Bluebrain.doc

A TECHNICAL SEMINAR REPORT
ON
BLUE BRAIN
Submitted by
ARUN.R.NAIR
(2220213101)
in partial fulfilment for the award of the degree
of
MASTER OF TECHNOLOGY
In
COMPUTER SCIENCE & TECHNOLOGY
GITAM UNIVERSITY
(Declared as Deemed to be University u/S 3 of UGC Act, 1956)
HYDERABAD CAMPUS
2013-2014

GITAM UNIVERSITY
(Declared as Deemed to be University u/S 3 of UGC Act,
1956)
HYDERABAD CAMPUS
DEPARTMENT OF COMPUTER SCIENCE
BONAFIDE CERTIFICATE
Certified that this seminar report titled “Blue Brain” is the
bonafide work done by Arun.R.Nair who carried out the work under my
supervision.
SEMINAR INCHARGE HEAD OF THE DEPARTMENT
SHANTHI.M M.TECH. (PHD) Dr.S.PHANI KUMAR M.TECH.PH.D
INTERNAL EXAMINER

ACKNOWLEDGMENT
The elation and gratification of this seminar will be incomplete without
mentioning all the people who helped me to make it possible, whose gratitude and
encouragement were invaluable to me.
Firstly, I would like to thank GOD, almighty, our supreme guide, for
bestowing his blessings upon me in my entire endeavour. I express my sincere
gratitude to Dr.S.Phani Kumar, Head of Department for his support and guidance.
I also like to thank Mrs.M.Shanthi (Assistant Professor) for her valuable
words of advice.
I am also thankful to all the other lecturers in our department and students of
my class for their support and suggestions.
ARUN.R.NAIR
i

ABSTRACT
Today scientists are in research to create an artificial brain that can think,
respond, 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 a person we will not lose the knowledge, intelligence, personalities, feelings
and memories of man, that can be used for the development of the human society.
Technology is growing faster than everything. 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. IBM, in partnership with scientists at Switzerland’s Ecole Poly Technique
Federale de Lausanne’s (EPFL) Brain and Mind Institute will begin simulating the
brain’s biological systems and output the data as a working 3-dimensional model that
will recreate the high-speed electro-chemical interactions that take place within the
brain’s interior. These include cognitive functions such as language, learning,
perception and memory in addition to brain malfunction such as psychiatric disorders
like depression and autism. From there, the modelling will expand to other regions of
the brain and, if successful, shed light on the relationships between genetic,
molecular and cognitive functions of the brain.
ii

TABLE OF CONTENTS
Abstract Ii
List of Figures V
CHAPTER 1. INTRODUCTION 1
1.1 Blue Brain . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.2 What is Virtual Brain? . . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.3 Why we need Virtual Brain? . . . . . . . . . . . . . . . . . . . . . . . 2
1.4 How it is possible? . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
CHAPTER 2. WORKING OF NATURAL BRAIN 5
2.1 Getting to know more about Human Brain . . . . . . . . . . . . . . . 5
2.1.1 Sensory Input . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
2.1.2 Integration . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
2.1.3 Motor Output . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
2.2 How we see, hear, feel, & smell? . . . . . . . . . . . . . . . . . . . . 7
2.2.1 Nose . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
2.2.2 Eye . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
2.2.3 Tongue . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
2.2.4 Ear . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
CHAPTER 3. BRAIN SIMULATION 9
CHAPTER 4. HOW THE BLUE BRAIN PROJECT WILL WORK? 11
4.1 Goals & Objectives . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
4.2 Architecture of Blue Gene . . . . . . . . . . . . . . . . . . . . . . . . 11
4.3 Modelling the Microcircuit . . . . . . . . . . . . . . . . . . . . . . . 13
4.4 Simulating the Microcircuit . . . . . . . . . . . . . . . . . . . . . . . 17
4.5 Interpreting the Results . . . . . . . . . . . . . . . . . . . . . . . . . 18
4.6 Data Manipulation Cascade . . . . . . . . . . . . . . . . . . . . . . . 19

4.7 Whole Brain Simulations . . . . . . . . . . . . . . . . . . . . . . . . 23
CHAPTER 5. APPLICATIONS OF BLUE BRAIN PROJECT 26
5.1 What can we learn from Blue Brain? . . . . . . . . . . . . . . . . . . 26
5.1.1 Defining functions of the basic elements . . . . . . . . . . . . 26
5.1.2 Understanding complexity . . . . . . . . . . . . . . . . . . . . 26
5.1.3 Exploring the role of dendrites. . . . . . . . . . . . . . . . . . 27
5.1.4 Revealing functional diversity . . . . . . . . . . . . . . . . . . 27
5.1.5 Tracking the emergence of intelligence . . . . . . . . . . . . . 27
5.1.6 Identifying points of vulnerability . . . . . . . . . . . . . . . . 27
5.1.7 Simulating disease and developing treatments . . . . . . . . . . 28
5.1.8 Providing a circuit design platform . . . . . . . . . . . . . . . 28
5.2 Applications of Blue Brain . . . . . . . . . . . . . . . . . . . . . . . 28
5.2.1 Gathering and Testing 100 Years of Data . . . . . . . . . . . . 28
5.2.2 Cracking the Neural Code . . . . . . . . . . . . . . . . . . . . 28
5.2.3 Understanding Neocortical Information Processing . . . . . . . 29
5.2.4 A Novel Tool for Drug Discovery for Brain Disorders . . . . . 29
5.2.5 A Global Facility . . . . . . . . . . . . . . . . . . . . . . . . . 29
5.2.6 A Foundation for Whole Brain Simulations . . . . . . . . . . . 30
5.2.7 A Foundation for Molecular Modelling of Brain Function . . . 30
CHAPTER 6. ADVANTAGES AND LIMITATIONS 31
6.1 Advantages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
6.2 Limitations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
CHAPTER 7. FUTURE PERSPECTIVE 33
CHAPTER 8. CONCLUSION 35
REFERENCES 36

LIST OF FIGURES
2.1 Medial view of the left hemisphere of human brain. . . . . . . . . . . 6
4.1 The Blue Gene/L supercomputer architecture . . . . . . . . . . . . . 13
4.2 Elementary building blocks of neural microcircuits. . . . . . . . . . . 14
4.3 Reconstructing the neocortical column. . . . . . . . . . . . . . . . . 17
4.4 The data manipulation cascade . . . . . . . . . . . . . . . . . . . . . 24

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 up load the contents of natural brain into it?
1.1 Blue Brain
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 a person we will not lose 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 whatever man has created
today always he has followed the nature.
1

When man does not have a device called computer, it was a big question for
all. Technology is growing faster than everything. 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. Within 30 years, we will be able to scan ourselves into the computers. Is
this the beginning of eternal life?
1.2 What is Virtual Brain?
Virtual brain is an artificial brain, which does not actually the natural brain,
but can act as the 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.
1.3 Why we need Virtual 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 always is in
need of such intelligence and such an intelligent brain to have with.
2

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?
1.4 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 noninvasive 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. Traveling 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.
3

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 possess a soul, while
some very technical people believe that quantum forces contribute to our awareness.
But we have to now think technically. 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.
4

CHAPTER 2
WORKING OF NATURAL BRAIN
2.1 Getting to know more about Human Brain
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, sub thalamus,
midbrain, pons, medulla oblongata and 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 world’s most “intricately organized” electron mechanisms is the nervous
system.
5

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.
Fig. 2.1. Medial view of the left hemisphere of human brain.
2.1.1 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 action of
getting information from your surrounding environment is called sensory input because
we are putting things in your brain by way of your senses.
2.1.2 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.
6

This process is all accomplished in the brain where many, many neurons work
together to understand the environment.
2.1.3 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.
2.2 How we see, hear, feel, & smell?
2.2.1 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.
2.2.2 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.
7

2.2.3 Tongue
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 fibre. 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.
2.2.4 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
interpretation and memory.
8

CHAPTER 3
BRAIN SIMULATION
A comparative discussion of Natural Brain and Simulated Brain is given below.
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
passing. The body receives the input has already created artificial neurons by
by the sensory cells. These sensory replacing them with the silicon chip. It
cells produces electric impulses which are has also been tested that these neurons
received by the neurons. The neurons can receive the input from the sensory
transfer these electric impulses to the cells. So, the electric impulses from
brain. the sensory cells can be received through
these artificial neurons and send to a super
computer for the interpretation.
2. INTERPRETATION 2. INTERPRETATION
The electric impulses received by the The interpretation of the electric impulses
brain from the neurons are interpreted in received by the artificial neuron can be
the brain. The interpretation in the brain done by means of a set of register. The
is accomplished by the means of certain different values in these register will
states of many neurons. represent different states of the brain.
3. OUTPUT 3. OUTPUT
Based on the states of the neurons the Similarly based on the states of the
brain sends the electric impulses repre- register the output signal can be given to
senting the responses which are further the artificial neurons in the body which
received by the sensory cell of our body will be received by the sensory cell.
to respond. The sensory cells of which
part of our body is going to receive that, it
depends upon the state of the neurons in
the brain at that time.
9

10
NATURAL BRAIN SIMULATED BRAIN
4. MEMORY. 4. MEMORY
There are certain neurons in our brain It is not impossible to store the data
which represent certain states perma- permanently by using the secondary
nently. When required these state is inter- memory. In the similar way the required
preted by our brain and we can remember states of the registers can be stored perma-
the past things. To remember thing we nently. And when required these infor-
force the neurons to represent certain mation can be retrieved and used.
states of the brain permanently or 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 circuitry. The past performing some arithmetic and logical
experience stored and the current input calculations.
received are used and the states of certain
neurons are changed to give the output.

CHAPTER 4
HOW THE BLUE BRAIN PROJECT WILL WORK?
4.1 Goals & Objectives
The Blue 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.
4.2 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.
11

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.
12

Fig. 4.1. The Blue Gene/L supercomputer architecture
4.3 Modelling the Microcircuit
The scheme shows the minimal essential building blocks required to recon-
struct 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 arborization 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.
13

Fig. 4.2. Elementary building blocks of neural microcircuits.
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 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.
14

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.
15

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 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.
16

Fig. 4.3. Reconstructing the neocortical column.
4.4 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. As the
electrical impulse travels from neuron to neuron, the results are communicated via
inter- processor communication (MPI). Currently, the time required to simulate the
circuit is about two orders of magnitude larger than the actual biological time
simulated.
17

The Blue Brain team is working to streamline the computation so that the circuit can
function in real time - meaning that 1 second of activity can be modelled in one
second.
4.5 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 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.
18

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.
4.6 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 electrical diversity. A
database of biologically accurate Hodgkin-Huxley ion channel models is being
produced.
19

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 three-
dimensional morphology of each neuron.
20

The synapses are functionalized according to the synaptic parameters for
different classes of synaptic connection within statistical variations 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 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 Neocortical Simulator (NCS), which was developed by Philip Goodman,
to manage the communication between NEURON-simulated neurons distributed on
different processors.
21

The latter simulator will allow embedding of a detailed NCC model into a
simplified large-scale model of the whole brain. Both of these software’s have
already been tested, produce identical results and can simulate tens of thousands of
morphologically and electrically 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 visualization 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.
22

4.7 Whole Brain Simulations
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 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.
23

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
Fig. 4.4. The data manipulation cascade
24

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
arborisations damaged during slice preparation.
The morphological statistics for a class of neurons are used to clone multiple copies
of neurons to generate the full morphological diversity and the thousands of neurons
required in the simulation. A spectrum of ion channels is inserted, and conductance
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 for feedback
stimulation.
25

CHAPTER 5
APPLICATIONS OF BLUE BRAIN PROJECT
5.1 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,
5.1.1 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.
5.1.2 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.
26

5.1.3 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.
5.1.4 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.
5.1.5 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.
5.1.6 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.
27

5.1.7 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.
5.1.8 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.
5.2 Applications of Blue Brain
5.2.1 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.
5.2.2 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.
28

5.2.3 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
experiments are essential to build an accurate copy of the NCC. These iterations are
therefore expected to reveal the function of individual elements (neurons, synapses,
ion channels, and receptors), pathways (mono-synaptic, disynaptic, multisynaptic
loops) and physiological processes (functional properties, learning, reward, goal-
oriented behaviour).
5.2.4 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 neurological and psychiatric diseases. The impact of receptor, ion
channel, cellular and synaptic deficits could be tested in simulations and the optimal
experimental tests can be determined.
5.2.5 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.
29

5.2.6 A Foundation for Whole Brain Simulations
With current and envisage able 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
capabilities, 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.
5.2.7 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.
30

CHAPTER 6
ADVANTAGES AND LIMITATIONS
6.1 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.
6.2 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.
31

The real threat, however, is the fear that people will have of new technologies.
That fear may culminate in a large resistance. Clear evidence of this type of fear
is found today with respect to human cloning.
32

CHAPTER 7
FUTURE PERSPECTIVE
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 pre-existing 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 dysfunction 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.
33

A model of the entire brain at the cellular level will probably take the next
decade. There is no fundamental obstacle to modelling 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.
34

CHAPTER 8
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.
The only serious threats raised are also overcome as we note the combination of
biological and digital technologies.
35

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] “Project Milestones”. Blue Brain.
http://bluebrain.epfl.ch/Jahia/site/bluebrain/op/edit/pid/19085
[5] Graham-Rowe, Duncan. “Mission to build a simulated brain
begins”, NewSci-entist, June 2005. pp. 1879-85.
[6] Blue Gene: http://www.research.ibm.com/bluegene
[7] The Blue Brain Project: http://bluebrainproject.epfl.ch
36

Bluebrain.doc

More Related Content

What's hot (20)

Viewers also liked (20)

Similar to Bluebrain.doc (20)

Recently uploaded (20)

Bluebrain.doc