Blue brain doc

SEMINAR REPORT

ON

BLUE-BRAIN

Submitted By

PREJITH S.
Roll No: 73
S7 AE&I

Department of Applied Electronics & Instrumentation Engineering
GOVERNMENT ENGINEERING COLLEGE
KOZHIKODE-673 005

December 2010

ACKNOWLEDGMENTS

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.C.Sathish Kumar, Head of Department for his support and guidance.

I also like to thank Mrs.Sangeetha (Asst Professor), Mrs.G.Sreelatha
(Sr.lecturer), Mrs.Shanthini K.S. (lecturer) and Mrs.Agnes Jacob (lecturer) for their
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.

PREJITH S.

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 loose the knowledge, intelligence, personalities, feelings
and memories of that man, that can be used for the development of the human society.
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. IBM, in partnership with scientists at Switzerland’s Ecole Polytech-
nique 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 modeling 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

Acknowledgments i

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? . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2

CHAPTER 2. WORKING OF NATURAL BRAIN 4
2.1 Getting to know more about Human Brain . . . . . . . . . . . . . . . 4
2.1.1 Sensory Input . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
2.1.2 Integration . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
2.1.3 Motor Output . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
2.2 How we see, hear, feel, & smell? . . . . . . . . . . . . . . . . . . . . 6
2.2.1 Nose . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
2.2.2 Eye . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
2.2.3 Tongue . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
2.2.4 Ear . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

CHAPTER 3. BRAIN SIMULATION 7

CHAPTER 4. HOW THE BLUE BRAIN PROJECT WILL WORK? 9
4.1 Goals & Objectives . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
4.2 Architecture of Blue Gene . . . . . . . . . . . . . . . . . . . . . . . . 9
4.3 Modelling the Microcircuit . . . . . . . . . . . . . . . . . . . . . . . 10
4.4 Simulating the Microcircuit . . . . . . . . . . . . . . . . . . . . . . . 13
4.5 Interpreting the Results . . . . . . . . . . . . . . . . . . . . . . . . . 14
4.6 Data Manipulation Cascade . . . . . . . . . . . . . . . . . . . . . . . 15
4.7 Whole Brain Simulations . . . . . . . . . . . . . . . . . . . . . . . . 17

iii

CHAPTER 5. APPLICATIONS OF BLUE BRAIN PROJECT 20
5.1 What can we learn from Blue Brain? . . . . . . . . . . . . . . . . . . 20
5.1.1 Deﬁning functions of the basic elements . . . . . . . . . . . . 20
5.1.2 Understanding complexity . . . . . . . . . . . . . . . . . . . . 20
5.1.3 Exploring the role of dendrites. . . . . . . . . . . . . . . . . . 20
5.1.4 Revealing functional diversity . . . . . . . . . . . . . . . . . . 21
5.1.5 Tracking the emergence of intelligence . . . . . . . . . . . . . 21
5.1.6 Identifying points of vulnerability . . . . . . . . . . . . . . . . 21
5.1.7 Simulating disease and developing treatments . . . . . . . . . . 21
5.1.8 Providing a circuit design platform . . . . . . . . . . . . . . . 21
5.2 Applications of Blue Brain . . . . . . . . . . . . . . . . . . . . . . . 22
5.2.1 Gathering and Testing 100 Years of Data . . . . . . . . . . . . 22
5.2.2 Cracking the Neural Code . . . . . . . . . . . . . . . . . . . . 22
5.2.3 Understanding Neocortical Information Processing . . . . . . . 22
5.2.4 A Novel Tool for Drug Discovery for Brain Disorders . . . . . 22
5.2.5 A Global Facility . . . . . . . . . . . . . . . . . . . . . . . . . 23
5.2.6 A Foundation for Whole Brain Simulations . . . . . . . . . . . 23
5.2.7 A Foundation for Molecular Modeling of Brain Function . . . . 23

CHAPTER 6. ADVANTAGES AND LIMITATIONS 24
6.1 Advantages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
6.2 Limitations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24

CHAPTER 7. FUTURE PERSPECTIVE 25

CHAPTER 8. CONCLUSION 26

References 27

iv

LIST OF FIGURES

2.1 Medial view of the left hemisphere of human brain. . . . . . . . . . . 5

4.1 The Blue Gene/L supercomputer architecture . . . . . . . . . . . . . 10
4.2 Elementary building blocks of neural microcircuits. . . . . . . . . . . 11
4.3 Reconstructing the neocortical column. . . . . . . . . . . . . . . . . 13
4.4 The data manipulation cascade . . . . . . . . . . . . . . . . . . . . . 18

v

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 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?

1

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 can not be created. Some people have this quality, so that they can think
up to such an extent where other can not 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 intelli-
gence 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.

2

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. 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.

3

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, 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.

4

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. 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.

5

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.

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 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.

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 interpre-
tation and memory.

6

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 o f the neurons in
the brain at that time.

7

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.

8

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. Biologi-
cally 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. 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

9

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.

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

10

Fig. 4.2. Elementary building blocks of neural microcircuits.

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. 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. 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-

11

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 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

12

Fig. 4.3. Reconstructing the neocortical column.

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.

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 elec-
trical impulse travels from neuron to neuron, the results are communicated via inter-

13

processor communication (MPI). Currently, the time required to simulate the circuit

is about two orders of magnitude larger than the actual biological time simulated.

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 modeled 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. 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

14

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. 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

15

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 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 Simu-
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

16

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.

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

17

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

Fig. 4.4. The data manipulation cascade

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 copies of neurons to generate the full morpho-
logical diversity and the thousands of neurons required in the simulation. A spectrum

18

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 for feedback
stimulation.

19

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.

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.

20

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.

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 imple-
mented into silicone chips for use as intelligence devices in industry.

21

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.

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 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).

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 experi-

22

mental 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.

5.2.6 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.

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 engi-
neering 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 devel-
opment.

23

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 interpre-
tation 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.

• 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.

24

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 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.

25

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.

26

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

27

Blue brain doc

More Related Content

What's hot (20)

Viewers also liked (20)

Similar to Blue brain doc (20)

Recently uploaded (20)

Blue brain doc