An interactive ppt based on the Blue Brain Project

1. CAN YOU THINK FROM
YOUR HEART?

2. THINKING?

3. STILL THINKING?

4. YES, YOU CAN THINK
FROM THE HEART OF
YOUR CNS

5. • Thinking has been one of the most
contrasting feature of humans to other
animals.
• It is mainly attributed to the brain that
humans posses.
• Human brain has millions of neurons
which acts as a circuit in maintaining
human thoughts and actions.

6. EVER THOUGHT OF
HOW A BRAIN CAN
BE BUILT UP?

7. IT HAS NOW BEEN PROVEN BY A
SWISS PROFESSOR “HENRY
MARKARM” WHERE HE IS TRYING TO
BUILD THE HUMAN BRAIN USING
CIRCUITS.

8. Presentation by
REJESH.B
NIRANJANA.J
III B. Sc
BIOTECHNOLOGY

9. It is an attempt to create a synthetic brain by
reverse engineering mammalian brain circuitry.
The aim of the project, founded in May 2005 by
Brain and Mind Institute of EPEL in Switzerland.
The end of the first phase was reported in Nov,2007
What???

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

11. • The goal of the Blue Brain Project is to build
biologically detailed digital reconstructions
and simulations of the rodent, and ultimately
the human brain.
• The supercomputer-based reconstructions and
simulations built by the project offer a
radically new approach for understanding the
multilevel structure and function of the brain.

12. Motivation:
Four broad motivations behind the Blue
Brain Project are:
• Brain disease treatments
• Scientific curiosity about consciousness and
the human mind
• Integration of all neuroscientific research
results worldwide
• Progress towards building thinking machines

13. • The living brain is very difficult to study both
from a technical perspective and a moral one.
• A virtual model, however, makes direct
observations possible.
• Experiments on models are also more efficient
and limit the need for laboratory animals.
• The Blue Brain Project, by including
molecular-level simulations, could be used to
study the effect of new pharmaceutical
compounds on virtual brains of any species,
age, and stage of disease.

14. IBM’s BLUE GENE:
• The primary machine used by the Blue Brain
Project is a Blue Gene supercomputer built
by IBM.
• This is where the name "Blue Brain"
originates from. IBM agreed in June 2005 to
supply EPFL with a Blue Gene/L as a
"technology demonstrator".
• The brain simulations generally run all day,
and one day per week (usually Thursdays).
The rest of the week is used to prepare
simulations and to analyze the resulting data.

15. Blue Gene technical specifications:
• 4,096 quad-core nodes (16,384 cores in total)
• Each core is a PowerPC 450, 850 MHz
• Total: 56 teraflops, 16 terabytes of memory
• 4 racks, one row, wired as a 16x16x16 3D
torus
• 1 PB of disk space, GPFS parallel file system
• Operating system: Linux SuSE SLES 10

17. There are three main steps to building the virtual
brain
 Data Acquisition
 Simulation
 visualisation of
results

18. 1. DATA Acquisition:
• Data acquisition involves taking brain slices,
placing them under a microscope, and
measuring the shape and electrical activity
of individual neurons.
• The neurons are typed by morphology,
electrophysiological behaviour, location
within the cortex, and their population
density.

19. • These observations are translated into
mathematical algorithms which describe
the form, function, and positioning of
neurons.
• The algorithms are then used to generate
biologically-realistic virtual neurons ready
for simulation.

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

22. • Around 200 different types of ion channel are
found in the cell membranes of cortical
neurons.
• Different types of neuron have different mixes of
channels - and this contributes to differences in
their electrical behaviour.
• The genes for these channels are cloned at the
lab, overexpressed in cultured cells, and their
electrical behaviour recorded.
• Over 270 genes are known to be associated with
voltage-gated ion channels in the rat.

23. 2. SIMULATION:
• The primary software used by the BBP for
neural simulations is a package called
NEURON.
• This was developed starting in the 1990s by
Michael Hines at Yale University and John
Moore at Duke University.
• It is written in C, C++, and FORTRAN. The
software continues to be under active
development

24. A screenshotof
NEURON

25. • Doubling the size of the neural network
doubles the time it takes to simulate.
• Currently the primary goal is biological
validity rather than performance.
• Once it's understood which factors are
biologically important for a given effect it
might be possible to trim components that
don't contribute in order to improve
performance.
• The simulation timestep for the numerical
integrations is 0.025 ms and the timestep for
writing the output to disk is 0.1 ms.

26. • The simulation step involves synthesising
virtual cells using the algorithms that were
found to describe real neurons.
• The algorithms and parameters are adjusted
for the age, species, and disease stage of the
animal being simulated.
• Every single protein is simulated, and there
are about a billion of these in one cell.

27. • First a network skeleton is built from all the
different kinds of synthesised neurons.
• Then the cells are connected together
according to the rules that have been found
experimentally.
• Finally the neurons are functionalised and the
simulation brought to life.
• The patterns of emergent behaviour are
viewed with visualisation software.

28. • A basic unit of the cerebral cortex is the
cortical column.
• Each column can be mapped to one
function, e.g. in rats one column is devoted
to each whisker.
• Every two weeks a column model is run.
• The simulations reproduce observations that
are seen in living neurons.
• Emergent properties are seen that require
larger and larger networks.
• The plan is to build a generalised simulation
tool, one that makes it easy to build circuits.

29. • There are also plans to couple the brain
simulations to avatars living in a virtual
environment, and eventually also to robots
interacting with the real world.
• The ultimate aim is to be able to understand
and reproduce human consciousness.

30. 3.VISUALISATION OF RESULT:
• RTNeuron is the primary application used by
the BBP for visualisation of neural
simulations.
• The software was developed internally by the
BBP team. It is written in C++ and OpenGL.
• RTNeuron is ad-hoc software written
specifically for neural simulations, i.e. it is
not generalizable to other types of simulation

31. • RTNeuron takes the output from Hodgkin-
Huxley simulations in NEURON and renders
them in 3D.
• This allows researchers to watch as activation
potentials propogate through a neuron and
between neurons.
• The animations can be stopped, started and
zoomed, thus letting researchers interact with
the model.
• The visualisations are multi-scale, that is they
can render individual neurons or a whole
cortical column.

32. JuQUEEN:
• JuQUEEN is an IBM Blue Gene supercomputer
that was installed at the Jülich Research Center
in Germany in May 2012.
• It currently performs at 1.6 petaflops and was
ranked the world's 8th fastest supercomputer in
June 2012.
• The JuQUEEN machine is also to be used by the
Ju Brain (Jülich Brain Model) research
initiative.
• This aims to develop a three-dimensional,
realistic model of the human brain.

34. DEEP - Dynamical Exascale Entry Platform:
• DEEP (deep-project.eu) is an exascale
supercomputer built at the Jülich Research
Center in Germany.
• The project started in December 2011 and is
funded by the European Union's 7th
framework programme.
• The Blue Brain Project simulations will be
ported to the DEEP prototype to help test the
system's performance.

35. • If successful, a future exascale version of this
machine could provide the 1 exaflops of
performance required for a complete human
brain simulation by the 2020s.

36. AT PRESENT:
•Blue brain project releases open source software
providing model parameter optimization for
neuro scientist.
•Allen brain institute collaborates with BBP to
modal neurons from mouse visual cortex.
•The BBP has announced the opening of the
neocortical microcircuit collaboration portal.
finally a cellular human brain is predicted
possible by 2023- equivalent to 100 rat brain with
a total of a hundred billion cells.

37. REFERENCE:
• http://www.artificialbrains.com/blue-brain-
project
• https://en.wikipedia.org/wiki/Blue_Brain_Proje
ct
• https://en.wikipedia.org/wiki/Henry_Markram
• https://en.wikipedia.org/wiki/Brain_simulation
• http://bluebrain.epfl.ch/