The Blue Brain Project, led by Dr. Henry Markram, aims to create a synthetic replica of the human brain using advanced supercomputing technology to better understand brain function and diseases. The project involves simulating the brain down to its molecular level, starting with rat brain models, and utilizes sophisticated techniques and hardware to analyze and visualize neural activity. Funded largely by the European Union, the initiative represents a significant collaborative effort involving hundreds of researchers across multiple institutions to tackle fundamental questions in neuroscience and medicine.

1. SEMINAR PROJECT ON
BLUE BRAIN
THE $1.3B QUEST TO
CREATE A REPLICA OF
THE HUMAN BRAIN
SURYADAY NATH
E and I
KALINGA INSTITUTE OF INDUSTRIAL TECHNOLOGY
BHUBANESWAR

2. PROLOGUE• The brain is a phenomenal processor that in a year's time can generate roughly 300,000
petabytes of data -- 30,000 times the amount generated by the Large Hadron Collider.Trying
to decipher its signals is a daunting prospect.
• A 100 billion neurons connected by a 100 thousand billion synapses the human brain is the
most complex machine we know of and the most mysterious.
• There have been issues in Neuro-science about the working and objectively diagnose and
treat brain diseases.
• Brain disease in Europe like Alzheimer’s disease, Parkinson’s
disease, hypertension, depression are more than heart diseases and cancer combined.
• In Europe it has been estimated that 35% of all disease burden is attributable to brain
disorders .
• EU researchers, from leading European researches, headed by Dr Henry Markram, have
come together for the most ambitious Neuro-science project ideate to simulate a complete
human brain in a super computer.
• Their aim is to study neurons, collect and consolidate and integrate them into a
supercomputer and create a Virtual Brain that the world has never seen before.

3. THE MISSION
The goal of the Human Brain Project is to
build a completely new information
computing technology infrastructure for
neuroscience and for brain-related research
in medicine and computing, catalysing a
global collaborative effort to understand the
human brain and its diseases and ultimately
to emulate its computational capabilities.

4. What is Blue Brain?
• The project is the brain-child of Professor Henry Markram.
• The Human Brain Project (HBP) is a large scientific research
project, directed by the École polytechnique fédérale de Lausanne and
largely funded by the European Union, which aims to simulate the
complete human brain on supercomputers to better understand how it
functions.
• The Blue Brain Project is an attempt to create a synthetic brain
by reverse-engineering the mammalian brain down to the molecular
level. This bizarre creation is capable of simulating a natural brain, cell-
for-cell. The Swiss scientists, who created what they have dubbed "Blue
Brain", believe it will soon offer a better understanding of human brain.
• The Blue Brain Project is an attempt to create a synthetic brain
by reverse-engineering the mammalian brain down to the molecular
level.

5. THE MAN
BEHIND
ONE OF THE
MOST
AUDACIOUS
PROJECT DARED
BY MAN

6. How will it be possible?
• The Blue Brain Project is an attempt to create a synthetic brain by reverse-
engineering the mammalian brain down to the molecular level.
• But to create a human brain model, first they have to create a model based
on a rat’s.
• The rat motor cortex is parcellated into distinct subregions that perform
specific functions, and this result appears to be similar to what is seen in
the primate brain.
• After opening the rat skulls and slicing their brains into thin sections, the
scientists kept the slices alive.
• Tiny sensors picked up individual neurons, recorded how the cells fired off
neurons and the adjacent cells’ responses.
• In this way the scientists were able to collect entire repertoires of actual rat
behavior- basically how a rat would respond in different situations
throughout a rat's life.

7. The research involves studying slices of living brain tissue using microscopes and patch clamp electrodes. Data is
collected about all the many different neuron types. This data is used to build biologically realistic models of
neurons and networks of neurons in the cerebral cortex. The simulations are carried out on a Blue Gene
supercomputer built by IBM.
A Wistar Rat
A Patch Clamp ElectrodeA Super Computer

8. WHAT IS A PATCH CLAMP ELECTR
• The patch clamp technique is a laboratory technique in
electrophysiology that allows the study of single or
multiple ion channels in cells.
• The technique can be applied to a wide variety of
cells, but is especially useful in the study of excitable
cells such as neurons, cardiomyocytes, muscle fibers
and pancreatic beta cells.
• It can also be applied to the study of bacterial ion
channels in specially prepared giant spheroplasts.
• Patch clamp recording uses, as an electrode, a glass
micropipette that has an open tip diameter of about
one micrometer, a size enclosing a membrane surface
area or "patch" that often contains just one or a few ion
channel molecules. This type of electrode is sealed
onto the surface of the cell membrane, rather than
inserted through it.

9. • In some experiments, the micropipette tip is heated in a
microforge to produce a smooth surface that assists in forming a
high resistance seal with the cell membrane.
• The interior of the pipette is filled with a solution matching the
ionic composition of the bath solution, as in the case of cell-
attached recording, or the cytoplasm for whole-cell recording.
• A chlorided silver wire is placed in contact with this solution
and conducts electric current to the amplifier. The investigator
can change the composition of this solution or add drugs to
study the ion channels under different conditions.
• The micropipette is pressed against a cell membrane and
suction is applied to assist in the formation of a high resistance
seal between the glass and the cell membrane (a "gigaohm seal"
or "gigaseal," since the electrical resistance of that seal is in
excess of a gigaohm).
• The high resistance of this seal makes it possible to
electronically isolate the currents measured across the
membrane patch with little competing noise, as well as
providing some mechanical stability to the recording.

10. HARDWARE USED
AN IBM BLUE GENE SUPERCOMPUTER
4,096 quad-core nodes (16,384 cores
in total)
Total: 56 teraflops, 16 terabytes of
memory
Operating system: Linux SuSE SLES
10
This machine peaked at 99th fastest
supercomputer in the world in
November 2009.
By June 2011 it had dropped to 343th
in the world.
It has since dropped out of the top
500.
A Silicon Graphics Inc. (SGI) system
with 300 Gb of shared memory is

11. Ju QUEEN is an IBM Blue Gene/Q supercomputer that was installed at the Jülich Research Center in
Germany in May 2013. It currently performs at 1.6 petaflops and was ranked the world's 8th fastest
supercomputer in June 2013. It's likely that this machine will be used for BBP simulations starting in
2014, provided funding is granted via the Human Brain Project.

12. SOFTWARE USED
The primary software used by the BBP for
neural simulations is a package called
NEURON.
This was developed starting in the 1990s by
Michael Hines at Yale University and John
Moore at Duke University. It is written in
C, C++, and FORTRAN.
The software continues to be under active
development and, as of July 2012, is currently
at version 7.2.
It is free and open source software, both the
code and the binaries are freely available on
the website.
Michael Hines and the BBP team collaborated
in 2005 to port the package to the massively
parallel Blue Gene supercomputer.

13. RTNeuron is the primary application used by the BBP for
visualisation of neural simulations.
It is written in C++ and OpenGL.
RTNeuron is ad-hoc software written specifically for neural
simulations, i.e. it is not generalisable to other types of
simulation.
RTNeuron takes the output from simulations in NEURON and
renders them in 3D.
This allows researchers to watch as activation potentials
propogate through a neuron and between neurons.
The animations can be stopped, started and zoomed, thus
letting researchers interact with the model.
The visualisations are multi-scale, that is they can render
individual neurons or a whole cortical column.
RT Neuron

14. There are three main steps to building the virtual brain: 1) data acquisition, 2) simulation, 3)
visualisation of results.
• Data acquisition involves taking brain slices, placing them under a microscope, and measuring
the shape and electrical activity of individual neurons. This is how the different types of neuron
are studied and catalogued. The neurons are typed by morphology (i.e. their
shape), electrophysiological behaviour, location within the cortex, and their population density.
These observations are translated into mathematical algorithms which describe the
form, function, and positioning of neurons. The algorithms are then used to generate
biologically-realistic virtual neurons ready for simulation.
• One of the methods is to take 300 µm-thick sagittal brain slices from the somatosensory cortex
(SA1) of juvenile Wistar rats (aged 14 to 16 days). The tissue is stained with biocytin and viewed
through a bright field microscope. Neuronal 3D morphologies are then reconstructed using the
Neurolucida software package (pictured below, far right) which runs on Windows workstations.
Staining leads to a shrinkage of 25% in thickness and 10% in length, so the reconstruction
process corrects for this. Slicing also severs 20% to 40% of axonal and dendritic arbors, so
these are regrown algorithmically.
STEPS TO CREATE THE VIRTUAL B

15. Funding The project involves hundreds of researchers, from 135 partner
institutions in 26 countries.
Its total costs are estimated at 1.190 billion €, of which 555 million
would go to personnel, to compensate 7148 person-years of effort.
It is funded by the European Commission through its Future and
Emerging Technologies (FET) Flagship grant. 86 institutions across
Europe are now involved and will receive one billion euro in funding
over ten years.
In March 2012 the ETH Board requested €70 m from the Swiss
government to fund the Blue Brain Project during 2013 to 2016.
IBM has not funded the project, but they sold their Blue Gene
supercomputer to EPFL at a reduced cost. This was because at the time
the computer was a prototype and IBM was interested in testing the
machine on different applications.

16. A Timeline of the BLUE BRAIN
2002 Henry Markram founds the Brain Mind Institute (BMI) at EPFL.
2005 June - EPFL and IBM agree to launch Blue Brain Project, IBM installs Blue Gene
Basic simulation of single neurons achieved.
2007 November - modelling and simulation of first rat cortical column.
2008 Cortical column construction and simulations
Neocortical column (10,000 cells)
Research on determining position and size of functional cortical columns.
2009 June - BlueGene/L replaced by BlueGene/P, doubling of processors
Simulations of cortical construction continue.
2013 February - decision on Human Brain Project funding of €1 billion over 10 years from the EU
Simulations using NEURON software ported to the Blue Gene/Q system in Jülich.
2014 Cellular-level simulation of the entire rat brain neocortex, ~100 mesocircuits
NEURON simulation software ported to the DEEP Cluster-Booster prototype system in Jülich
2023 Cellular-level simulation of the entire human brain, equivalent to 1,000x the size of the rat brain

17. APPLICATIONSResearch Areas
The HBP will make fundamental contributions to neuroscience, to medicine and to future computing technology.
In neuroscience, the project will use neuroinformatics and brain simulation to collect and integrate experimental
data, identifying and filling gaps in our knowledge, and prioritising future experiments.
In medicine, the HBP will use medical informatics to identify biological signatures of brain disease, allowing diagnosis at an
early stage, before the disease has done irreversible damage, and enabling personalized treatment, adapted to the needs of
individual patients. Better diagnosis, combined with disease and drug simulation, will accelerate the discovery of new
treatments, drastically lowering the cost of drug discovery.
In computing, new techniques of interactive supercomputing, driven by the needs of brain simulation, will impact a vast range
of industries. Devices and systems, modelled after the brain, will overcome fundamental limits on the energy-
efficiency, reliability and programmability of current technologies, clearing the road for systems with brain-like intelligence.
The Future of Brain Research
Applying ICT to brain research and its applications promises huge economic and social benefits. But to realise these
benefits, the technology needs to be made accessible to scientists – in the form of research platforms they can use for basic
and clinical research, drug discovery and technology development. As a foundation for this effort, the HBP will build an
integrated system of ICT-based research platforms, Building and operating the platforms will require a clear
vision, strong, flexible leadership, long-term investment in research and engineering, and a strategy that leverages the
diversity and strength of European research. It will also require continuous dialogue with civil society, creating consensus and
ensuring the project has a strong grounding in ethical standards.

18. THANK YOU