Blue Brain Project

In 2006, the project made its first model of a neocortical column with simplified neurons.{{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}} 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.{{Cite news |last=Witchalls |first=Clint |date=2007-12-20 |title=Lab comes one step closer to building artificial human brain |url=https://www.theguardian.com/technology/2007/dec/20/research.it |access-date=2024-05-10 |work=The Guardian |language=en-GB |issn=0261-3077}}{{cite web |title=News and Media information |url=http://bluebrain.epfl.ch/page18700.html |url-status=dead |archive-url=https://web.archive.org/web/20080919051656/http://bluebrain.epfl.ch/page18700.html |archive-date=2008-09-19 |access-date=2008-08-11 |work=Blue Brain}}

Neocortical columns are considered by some researchers to be the smallest functional units of the neocortex,{{cite journal | vauthors = Horton JC, Adams DL | title = The cortical column: a structure without a function | journal = Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences | volume = 360 | issue = 1456 | pages = 837–62 | date = April 2005 | pmid = 15937015 | pmc = 1569491 | doi = 10.1098/rstb.2005.1623 }}{{cite journal | vauthors = Rakic P | title = Confusing cortical columns | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 105 | issue = 34 | pages = 12099–100 | date = August 2008 | pmid = 18715998 | pmc = 2527871 | doi = 10.1073/pnas.0807271105 | doi-access = free | bibcode = 2008PNAS..10512099R }} and they are thought to be responsible for higher functions such as conscious thought. In humans, each column is about {{Convert|2|mm|inch|abbr=on}} in length, has a diameter of {{Convert|0.5|mm|inch|abbr=on}} and contains about 60,000 neurons. Rat neocortical columns are very similar in structure but contain only 10,000 neurons and 10⁸ synapses.

In 2009, Henry Markram claimed that a "detailed, functional artificial human brain can be built within the next 10 years".{{Cite news |date=2009-07-22 |title=Artificial brain '10 years away' |url=http://news.bbc.co.uk/2/hi/8164060.stm |access-date=2024-05-10 |work=BBC |language=en-GB}} He conceived the Human Brain Project, to which the Blue Brain Project contributed, and which became funded in 2013 by the European Union with up to $1.3 billion.{{Cite news |last=Requarth |first=Tim |date=2013-03-18 |title=Bringing a Virtual Brain to Life |url=https://www.nytimes.com/2013/03/19/science/bringing-a-virtual-brain-to-life.html |access-date=2024-05-10 |work=The New York Times |language=en-US |issn=0362-4331}}

In 2015, the project simulated part of a rat brain with 30,000 neurons.{{Cite news |last=Sample |first=Ian |date=2015-10-08 |title=Complex living brain simulation replicates sensory rat behaviour |url=https://www.theguardian.com/science/2015/oct/08/complex-living-brain-simulation-replicates-sensory-rat-behaviour |access-date=2024-05-10 |work=The Guardian |language=en-GB |issn=0261-3077}} Also in 2015, scientists at École Polytechnique Fédérale de Lausanne (EPFL) developed a quantitative model of the previously unknown relationship between the neurons and the astrocytes. This model describes the energy management of the brain through the function of the neuro-glial vascular unit (NGV). The additional layer of neuron and glial cells is being added to Blue Brain Project models to improve functionality of the system.{{cite journal | vauthors = Jolivet R, Coggan JS, Allaman I, Magistretti PJ | title = Multi-timescale modeling of activity-dependent metabolic coupling in the neuron-glia-vasculature ensemble | journal = PLOS Computational Biology | volume = 11 | issue = 2 | pages = e1004036 | date = February 2015 | pmid = 25719367 | pmc = 4342167 | doi = 10.1371/journal.pcbi.1004036 | doi-access = free | bibcode = 2015PLSCB..11E4036J }}

In 2017, Blue Brain Project discovered that neural cliques connected to one another in up to eleven dimensions. The project's director suggested that the difficulty of understanding the brain is partly because the mathematics usually applied for studying neural networks cannot detect that many dimensions. The Blue Brain Project was able to model these networks using algebraic topology.{{cite web | url = https://blog.frontiersin.org/2017/06/12/blue-brain-team-discovers-a-multi-dimensional-universe-in-brain-networks/ | title = Blue Brain Team Discovers a Multi-Dimensional Universe in Brain Networks | work = Frontiers Science News | date = June 12, 2017 }}

In 2018, Blue Brain Project released its first digital 3D brain cell atlas{{Cite web |title=Blue Brain Cell Atlas |url=https://bbp.epfl.ch/nexus/cell-atlas/?v=v2&std=1 |access-date=2024-05-10 |website=bbp.epfl.ch}} which, according to ScienceDaily, is like "going from hand-drawn maps to Google Earth", providing information about major cell types, numbers, and positions in 737 regions of the brain.{{Cite journal |date=November 28, 2018 |access-date=18 April 2019 |journal=ScienceDaily |url=https://www.sciencedaily.com/releases/2018/11/181128082718.htm |title=Blue Brain Project releases first-ever digital 3D brain cell atlas}}

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 an artificial neural network (see citation for details).{{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 }}

In 2022, scientists at the Blue Brain Project used algebraic topology to create an algorithm, Topological Neuronal Synthesis, that generates a large number of unique cells using only a few examples, synthesizing millions of unique neuronal morphologies. This allows them to replicate both healthy and diseased states of the brain. In a paper Kenari et al. were able to digitally synthesize dendritic morphologies from the mouse brain using this algorithm. They mapped entire brain regions from just a few reference cells. Since it is open source, this will enable the modelling of brain diseases and eventually, the algorithm could lead to digital twins of brains.[https://news.epfl.ch/news/blue-brain-builds-neurons-with-mathematics-2/ Blue Brain builds neurons with mathematics] Kate Mullins, EPFL news. June 4th, 2022

The Blue Brain Project has developed a number of software to reconstruct and to simulate the mouse brain. All software tools mentioned below are open source software and available for everyone on GitHub.{{Citation |title=BlueBrain/nexus |date=2021-06-03 |url=https://github.com/BlueBrain/nexus |access-date=2021-06-04 |publisher=The Blue Brain Project}}{{Citation |title=BlueBrain/BluePyOpt |date=2020-12-16 |url=https://github.com/BlueBrain/BluePyOpt |access-date=2020-12-16 |publisher=The Blue Brain Project}}{{Citation |title=BlueBrain/CoreNeuron |date=2020-12-15 |url=https://github.com/BlueBrain/CoreNeuron |access-date=2020-12-16 |publisher=The Blue Brain Project}}{{Citation |title=BlueBrain/NeuroMorphoVis |date=2020-12-15 |url=https://github.com/BlueBrain/NeuroMorphoVis |access-date=2020-12-16 |publisher=The Blue Brain Project}}{{Citation |title=BlueBrain/sonata |date=2018-04-28 |url=https://github.com/BlueBrain/sonata |access-date=2020-12-24 |publisher=The Blue Brain Project}}{{Citation |title=AllenInstitute/sonata |date=2020-12-02 |url=https://github.com/AllenInstitute/sonata |access-date=2020-12-24 |publisher=Allen Institute}}

Blue Brain Nexus{{Cite web|title=Building the Blue Brain Nexus|url=https://www.technologynetworks.com/informatics/articles/building-the-blue-brain-nexus-295851|access-date=2021-06-04|website=Informatics from Technology Networks|language=en}}{{Cite web|title=The Nexus Ecosystem: Better (Research) Data Management|url=https://bluebrainnexus.io|access-date=2021-06-04|website=bluebrainnexus.io}}{{cite journal |last1 =Sy |first1 = Mohameth François

|last2 = Roman |first2 = Bogdan

|last3 = Kerrien |first3= Samuel Claude

|last4 = Montero |first4 = Didac Mendez

|last5 = Genet |first5 = Henry

|last6 = Wajerowicz |first6 = Wojciech

|last7 = Dupont |first7 = Michäel

|last8 = Lavriushev |first8 = Ian

|last9 = Machon |first9 = Julien

|last10 = Pirman |first10 = Kenneth

|last11 = mana |first11 = Dhanesh Neela

|last12 = Stafeeva |first12 = Natalia

|last13 = Kaufmann |first13 = Anna-Kristin

|last14 = Huanxiang Lu |last15 = Lurie |first15 = Jonathan

|last16 = Fonta |first16 = Pierre-Alexandre

|last17 = Rojas Martinez |first17 = Alejandra Garcia

|last18 = Ulbrich |first18 = Alexander D.

|last19 = Lindqvist |first19 = Carolina

|last20 = Jimenez |first20 = Silvia

|last21 = Rotenberg |first21 = David

|last22 = Markram |first22 = Henry

|last23 = Hill |first23 = Sean L. |date=August 2022 |title=Blue Brain Nexus: An open, secure, scalable system for knowledge graph management and data-driven science |journal=Semantic Web |volume = 14

|issue = 4

|pages = 697–727

|doi=10.3233/SW-222974|s2cid = 251964238

|doi-access = free }} is a data integration platform which uses a knowledge graph to enable users to search, deposit, and organise data. It stands on the FAIR data principles to provide flexible data management solutions beyond neuroscience studies.

BluePyOpt{{cite journal | vauthors = Van Geit W, Gevaert M, Chindemi G, Rössert C, Courcol JD, Muller EB, Schürmann F, Segev I, Markram H | display-authors = 6 | title = BluePyOpt: Leveraging Open Source Software and Cloud Infrastructure to Optimise Model Parameters in Neuroscience | language = English | journal = Frontiers in Neuroinformatics | volume = 10 | pages = 17 | date = 2016 | pmid = 27375471 | pmc = 4896051 | doi = 10.3389/fninf.2016.00017 | arxiv = 1603.00500 | doi-access = free }} is a tool that is used to build electrical models of single neurons. For this, it uses evolutionary algorithms to constrain the parameters to experimental electrophysiological data. Attempts to reconstruct single neurons using BluePyOpt are reported by Rosanna Migliore,{{cite journal | vauthors = Migliore R, Lupascu CA, Bologna LL, Romani A, Courcol JD, Antonel S, Van Geit WA, Thomson AM, Mercer A, Lange S, Falck J, Rössert CA, Shi Y, Hagens O, Pezzoli M, Freund TF, Kali S, Muller EB, Schürmann F, Markram H, Migliore M | display-authors = 6 | title = The physiological variability of channel density in hippocampal CA1 pyramidal cells and interneurons explored using a unified data-driven modeling workflow | journal = PLOS Computational Biology | volume = 14 | issue = 9 | pages = e1006423 | date = September 2018 | pmid = 30222740 | pmc = 6160220 | doi = 10.1371/journal.pcbi.1006423 | bibcode = 2018PLSCB..14E6423M | doi-access = free }} and Stefano Masori.{{cite journal | vauthors = Masoli S, Rizza MF, Sgritta M, Van Geit W, Schürmann F, D'Angelo E | title = Single Neuron Optimization as a Basis for Accurate Biophysical Modeling: The Case of Cerebellar Granule Cells | language = English | journal = Frontiers in Cellular Neuroscience | volume = 11 | pages = 71 | date = 2017 | pmid = 28360841 | pmc = 5350144 | doi = 10.3389/fncel.2017.00071 | doi-access = free }}

CoreNEURON{{cite journal | vauthors = Kumbhar P, Hines M, Fouriaux J, Ovcharenko A, King J, Delalondre F, Schürmann F | title = CoreNEURON : An Optimized Compute Engine for the NEURON Simulator | language = English | journal = Frontiers in Neuroinformatics | volume = 13 | pages = 63 | date = 2019 | pmid = 31616273 | pmc = 6763692 | doi = 10.3389/fninf.2019.00063 | arxiv = 1901.10975 | doi-access = free }} is a supplemental tool to NEURON, which allows large scale simulation by boosting memory usage and computational speed.

NeuroMorphoVis{{cite journal | vauthors = Abdellah M, Hernando J, Eilemann S, Lapere S, Antille N, Markram H, Schürmann F | title = NeuroMorphoVis: a collaborative framework for analysis and visualization of neuronal morphology skeletons reconstructed from microscopy stacks | journal = Bioinformatics | volume = 34 | issue = 13 | pages = i574–i582 | date = July 2018 | pmid = 29949998 | pmc = 6022592 | doi = 10.1093/bioinformatics/bty231 }} is a visualisation tool for morphologies of neurons.

SONATA{{cite journal | vauthors = Dai K, Hernando J, Billeh YN, Gratiy SL, Planas J, Davison AP, Dura-Bernal S, Gleeson P, Devresse A, Dichter BK, Gevaert M, King JG, Van Geit WA, Povolotsky AV, Muller E, Courcol JD, Arkhipov A | display-authors = 6 | title = The SONATA data format for efficient description of large-scale network models | journal = PLOS Computational Biology | volume = 16 | issue = 2 | pages = e1007696 | date = February 2020 | pmid = 32092054 | pmc = 7058350 | doi = 10.1371/journal.pcbi.1007696 | bibcode = 2020PLSCB..16E7696D | doi-access = free }} is a joint effort between Blue Brain Project and Allen Institute for Brain Science, to develop a standard for data format, which realises a multiple platform working environment with greater computational memory and efficiency.

The project was funded primarily by the Swiss government and the Future and Emerging Technologies (FET) Flagship grant from the European Commission,{{cite journal | vauthors = Abbott A |title=Brain-simulation and graphene projects win billion-euro competition |journal=Nature |date=23 January 2013 |doi=10.1038/nature.2013.12291 |s2cid=61977896 }} and secondarily by grants and donations from private individuals. The EPFL bought the Blue Gene computer at a reduced cost because it was still a prototype and IBM was interested in exploring how applications would perform on the machine. BBP was viewed as a validation of the Blue Gene supercomputer concept.{{cite web|url=http://technology-report.com/2009/01/blue-brain-project-ibm-has-not-withdrawn-support/|title=Blue Brain Project - IBM has not withdrawn support|work=Henry Markram, Project Director as quoted by IBM Switzerland to Technology Report on January 19, 2009| access-date=2009-04-14}}

Although the Blue Brain Project is often associated with the Human Brain Project (HBP), it is important to distinguish between the two. While the Blue Brain Project was a key participant of the HBP, much of the criticism regarding targets and management issues actually pertains to the Human Brain Project rather than the Blue Brain Project itself.{{cite web|url=https://www.theatlantic.com/science/archive/2019/07/ten-years-human-brain-project-simulation-markram-ted-talk/594493/|title=The Human Brain Project Hasn't Lived Up to Its Promise|work=By Ed Yong, The Atlantic, July 22, 2019|date=22 July 2019 }}{{cite web|url=https://www.horizons-mag.ch/2022/09/01/charting-new-worlds-or-running-aground/|title=Charting new worlds or running aground?|work=By Edwin Cartlidge, Horizons - The Swiss Research Magazine, September 1, 2022|date=September 2022 }}

Voices raised as early as September 2014 highlighted concerns over the trajectory of the Human Brain Project, noting challenges in meeting its high-level goals and questioning its organizational structure and the project's key promoter, Professor Henry Markram.{{cite web|last1=Epstein|first1=Robet|title=The Empty Brain|url=https://aeon.co/essays/your-brain-does-not-process-information-and-it-is-not-a-computer|website=Aeon|access-date=8 January 2018}}{{cite journal|last1=Theil|first1=Stefan|title=Why the Human Brain Project Went Wrong—and How to Fix It|url=https://www.scientificamerican.com/article/why-the-human-brain-project-went-wrong-and-how-to-fix-it/|website=Scientific American|date=October 2015 |doi=10.1038/scientificamerican1015-36 |access-date=8 January 2018|url-access=subscription}} In 2016, the HBP underwent a restructuring with resources originally earmarked for brain simulation redistributed to support a wider array of neuroscience research groups. Since then, scientists and engineers from the Blue Brain Project have contributed to various aspects of the HBP, including the Neuroinformatics, EBRAINS, Neurorobotics, and High-Performance Computing Platforms.{{Cite web |title=Blue Brain Project |url=https://bbp.epfl.ch/bbp/research/domains/bluebrain/index.html?p=7604.html |access-date=2025-02-03 |website=EPFL |language=en-GB}} This distinction is important because some of the criticism directed at the initial incarnation of HBP may have been misattributed to the Blue Brain Project due to their shared leadership and early involvement in the initiative.

Image:UPM-CeSViMa-SupercomputadorMagerit.jpg supercomputer (CeSViMa)]]

The Cajal Blue Brain Project is coordinated by the Technical University of Madrid led by Javier de Felipe and uses the facilities of the Supercomputing and Visualization Center of Madrid and its supercomputer Magerit.{{cite web |url= http://cajalbbp.cesvima.upm.es |title= Cajal Blue Brain Project |access-date= 2011-01-07 |archive-url= https://web.archive.org/web/20110319033234/http://cajalbbp.cesvima.upm.es/ |archive-date= 2011-03-19 |url-status= dead }} The Cajal Institute also participates in this collaboration. The main lines of research currently being pursued at Cajal Blue Brain include neurological experimentation and computer simulations.{{Cite web |title=Cajal Blue Brain Project |url=https://cajalbbp.es/ |access-date=2023-02-07 |website=cajalbbp.es}} Nanotechnology, in the form of a newly designed brain microscope, plays an important role in its research plans.{{cite web|url= http://www.azonano.com/news.asp?newsID=11626 |title=Nanotechnology Microscope for Brain Studies |date=21 May 2009 |access-date=2011-01-07}}

Noah Hutton created the documentary film In Silico over a 10-year period. The film was released in April 2021.{{cite web|url=https://filmmakermagazine.com/111872-allowing-room-for-shifts-to-happen-noah-hutton-on-the-decade-long-making-of-his-brain-science-doc-in-silico/|title= Allowing Room for Shifts to Happen: Noah Hutton on the Decade-Long Making of His Brain Science Doc In Silico|date= 21 June 2021}} The film covers the "shifting goals and landmarks"{{cite web|url=https://www.austinchronicle.com/events/film/2021-04-30/in-silico/|title= In Silico|date= 30 April 2021}} of the Blue Brain Project as well as the drama, "In the end, this isn’t about science. It’s about the universals of power, greed, ego, and fame."{{cite web|url=https://easyreadernews.com/in-silico-the-future-is-now-or-is-it-movie/|title= "In Silico" – the future is now, or is it?|date= 11 November 2020}}{{Cite journal |last=Abbott |first=Alison |date=2020-12-07 |title=Documentary follows implosion of billion-euro brain project |url=https://www.nature.com/articles/d41586-020-03462-3 |journal=Nature |language=en |volume=588 |issue=7837 |pages=215–216 |doi=10.1038/d41586-020-03462-3|pmid=33288920 |bibcode=2020Natur.588..215A |s2cid=227950069 |url-access=subscription }}

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{{Reflist}}

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• {{cite web |first=Manfred |last=Dworschak |url=http://www.spiegel.de/international/spiegel/0,1518,466789,00.html |title=Growing a Brain in Switzerland |work=Der Spiegel |date=7 February 2007}}
• {{cite web |first=Jonah |last=Lehrer |url=http://seedmagazine.com/news/2008/03/out_of_the_blue.php |archive-url=https://web.archive.org/web/20090207113305/http://seedmagazine.com/news/2008/03/out_of_the_blue.php |archive-date=2009-02-07 |title=Out of the Blue: Can a thinking, remembering, decision-making, biologically accurate brain be built from a supercomputer? |work=Seed Magazine |date=3 March 2008}}
• {{cite journal | last = Markram | first = H. | title = The blue brain project | journal = Nature Reviews. Neuroscience | volume = 7 | issue = 2 | pages = 153–60 | date = February 2006 | pmid = 16429124 | doi = 10.1038/nrn1848 | s2cid = 15752137 }}
• {{cite web | last = Ray | first= S. | 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 | date = 6 June 2005 }}

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{{Commons category|Blue Brain Project}}

• [http://bluebrain.epfl.ch/ Blue Brain Project], Lausanne.
• [https://portal.bluebrain.epfl.ch/ Blue Brain Portal] - Knowledge Space for Neuroscience.
• {{YouTube|Bz5IUaRr8No|The Blue Brain Project}}: an Interview with Idan Segev.
• [https://cajalbbp.es/press/Newsletter-2018-december.pdf Cajal Blue Brain Project].
• [https://web.archive.org/web/20070127195551/http://bluebrain.epfl.ch/page18924.html FAQ on Blue Brain].
• [https://web.archive.org/web/20060206160215/http://brain.cse.unr.edu/ncsDocs/ NCS documentation].
• [https://web.archive.org/web/20110706225700/http://ditwww.epfl.ch/cgi-perl/EPFLTV/home.pl?page=start_video&lang=2&connected=0&id=365&video_type=10&win_close=0 Reconstructing the Heart of Mammalian Intelligence] Henry Markram's Lecture, March 4, 2008.
• [https://web.archive.org/web/20140110184236/https://www.ted.com/talks/henry_markram_supercomputing_the_brain_s_secrets.html Henry Markram: A brain in a supercomputer] TED Conference. July 2009.

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