"Blue Brain - A Virtual Brain": A Seminar Report On

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A

Seminar Report
On

“BLUE BRAIN – A VIRTUAL BRAIN”

Submitted in partial fulfillment for the award of degree of


BACHELOR OF TECHNOLOGY
In
COMPUTER SCIENCE ENGINEERING

Submitted To Submitted By
Mrs. Aastha Joshi Sunny Kumar
(Assistant Professor) 15EGJCS739
Miss Poonam Saini
(Assistant Professor)

DEPARTMENT OF COMPUTER SCIENCE ENGINEERING


GLOBAL INSTITUTE OF TECHNOLOGY
JAIPUR (RAJASTHAN)-302022
2018-19

i
ACKNOWLEDGEMENT

It is my pleasure to be indebted to various people, who directly or indirectly contributed


in the development of this work and who influenced my thinking, behavior, and acts
during the course of study. This formal piece of acknowledgement is an attempt to express
the feeling of gratitude towards people who helpful me in successfully completing of my
seminar.

I would like to express my sincere appreciation to Mrs. Aastha joshi and Miss Poonam
Saini, who provided their valuable suggestions and precious time for providing healthy
competitive and comfortable environment throughout the completion of my learning.
They were always there with their competent support and valuable suggestion throughout
the pursuance of the learning.

A special thanks goes out to the HEAD OF DEPARTMENT (Computer Science &
Engineering) Dr. Smita Agrawal who has always given a patient hearing to all out doubts
and provided useful suggestions for completing the project and report.

I would also like to place of appreciation to all my friends, colleagues for their
cooperation and important support.

Above all no words can express my feelings to my parents who always supported me at
every step, guided me, inspired me, and provided me all facilities so that I can achieve my
goals. Last but not the least I would like to thanks the Almighty God for everything.

Sunny Kumar
University Roll No. : 15EGJCS739
B. Tech. VIII Sem.
Computer Science & Engineering.

ii
ACKNOWLEDGEMENT

I express my sincere thanks to my seminar mentors, for guiding me right from the inception
till the successful completion of this report. I sincerely acknowledge them for extending their
valuable guidance, support for literature, critical reviews of project and the report and above
all the moral support they had provided to me with all the stages of this seminar. I would like
to express my deepest appreciation to all those who provided me the possibility to complete
this seminar report.

I would also like to thanks the supporting staff of Department of CSE (GIT) for their
help and cooperation throughout the seminar.

Sunny Kumar

Roll No. - 15EGJCS739

IV Year, VIII Semester

Computer Engineering

GIT, Jaipur

ii
ABSTRACT

The human brain has about 100 billion neurons, nerve cells which enable us to adapt quickly
to an immense array of stimuli. We use them to respond to

anything such as bright sunlight, the smell of chicken frying, a honking horn and anything
else our sensors detect. Researchers had launched an ambitious project called Blue Brain, to
better understand some of those responses. They are in research to create an artificial brain
that can think, response, take decision, and store anything in memory. The main aim is to
upload human brain into a machine so that man can think, take decision without much
efforts. After the death of the body, the virtual brain will act as the man's brain. Such models
will shed light on how memories are stored and retrieved. This could reveal many exciting
aspects of the brain, such as the form of memories, memory capacity and how memories are
lost. In this paper, we explain the concept and functioning model of blue brain, motivations
behind it, limitations and many more.

The Blue Brain Project is delighted to announce that it will be hosting in May this year, the
second Neuromodulation of Neural Microcircuits NM² Conference.

The overarching goal of the second NM² Conference is to provide a unifying and mechanistic
view by which an ever increasing number of neuromodulators, including monoamines, and
peptides – the master switches – control genes, proteins, neurons and glia, dendrites,
synapses, and emergent states in neural microcircuits across different brain regions in health
and disease.

iii
CONTENTS
TOPIC PAGE NO.

ACKNOWLEDGEMENT ii

ABSTRACT iii

LIST OF CONTENTS iv

LIST OF FIGURES vi

LIST OF TABLES vii

CHAPTER 1: INTRODUCTION 1

1.1What is Virtual Brain? 2

1.2 History of Virtual Brain 4

CHAPTER 2: ABOUT THE PROJECT: BLUE BRAIN 6

2.1 Blue Brain Project 6

2.2 Why we need Blue Brain? 8

2.3 How it is possible? 9

CHAPTER 3: DESCRIPTION OF NATURAL BRAIN 11

3.1 General Description 11

3.2 How we see, hear, feel & smell? 13

CHAPTER 4: BRAIN SIMULATION 20

CHAPTER 5: BUILDING BLUE BRAIN 23

5.1 Introduction 23

5.2 Neural Network 23

5.3 Design 25

iv
CHAPTER 6: WORKING OF BLUE BRAIN 30
6.1 Goals & Objectives 30

6.2 Architecture of Blue Gene 31

6.3 Modelling the Microcircuit 32

6.4 Simulating the Microcircuit 34

6.5 Interpreting the Results 34

6.6 Data Manipulation Cascade 35

6.7 Whole Brain Simulation 37

CHAPTER 7: APPLICATIONS OF BLUE BRAIN 40

7.1 What can we learn from Blue Brain? 40

7.2 Applications of Blue Brain 41

CHAPTER 8: ADVANTAGES AND LIMITATINS 44

8.1 Advantages 44

8.2 Limitations 44

CHAPTER 9: FUTURE PERSPECTIVES 46

CHAPTER 10: CONCLUSION 47

REFERENCES 48

v
List of Figures

Fig. No. Name of Figure Page No.


1 3.1: Medial view of the left hemisphere of human 12

brain
2 6.1: The Blue Gene/L supercomputer architecture 32

vi
List of Tables

Fig. No. Name of Table Page No.

1 4.1: Simulation Comparison 22

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BLUE BRAIN GIT DCSE

Chapter 1

INTRODUCTION

Human brain is the most valuable creation of God. The man is called intelligent because of
the brain. The brain translates the information delivered by the impulses, which then enables
the person to react. But we loss the knowledge of a brain when the body is destroyed after the
death of man. That knowledge might have been used for the development of the human
society. What happen if we create a brain and upload the contents of natural brain into it?

The Blue Brain Project is an attempt to reverse engineer the human brain and recreate it at
the cellular level inside a computer simulation. The project was started in May 2005 by
Henry Markram at the EPFL in Lausanne, Switzerland. Main goals of the project are to gain
a complete understanding of the brain and to enable better and faster development of brain
disease treatments. The research involved studying slices of living brain tissue using
instruments such as microscopes and patch clamp electrodes. Data is collected about many
different neuron types. This collected 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. Hence the name "Blue Brain". The
simulation software is based around Michael Hines's NEURON, together with other custom-
built components. Human brain is the most

valuable creation of God. Man is intelligent because of this valuable creation "brain". ―Blue
brain‖ is the name of the world’s first virtual brain. That means a machine that can function as
human brain. Today scientists are in research to create an artificial brain that can think,
response, take decision, and store anything in memory. The main aim is to upload human
brain into a machine so that man can think, take decision without much efforts. After the
death of the body, the virtual brain will act as the man's brain .So, even after the death of a
person we will not lose the knowledge, personalities,

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Feelings, intelligence and memories of that man that can be used for the development of the
human society. Brain simulation is unbelievably inter-disciplinary research. It involves the
domains like brain imaging,

Neuroscience, computer science, nanotechnology, AI, biotechnology, psychology,


philosophy, and many more. A typical human brain usually consists of approximately 85.5
billion nerve cells called neurons. Each neuron is individually linked to other neurons
through axons and dendrites. Signals at the biological level of these connections are
transmitted by releasing and detecting chemicals known as neurotransmitters. Neuroscientists
have stated that important functions that a mind performs such as consciousness, memory,
and learning, have been possible due to completely physical and electrochemical processes in
the brain.

1.1 What is Virtual Brain?

Virtual brain is an artificial brain, which does not actually the natural brain, but can act as the
natural brain. It can think like brain, take decisions based on the past experience, and
response as the natural brain can. It is possible by using a super computer, with a huge
amount of storage capacity, processing power and an interface between the human brain and
this artificial one. Through this interface the data stored in the natural brain can be up loaded
into the computer. So the brain and the knowledge, intelligence of anyone can be kept and
used for ever, even after the death of the person. The Virtual Brain Initiative is one of the best
known trials to understand and organize brain data in a useful way. It is a way through neuro
informatics platform that tries to simulate the brain organization on the macroscopic levels of
details. This tool is based on the ideas of taking advantage of available functional and
structural brain data generated by imaging techniques such as MRI, functional MRI and
trans-cranial magnetic stimulation.

The virtual brain will try to gather important information related to neuronal connectivity and
structure of the brain. It will inform us about activated groups of neurons, their connections,
their respective distances, the time and the speed of their communications. This software will

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also collect data related to the structure of the brain like 3D cortex geometry and the exact
location of neuron groups. After identifying the involved population of neurons, they will be
assembled in large neuronal networks to finally construct a brain model.

As the model is developed, a knowledge library of brain anatomy and physiology will be
used to guide the building process. This later step guarantees that the model reflects the
natural phenomena regulating normal brain physiology.

An ideal computational brain model should consider the functions and connections of
individual neurons. However, just to assemble this model we will need very powerful
computational resources that are not yet available. Even if we achieve this colossal task, we
still won’t be able to explain how cognitive and psychological process are born in the mind
and how are they related to the organic structure of the brain.

Moreover, some studies showed that the behavior of the single neuron is irrelevant for the
prediction of complex functions of the brain and probably even less for understanding the
cognitive functions. In this regard, virtual brain has the advantage of working on the
macroscopic and mesoscopic levels (the micrometer range) where not so much computer
power is needed.

This approach is not new in science, and the attempts to build macroscopic models based on
the mesoscopic level of details were shown to be useful. In the virtual brain, this philosophy
is used to predict the global brain behavior and function starting from small groups of
neurons.

The virtual brain is a great tool for research that will allow us to monitor the dynamics of
communications between different brain regions and see how the functions of the brain are
related to its structure. Scientists can use the virtual brain to understand how changes in the
brain structure affect neuron communications and in turn lead to modifications in behaviour
and cognitive processes.

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1.2 History of Virtual Brain

The Virtual Brain, a Swiss national brain initiative, aims to create a digital reconstruction of
the brain by reverse-engineering mammalian brain circuitry. The mission of the project,
founded in May 2005 by the Brain and Mind Institute of the École Polytechnique Fédérale de
Lausanne (EPFL) in Switzerland, is to use biologically-detailed digital reconstructions and
simulations of the mammalian brain (brain simulation) to identify the fundamental principles
of brain structure and function in health and disease.

The project is headed by the founding director Henry Markram, who also launched the
European Human Brain Project, and co-directed by Felix Schürmann and Sean Hill. Using a
Blue Gene supercomputer running Michael Hines's NEURON software, the simulation does
not consist simply of an artificial neural network, but involves a biologically realistic model
of neurons, and an empirically reconstructed model connectome. It is hoped that it will
eventually shed light on the nature of consciousness.

There are a number of sub-projects, including the Cajal Blue Brain, coordinated by the
Supercomputing and Visualization Center of Madrid (CeSViMa), and others run by
universities and independent laboratories.

The initial goal of the project, completed in December 2006,was the simulation of a rat
neocortical column, which is considered by some researchers to be the smallest functional
unit of the neo cortex (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 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, the project reported the end of the first phase, delivering a data-driven
process for creating, validating, and researching the neocortical column.

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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.

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,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).

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.

Recently, Virtual Brain Project releases first-ever digital 3D brain cell atlas:- The Blue Brain
Cell Atlas is like 'going from hand-drawn maps to Google Earth' -- providing previously
unavailable information on major cell types, numbers and positions in all 737 brain regions.
This comprehensive, interactive and dynamic online resource allows anyone to visualize
every region in the mouse brain, cell-by-cell and in 3D, and freely download data for new
analyses and modelling. It can also be continuously be updated with new findings.

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Chapter 2

ABOUT THE PROJECT: BLUE BRAIN

2.1 Blue Brain Project

The name of the world’s first virtual brain. That means a machine that can function as human
brain. Today scientists are in research to create an artificial brain that can think, response,
take decision, and keep anything in memory. The main aim is to upload human brain into
machine. So that man can think, take decision without any effort. After the death of the body,
the virtual brain will act as the man .So, even after the death of person we will not loose the
knowledge, intelligence, personalities, feelings and memories of that man that can be used
for the development of the human society. No one has ever understood the complexity of
human brain. It is complex than any circuitry in the world. So, question may arise ―Is it
really possible to create a human brain?‖ The answer is ―Yes‖. Because what ever man has
created today always he has followed the nature. When man does not have a device called
computer, it was a big question for all. Technology is growing faster than every thing. IBM is
now in research to create a virtual brain, called ―Blue brain‖. If possible, this would be the
first virtual brain of the world. With in 30 years, we will be able to scan ourselves into the
computers. Is this the beginning of eternal life.

Blue Brain also named as ‖Virtual Brain‖, was the first intellectual brain which attempted
reverse-engineering on the brain of mammals. This process helps to study the detailed
stimulation and functionality of Pink brain. The project was initialized b Prof.Henry
Markram from Brain and Mind Institute at EPFL (Ecole Polytechique Federale de Lausanne)
in Lausanne, Switzerland. IBM collaborated on this project to provide technical assistance.
Recreating one of the most valuable advantages of Pink brain - the Brain Uploading even
after the death of a person, was a great challenge during the project. The aim of introducing
Blue brain is to enable extremely fast development on recovery for Brain diseases. This has

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been a very useful tool for Short-term memory patients. They can remember their lost
memories through this feature. Research is done on an actual living brain, slicing down
through human brain tissues and applying Microscopes and Clamp electrodes for detailed
study. Data from each neuron is collected. The real role of IBM is to create a neuron model
for this project. The collected data is used to create a biological-realistic model and network
of neurons. Stimulation is performed using Blue Gene supercomputer built by IBM.

In a similar way an artificial nervous system can be created. Scientists have created artificial
neurons by replacing them with the silicon chip. Tests have also been completed to show that
these neurons can receive input from the sensory cells. So, the electric impulses from the
sensory cells can be received through these artificial neurons. The interpretation of the
electric impulses received by the artificial neuron can be completed by means of registers.
The different values in these registers will represent different states of the brain. Based on the
states of the register the output signal can be sent to the artificial neurons in the body, which
will be received by the sensory cell. It is possible to store the data permanently by using the
secondary memory. In a similar way the required states of the registers can be stored
permanently and when required this information can be received and used.

The decision-making can be performed by the computer by using some stored states and the
received input and performing some arithmetic and logical calculations. The computer chip,
which is implanted into the brain, monitors brain activity and converts the intention of the
user into computer commands. These applications may include novel communications
interfaces for motor impaired patients, as well as the monitoring and treatment of certain
diseases which manifest themselves in patterns of brain activity, such as epilepsy and
depression.

Currently the chip uses 100 hair-thin electrodes that sense the electro-magnetic signature of
neurons firing in specific areas of the brain, for example, the area that controls arm
movement. The activities are translated into electrically charged signals and are then sent and
decoded using a program.

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The simulation step involves synthesizing virtual cells using the algorithms that were found
to describe real neurons. The algorithms and parameters are adjusted for the age, species, and
disease stage of the animal being simulated. Every single protein is simulated, and there are
about a billion of these in one cell. First a network skeleton is built from all the different
kinds of synthesized neurons. Then the cells are connected together according to the rules
that have been found experimentally. Finally the neurons are functioned and the simulation
brought to life. The patterns of emergent behaviour are viewed with visualization software.

2.2 Why we need Blue Brain?

Today we are developed because of our intelligence. Intelligence is the inborn quality that
cannot be created. Some people have this quality, so that they can think up to such an extent
where other cannot reach. Human society is always need of such intelligence and such an
intelligent brain to have with. But the intelligence is lost along with the body after the death.
The virtual brain is a solution to it. The brain and intelligence will alive even after the death.
We often face difficulties in remembering things such as people’s names, their birthdays, and
the spellings of words, proper grammar, important dates, history, facts etc... In the busy life
every one want to be relaxed. Can’t we use any machine to assist for all these? Virtual brain
may be the solution to it. What if we upload ourselves into computer, we were simply aware
of a computer, or maybe, what if we lived in a computer as a program?

Four broad motivations behind the Blue Brain Project are:

• Brain disease treatments

• Scientific curiosity about consciousness and the human mind

• Integration of all neuro-scientific research results worldwide

• Progress towards building thinking machines(bottom up approach)

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One in four people will suffer from one of around 560 brain diseases during their lifetime.
Therefore it is important to have a good strategy for understanding these diseases and finding
suitable treatments. The living brain is very difficult to study. Both from a technical
perspective, and a moral one. A virtual model, however, makes direct observations possible.
Experiments on models are also more efficient and limit the need for laboratory animals. The
Blue Brain Project, by including molecular-level simulations, could be used to study the
effect of new pharmaceutical compounds on virtual brains of any species, age, and stage of
disease. Another aim of the Blue Brain Project is to provide a centrally coordinated resource
for the 200,000 active neuroscientists in the world. Previously each researcher has focused on
their own specialist field without the results being shared and easily available to all.

2.2 How it is possible?

First, it is helpful to describe the basic manners in which a person may be uploaded into a
computer. Raymond Kurzweil recently provided an interesting paper on this topic. In it, he
describes both invasive and noninvasively techniques. The most promising is the use of very
small robots, or nanobots. These robots will be small enough to travel throughout our
circulatory systems. Travelling into the spine and brain, they will be able to monitor the
activity and structure of our central nervous system. They will be able to provide an interface
with computers that is as close as our mind can be while we still reside in our biological
form. Nanobots could also carefully scan the structure of our brain, providing a complete
readout of the connections between each neuron. They would also record the current state of
the brain. This information, when entered into a computer, could then continue to function as
us. All that is required is a computer with large enough storage space and processing power.
Is the pattern and state of neuron connections in our brain truly all that makes up our
conscious selves? Many people believe firmly those we posses a soul, while some very
technical people believe that quantum forces contribute to our awareness. But we have to
now think technically.

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Note, however, that we need not know how the brain actually functions, to transfer it to a
computer. We need only know the media and contents. The actual mystery of how we
achieved consciousness in the first place, or how we maintain it, is a separate discussion.
Really this concept appears to be very difficult and complex to us. For this we have to first
know how the human brain actually works.

It is the creation of synthetic brain by reverse engineering, the mammalian brains down to the
molecular level. That means a machine can function as human brain. No one can ever
understand the complexity of human brain. It is more complex than any circuitry in the
world. Is it possible to create a virtual brain? Yes, the scientists today are in research to create
an artificial brain that can think, respond, take decision, and keep everything in memory.
Ultimately, it is to upload human brain into machine so that man can think , take decisions
without any effort. After the death of the body, we will not lose knowledge, intelligence,
feelings and memory of that man and can be used for the welfare of human society. Within
30 years, we will be able to scan ourselves into the computers.

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Chapter 3

DESCRIPTION OF NATURAL BRAIN

3.1 General Description

The brain essentially serves as the body’s information processing centre. It receives signals
from sensory neurons (nerve cell bodies and their axons and dendrites) in the central and
peripheral nervous systems, and in response it generates and sends new signals that instruct
the corresponding parts of the body to move or react in some way. It also integrates signals
received from the body with signals from adjacent areas of the brain, giving rise to
perception and consciousness. The brain weighs about 1,500 grams (3 pounds) and
constitutes about 2 percent of total body weight. It consists of three major divisions;

 The massive paired hemispheres of the cerebrum

 The brainstem, consisting of the thalamus, hypothalamus, epithalamus, subtha-lamus,


midbrain, pons, and medulla oblongata

 The cerebellum.

The human ability to feel, interpret and even see is controlled, in computer like calculations,
by the magical nervous system. The nervous system is quite like magic because we can’t see
it, but its working through electric impulses through your body. One of the worlds most
―intricately organized‖ electron mechanisms is the nervous system. Not even engineers have
come close to making circuit boards and computers as delicate and precise as the nervous
system. To understand this system, one has to know the three simple functions that it puts
into action; sensory input, integration & motor output.

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Figure 3.1: Medial view of the left hemisphere of human brain.

3.1.1 Sensory Input

When our eyes see something or our hands touch a warm surface, the sensory cells, also
known as Neurons, send a message straight to your brain. This actionof getting information
from your surrounding environment is called sensory input because we are putting things in
your brain by way of your senses.

The sensory system axons are connected to nuclei in the thalamus which, in turn, project
their axons into subcortical structures such as the basal ganglia and hypothalamus to transmit
impulses. Other neurons in the thalamus act as cortical relays. They receive fibers from the
sensory tracts, cerebellum, reticular system, and basal ganglia. These neurons project their
axons into the cerebral cortex. Association neurons have input links only with other
diencephalar cells, but they project their output fibers to the association areas of the
cerebrum.

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Sensory impulses result from some outside stimulation or input, such as incoming light from
the retina. In the eye, photosensitive cells react to light intensity and color to begin
electrochemical chain-reactions in the brain (I’ll cover those chemical reactions in future
posts). These inputs can trigger responses such as looking at something interesting in the
field of view. This means that incoming stimuli, besides being interpreted, may be acted upon
immediately.

3.1.2 Integration

Integration is best known as the interpretation of things we have felt, tasted, and touched with
our sensory cells, also known as neurons, into responses that the body recognizes. This
process is all accomplished in the brain where many, many neurons work together to
understand the environment.

3.1.3 Motor Output

Once our brain has interpreted all that we have learned, either by touching, tasting, or using
any other sense, then our brain sends a message through neurons to effecter cells, muscle or
gland cells, which actually work to perform our requests and act upon our environment.

3.2 How we see, hear, feel, & smell?

The brain essentially serves as the body’s information processing centre. It receives signals
from sensory neurons (nerve cell bodies and their axons and dendrites) in the central and
peripheral nervous systems, and in response it generates and sends new signals that instruct
the corresponding parts of the body to move or react in some way. It also integrates signals
received from the body with signals from adjacent areas of the brain, giving rise to
perception and consciousness.

The human ability to feel, interpret and even see is controlled, in computer like calculations,
by the magical nervous system. The nervous system is quite like magic because we can’t see
it, but its working through electric impulses through your body. One of the world’s most

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―intricately organized‖ electron mechanisms is the nervous system. Not even engineers have
come close to making circuit boards and computers as delicate and precise as the nervous
system. To understand this system, one has to know the three simple functions that it puts
into action; sensory input, integration & motor output.

Feeling is the nominalization of the verb to feel. The word was first used in the English
language to describe the physical sensation of touch through either experience or perception.
The word is also used to describe experiences other than the physical sensation of touch, such
as "a feeling of warmth" and of sentience in general. In Latin, sentire meant to feel, hear or
smell. In psychology, the word is usually reserved for the conscious subjective experience of
emotion. Phenomenology and hetero phenomenology are philosophical approaches that
provide some basis for knowledge of feelings. Many schools of psychotherapy depend on the
therapist achieving some kind of understanding of the client's feelings, for which
methodologies exist.

Perception of the physical world does not necessarily result in a universal reaction among
receivers (see emotions), but varies depending upon one's tendency to handle the situation,
how the situation relates to the receiver's past experiences, and any number of other factors.
Feelings are also known as a state of consciousness, such as that resulting from emotions,
sentiments or desires.

People buy products in hopes that the product will make them feel a certain way: either
happy, excited or beautiful. Or, they find the product useful in some way, even indirectly
such as to support a charity or for altruistic economic reasons. Some people buy beauty
products in hopes of achieving a state of happiness or a sense of self beauty or as an act or
expression of beauty. Past events are used in our lives to form schemas in our minds, and
based on those past experiences, we expect our lives to follow a certain script. However,
storytelling, commemoration and reservation of commemoration (the unwillingness to
overtly impose remembrances), research and investigation, and many other activities can
help settle uneasy feelings without "scripting", without the ambivalence that feeling can only
be "handled" by proxy, which is not always true.

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A social psychologist, Daniel Gilbert, conducted a study on the influence of feelings on


events alongside other researchers. The results showed that when the participants predicted a
positive feeling for an event, the higher the chances that they wanted to relive the event.
Predicted feelings were either short-lived or did not correlate to what the participant
expected.

Sensation is an animal's, including humans', detection of external or internal stimulation (e.g.,


eyes detecting light waves, ears detecting sound waves). It is different from perception,
which is about making sense of, or describing, the stimulation (e.g., seeing a chair, hearing a
guitar).

Sensation involves three steps:

 Sensory receptors detect stimuli.

 Sensory stimuli are transduced into electrical impulses (action potentials) to be


decoded by the brain.

 Electrical impulses move along neural pathways to specific parts of the brain
wherein the impulses are decoded into useful information (perception).

For example, when touched by a soft feather, mechanoreceptors – which are sensory
receptors in the skin – register that the skin has been touched. That sensory information is
then turned into neural information through a process called transduction. Next, the neural
information travels down neural pathways to the appropriate part of the brain, wherein the
sensations are perceived as the touch of a feather.

Children are often taught five basic senses: seeing (i.e., vision), hearing (i.e., audition),
tasting (i.e., gustation), smelling (i.e., olfaction), and touching. However, there are actually
many more senses including vestibular sense, kinesthetic sense, sense of thirst, sense of
hunger, and cutaneous sense.

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3.2.1 Nose

Once the smell of food has reached your nose, which is lined with hairs, it travels to an
olfactory bulb, a set of sensory nerves. The nerve impulses travel through the olfactory tract,
around, in a circular way, the thalamus, and finally to the smell sensory cortex of our brain,
located between our eye and ear, where it is interpreted to be understood and memorized by
the body.

The human nose is the most protruding part of the face that bears the nostrils and is the first
organ of the respiratory system. The nose is also the principal organ in the olfactory system.
The shape of the nose is determined by the nasal bones and the nasal cartilages, including the
nasal septum which separates the nostrils and divides the nasal cavity into two. On average
the nose of a male is larger than that of a female.

The main function of the nose is respiration, and the nasal mucosa lining the nasal cavity and
the paranasal sinuses carries out the necessary conditioning of inhaled air by warming and
moistening it. Nasal conchae, shell-like bones in the walls of the cavities play a major part in
this process. Filtering of the air by nasal hair in the nostrils prevents large particles from
entering the lungs. Sneezing is a reflex to expel unwanted particles from the nose that irritate
the mucosal lining. Sneezing can transmit infections, because aerosols are created in which
the droplets can harbour pathogens.

Another major function of the nose is olfaction, the informing of odours that the sense of
smell carries out. The area of olfactory epithelium, in the upper nasal cavity contains
specialised olfactory cells responsible for this function.

The nose is also involved in the function of speech. Nasal vowels and nasal consonants are
produced in the process of nasalisation. The nasal cavity is the third most effective vocal
resonator.

There are many plastic surgery procedures on the nose, known as rhinoplasties available to
correct various structural defects or to change the shape of the nose. Defects may be
congenital, result from nasal disorders or from trauma and these are carried out by

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reconstructive surgery. Procedures used to change a nose shape electively are carried out by
cosmetic surgeries.

3.2.2 Eye

Seeing is one of the most pleasing senses of the nervous system. This cherished action
primarily conducted by the lens, which magnifies a seen image, vitreous disc, which bends
and rotates an image against the retina, which translates the image and light by a set of cells.
The retina is at the back of the eye ball where rods and cones structure along with other cells
and tissues covert the image into nerve impulses which are transmitted along the optic nerve
to the brain where it is kept for memory.

Eyes are organs of the visual system. They provide organisms with vision, the ability to
receive and process visual detail, as well as enabling several photo response functions that
are independent of vision. Eyes detect light and convert it into electro-chemical impulses in
neurons. In higher organisms, the eye is a complex optical system which collects light from
the surrounding environment, regulates its intensity through a diaphragm, focuses it through
an adjustable assembly of lenses to form an image, converts this image into a set of electrical
signals, and transmits these signals to the brain through complex neural pathways that
connect the eye via the optic nerve to the visual cortex and other areas of the brain. Eyes with
resolving power have come in ten fundamentally different forms, and 96% of animal species
possess a complex optical system. Image-resolving eyes are present in molluscs, chordates
and arthropods.

The simplest "eyes", such as those in microorganisms, do nothing but detect whether the
surroundings are light or dark, which is sufficient for the entrainment of circadian
rhythms.From more complex eyes, retinal photosensitive ganglion cells send signals along
the retinohypothalamic tract to the suprachiasmatic nuclei to effect circadian adjustment and
to the pretectal area to control the pupillary light reflex.

3.2.3 Tongue

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A set of microscopic buds on the tongue divide everything we eat and drink into four kinds of
taste: bitter, sour, salty, and sweet. These buds have taste pores, which convert the taste into a
nerve impulse and send the impulse to the brain by a sensory nerve fiber. Upon receiving the
message, our brain classifies the different kinds of taste. This is how we can refer the taste of
one kind of food to another.

The tongue is a muscular organ in the mouth of most vertebrates that manipulates food for
mastication, and is used in the act of swallowing. It is of importance in the digestive system
and is the primary organ of taste in the gustatory system. The tongue's upper surface
(dorsum) is covered by taste buds housed in numerous lingual papillae. It is sensitive and
kept moist by saliva, and is richly supplied with nerves and blood vessels. The tongue also
serves as a natural means of cleaning the teeth. A major function of the tongue is the enabling
of speech in humans and vocalization in other animals.

The human tongue is divided into two parts, an oral part at the front and a pharyngeal part at
the back. The left and right sides are also separated along most of its length by a vertical
section of fibrous tissue (the lingual septum) that results in a groove, the median sulcus on
the tongue's surface.

There are two groups of muscles of the tongue. The four intrinsic muscles alter the shape of
the tongue and are not attached to bone. The four paired extrinsic muscles change the
position of the tongue and are anchored to bone.

3.2.4 Ear

Once the sound or sound wave has entered the drum, it goes to a large structure called the
cochlea. In this snail like structure, the sound waves are divided into pitches. The vibrations
of the pitches in the cochlea are measured by the Corti. This organ transmits the vibration
information to a nerve, which sends it to the brain for interpre-tation and memory.

The ear is the organ of hearing and, in mammals, balance. In mammals, the ear is usually
described as having three parts—the outer ear, middle ear and the inner ear. The outer ear
consists of the pinna and the ear canal. Since the outer ear is the only visible portion of the

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ear in most animals, the word "ear" often refers to the external part alone.The middle ear
includes the tympanic cavity and the three ossicles. The inner ear sits in the bony labyrinth,
and contains structures which are key to several senses: the semicircular canals, which enable
balance and eye tracking when moving; the utricle and saccule, which enable balance when
stationary; and the cochlea, which enables hearing. The ears of vertebrates are placed
somewhat symmetrically on either side of the head, an arrangement that aids sound
localisation.

The ear develops from the first pharyngeal pouch and six small swellings that develop in the
early embryo called otic placodes, which are derived from ectoderm.

The ear may be affected by disease, including infection and traumatic damage. Diseases of
the ear may lead to hearing loss, tinnitus and balance disorders such as vertigo, although
many of these conditions may also be affected by damage to the brain or neural pathways
leading from the ear.

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Chapter 4

BRAIN SIMULATION

Brain simulation is the concept of creating a functioning computer model of a brain or part of
a brain. Modelling a brain (or brain subsystem) involves both modelling neurons' electrical
and bulk chemical properties (e.g. extracellular serotonin gradients). A model of the neural
connectome of the target organism is also required. The connectome is extremely complex,
and its detailed wiring is not yet understood; thus it is presently being modeled empirically in
smaller mammals by projects like the Blue Brain Project.

The Blue Brain Project intends to create a computer simulation of a mammalian cortical
column down to the molecular level.[citation needed] By one estimate, a full reconstruction
of the human connectome using the methodology of the Blue Brain Project would require a
zettabyte of data storage. In 2013, Human Brain Project created a Brain Simulation Platform
(BSP), which is an internet-accessible collaborative platform designed for the simulation of
brain models. The Human Brain Project has utilized techniques used by the Blue Brain
Project and built upon them.

Brain simulation projects intend to contribute to a complete understanding of the brain, and
eventually assist the process of treating and diagnosing brain diseases.

The connectivity of the neural circuit for touch sensitivity of the simple C. elegans nematode
(roundworm) was mapped in 1985 and partly simulated in 1993.Since 2004, many software
simulations of the complete neural and muscular system have been developed, including
simulation of the worm's physical environment. Some of these models have been made
available for download. However, there is still a lack of understanding of how the neurons
and the connections between them generate the surprisingly complex range of behaviors that
are observed in the relatively simple organism. This contrast between the apparent simplicity
of how the mapped neurons interact with their neighbours, and exceeding complexity of the

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overall brain function, is an example of an emergent property. This kind of emergent property
is paralleled within artificial neural networks, the neurons of which are exceedingly simple
compared to their often complex, abstract outputs.

A comparative discussion of Natural Brain and Simulated Brain is given below.

Figure 4.1: Simulation Comparision

NATURAL BRAIN SIMULATED BRAIN


1. INPUT 1. INPUT
In the nervous system in our body the In a similar way the artificial nervous

neurons are responsible for the message system can be created. The scientist has

passing. The body receives the input by already created artificial neurons by

the sensory cells. These sensory replacing them with the silicon chip. It has

cells produces electric impulses which are also been tested that these neurons can

received by the neurons. The neurons receive the input from the sensory cells.

transfer these electric impulses to the So, the electric impulses from the sensory

brain. cells can be received through these

artificial neurons and send to a super

computer for the interpretation.

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3. OUTPUT 3. OUTPUT
Based on the states of the neurons the Similarly based on the states of the

brain sends the electric impulses register the output signal can be given to

representing the responses which are the artificial neurons in the body which

further received by the sensory cell of our will be received by the sensory cell.

body to respond.

4. MEMORY. 4. MEMORY
There are certain neurons in our brain It is not impossible to store the data
which represent certain states permanently by using the secondary
permanently. When required these state is memory. In the similar way the required
interpreted by our brain and we can states of the registers can be stored
remember the past things. To remember permanently.
thing we force the neurons to represent And when required these information
certain states of the brain permanently or can be retrieved and used.
for any interesting or serious matter this is
happened implicitly.

5. PROCESSING 5. PROCESSING
When we take decision, think about In a similar way the decision making can
something, or make any computation, be done by the computer by using some
Logical and arithmetic calculations are stored states and the received input & by
done in our neural circuit. performing some arithmetic and logical
calculations.

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Chapter 5

BUILDING BLUE BRAIN

5.1 Introduction

The ability of a man to control the environment in which he lives is what makes him
distinctively different from the other species. His intellectual skills place him at the most
superior level of the animal kingdom. Thus, underlying all human abilities lie the essential
attributes of intelligence.

Intelligence refers to the ability to understand, think, act, interpret and predict the future to
achieve and handle relationships, concepts etc. It helps in decision making, problem solving,
learning and reasoning. Intelligence thus

plays a very important role in survival and progress beyond the present. Technology has been
progressing to a great extend such that even the human brains are being created artificially
through the science of artificial intelligence. Artificial intelligence is the simulation of
intelligence in machines which makes it behave like a human being. It is the study and design
of intelligent agents where an intelligent agent is a system that perceives its environment and
takes actions that maximize its chances of success.

5.2 Neural Network

Neural network is an extremely simplified model of the brain. The building blocks of the neural
networks are called the neurons. An artificial neuron is a computational model inspired in the
natural neurons. Natural neurons receive signals through synapses located on the dendrites or
membrane of the neuron. When the signals received are strong enough ,surpass a certain
threshold , the neuron is activated and emits a signal though the axon. This signal might be sent
to another synapse, and might activate other neurons. Each neuron

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receives inputs from many other neurons, changes its state base on the current input and send
one output signal to many other neurons.

The complexity of real neurons is highly abstracted when modelling artificial neurons. These
basically consist of inputs (like synapses), which are multiplied by weights (strength of the
respective signals), and then computed by a mathematical function which determines the
activation of the neuron. Another function computes the output of the artificial neuron. ANNs
combine artificial neurons in order to process information. Information is transmitted as a
series of electric impulses, so-called spikes. The frequency and phase of these spikes encodes
the information. In biological systems, one neuron can be connected to as many as 10,000
other neurons. Usually, a neuron receives its information from other neurons in a confined
area, its so-called receptive field.

The higher a weight of an artificial neuron is, the stronger the input which is multiplied by it
will be. Weights can also be negative, so we can say that the signal is inhibited by the
negative weight. Depending on the weights, the computation of the neuron will be different.
By adjusting the weights of an artificial neuron we can obtain the output we want for specific
inputs. But when we have an ANN of hundreds or thousands of neurons, it would be quite
complicated to find by hand all the necessary weights. But we can find algorithms which can
adjust the weights of the ANN in order to obtain the desired output from the network. This
process of adjusting the weights is called learning or training. The number of types of ANNs
and their uses is very high. Since the first neural model by McCulloch and Pitts (1943) there
have been developed hundreds of different models considered as ANNs. The differences in
them might be the functions, the accepted values, the topology, the learning algorithms, etc.
Also there are many hybrid models where each neuron has more properties than the ones we
are reviewing here. Because of matters of space, we will present only an ANN which learns
using the backpropagation algorithm for learning the appropriate weights, since it is one of
the most common models used in ANNs, and many others are based on it. Since the function
of ANNs is to process information, they are used mainly in fields related with it. There are a
wide variety of ANNs that are used to model real neural networks, and study behaviour and

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control in animals and machines, but also there are ANNs which are used for engineering
purposes, such as pattern recognition, forecasting, and data compression.

5.3 Design

There are three main steps to building the blue brain:

 Data Acquisition

 Simulation

 Visualisation of results.

5.1.1 Data acquisition:

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
biologicallyrealistic 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.The electrophysiological behaviour of neurons is studied using a 12
patch clamp instrument. This tool was developed for the Blue Brain Project and it forms a
foundation of the research. It enables twelve living neurons to be concurrently patched and
their electrical activity recorded. The Nomarski microscope enhances the contrast of the

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unstained samples of living neural tissue. Carbon nanotube-coated electrodes can be used to
improve recording. Different types of neuron have different mixes of channels - and this
contributes to differences in their electrical behaviour. The genes for these channels are
cloned at the lab, over expressed in cultured cells, and their electrical behaviour recorded.
Over 270 genes are known to be associated with voltage-gated ion channels in the rat.

5.1.2 Simulation:

The simulation step involves synthesising virtual cells using the algorithms that were found
to describe real neurons. The algorthims and parameters are adjusted for the age, species, and
disease stage of the animal being simulated. Every single protein is simulated, and there are
about a billion of these in one cell. First a network skeleton is built from all the different
kinds of synthesised neurons. Then the cells are connected together according to the rules
that have been found experimentally. Finally the neurons are functionalised and the
simulation brought to life. The patterns of emergent behaviour are viewed with visualisation
software. A basic unit of the cerebral cortex is the cortical column. Each column can be
mapped to one function, e.g. in rats one column is devoted to each whisker. A rat cortical
column has about 10,000 neurons and is about the size of a pinhead. The latest simulations,
as of November 2011, contain about 100 columns, 1 million neurons, and 1 billion synapses.
A real life rat has about 100,000 columns in total, and humans have around 2 million.
Techniques are being developed for multiscale simulation whereby active parts of the brain
are simulated in great detail while quiescent parts are not so detailed. Every two weeks a
column model is run. The simulations reproduce observations that are seen in living neurons.
Emergent properties are seen that require larger and larger networks. The plan is to build a
generalised simulation tool, one that makes it easy to build circuits. There are also plans to
couple the brain simulations to avatars living in a virtual environment, and eventually also to
robots interacting with the real world. The ultimate aim is to be able to understand and
reproduce human consciousness.

In the 1990s, a software package known as NEURON was developed by Michael Hines. This
is used for neural simulations. It is written in languages like C, C++, and FORTRAN. The
current version at which software is working is 7.2 and it is still under development.

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Data Simulation has two major aspects:

• Simulation speed

• Simulation workflow

1) Simulation speed- Simulations of one cortical column (more than 10,100 neurons) run
about two hundred times slower than real time. It takes about five minutes to complete one
second of stimulated time. And display unevenly line scaling. It might be possible to trim
components in order to improve performance, if the biological validity is understood. The
simulation timestep varies as it is 0.025 ms for numerical integrations and 0.1 ms for writing
the output to the disk.

2) Simulation overflow- Main work of this step is to make virtual cells use the algorithms,
written to define the real neurons. According to the characteristics of the stage species like
their age, type and disease that it has, of the animal is being simulated. In a single cell, there
are hundreds of millions of proteins and each protein is simulated. First a body or structure of
network is built using all the different kinds of synthesized neurons. After this, cells are
connected with experimentally defined rules. And, finally the neurons become functional and
the simulation is achieved. The blueprints showing the changing behavior of neurons are seen
via visualization software. Every two weeks a column model is run; column here is cortical
column that is the basic unit of cerebral cortex and each of them can be mapped into one
function. The results that are seen in living neurons are simulations causing to reproduce
serving our ultimate aim.

3) BBP-SDK- Abbreviated as Blue Brain Project - Software Development Kit, it is a set of


software classes that allows researchers to examine models and simulations and use them.
The software kit is a C++ library enfolded in Java and Python.

5.1.3 Visualisation of results:

RTNeuron: RTNeuron is the primary application used by the BBP for visualisation of neural
simulations. The software was developed internally by the BBP team. It is written in C++

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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 Hodgkin-
Huxley 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.

RTNeuron is a scalable real-time rendering tool for the visualisation of neuronal simulations
based on cable models. Its main utility is twofold: the interactive visual inspection of
structural and functional features of the cortical column model and the generation of high
quality movies and images for presentations and publications. The package provides three
main components:

• A high level C++ library.

• A Python module that wraps the C++ library and provides additional tools.

• The Python application script rtneuron-app.py

A wide variety of scenarios is covered by rtneuron-app.py. In case the user needs a finer
control of the rendering, such as in movie production or to speed up the exploration of
different data sets, the Python wrapping is the way to go. The Python wrapping can be used
through an IPython shell started directly from rtneuron-app.py or importing the module
rtneuron into own Python programs. GUI overlays can be created for specific use c ases
using PyQt and QML.

RTNeuron is available on the pilot system JULIA and on JURECA as environment module.
Neuron is a simulation environment for modeling individual and networks of neurons. It was
primarily developed by Michael Hines, John W. Moore, and Ted Carnevale at Yale and Duke.

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Neuron models individual neurons via the use of sections that are automatically subdivided
into individual compartments, instead of requiring the user to manually create compartments.
The primary scripting language is hoc but a Python interface is also available. Programs can
be written interactively in a shell, or loaded from a file. Neuron supports parallelization via
the MPI protocol.

Neuron is capable of handling diffusion-reaction models, and integrating diffusion functions


into models of synapses and cellular networks. Parallelization is possible via internal
multithreaded routines, for use on multi-core computers. The properties of the membrane
channels of the neuron are simulated using compiled mechanisms written using the NMODL
language or by compiled routines operating on internal data structures that are set up with
Channel Builder.

Along with the analogous software platform GENESIS, Neuron is the basis for instruction in
computational neuroscience in many courses and laboratories around the world.

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Chapter 6

WORKING OF BLUE BRAIN

6.1 Goals & Objectives

The Virtual Brain Project is the first comprehensive attempt to reverse-engineer the
mammalian brain, in order to understand brain function and dysfunction through detailed
simulations. The mission in undertaking The Blue Brain Project is to gather all existing
knowledge of the brain, accelerate the global research effort of reverse engineering the
structure and function of the components of the brain, and to build a complete theoretical
framework that can orchestrate the reconstruction of the brain of mammals and man from the
genetic to the whole brain levels, into computer models for simulation, visualization and
automatic knowledge archiving by 2015. Biologically accurate computer models of
mammalian and human brains could provide a new foundation for understanding functions
and malfunctions of the brain and for a new generation of information-based, customized
medicine.

The goal of the Virtual 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).

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 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.

6.2 Architecture of Blue Gene

Blue Gene/L is built using system-on-a-chip technology in which all functions of a node
(except for main memory) are integrated onto a single application-specific integrated circuit
(ASIC). This ASIC includes 2 PowerPC 440 cores running at 700 MHz. Associated with each
core is a 64-bit ―double‖ floating point unit (FPU) that can operate in single instruction,
multiple data (SIMD) mode. Each (single) FPU can execute up to 2 ―multiply-adds‖ per
cycle, which means that the peak performance of the chip is 8 floating point operations per
cycle (4 under normal conditions, with no use of SIMD mode). This leads to a peak
performance of 5.6 billion floating point operations per second (gigaFLOPS or GFLOPS) per
chip or node, or 2.8 GFLOPS in non- SIMD mode. The two CPUs (central processing units)
can be used in ―co-processor‖ mode (resulting in one CPU and 512 MB RAM (random
access memory) for computation, the other CPU being used for processing the I/O
(input/output) of the main CPU) or in ―virtual node‖ mode (in which both CPUs with 256
MB each are used for computation). So, the aggregate performance of a processor card in
virtual node mode is: 2 x node = 2 x 2.8 GFLOPS = 5.6 GFLOPS, and its peak performance
(optimal use of double FPU) is: 2 x 5.6 GFLOPS = 11.2 GFLOPS. A rack (1,024 nodes =
2,048 CPUs) therefore has 2.8 teraFLOPS or TFLOPS, and a peak of 5.6 TFLOPS. The Blue
Brain Projects Blue Gene is a 4-rack system that has 4,096 nodes, equal to 8,192 CPUs, with
a peak performance of 22.4 TFLOPS. A 64-rack machine should provide 180 TFLOPS, or
360 TFLOPS at peak performance.

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Figure 6.1: The Blue Gene/L supercomputer architecture

6.3 Modelling the Microcircuit

The scheme shows the minimal essential building blocks required to reconstruct a neural
microcircuit. Microcircuits are composed of neurons and synaptic connections. To model
neurons, the three-dimensional morphology, ion channel composition, and distributions and
electrical properties of the different types of neuron are required, as well as the total numbers
of neurons in the microcircuit and the relative proportions of the different types of neuron. To
model synaptic connections, the physiological and pharmacological properties of the different
types of synapse that connect any two types of neuron are required, in addition to statistics on
which part of the axonal arborisation is used (presynaptic innervation pattern) to contact
which regions of the target neuron (postsynaptic innervations pattern), how many synapses
are involved in forming connections, and the connectivity statistics between any two types of
neuron. Neurons receive inputs from thousands of other neurons, which are intricately
mapped onto different branches of highly complex dendritic trees and require tens of
thousands of compartments to accurately represent them. There is therefore a minimal size of
a microcircuit and a minimal complexity of a neuron’s morphology that can fully sustain a

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neuron. A massive increase in computational power is required to make this quantum leap -
an increase that is provided by IBM’s Blue Gene supercomputer. By exploiting the
computing power of Blue Gene, the Blue Brain Project1 aims to build accurate models of the
mammalian brain from first principles. The first phase of the project is to build a cellular-
level (as opposed to a genetic- or molecular-level) model of a 2-week-old rat somatosensory
neocortex corresponding to the dimensions of a neocortical column (NCC) as defined by the
dendritic arborizations of the layer 5 pyramidal neurons. The combination of infrared
differential interference microscopy in brain slices and the use of multi-neuron patch-
clamping allowed the systematic quantification of the molecular, morphological and electrical
properties of the different neurons and their synaptic pathways in a manner that would allow
an accurate reconstruction of the column. Over the past 10 years, the laboratory has prepared
for this reconstruction by developing the multi-neuron patch-clamp approach, recording from
thousands of neocortical neurons and their synaptic connections, and developing quantitative
approaches to allow a complete numerical breakdown of the elementary building blocks of
the NCC. The recordings have mainly been in the 14-16-day-old rat somatosensory cortex,
which is a highly accessible region on which many researchers have converged following a
series of pioneering studies driven by Bert Sakmann. Much of the raw data is located in our
databases, but a major initiative is underway to make all these data freely available in a
publicly accessible database. The so-called ’blue print’ of the circuit, although not entirely
complete, has reached a sufficient level of refinement to begin the reconstruction at the
cellular level. Highly quantitative data are available for rats of this age, mainly because
visualization of the tissue is optimal from a technical point of view. This age also provides an
ideal template because it can serve as a starting point from which to study maturation and
ageing of the NCC. As NCCs show a high degree of stereotypy, the region from which the
template is built is not crucial, but a sensory region is preferred because these areas contain a
prominent layer 4 with cells specialized to receive input to the neocortex from the thalamus;
this will also be required for later calibration with in vivo experiments. The NCC should not
be overly specialized, because this could make generalization to other neocortical regions
difficult, but areas such as the barrel cortex do offer the advantage of highly controlled in
vivo data for comparison. The mouse might have

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been the best species to begin with, because it offers a spectrum of molecular approaches
with which to explore the circuit, but mouse neurons are small, which prevents the detailed
dendritic recordings that are important for modelling the nonlinear properties of the complex
dendritic trees of pyramidal cells (75-80% of the neurons).

The image shows the Microcircuit in various stages of reconstruction. Only a small fraction
of reconstructed, three dimensional neurons is shown. Red indicates the dendritic and blue
the axonal arborizations. The columnar structure illustrates the layer definition of the NCC.

 The microcircuits (from left to right) for layers 2, 3, 4 and 5.

 A single thick tufted layer 5 pyramidal neuron located within the column.

 One pyramidal neuron in layer 2, a small pyramidal neuron in layer 5 and the large
thick tufted pyramidal neuron in layer

 An image of the NCC, with neurons located in layers 2 to 5.

6.4 Simulating the Microcircuit

Once the microcircuit is built, the exciting work of making the circuit function can begin. All
the 8192 processors of the Blue Gene are pressed into service, in a massively parallel
computation solving the complex mathematical equations that govern the electrical activity
in each neuron when a stimulus is applied. Currently, the time required to simulate the circuit
is about two orders of magnitude larger than the actual biological time simulated.

6.5 Interpreting the Results

Running the Blue Brain simulation generates huge amounts of data. Analyses of individual
neurons must be repeated thousands of times. And analyses dealing with the network activity
must deal with data that easily reaches hundreds of gigabytes per second of simulation. Using

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massively parallel computers the data can be analyzed where it is created (server-side
analysis for experimental data, online analysis during simulation). Given the geometric
complexity of the column, a visual exploration of the circuit is an important part of the
analysis. Mapping the simulation data onto the morphology is invaluable for an immediate
verification of single cell activity as well as network phenomena. Architects at EPFL have
worked with the Blue Brain devel-opers to design a visualization interface that translates the
Blue Gene data into a 3D visual representation of the column. A different supercomputer is
used for this compu-tationally intensive task. The visualization of the neurons’ shapes is a
challenging task given the fact that a column of 10,000 neurons rendered in high quality
mesh accounts for essentially 1 billion triangles for which about 100GB of management data
is required. Simulation data with a resolution of electrical compartments for each neuron
accounts for another 150GB. As the electrical impulse travels through the column, neurons
light up and change color as they become electrically active. A visual interface makes it
possible to quickly identify areas of interest that can then be studied more extensively using
further simulations. A visual representation can also be used to compare the simulation
results with experiments that show electrical activity in the brain.

6.6 Data Manipulation Cascade

Building the Blue Column requires a series of data manipulations .The first step is to parse
each three-dimensional morphology and correct errors due to the in vitro preparation and
reconstruction. The repaired neurons are placed in a database from which statistics for the
different anatomical classes of neurons are obtained. These statistics are used to clone an
indefinite number of neurons in each class to capture the full morphological diversity. The
next step is to take each neuron and insert ion channel models in order to produce the array of
electrical types. The field has reached a sufficient stage of convergence to generate efforts to
classify neurons, such as the Petilla Convention - a conference held in October 2005 on
anatomical and electrical types of neocortical interneuron, established by the community.
Single-cell gene expression studies of neocortical interneurons now provide detailed
predictions of the specific combinations of more than 20 ion channel genes that underlie

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electrical diversity. A database of biologically accurate Hodgkin-Huxley ion channel models


is being produced. The simulator NEURON is used with automated fitting algorithms
running on Blue Gene to insert ion channels and adjust their parameters to capture the
specific electrical properties of the different electrical types found in each anatomical class.
The statistical variations within each electrical class are also used to generate subtle
variations in discharge behaviour in each neuron.

So, each neuron is morpho-logically and electrically unique. Rather than taking 10,000 days
to fit each neuron’s electrical behaviour with a unique profile, density and distribution of ion
channels, applications are being prepared to use Blue Gene to carry out such a fit in a day.
These functionalized neurons are stored in a database. The three-dimensional neurons are
then imported into Blue Builder, a circuit builder that loads neurons into their layers
according to a ―recipe‖ of neuron numbers and proportions. A collision detection algorithm
is run to determine the structural positioning of all axo-dendritic touches, and neurons are
jittered and spun until the structural touches match experimentally derived statistics.
Probabilities of connectivity between different types of neuron are used to determine which
neurons are connected, and all axo-dendritic touches are converted into synaptic connections.
The manner in which the axons map onto the dendrites between specific anatomical classes
and the distribution of synapses received by a class of neurons are used to verify and fine-
tune the biological accuracy of the synaptic mapping between neurons. It is therefore
possible to place 10-50 million synapses in accurate three-dimensional space, distributed on
the detailed threedimen-sional morphology of each neuron. The synapses are functionalized
according to the synaptic parameters for different classes of synaptic connection within
statistical vari-ations of each class, dynamic synaptic models are used to simulate
transmission, and synaptic learning algorithms are introduced to allow plasticity. The
distance from the cell body to each synapse is used to compute the axonal delay, and the
circuit configuration is exported. The configuration file is read by a NEURON subroutine
that calls up each neuron and effectively inserts the location and functional properties of
every synapse on the axon, soma and dendrites. One neuron is then mapped onto each
processor and the axonal delays are used to manage communication between neurons and
processors. Effectively, processors are converted into neurons, and MPI (message-passing

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interface)- based communication cables are converted into axons interconnecting the neurons
- so the entire Blue Gene is essentially converted into a neocortical microcircuit. We
developed two software programs for simulating such large-scale networks with
morphologically complex neurons. A new MPI version of NEURON has been adapted by
Michael Hines to run on Blue Gene. The second simulator uses the MPI messaging
component of the large-scale NeoCorticalSimu-lator (NCS), which was developed by Philip
Goodman, to manage the communication between NEURON-simulated neurons distributed
on different processors. The latter simulator will allow embedding of a detailed NCC model
into a simplified large-scale model of the whole brain. Both of these softwares have already
been tested, produce identical results and can simulate tens of thousands of morphologically
and electri-cally complex neurons (as many as 10,000 compartments per neuron with more
than a dozen Hodgkin-Huxley ion channels per compartment). Up to 10 neurons can be
mapped onto each processor to allow simulations of the NCC with as many as 100,000
neurons. Optimization of these algorithms could allow simulations to run at close to real
time. The circuit configuration is also read by a graphic application, which renders the entire
circuit in various levels of textured graphic formats. Real-time stereo visu-alization
applications are programmed to run on the terabyte SMP (shared memory processor) Extreme
series from SGI (Silicon Graphics, Inc.). The output from Blue Gene (any parameter of the
model) can be fed directly into the SGI system to perform in silico imaging of the activity of
the inner workings of the NCC. Eventually, the simulation of the NCC will also include the
vasculature, as well as the glial network, to allow capture of neuron-glia interactions.
Simulations of extracellular currents and field potentials, and the emergent
electroencephalogram (EEG) activity will also be modelled.

6.7 Whole Brain Simulation

The main limitations for digital computers in the simulation of biological processes are the
extreme temporal and spatial resolution demanded by some biological processes, and the
limitations of the algorithms that are used to model biological processes. If each atomic
collision is simulated, the most powerful super-computers still take days to simulate a

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microsecond of protein folding, so it is, of course, not possible to simulate complex


biological systems at the atomic scale. However, models at higher levels, such as the
molecular or cellular levels, can capture lower-level processes and allow complex large-scale
simulations of biological processes. The Blue Brain Project’s Blue Gene can simulate a NCC
of up to 100,000 highly complex neurons at the cellular or as many as 100 million simple
neurons (about the same number of neurons found in a mouse brain). However, simulating
neurons embedded in microcircuits, microcircuits embedded in brain regions, and brain
regions embedded in the whole brain as part of the process of understanding the emergence
of complex behaviors of animals is an inevitable progression in understanding brain function
and dysfunction, and the question is whether whole-brain simulations are at all possible.
Computational power needs to increase about 1-million-fold before we will be able to
simulate the human brain, with 100 billion neurons, at the same level of detail as the Blue
Column. Algorithmic and simulation efficiency (which ensure that all possible FLOPS are
exploited) could reduce this requirement by two to three orders of magnitude. Simulating the
NCC could also act as a test-bed to refine algorithms required to simulate brain function,
which can be used to produce field programmable gate array (FPGA)-based chips. FPGAs
could increase computational speeds by as much as two orders of magnitude. The FPGAs
could, in turn, provide the testing ground for the production of specialized NEURON solver
application-specific integrated circuits (ASICs) that could further increase computational
speed by another one to two orders of magnitude. It could therefore be possible, in principle,
to simulate the human brain even with current technology. The computer industry is facing
what is known as a discontinuity, with increasing processor speed leading to unacceptably
high power consumption and heat production. This is pushing a qualita-tively new transition
in the types of processor to be used in future computers. These advances in computing should
begin to make genetic- and molecular-level simulations possible. Software applications and
data manipulation required to model the brain with biological accuracy.

Experimental results that provide the elementary building blocks of the microcircuit are
stored in a database. Before three-dimensional neurons are modelled electrically, the
morphology is parsed for errors, and for repair of arboriza-tions damaged during slice
preparation. The morphological statistics for a class of neurons are used to clone multiple

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copies of neurons to generate the full morpho-logical diversity and the thousands of neurons
required in the simulation. A spectrum of ion channels is inserted, and conductances and
distributions are altered to fit the neurons electrical properties according to known statistical
distributions, to capture the range of electrical classes and the uniqueness of each neurons
behaviour (model fitting/electrical capture). A circuit builder is used to place neurons within
a three-dimensional column, to perform axo-dendritic collisions and, using structural and
functional statistics of synaptic connectivity, to convert a fraction of axo-dendritic touches
into synapses. The circuit configuration is read by NEURON, which calls up each modelled
neuron and inserts the several thousand synapses onto appropriate cellular locations. The
circuit can be inserted into a brain region using the brain builder. An environment builder is
used to set up the stimulus and recording conditions. Neurons are mapped onto processors,
with integer numbers of neurons per processor. The output is visualized, analysed and/or fed
into real-time algorithms

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Chapter 7

APPLICATIONS OF BLUE BRAIN

7.1 What can we learn from Blue Brain?

Detailed, biologically accurate brain simulations offer the opportunity to answer some
fundamental questions about the brain that cannot be addressed with any current
experimental or theoretical approaches. These include,

7.1.1 Defining functions of the basic elements

Despite a century of experimental and theoretical research, we are unable to provide a


comprehensive definition of the computational function of different ion channels, receptors,
neurons or synaptic pathways in the brain. A detailed model will allow fine control of any of
these elements and allow a systematic investigation of their contribution to the emergent
behaviour.

7.1.2 Understanding complexity

At present, detailed, accurate brain simulations are the only approach that could allow us to
explain why the brain needs to use many different ion channels, neurons and synapses, a
spectrum of receptors, and complex dendritic and axonal arborizations, rather than the
simplified, uniform types found in many models.

7.1.3 Exploring the role of dendrites.

This is the only current approach to explore the dendritic object theory, which proposes that
three-dimensional voltage objects are generated continuously across dendritic segments
regardless of the origin of the neurons, and that spikes are used to maintain such dendritic
objects.

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7.1.4 Revealing functional diversity

Most models engineer a specific function, whereas a spectrum of functions might be possible
with a biologically based design. Understanding memory storage and retrieval. This approach
offers the possibility of determining the manner in which representations of information are
imprinted in the circuit for storage and retrieval, and could reveal the part that different types
of neuron play in these crucial functions.

7.1.5 Tracking the emergence of intelligence

This approach offers the possibility to re-trace the steps taken by a network of neurons in the
emergence of electrical states used to embody representations of the organism and its world.

7.1.6 Identifying points of vulnerability

Although the neocortex confers immense computational power to mammals, defects are
common, with catastrophic cognitive effects. At present, a detailed model is the only
approach that could produce a list of the most vulnerable circuit parameters, revealing likely
candidates for dysfunction and targets for treatment.

7.1.7 Simulating disease and developing treatments

Such simulations could be used to test hypotheses for the pathogenesis of neurological
and psychiatric diseases, and to develop and test new treatment strategies.

7.1.8 Providing a circuit design platform

Detailed models could reveal powerful circuit designs that could be implemented into
silicone chips for use as intelligence devices in industry.

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7.2 Applications of Blue Brain

7.2.1 Gathering and Testing 100 Years of Data

The most immediate benefit is to provide a working model into which the past 100 years
knowledge about the microstructure and workings of the neocortical column can be gathered
and tested. The Blue Column will therefore also produce a virtual library to explore in 3D the
microarchitecture of the neocortex and access all key research relating to its structure and
function.

7.2.2 Cracking the Neural Code

The Neural Code refers to how the brain builds objects using electrical patterns. In the same
way that the neuron is the elementary cell for computing in the brain, the NCC is the
elementary network for computing in the neocortex. Creating an accurate replica of the NCC
which faithfully reproduces the emergent electrical dynamics of the real microcircuit, is an
absolute requirement to revealing how the neocortex processes, stores and retrieves
information.

7.2.3 Understanding Neocortical Information Processing

The power of an accurate simulation lies in the predictions that can be generated about the
neocortex. Indeed, iterations between simulations and exper-iments are essential to build an
accurate copy of the NCC. These iterations are therfore expected to reveal the function of
individual elements (neurons, synapses, ion channels, receptors), pathways (mono-synaptic,
disynaptic, multisynaptic loops) and physiological processes (functional properties, learning,
reward, goal-oreinted behavior).

7.2.4 A Novel Tool for Drug Discovery for Brain Disorders

Understanding the functions of different elements and pathways of the NCC will provide a
concrete foundation to explore the cellular and synaptic bases of a wide spectrum of

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neurological and psychiatric diseases. The impact of receptor, ion channel, cellular and
synaptic deficits could be tested in simulations and the optimal experiments.

7.2.5 A Global Facility

A software replica of a NCC will allow researchers to explore hypotheses of brain function
and dysfunction accelerating research. Simulation runs could determine which parameters
should be used and measured in the experiments. An advanced 2D, 3D and 3D immersive
visualization system will allow ―imaging‖ of many aspects of neural dynamics during
processing, storage and retrieval of information. Such imaging experiments may be
impossible in reality or may be prohibitively expensive to perform.

7.2.6 A Foundation for Whole Brain Simulations

With current and envisageable future computer technology it seems unlikely that a
mammalian brain can be simulated with full cellular and synaptic complexity (above the
molecular level). An accurate replica of an NCC is therefore required in order to generate
reduced models that retain critical functions and computational capa-bilities, which can be
duplicated and interconnected to form neocortical brain regions. Knowledge of the NCC
architecture can be transferred to facilitate reconstruction of subcortical brain regions.

7.2.7 A Foundation for Molecular Modeling of Brain Function

An accurate cellular replica of the neocortical column will provide the first and essential step
to a gradual increase in model complexity moving towards a molecular level description of
the neocortex with biochemical pathways being simulated. A molecular level model of the
NCC will provide the substrate for interfacing gene expression with the network structure
and function. The NCC lies at the interface between the genes and complex cognitive
functions. Establishing this link will allow predictions of the cognitive consequences of
genetic disorders and allow reverse engineering of cognitive deficits to determine the genetic
and molecular causes. This level of simulation will become a reality with the most advanced
phase of Blue Gene development.

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Chapter 8

ADVANTAGES AND LIMITATIONS

8.1 ADVANTAGES

 We can remember things without any effort.

 Decision can be made without the presence of a person.

 Even after the death of a man his intelligence can be used.

 The activity of different animals can be understood. That means by interpretation of the
electric impulses from the brain of the animals, their thinking can be understood easily.

 It would allow the deaf to hear via direct nerve stimulation, and also be helpful for many
psychological diseases. By down loading the contents of the brain that was uploaded into
the computer, the man can get rid from the madness.

8.2 LIMITATIONS

 Further, there are many new dangers these technologies will open. We will be
susceptible to new forms of harm.

 We become dependent upon the computer systems. Others may use technical
knowledge against us.

 Computer viruses will pose an increasingly critical threat.

 The real threat, however, is the fear that people will have of new technologies.

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 That fear may culminate in a large resistance. Clear evidence of this type of fear is
found today with respect to human cloning.

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Chapter 9

FUTURE PERSPECTIVES

The synthesis era in neuroscience started with the launch of the Human Brain Project and is
an inevitable phase triggered by a critical amount of fundamental data. The data set does not
need to be complete before such a phase can begin. Indeed, it is essential to guide
reductionist research into the deeper facets of brain structure and function. As a complement
to experimental research, it offers rapid assessment of the probable effect of a new finding on
preexisting knowledge, which can no longer be managed completely by any one researcher.
Detailed models will probably become the final form of databases that are used to organize
all knowledge of the brain and allow hypothesis testing, rapid diagnoses of brain malfunction,
as well as development of treatments for neurological disorders. In short, we can hope to
learn a great deal about brain function and disfunction from accurate models of the brain .The
time taken to build detailed models of the brain depends on the level of detail that is captured.
Indeed, the first version of the Blue Column, which has 10,000 neurons, has already been
built and simulated; it is the refinement of the detailed properties and calibration of the circuit
that takes time. A model of the entire brain at the cellular level will probably take the next
decade. There is no fundamental obstacle to modeling the brain and it is therefore likely that
we will have detailed models of mammalian brains, including that of man, in the near future.
Even if overestimated by a decade or two, this is still just a ’blink of an eye’ in relation to the
evolution of human civilization. As with Deep Blue, Blue Brain will allow us to challenge the
foundations of our understanding of intelligence and generate new theories of consciousness.

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Chapter 10

CONCLUSION

In conclusion, we will be able to transfer ourselves into computers at some point. Most
arguments against this outcome are seemingly easy to circumvent. They are either simple
minded, or simply require further time for technology to increase. It can be said that focusing
on preserving the original vision of reconstruction and simulation of the brain, this project
promises to have a profound impact on neuroscience, neuroinformatics, neurorobotics & high
performance computing. Although, it’s potential goes far beyond the limitations of
neurobiology and above mentioned fields as transforming whole human brain into a
computational machine that processes on multi scales is way beyond exceptional.
Understanding the natural brain’s biological functioning through a virtual brain will not only
make it easier for people with psychological disorders and other brain diseases but will also
benefit the other areas of science. And one of the important things to remember is to make
use of connectivity available to other scientists and also provide the infrastructure to enable
several applications mentioned. The only serious threats raised are also overcome as we note
the combination of biological and digital technologies.

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REFERENCES

1. ―Engineering in Medicine and Biology Society‖, 2008. EMBS 2008. 30th Annual
International Conference of the IEEE.

2. Henry Markram, ―The Blue Brain Project‖, Nature Reviews Neuroscience 2006
February.

3. Simulated brain closer to thought BBC News 22 April 2009.

4. http://bluebrain.epfl.ch/Jahia/site/bluebrain/op/edit/pid/19085

5. Graham-Rowe, Duncan. ―Mission to build a simulated brain begins‖, New Scientist,


June 2005. pp. 1879-85.

6. Blue Gene: http://www.research.ibm.com/bluegene.

7. The Blue Brain Project: http://bluebrainproject.epfl.ch

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