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{{Short description|Creating a computer model of all or part of a brain}}
{{update|date=January 2018}}
{{Use dmy dates|date=November 2023}}
'''Brain simulation''' is the concept of creating a functioning [[Computer simulation|computer model]] of a brain or part of a brain.<ref>{{Cite journal|last1=Fan|first1=Xue|last2=Markram|first2=Henry|date=2019|title=A Brief History of Simulation Neuroscience|journal=Frontiers in Neuroinformatics|language=English|volume=13|page=32|doi=10.3389/fninf.2019.00032|pmid=31133838|pmc=6513977|issn=1662-5196|doi-access=free}}</ref> Modelling a brain (or brain subsystem) involves both modelling neurons' electrical and bulk chemical properties (e.g. extracellular [[serotonin]] gradients). A model of the neural [[connectome]] of the target organism is also required. The connectome is extremely complex, and its detailed wiring is not yet understood; thus it is presently being modeled empirically in smaller mammals by projects like the [[Blue Brain Project]].
In the field of [[computational neuroscience]], '''brain simulation''' is the concept of creating a functioning [[Computer simulation|computer model]] of a brain or part of a brain.<ref>{{cite journal |last1=Fan |first1=Xue |last2=Markram |first2=Henry |title=A Brief History of Simulation Neuroscience |journal=Frontiers in Neuroinformatics |date=7 May 2019 |volume=13 |page=32 |doi=10.3389/fninf.2019.00032 |pmid=31133838 |pmc=6513977 |doi-access=free }}</ref> Brain simulation projects intend to contribute to a complete understanding of the brain, and eventually also assist the process of treating and diagnosing [[brain disease]]s.<ref>{{Cite news|title=Neuroinformatics and The Blue Brain Project|work=Informatics from Technology Networks|url=https://www.technologynetworks.com/informatics/articles/neuroinformatics-and-the-blue-brain-project-part-1-295850|access-date=2018-01-30}}</ref><ref>{{cite journal |last1=Colombo |first1=Matteo |title=Why build a virtual brain? Large-scale neural simulations as jump start for cognitive computing |journal=Journal of Experimental & Theoretical Artificial Intelligence |date=4 March 2017 |volume=29 |issue=2 |pages=361–370 |doi=10.1080/0952813X.2016.1148076 |bibcode=2017JETAI..29..361C |s2cid=205634599 |doi-access=free }}</ref> Simulations utilize [[Biological neuron model|mathematical models of biological neurons]], such as the [[Hodgkin–Huxley model|hodgkin-huxley model]], to simulate the behavior of [[neurons]], or other cells within the brain.


The Blue Brain Project intends to create a computer simulation of a mammalian [[cortical column]] down to the molecular level.<ref name=":1" /> By one estimate, a full reconstruction of the human connectome using the methodology of the Blue Brain Project would require a [[zettabyte]] of data storage.<!-- [[The Brain with David Eagleman]] (2015) has a principal researcher in a Swiss lab face the camera and say this; this surely rivals CERN or LIGO or a complete Hubble-resolution astronomical map --> In 2013, [[Human Brain Project]] created a Brain Simulation Platform (BSP), which is an internet-accessible collaborative platform designed for the simulation of brain models. The Human Brain Project has utilized techniques used by the Blue Brain Project and built upon them.<ref name=":0">Human Brain Project, Framework Partnership Agreement https://www.humanbrainproject.eu/documents/10180/538356/FPA++Annex+1+Part+B/41c4da2e-0e69-4295-8e98-3484677d661f {{Webarchive|url=https://web.archive.org/web/20170202001252/https://www.humanbrainproject.eu/documents/10180/538356/FPA++Annex+1+Part+B/41c4da2e-0e69-4295-8e98-3484677d661f |date=2017-02-02 }}</ref>
Various simulations from around the world have been fully or partially released as [[open source|open source software]], such as [[Caenorhabditis elegans|C. elegans]],<ref name="C. elegans on GitHub">[https://github.com/Flowx08/Celegans-simulation C. Elegans simulation], Open source software project at Github</ref> and the Blue Brain Project Showcase.<ref name=":3">{{cite web|url=http://opensourcebrain.org/projects/blue-brain-project-showcase|website=Open Source Brain|title=Overview - Blue Brain Project Showcase - Open Source Brain|accessdate=May 5, 2020|archive-date=November 26, 2020|archive-url=https://web.archive.org/web/20201126013330/https://www.opensourcebrain.org/projects/blue-brain-project-showcase/|url-status=dead}}</ref> In 2013 the [[Human Brain Project]], which has utilized techniques used by the Blue Brain Project and built upon them,<ref name=":0">Human Brain Project, Framework Partnership Agreement https://www.humanbrainproject.eu/documents/10180/538356/FPA++Annex+1+Part+B/41c4da2e-0e69-4295-8e98-3484677d661f {{Webarchive|url=https://web.archive.org/web/20170202001252/https://www.humanbrainproject.eu/documents/10180/538356/FPA++Annex+1+Part+B/41c4da2e-0e69-4295-8e98-3484677d661f |date=2017-02-02 }}</ref> created a Brain Simulation Platform (BSP), an internet-accessible [[Open collaboration|collaborative platform]] designed for the simulation of brain models.


Brain simulations can be done at varying levels of detail, with more detail requiring significantly higher computation capabilities. Some simulations may only consider the behaviour of areas without modeling individual neurons. Other simulations model the behaviour of individual neurons, the strength of the connections between neurons and how these connections change.<ref>{{Cite web |last=Fan |first=Shelly |date=2019-05-30 |title=The Crucial Role of Brain Simulation in Future Neuroscience |url=https://singularityhub.com/2019/05/30/the-crucial-role-of-brain-simulation-in-future-neuroscience/ |access-date=2024-03-29 |website=Singularity Hub |language=en-US}}</ref> This requires having a map of the target organism neurons and their connections, called a [[connectome]].<ref>{{Cite web |last=Seung |first=Sebastian |title=Another Perspective on Massive Brain Simulations |url=https://www.scientificamerican.com/article/massive-brain-simulators-seung-conntectome/ |access-date=2024-03-29 |website=Scientific American |language=en}}</ref> Highly detailed simulations may precisely model the [[Electrophysiological|electrophysiology]] of each individual neuron, potentially even their [[metabolome]] and [[proteome]], and the state of their [[Protein complex|protein complexes]].<ref name=":5">{{Cite web |last1=Sandberg |first1=Anders |last2=Bostrom |first2=Nick |date=2008 |title=Whole Brain Emulation: A Roadmap |url=https://www.fhi.ox.ac.uk/brain-emulation-roadmap-report.pdf}}</ref>
Brain simulation projects intend to contribute to a complete understanding of the brain, and eventually assist the process of treating and diagnosing [[brain disease]]s.<ref>{{Cite news|url=https://www.technologynetworks.com/informatics/articles/neuroinformatics-and-the-blue-brain-project-part-1-295850|title=Neuroinformatics and The Blue Brain Project|work=Informatics from Technology Networks|access-date=2018-01-30}}</ref><ref>Colombo, M. (2017). Why Build a Virtual Brain? Large-Scale Neural Simulations as Jump Start for Cognitive Computing. Journal of Experimental & Theoretical Artificial Intelligence, 29, 361-370. doi: https://doi.org/10.1080/0952813X.2016.1148076</ref>


== Case studies ==
==Caenorhabditis elegans (roundworm)==
Over time, brain simulation research has focused on increasingly complex organisms, starting with primitive organisms like the nematode [[C. elegans]] and progressing towards simulations of human brains.

===Roundworm===
[[File:C.elegans-brain-network.jpg|thumb|right|[[Brain mapping|Brain map]] of the [[Caenorhabditis elegans|C. elegans]] roundworm 302 neurons, interconnected by 5000 synapses]]
[[File:C.elegans-brain-network.jpg|thumb|right|[[Brain mapping|Brain map]] of the [[Caenorhabditis elegans|C. elegans]] roundworm 302 neurons, interconnected by 5000 synapses]]
The connectivity of the neural circuit for touch sensitivity of the simple [[Caenorhabditis elegans|C. elegans]] nematode (roundworm) was mapped in 1985<ref>{{cite journal |display-authors=5|author=Chalfie M|author2=Sulston JE|author3=White JG|author4=Southgate E |authorlink4=Eileen Southgate |author5=Thomson JN|author6=Brenner S |title=The neural circuit for touch sensitivity in Caenorhabditis elegans |journal=The Journal of Neuroscience |volume=5 |issue=4 |pages=956–64 |date=April 1985 |doi=10.1523/JNEUROSCI.05-04-00956.1985|pmid=3981252 |pmc=6565008|url=http://www.jneurosci.org/cgi/pmidlookup?view=long&pmid=3981252}}</ref> and partly simulated in 1993.<ref>{{cite journal |author=Niebur E|author2=Erdös P |title=Theory of the locomotion of nematodes: control of the somatic motor neurons by interneurons |journal=Mathematical Biosciences |volume=118 |issue=1 |pages=51–82 |date=November 1993 |pmid=8260760 |doi=10.1016/0025-5564(93)90033-7}}</ref> Since 2004, many software simulations of the complete neural and muscular system have been developed, including simulation of the worm's physical environment. Some of these models including [[source code]] have been made available for download.<ref>{{cite conference |last1=Bryden |first1=J. |last2=Cohen |first2=N. |date=2004 |title=A simulation model of the locomotion controllers for the nematodode Caenorhabditis elegans |display-editors=4 |editor1-last=Schaal |editor1-first=S. |editor2-last=Ijspeert |editor2-first=A. |editor3-last=Billard |editor3-first=A. |editor4-last=Vijayakumar |editor4-first=S. |editor5-last=Hallam |editor5-first=J. |editor6-last=Meyer |editor6-first=J.-A. |conference=From Animals to Animats 8: Proceedings of the eighth international conference on the Simulation of Adaptive Behaviour |pages=183–92 |url=http://eprints.whiterose.ac.uk/7961/}}</ref><ref name="C. elegans on GitHub">[https://github.com/Flowx08/Celegans-simulation C. Elegans simulation], Open source software project at Github</ref> However, there is still a lack of understanding of how the neurons and the connections between them generate the surprisingly complex range of behaviors that are observed in the relatively simple organism.<ref>[http://itee.uq.edu.au/~markw/celegans/ Mark Wakabayashi] {{webarchive |url=https://web.archive.org/web/20130512215753/http://itee.uq.edu.au/~markw/celegans/ |date=May 12, 2013 }}, with links to MuCoW simulation software, a demo video and the doctoral thesis Computational Plausibility of Stretch Receptors as the Basis for Motor Control in ''C. elegans'', 2006.</ref><ref>{{Cite book | last1 = Mailler | first1 = R. | last2 = Avery | first2 = J. | last3 = Graves | first3 = J. | last4 = Willy | first4 = N. | chapter = A Biologically Accurate 3D Model of the Locomotion of Caenorhabditis Elegans | doi = 10.1109/BioSciencesWorld.2010.18 | title = 2010 International Conference on Biosciences | pages = 84–90 | date = 7–13 March 2010| isbn = 978-1-4244-5929-2 | s2cid = 10341946 | url = http://www.personal.utulsa.edu/~roger-mailler/publications/BIOSYSCOM2010.pdf}}</ref> This contrast between the apparent simplicity of how the mapped neurons interact with their neighbours, and exceeding complexity of the overall brain function, is an example of an [[Emergence|emergent property]]. <ref>{{Cite news|url=https://phys.org/news/2013-08-complex-behavior-spontaneously-emerge-brain.html|title=How does complex behavior spontaneously emerge in the brain?|access-date=2018-02-27}}</ref> This kind of emergent property is paralleled within [[Artificial neural network|artificial neural networks]], the neurons of which are exceedingly simple compared to their often complex, abstract outputs.
The connectivity of the neural circuit for touch sensitivity of the simple [[Caenorhabditis elegans|C. elegans]] nematode (roundworm) was mapped in 1985<ref>{{cite journal |display-authors=5|author=Chalfie M|author2=Sulston JE|author3=White JG|author4=Southgate E |authorlink4=Eileen Southgate |author5=Thomson JN|author6=Brenner S |title=The neural circuit for touch sensitivity in Caenorhabditis elegans |journal=The Journal of Neuroscience |volume=5 |issue=4 |pages=956–64 |date=April 1985 |doi=10.1523/JNEUROSCI.05-04-00956.1985|pmid=3981252 |pmc=6565008|url=}}</ref> and partly simulated in 1993.<ref>{{cite journal |author=Niebur E|author2=Erdös P |title=Theory of the locomotion of nematodes: control of the somatic motor neurons by interneurons |journal=Mathematical Biosciences |volume=118 |issue=1 |pages=51–82 |date=November 1993 |pmid=8260760 |doi=10.1016/0025-5564(93)90033-7}}</ref> Since 2004, many software simulations of the complete neural and muscular system have been developed, including simulation of the worm's physical environment. Some of these models including [[source code]] have been made available for download.<ref>{{cite conference |last1=Bryden |first1=J. |last2=Cohen |first2=N. |date=2004 |title=A simulation model of the locomotion controllers for the nematodode Caenorhabditis elegans |display-editors=4 |editor1-last=Schaal |editor1-first=S. |editor2-last=Ijspeert |editor2-first=A. |editor3-last=Billard |editor3-first=A. |editor4-last=Vijayakumar |editor4-first=S. |editor5-last=Hallam |editor5-first=J. |editor6-last=Meyer |editor6-first=J.-A. |conference=From Animals to Animats 8: Proceedings of the eighth international conference on the Simulation of Adaptive Behaviour |pages=183–92 |url=http://eprints.whiterose.ac.uk/7961/}}</ref><ref name="C. elegans on GitHub" /> However, there is still a lack of understanding of how the neurons and the connections between them generate the surprisingly complex range of behaviors that are observed in the relatively simple organism.<ref>[http://itee.uq.edu.au/~markw/celegans/ Mark Wakabayashi] {{webarchive |url=https://web.archive.org/web/20130512215753/http://itee.uq.edu.au/~markw/celegans/ |date=May 12, 2013 }}, with links to MuCoW simulation software, a demo video and the doctoral thesis Computational Plausibility of Stretch Receptors as the Basis for Motor Control in ''C. elegans'', 2006.</ref><ref>{{Cite book | last1 = Mailler | first1 = R. | last2 = Avery | first2 = J. | last3 = Graves | first3 = J. | last4 = Willy | first4 = N. | chapter = A Biologically Accurate 3D Model of the Locomotion of Caenorhabditis Elegans | doi = 10.1109/BioSciencesWorld.2010.18 | title = 2010 International Conference on Biosciences | pages = 84–90 | date = 7–13 March 2010 | isbn = 978-1-4244-5929-2 | s2cid = 10341946 | url = http://www.personal.utulsa.edu/~roger-mailler/publications/BIOSYSCOM2010.pdf | access-date = 14 October 2015 | archive-date = 18 July 2019 | archive-url = https://web.archive.org/web/20190718140743/http://www.personal.utulsa.edu/~roger-mailler/publications/BIOSYSCOM2010.pdf | url-status = dead }}</ref> This contrast between the apparent simplicity of how the mapped neurons interact with their neighbours, and exceeding complexity of the overall brain function, is an example of an [[Emergence|emergent property]].<ref>{{Cite news|url=https://phys.org/news/2013-08-complex-behavior-spontaneously-emerge-brain.html|title=How does complex behavior spontaneously emerge in the brain?|access-date=2018-02-27}}</ref> This kind of emergent property is paralleled within [[Artificial neural network|artificial neural networks]], the neurons of which are exceedingly simple compared to their often complex, abstract outputs. To quote a common saying, a group (in this case a brain) is stronger than the sum of its parts.


==Drosophila neural system==
===Drosophila===
{{see|Insect brain}}
{{see|Insect brain}}
The brain of the fruit fly, [[Drosophila]], has also been thoroughly studied. A simulated model of the fruit fly's brain offers a unique model of sibling neurons.<ref>Arena, P.; Patane, L.; Termini, P.S.; [https://scholar.google.se/scholar?cluster=12345296403665184996&hl=sv&as_sdt=0,5 An insect brain computational model inspired by Drosophila melanogaster: Simulation results], The 2010 International Joint Conference on Neural Networks (IJCNN).</ref> Like the roundworm, this has been made available as [[open-source software]].<ref name=":2">[https://github.com/neurokernel/neurokernel], Neurokernel open-source fruit fly brain simulation</ref>
The brain of the fruit fly, [[Drosophila]], has also been thoroughly studied. A simulated model of the fruit fly's brain offers a unique model of sibling neurons.<ref>Arena, P.; Patane, L.; Termini, P.S.; [https://scholar.google.se/scholar?cluster=12345296403665184996&hl=sv&as_sdt=0,5 An insect brain computational model inspired by Drosophila melanogaster: Simulation results], The 2010 International Joint Conference on Neural Networks (IJCNN).</ref> Like the roundworm, this has been made available as [[open-source software]].<ref name=":2">[https://github.com/neurokernel/neurokernel], Neurokernel open-source fruit fly brain simulation</ref>


==Mouse brain mapping and simulation==
===Mouse and rat===
In 2006, the [[Blue Brain Project]], led by [[Henry Markram]], made its first model of a [[neocortical column]] with simplified neurons. And in November 2007, it completed an initial model of the rat neocortical column. This marked the end of the first phase, delivering a data-driven process for creating, validating, and researching the neocortical column.<ref name=":02">{{Cite web |title=Timeline and Achievements |url=https://www.epfl.ch/research/domains/bluebrain/blue-brain/about/timeline/ |archive-url=https://web.archive.org/web/20240411075924/https://www.epfl.ch/research/domains/bluebrain/blue-brain/about/timeline/ |archive-date=2024-04-11 |access-date=2024-05-10 |website=EPFL |language=en-GB}}</ref><ref>{{cite web |title=News and Media information |url=http://bluebrain.epfl.ch/page18700.html |url-status=dead |archiveurl=https://web.archive.org/web/20080919051656/http://bluebrain.epfl.ch/page18700.html |archivedate=2008-09-19 |accessdate=2008-08-11 |work=Blue Brain}}</ref> The neocortical column is considered the smallest functional unit of the [[neocortex]]. The neocortex is the part of the brain thought to be responsible for higher-order functions like conscious thought, and contains 10,000 neurons in the rat brain (and 10<sup>8</sup> [[synapse]]s).
[[Henry Markram]] mapped the types of neurons within the [[mouse brain]] and their connections between 1995 and 2005.{{cn|date=January 2018}}

⚫
An [[artificial neural network]] described as being "as big and as complex as half of a mouse brain"<ref>{{Cite news|url=https://www.huffingtonpost.com/2007/04/28/supercomputer-mimics-mous_n_47135.html|title=Supercomputer Mimics Mouse's Brain|date=2008-03-28|work=Huffington Post|access-date=2018-06-05|language=en-US}}</ref> with 8 million of neurons and 6300 synapses per neuron was run on an IBM [[Blue Gene]] supercomputer by the University of Nevada's research team and [[IBM Almaden]] in 2007.<ref>[https://dominoweb.draco.res.ibm.com/reports/rj10404.pdf IBM research report] IBM</ref> Each second of simulated time took ten seconds of computer time. The researchers claimed to observe "biologically consistent" nerve impulses that flowed through the virtual cortex. However, the simulation lacked the structures seen in real mice brains, and they intend to improve the accuracy of the neuron and synapse models.<ref>{{Cite news |url=http://news.bbc.co.uk/1/hi/technology/6600965.stm |work=[[BBC News]] |date=27 April 2007 |title=Mouse brain simulated on computer}}</ref> IBM later in the same year increased the number of neurons to 16 million and 8000 synapses per neuron, 5 seconds of which was modelled in 265 s of real time.<ref>{{cite journal |last1=Ananthanarayanan |first1=Rajagopal |last2=Modha |first2=Dharmendra S |title=Scaling, stability and synchronization in mouse-sized (and larger) cortical simulations |journal=BMC Neuroscience |date=July 2007 |volume=8 |issue=S2 |pages=187 |doi=10.1186/1471-2202-8-S2-P187 |pmc=4436247 |doi-access=free }}</ref> By 2009, the researchers were able to ramp up the numbers to 1.6 billion neurons and 9 trillion synapses, saturating entire 144 TB of supercomputer RAM.<ref>{{cite journal |last1=Ananthanarayanan |first1=Rajagopal |last2=Esser |first2=Steven K. |last3=Simon |first3=Horst D. |last4=Modha |first4=Dharmendra S. |date=14 November 2009 |title=The cat is out of the bag: cortical simulations with 10 9 neurons, 10 13 synapses |journal=Conference on High Performance Computing Networking, Storage and Analysis |pages=1–12 |doi=10.1145/1654059.1654124 |s2cid=6110450}}</ref>

In 2019, Idan Segev, one of the computational neuroscientists working on the Blue Brain Project, gave a talk titled: "Brain in the computer: what did I learn from simulating the brain." In his talk, he mentioned that the whole cortex for the mouse brain was complete and virtual EEG experiments would begin soon. He also mentioned that the model had become too heavy on the supercomputers they were using at the time, and that they were consequently exploring methods in which every neuron could be represented as a neural network (see citation for details).<ref>{{Cite web|url=https://www.youtube.com/watch?v=sEiDxti0opE|title = Brain in the computer: What did I learn from simulating the brain - Idan Segev|website = [[YouTube]]| date=3 June 2019 }}</ref>


In 2023, researchers from Duke University performed a particularly high-resolution scan of a mouse brain.<ref name=":15">{{Cite web |last=Thornton |first=Angela |date=2023-06-26 |title=How uploading our minds to a computer might become possible |url=http://theconversation.com/how-uploading-our-minds-to-a-computer-might-become-possible-206804 |access-date=2023-11-08 |website=The Conversation |language=en-US}}</ref>
In December 2006,<ref>{{cite web|url=http://bluebrain.epfl.ch/Jahia/site/bluebrain/op/edit/pid/19085|title=Project Milestones|work=Blue Brain|accessdate=2008-08-11}}</ref> the [[Blue Brain]] project completed a simulation of a rat's [[cortical column|neocortical column]]. The neocortical column is considered the smallest functional unit of the [[neocortex]]. The neocortex is the part of the brain thought to be responsible for higher-order functions like conscious thought, and contains 10,000 neurons in the rat brain (and 10<sup>8</sup> [[synapse]]s). In November 2007,<ref>{{cite web|url=http://bluebrain.epfl.ch/page18700.html|title=News and Media information|work=Blue Brain|accessdate=2008-08-11|url-status=dead|archiveurl=https://web.archive.org/web/20080919051656/http://bluebrain.epfl.ch/page18700.html|archivedate=2008-09-19}}</ref> the project reported the end of its first phase, delivering a data-driven process for creating, validating, and researching the neocortical column.


==== Blue Brain ====
⚫
An [[artificial neural network]] described as being "as big and as complex as half of a mouse brain"<ref>{{Cite news|url=https://www.huffingtonpost.com/2007/04/28/supercomputer-mimics-mous_n_47135.html|title=Supercomputer Mimics Mouse's Brain|date=2008-03-28|work=Huffington Post|access-date=2018-06-05|language=en-US}}</ref> was run on an IBM [[Blue Gene]] supercomputer by the University of Nevada's research team in 2007. Each second of simulated time took ten seconds of computer time. The researchers claimed to observe "biologically consistent" nerve impulses that flowed through the virtual cortex. However, the simulation lacked the structures seen in real mice brains, and they intend to improve the accuracy of the neuron and synapse models.<ref>{{Cite news |url=http://news.bbc.co.uk/1/hi/technology/6600965.stm |work=[[BBC News]] |date=27 April 2007 |title=Mouse brain simulated on computer}}</ref>
⚫
[[Blue Brain]] is a project that was launched in May 2005 by [[IBM]] and the [[École Polytechnique Fédérale de Lausanne|Swiss Federal Institute of Technology]] in [[Lausanne]]. The intention of the project was to create a [[computer simulation]] of a mammalian [[cortical column]] down to the molecular level.<ref name=":1">{{cite news| url=https://www.forbes.com/technology/sciences/2005/06/06/cx_mh_0606ibm.html| archive-url=https://web.archive.org/web/20050608010310/http://www.forbes.com/technology/sciences/2005/06/06/cx_mh_0606ibm.html| url-status=dead| archive-date=June 8, 2005| title=IBM Aims To Simulate A Brain| work=Forbes| first=Matthew| last=Herper| date=June 6, 2005| accessdate=2006-05-19}}</ref> The project uses a [[supercomputer]] based on IBM's [[Blue Gene]] design to simulate the electrical behavior of neurons based upon their synaptic connectivity and ion permeability. The project seeks to eventually reveal insights into human cognition and various psychiatric disorders caused by malfunctioning neurons, such as [[autism]], and to understand how pharmacological agents affect network behavior.


==Blue Brain and the rat==
=== Human ===
{{Related article|Whole brain emulation}}[[File:Whole brain emulation.svg|thumb|330x330px|Estimates of how much processing power is needed to emulate a human brain at various levels of detail, on a logarithmic scale.<ref name=":5" />]]Human brains contain 86 billion neurons,<ref>{{Cite journal |last=Herculano-Houzel |first=Suzana |date=November 2009 |title=The Human Brain in Numbers: A Linearly Scaled-up Primate Brain |journal=Frontiers in Human Neuroscience|volume=3 |page=31 |doi=10.3389/neuro.09.031.2009 |doi-access=free |pmid=19915731 |pmc=2776484 }}</ref> each with an approximate average of 10,000 connections. By one estimate, a very detailed full reconstruction of the human [[connectome]] would require a [[zettabyte]] (10<sup>21</sup> bytes) of data storage.<ref>{{Cite news |last=Gorman |first=James |date=May 26, 2014 |title=All Circuits Are Busy |url=https://www.nytimes.com/2014/05/27/science/all-circuits-are-busy.html |work=The New York Times}}</ref>


A supercomputer having similar computing capability as the human brain is scheduled to go online in April 2024.<ref>{{Cite web |last=Vicinanza |first=Domenico |date=2023-12-18 |title=A new supercomputer aims to closely mimic the human brain — it could help unlock the secrets of the mind and advance AI |url=http://theconversation.com/a-new-supercomputer-aims-to-closely-mimic-the-human-brain-it-could-help-unlock-the-secrets-of-the-mind-and-advance-ai-220044 |access-date=2024-03-29 |website=The Conversation |language=en-US}}</ref> Called "DeepSouth", it could perform 228 trillions of ''synaptic'' operations per second.<ref>{{Cite web |last=Zolfagharifard |first=Ellie |title=The world's first human brain-scale supercomputer will go live next year |url=https://www.businessinsider.com/deepsouth-supercomputer-simulates-human-brain-go-online-next-year-2023-12 |access-date=2024-03-29 |website=Business Insider |language=en-US}}</ref>
⚫
[[Blue Brain]] is a project that was launched in May 2005 by [[IBM]] and the [[École Polytechnique Fédérale de Lausanne|Swiss Federal Institute of Technology]] in [[Lausanne]]. The intention of the project was to create a [[computer simulation]] of a mammalian cortical column down to the molecular level.<ref name=":1">{{cite news| url=https://www.forbes.com/technology/sciences/2005/06/06/cx_mh_0606ibm.html| title=IBM Aims To Simulate A Brain| work=Forbes| first=Matthew| last=Herper| date=June 6, 2005| accessdate=2006-05-19}}</ref> The project uses a [[supercomputer]] based on IBM's [[Blue Gene]] design to simulate the electrical behavior of neurons based upon their synaptic connectivity and ion permeability. The project seeks to eventually reveal insights into human cognition and various psychiatric disorders caused by malfunctioning neurons, such as [[autism]], and to understand how pharmacological agents affect network behavior.


==K computer and human brain==
==== K computer ====
In late 2013, researchers in Japan and Germany used the [[K computer]], then 4th fastest supercomputer, and the simulation software [[NEST (software)|NEST]] to simulate 1% of the human brain. The simulation modeled a network consisting of 1.73 billion nerve cells connected by 10.4 trillion synapses. To realize this feat, the program recruited 82,944 processors of the K Computer. The process took 40 minutes, to complete the simulation of 1 second of neuronal network activity in real, biological, time.<ref name="SD20130802">{{cite news| url=https://www.sciencedaily.com/releases/2013/08/130802080237.htm| title=Largest neuronal network simulation to date achieved using Japanese supercomputer| work=ScienceDaily| date=August 2, 2013| accessdate=2020-11-25}}</ref><ref name="Juelich20200802">{{cite news| url=https://www.fz-juelich.de/SharedDocs/Pressemitteilungen/UK/EN/2013/13-08-02LargestSimulation.html| title=Largest neuronal network simulation to date achieved using Japanese supercomputer| work=Jülich Forschungszentrum| date=August 2, 2013| accessdate=2020-11-25}}</ref>
In late 2013, researchers in Japan and Germany used the [[K computer]], then 4th fastest supercomputer, and the simulation software [[NEST (software)|NEST]] to simulate 1% of the human brain. The simulation modeled a network consisting of 1.73 billion nerve cells connected by 10.4 trillion synapses. To realize this feat, the program recruited 82,944 processors of the K Computer. The process took 40 minutes, to complete the simulation of 1 second of neuronal network activity in real, biological, time.<ref name="SD20130802">{{cite news| url=https://www.sciencedaily.com/releases/2013/08/130802080237.htm| title=Largest neuronal network simulation to date achieved using Japanese supercomputer| work=ScienceDaily| date=August 2, 2013| accessdate=2020-11-25}}</ref><ref name="Juelich20200802">{{cite news| url=https://www.fz-juelich.de/SharedDocs/Pressemitteilungen/UK/EN/2013/13-08-02LargestSimulation.html| title=Largest neuronal network simulation to date achieved using Japanese supercomputer| work=Jülich Forschungszentrum| date=August 2, 2013| accessdate=2020-11-25}}</ref>


==Human Brain Project==
==== Human Brain Project ====
The [[Human Brain Project]] (HBP) is a 10-year program of research funded by the [[European Union]]. It began in 2013 and employs around 500 scientists across Europe. It includes 6 platforms:
The [[Human Brain Project]] (HBP) was a 10-year program of research funded by the [[European Union]]. It began in 2013 and employed around 500 scientists across Europe.<ref>{{Cite news |last=Holmgaard Mersh |first=Amalie |date=September 15, 2023 |title=Decade-long European research project maps the human brain |url=https://www.euractiv.com/section/health-consumers/news/decade-long-european-research-project-maps-the-human-brain/ |work=euractiv}}</ref> It includes 6 platforms:


*[[Neuroinformatics]] (shared databases),
*[[Neuroinformatics]] (shared databases),
Line 38: Line 48:
*[[Neurorobotics]] (robotic simulations).
*[[Neurorobotics]] (robotic simulations).


The Brain Simulation Platform (BSP) is a device for internet-accessible tools, which allows investigations that are not possible in the laboratory. They are applying Blue Brain techniques to other brain regions, such as the [[cerebellum]], [[hippocampus]], and the [[basal ganglia]].<ref>{{cite web|title=Brain Simulation Platform|url=https://www.humanbrainproject.eu/en/brain-simulation/brain-simulation-platform/|website=Human Brain Project|accessdate=20 January 2018}}</ref>
The Brain Simulation Platform (BSP) is a device for internet-accessible tools, which allows investigations that are not possible in the laboratory. They are applying Blue Brain techniques to other brain regions, such as the [[cerebellum]], [[hippocampus]], and the [[basal ganglia]].<ref name=":4">{{cite web|title=Brain Simulation Platform|url=https://www.humanbrainproject.eu/en/brain-simulation/brain-simulation-platform/|website=Human Brain Project|accessdate=20 January 2018}}</ref>


==Open-source brain simulation==
==Open source==
Various models of the brain have been released as [[open-source software]] (OSS) and are available on sites such as [[GitHub]] including the [[C. elegans]] roundworm,<ref name="C. elegans on GitHub" /> the [[Drosophila]] fruit fly,<ref name=":2" /> and the human brain models Elysia<ref>[https://github.com/elysia/elysia Elysia]</ref> and [[Spaun (Semantic Pointer Architecture Unified Network)|Spaun]],<ref>[https://github.com/xchoo/spaun2.0], spaun2.0 brain simulation</ref> which is the world's largest functional brain model and is based on the [[Neural Engineering Object|NENGO]] software architecture.<ref name="Spaun">Eliasmith, C., Stewart T. C., Choo X., Bekolay T., DeWolf T., Tang Y., Rasmussen, D. (2012). A large-scale model of the functioning brain. Science. Vol. 338 no. 6111 pp. 1202-1205. DOI: 10.1126/science.1225266.</ref>
Various models of the brain have been released as [[open-source software]] and are available on sites such as [[GitHub]], including the [[C. elegans]] roundworm,<ref name="C. elegans on GitHub" /> the [[Drosophila]] fruit fly,<ref name=":2" /> and the human brain models Elysia<ref>{{Cite web|url=https://github.com/elysia/elysia|title=elysia/elysia|date=8 November 2023|accessdate=22 November 2023|via=GitHub}}</ref> and [[Spaun (Semantic Pointer Architecture Unified Network)|Spaun]],<ref>[https://github.com/xchoo/spaun2.0], spaun2.0 brain simulation</ref> which are based on the [[Neural Engineering Object|NENGO]] software architecture.<ref name="Spaun">{{cite journal |last1=Eliasmith |first1=Chris |last2=Stewart |first2=Terrence C. |last3=Choo |first3=Xuan |last4=Bekolay |first4=Trevor |last5=DeWolf |first5=Travis |last6=Tang |first6=Yichuan |last7=Rasmussen |first7=Daniel |title=A Large-Scale Model of the Functioning Brain |journal=Science |date=30 November 2012 |volume=338 |issue=6111 |pages=1202–1205 |doi=10.1126/science.1225266 |pmid=23197532 |bibcode=2012Sci...338.1202E |s2cid=1673514 }}</ref> The Blue Brain Project Showcase likewise illustrates how models and data from the [[Blue Brain Project]] can be converted to [[NeuroML]] and PyNN ([[Python (programming language)|Python]] neuronal network models).<ref name=":3" />


The Brain Simulation Platform (BSP) is an internet-accessible [[open collaboration]] platform for brain simulation, created by the [[Human Brain Project]].<ref name=":4" />
The Blue Brain Project Showcase also illustrates how models and data from the [[Blue Brain Project]] can be converted to [[NeuroML]] and PyNN ([[Python (programming language)|Python]] neuronal network models).<ref>{{cite web|url=http://opensourcebrain.org/projects/blue-brain-project-showcase|website=Open Source Brain|title=Overview - Blue Brain Project Showcase - Open Source Brain|accessdate=May 5, 2020}}</ref>


== See also ==
== See also ==


* [[Whole brain emulation]]
* [[Mind uploading]]
* [[Artificial general intelligence]]
* [[Trion (neural networks)]]


==References==
==References==


{{reflist}}
{{reflist}}
{{Computer simulation}}


[[Category:Computational neuroscience]]
[[Category:Computational neuroscience]]

Latest revision as of 21:35, 11 October 2024

In the field of computational neuroscience, brain simulation is the concept of creating a functioning computer model of a brain or part of a brain.[1] Brain simulation projects intend to contribute to a complete understanding of the brain, and eventually also assist the process of treating and diagnosing brain diseases.[2][3] Simulations utilize mathematical models of biological neurons, such as the hodgkin-huxley model, to simulate the behavior of neurons, or other cells within the brain.

Various simulations from around the world have been fully or partially released as open source software, such as C. elegans,[4] and the Blue Brain Project Showcase.[5] In 2013 the Human Brain Project, which has utilized techniques used by the Blue Brain Project and built upon them,[6] created a Brain Simulation Platform (BSP), an internet-accessible collaborative platform designed for the simulation of brain models.

Brain simulations can be done at varying levels of detail, with more detail requiring significantly higher computation capabilities. Some simulations may only consider the behaviour of areas without modeling individual neurons. Other simulations model the behaviour of individual neurons, the strength of the connections between neurons and how these connections change.[7] This requires having a map of the target organism neurons and their connections, called a connectome.[8] Highly detailed simulations may precisely model the electrophysiology of each individual neuron, potentially even their metabolome and proteome, and the state of their protein complexes.[9]

Case studies

[edit]

Over time, brain simulation research has focused on increasingly complex organisms, starting with primitive organisms like the nematode C. elegans and progressing towards simulations of human brains.

Roundworm

[edit]
Brain map of the C. elegans roundworm 302 neurons, interconnected by 5000 synapses

The connectivity of the neural circuit for touch sensitivity of the simple C. elegans nematode (roundworm) was mapped in 1985[10] and partly simulated in 1993.[11] Since 2004, many software simulations of the complete neural and muscular system have been developed, including simulation of the worm's physical environment. Some of these models including source code have been made available for download.[12][4] However, there is still a lack of understanding of how the neurons and the connections between them generate the surprisingly complex range of behaviors that are observed in the relatively simple organism.[13][14] This contrast between the apparent simplicity of how the mapped neurons interact with their neighbours, and exceeding complexity of the overall brain function, is an example of an emergent property.[15] This kind of emergent property is paralleled within artificial neural networks, the neurons of which are exceedingly simple compared to their often complex, abstract outputs. To quote a common saying, a group (in this case a brain) is stronger than the sum of its parts.

Drosophila

[edit]
Further information: Insect brain

The brain of the fruit fly, Drosophila, has also been thoroughly studied. A simulated model of the fruit fly's brain offers a unique model of sibling neurons.[16] Like the roundworm, this has been made available as open-source software.[17]

Mouse and rat

[edit]

In 2006, the Blue Brain Project, led by Henry Markram, made its first model of a neocortical column with simplified neurons. And in November 2007, it completed an initial model of the rat neocortical column. This marked the end of the first phase, delivering a data-driven process for creating, validating, and researching the neocortical column.[18][19] The neocortical column is considered the smallest functional unit of the neocortex. The neocortex is the part of the brain thought to be responsible for higher-order functions like conscious thought, and contains 10,000 neurons in the rat brain (and 108 synapses).

An artificial neural network described as being "as big and as complex as half of a mouse brain"[20] with 8 million of neurons and 6300 synapses per neuron was run on an IBM Blue Gene supercomputer by the University of Nevada's research team and IBM Almaden in 2007.[21] Each second of simulated time took ten seconds of computer time. The researchers claimed to observe "biologically consistent" nerve impulses that flowed through the virtual cortex. However, the simulation lacked the structures seen in real mice brains, and they intend to improve the accuracy of the neuron and synapse models.[22] IBM later in the same year increased the number of neurons to 16 million and 8000 synapses per neuron, 5 seconds of which was modelled in 265 s of real time.[23] By 2009, the researchers were able to ramp up the numbers to 1.6 billion neurons and 9 trillion synapses, saturating entire 144 TB of supercomputer RAM.[24]

In 2019, Idan Segev, one of the computational neuroscientists working on the Blue Brain Project, gave a talk titled: "Brain in the computer: what did I learn from simulating the brain." In his talk, he mentioned that the whole cortex for the mouse brain was complete and virtual EEG experiments would begin soon. He also mentioned that the model had become too heavy on the supercomputers they were using at the time, and that they were consequently exploring methods in which every neuron could be represented as a neural network (see citation for details).[25]

In 2023, researchers from Duke University performed a particularly high-resolution scan of a mouse brain.[26]

Blue Brain

[edit]

Blue Brain is a project that was launched in May 2005 by IBM and the Swiss Federal Institute of Technology in Lausanne. The intention of the project was to create a computer simulation of a mammalian cortical column down to the molecular level.[27] The project uses a supercomputer based on IBM's Blue Gene design to simulate the electrical behavior of neurons based upon their synaptic connectivity and ion permeability. The project seeks to eventually reveal insights into human cognition and various psychiatric disorders caused by malfunctioning neurons, such as autism, and to understand how pharmacological agents affect network behavior.

Human

[edit]
See also: Whole brain emulation
Estimates of how much processing power is needed to emulate a human brain at various levels of detail, on a logarithmic scale.[9]

Human brains contain 86 billion neurons,[28] each with an approximate average of 10,000 connections. By one estimate, a very detailed full reconstruction of the human connectome would require a zettabyte (1021 bytes) of data storage.[29]

A supercomputer having similar computing capability as the human brain is scheduled to go online in April 2024.[30] Called "DeepSouth", it could perform 228 trillions of synaptic operations per second.[31]

K computer

[edit]

In late 2013, researchers in Japan and Germany used the K computer, then 4th fastest supercomputer, and the simulation software NEST to simulate 1% of the human brain. The simulation modeled a network consisting of 1.73 billion nerve cells connected by 10.4 trillion synapses. To realize this feat, the program recruited 82,944 processors of the K Computer. The process took 40 minutes, to complete the simulation of 1 second of neuronal network activity in real, biological, time.[32][33]

Human Brain Project

[edit]

The Human Brain Project (HBP) was a 10-year program of research funded by the European Union. It began in 2013 and employed around 500 scientists across Europe.[34] It includes 6 platforms:

The Brain Simulation Platform (BSP) is a device for internet-accessible tools, which allows investigations that are not possible in the laboratory. They are applying Blue Brain techniques to other brain regions, such as the cerebellum, hippocampus, and the basal ganglia.[35]

Open source

[edit]

Various models of the brain have been released as open-source software and are available on sites such as GitHub, including the C. elegans roundworm,[4] the Drosophila fruit fly,[17] and the human brain models Elysia[36] and Spaun,[37] which are based on the NENGO software architecture.[38] The Blue Brain Project Showcase likewise illustrates how models and data from the Blue Brain Project can be converted to NeuroML and PyNN (Python neuronal network models).[5]

The Brain Simulation Platform (BSP) is an internet-accessible open collaboration platform for brain simulation, created by the Human Brain Project.[35]

See also

[edit]

References

[edit]
  1. ^ Fan, Xue; Markram, Henry (7 May 2019). "A Brief History of Simulation Neuroscience". Frontiers in Neuroinformatics. 13: 32. doi:10.3389/fninf.2019.00032. PMC 6513977. PMID 31133838.
  2. ^ "Neuroinformatics and The Blue Brain Project". Informatics from Technology Networks. Retrieved 30 January 2018.
  3. ^ Colombo, Matteo (4 March 2017). "Why build a virtual brain? Large-scale neural simulations as jump start for cognitive computing". Journal of Experimental & Theoretical Artificial Intelligence. 29 (2): 361–370. Bibcode:2017JETAI..29..361C. doi:10.1080/0952813X.2016.1148076. S2CID 205634599.
  4. ^ a b c C. Elegans simulation, Open source software project at Github
  5. ^ a b "Overview - Blue Brain Project Showcase - Open Source Brain". Open Source Brain. Archived from the original on 26 November 2020. Retrieved 5 May 2020.
  6. ^ Human Brain Project, Framework Partnership Agreement https://www.humanbrainproject.eu/documents/10180/538356/FPA++Annex+1+Part+B/41c4da2e-0e69-4295-8e98-3484677d661f Archived 2017-02-02 at the Wayback Machine
  7. ^ Fan, Shelly (30 May 2019). "The Crucial Role of Brain Simulation in Future Neuroscience". Singularity Hub. Retrieved 29 March 2024.
  8. ^ Seung, Sebastian. "Another Perspective on Massive Brain Simulations". Scientific American. Retrieved 29 March 2024.
  9. ^ a b Sandberg, Anders; Bostrom, Nick (2008). "Whole Brain Emulation: A Roadmap" (PDF).
  10. ^ Chalfie M; Sulston JE; White JG; Southgate E; Thomson JN; et al. (April 1985). "The neural circuit for touch sensitivity in Caenorhabditis elegans". The Journal of Neuroscience. 5 (4): 956–64. doi:10.1523/JNEUROSCI.05-04-00956.1985. PMC 6565008. PMID 3981252.
  11. ^ Niebur E; Erdös P (November 1993). "Theory of the locomotion of nematodes: control of the somatic motor neurons by interneurons". Mathematical Biosciences. 118 (1): 51–82. doi:10.1016/0025-5564(93)90033-7. PMID 8260760.
  12. ^ Bryden, J.; Cohen, N. (2004). Schaal, S.; Ijspeert, A.; Billard, A.; Vijayakumar, S.; et al. (eds.). A simulation model of the locomotion controllers for the nematodode Caenorhabditis elegans. From Animals to Animats 8: Proceedings of the eighth international conference on the Simulation of Adaptive Behaviour. pp. 183–92.
  13. ^ Mark Wakabayashi Archived May 12, 2013, at the Wayback Machine, with links to MuCoW simulation software, a demo video and the doctoral thesis Computational Plausibility of Stretch Receptors as the Basis for Motor Control in C. elegans, 2006.
  14. ^ Mailler, R.; Avery, J.; Graves, J.; Willy, N. (7–13 March 2010). "A Biologically Accurate 3D Model of the Locomotion of Caenorhabditis Elegans". 2010 International Conference on Biosciences (PDF). pp. 84–90. doi:10.1109/BioSciencesWorld.2010.18. ISBN 978-1-4244-5929-2. S2CID 10341946. Archived from the original (PDF) on 18 July 2019. Retrieved 14 October 2015.
  15. ^ "How does complex behavior spontaneously emerge in the brain?". Retrieved 27 February 2018.
  16. ^ Arena, P.; Patane, L.; Termini, P.S.; An insect brain computational model inspired by Drosophila melanogaster: Simulation results, The 2010 International Joint Conference on Neural Networks (IJCNN).
  17. ^ a b [1], Neurokernel open-source fruit fly brain simulation
  18. ^ "Timeline and Achievements". EPFL. Archived from the original on 11 April 2024. Retrieved 10 May 2024.
  19. ^ "News and Media information". Blue Brain. Archived from the original on 19 September 2008. Retrieved 11 August 2008.
  20. ^ "Supercomputer Mimics Mouse's Brain". Huffington Post. 28 March 2008. Retrieved 5 June 2018.
  21. ^ IBM research report IBM
  22. ^ "Mouse brain simulated on computer". BBC News. 27 April 2007.
  23. ^ Ananthanarayanan, Rajagopal; Modha, Dharmendra S (July 2007). "Scaling, stability and synchronization in mouse-sized (and larger) cortical simulations". BMC Neuroscience. 8 (S2): 187. doi:10.1186/1471-2202-8-S2-P187. PMC 4436247.
  24. ^ Ananthanarayanan, Rajagopal; Esser, Steven K.; Simon, Horst D.; Modha, Dharmendra S. (14 November 2009). "The cat is out of the bag: cortical simulations with 10 9 neurons, 10 13 synapses". Conference on High Performance Computing Networking, Storage and Analysis: 1–12. doi:10.1145/1654059.1654124. S2CID 6110450.
  25. ^ "Brain in the computer: What did I learn from simulating the brain - Idan Segev". YouTube. 3 June 2019.
  26. ^ Thornton, Angela (26 June 2023). "How uploading our minds to a computer might become possible". The Conversation. Retrieved 8 November 2023.
  27. ^ Herper, Matthew (6 June 2005). "IBM Aims To Simulate A Brain". Forbes. Archived from the original on 8 June 2005. Retrieved 19 May 2006.
  28. ^ Herculano-Houzel, Suzana (November 2009). "The Human Brain in Numbers: A Linearly Scaled-up Primate Brain". Frontiers in Human Neuroscience. 3: 31. doi:10.3389/neuro.09.031.2009. PMC 2776484. PMID 19915731.
  29. ^ Gorman, James (26 May 2014). "All Circuits Are Busy". The New York Times.
  30. ^ Vicinanza, Domenico (18 December 2023). "A new supercomputer aims to closely mimic the human brain — it could help unlock the secrets of the mind and advance AI". The Conversation. Retrieved 29 March 2024.
  31. ^ Zolfagharifard, Ellie. "The world's first human brain-scale supercomputer will go live next year". Business Insider. Retrieved 29 March 2024.
  32. ^ "Largest neuronal network simulation to date achieved using Japanese supercomputer". ScienceDaily. 2 August 2013. Retrieved 25 November 2020.
  33. ^ "Largest neuronal network simulation to date achieved using Japanese supercomputer". Jülich Forschungszentrum. 2 August 2013. Retrieved 25 November 2020.
  34. ^ Holmgaard Mersh, Amalie (15 September 2023). "Decade-long European research project maps the human brain". euractiv.
  35. ^ a b "Brain Simulation Platform". Human Brain Project. Retrieved 20 January 2018.
  36. ^ "elysia/elysia". 8 November 2023. Retrieved 22 November 2023 – via GitHub.
  37. ^ [2], spaun2.0 brain simulation
  38. ^ Eliasmith, Chris; Stewart, Terrence C.; Choo, Xuan; Bekolay, Trevor; DeWolf, Travis; Tang, Yichuan; Rasmussen, Daniel (30 November 2012). "A Large-Scale Model of the Functioning Brain". Science. 338 (6111): 1202–1205. Bibcode:2012Sci...338.1202E. doi:10.1126/science.1225266. PMID 23197532. S2CID 1673514.
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