dimensional blocks, starting with rods (1D), then planks (2D), then cubes (3D), and then more complex geometries with 4D, 5D, etc. The progression of activity through the brain resembles a multi-dimensional sandcastle that materializes out of the sand and then disintegrates.”

The big question these researchers are asking now is whether the intricacy of tasks we can perform depends on the complexity of the multi-dimensional “sandcastles” the brain can build. Neuroscience has also been struggling to find where the brain stores its memories. “They may be ‘hiding’ in high-dimensional cavities,” Markram speculates.

Read the full paper: http://journal.frontiersin.org/article/10.3389/fncom.2017.00048/abstract

Citation: Reimann MW, Nolte M, Scolamiero M, Turner K, Perin R, Chindemi G, Dłotko P, Levi R, Hess K and Markram H (2017) Cliques of Neurons Bound into Cavities Provide a Missing Link between Structure and Function. Front. Comput. Neurosci. 11:48. doi: 10.3389/fncom.2017.00048

This research was funded by: ETH Domain for the Blue Brain Project (BBP) and the Laboratory of Neural Microcircuitry (LNMC); The Blue Brain Project’s IBM BlueGene/Q system, BlueBrain IV, funded by ETH Board and hosted at the Swiss National Supercomputing Center (CSCS); NCCR Synapsy grant of the Swiss National Science Foundation; GUDHI project, supported by an Advanced Investigator Grant of the European Research Council and hosted by INRIA.

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