Friday, September 29, 2023

The Blue Brain Project: Unraveling The Brain’s Mystery

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The human brain is the most remarkable creation of God and also the reason behind human intelligence. Blue Brain is the name of the worldís first virtual brainóa machine that works on the same lines as human brain. The Blue Brain System is an endeavour to reverse-engineer the human brain and rebuild it at the molecular level via computer simulation. The project was initiated in May 2005 by Prof. Henry Markram at Ecole Polytechnique FÈdÈrale de Lausanne (EPFL) in Lausanne, Switzerland.

Fig. 1: Professor Henry Markram, father of Blue Brain Project (Image courtesy: Frankenstein Project)

IBM (fondly known as The Big Blue) and Swiss University team, associated with fabricating a custom-made supercomputer based on IBMís Blue Gene design, have been working together on Blue Brain Project. IBM brings to the table expertise in visualisation, simulations, algorithms, Blue Gene optimisations and development of innovative computational methods.

Fig. 2: Blue Brain is the name of the worldís first virtual brain (Image courtesy:

Blue Brain Project expects researchers to develop their own models of various brain areas in dissimilar species and at altered levels of detail using Blue Brain Software for simulation on Blue Gene. The objective is to collect these models in a central Internet database from which Blue Brain Software can mine and link models together to form brain regions. This would finally lead to the first whole brain simulation.

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It is hoped that Blue Brain Project will enable building up the virtual brain, which will ultimately unravel the mysteries of the key facets of human cognition, such as perception, memory and, may be, consciousness, too. For the first time, we will be able to witness the electrical code our brains use to denote the world, in real-time basis. We also expect to gain an understanding of how certain failures of the brainís microcircuits lead to psychiatric disorders such as autism, schizophrenia and depression.

Reconstructing the enigmatic human brain using IT

Typically, a human brain has over 100 billion neurons or brain cells and about 100 trillion synapses, thus making it a very complex multilevel system. The inter-neuron connections make up a hierarchy of circuits that range from local microcircuits to macro-circuits that form the entire brain. At the unit level, each neuron and synapse is a complex molecular machine in itself. It is the interactions between these levels that leads to human behaviour, human emotion and human cognition, as we know it.

Blue Brain Project aspires to develop wide-ranging digital reconstructions, that is, computer models of the brain including its diverse levels of organisation and interactions. Blue Brain Projectís reconstruction approach pinpoints interdependencies in experimental data; for example, dependencies between the size of neurons and neuron densities, dependencies between the shapes of neurons and the synapses these form, and dependencies between the number of boutons on axons and synapse numbers. It then uses these to coerce the reconstruction procedure. Multiple and intersecting constraints enable the project to develop the most accurate reconstructions possible from the scanty experimental data available, thus doing away with the need to measure everything.

Digital reconstructions of the brain tissue characterise a snapshot of the anatomy and physiology of the brain at a single moment in time. Blue Brain Project simulations use mathematical models of individual neurons and synapses to calculate the electrical activity of the network as it progresses over time. This demands a very high computational power that can only be delivered via large supercomputers. In fact, the larger the volume of tissue that needs to be simulated and higher the accuracy, the higher is the required computing power.

The range of experiments that can be enabled is proportional to the size and accuracy of digital reconstructions. Blue Brain Project is now constructing neuro-robotics tools wherein brain simulations are coupled to simulated robots and a simulated environment, in a closed loop. These novel tools enable replication of cognitive and behavioural experiments in animals, wherein the sensory organs capture and encode data about their environment, and their brain produces a motor response. The supercomputer based reconstructions and simulations put together by the project suggest a profoundly new strategy for comprehending the multilevel structure and function of the brain.

The Blue Gene Supercomputer

The Blue Brain workflow demands large-scale computing and data infrastructure. The hardware typically consists of the following configuration:
1. IBM 65,536-core BlueGene/Q supercomputer for modelling and simulation (hosted at CSCS), providing extended capabilities for data-intensive supercomputing (Blue Gene Active Storage)
2. Fourty-node analysis and visualisation cluster
3. OpenStack/Ceph private Cloud running in two regions
4. Different storage systems for data archiving and neuroinformatics
5. Modern continuous integration, collaborative software-development platform

Fig. 3: Illustration showing the basic elements of the human brain (Image courtesy:

State-of-the-art technology for acquisition of data on various brain levels of the brain organisation comprises multi-patch clamp set-ups for studies of the electrophysiological behaviour of neural circuits, multi-electrode arrays enabling the stimulation of and recording from brain slices, services for the formation and study of cell lines expressing specific ion channels, a multiplicity of imaging systems and systems for the 3D reconstruction of neural morphologies.


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