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=== BluePyOpt ===
=== BluePyOpt ===
BluePyOpt<ref>{{Cite journal|last=Van Geit|first=Werner|last2=Gevaert|first2=Michael|last3=Chindemi|first3=Giuseppe|last4=Rössert|first4=Christian|last5=Courcol|first5=Jean-Denis|last6=Muller|first6=Eilif B.|last7=Schürmann|first7=Felix|last8=Segev|first8=Idan|last9=Markram|first9=Henry|date=2016|title=BluePyOpt: Leveraging Open Source Software and Cloud Infrastructure to Optimise Model Parameters in Neuroscience|url=https://www.frontiersin.org/articles/10.3389/fninf.2016.00017/full|journal=Frontiers in Neuroinformatics|language=English|volume=10|doi=10.3389/fninf.2016.00017|issn=1662-5196}}</ref> is a tool that is used to build electrical models of single neurons. For this, it uses [[Evolutionary algorithm|evolutionary algorithms]] to constrain the parameters to experimental electrophysiological data. It is open source and available for everyone on [[GitHub]]<ref>{{Citation|title=BlueBrain/BluePyOpt|date=2020-12-16|url=https://github.com/BlueBrain/BluePyOpt|publisher=The Blue Brain Project|access-date=2020-12-16}}</ref>.
BluePyOpt<ref>{{Cite journal|last=Van Geit|first=Werner|last2=Gevaert|first2=Michael|last3=Chindemi|first3=Giuseppe|last4=Rössert|first4=Christian|last5=Courcol|first5=Jean-Denis|last6=Muller|first6=Eilif B.|last7=Schürmann|first7=Felix|last8=Segev|first8=Idan|last9=Markram|first9=Henry|date=2016|title=BluePyOpt: Leveraging Open Source Software and Cloud Infrastructure to Optimise Model Parameters in Neuroscience|url=https://www.frontiersin.org/articles/10.3389/fninf.2016.00017/full|journal=Frontiers in Neuroinformatics|language=English|volume=10|doi=10.3389/fninf.2016.00017|issn=1662-5196}}</ref> is a tool that is used to build electrical models of single neurons. For this, it uses [[Evolutionary algorithm|evolutionary algorithms]] to constrain the parameters to experimental electrophysiological data. It is an [[Open-source software|open source software]] and available for everyone on [[GitHub]]<ref>{{Citation|title=BlueBrain/BluePyOpt|date=2020-12-16|url=https://github.com/BlueBrain/BluePyOpt|publisher=The Blue Brain Project|access-date=2020-12-16}}</ref>. Attempts to reconstruct single neutrons using BluePyOpt are reported by [[Rosanna Migliore]]<ref>{{Cite journal|last=Migliore|first=Rosanna|last2=Lupascu|first2=Carmen A.|last3=Bologna|first3=Luca L.|last4=Romani|first4=Armando|last5=Courcol|first5=Jean-Denis|last6=Antonel|first6=Stefano|last7=Van Geit|first7=Werner A. H.|last8=Thomson|first8=Alex M.|last9=Mercer|first9=Audrey|last10=Lange|first10=Sigrun|last11=Falck|first11=Joanne|date=2018-09-17|title=The physiological variability of channel density in hippocampal CA1 pyramidal cells and interneurons explored using a unified data-driven modeling workflow|url=https://journals.plos.org/ploscompbiol/article?rev=2&id=10.1371/journal.pcbi.1006423|journal=PLOS Computational Biology|volume=14|issue=9|pages=e1006423|doi=10.1371/journal.pcbi.1006423|issn=1553-7358|pmc=PMC6160220|pmid=30222740}}</ref>, and [[Stephano Masori]]<ref>{{Cite journal|last=Masoli|first=Stefano|last2=Rizza|first2=Martina F.|last3=Sgritta|first3=Martina|last4=Van Geit|first4=Werner|last5=Schürmann|first5=Felix|last6=D'Angelo|first6=Egidio|date=2017|title=Single Neuron Optimization as a Basis for Accurate Biophysical Modeling: The Case of Cerebellar Granule Cells|url=https://www.frontiersin.org/articles/10.3389/fncel.2017.00071/full|journal=Frontiers in Cellular Neuroscience|language=English|volume=11|doi=10.3389/fncel.2017.00071|issn=1662-5102}}</ref>.


=== CoreNEURON ===
=== CoreNEURON ===
CoreNEURON<ref>{{Cite journal|last=Kumbhar|first=Pramod|last2=Hines|first2=Michael|last3=Fouriaux|first3=Jeremy|last4=Ovcharenko|first4=Aleksandr|last5=King|first5=James|last6=Delalondre|first6=Fabien|last7=Schürmann|first7=Felix|date=2019|title=CoreNEURON : An Optimized Compute Engine for the NEURON Simulator|url=https://www.frontiersin.org/articles/10.3389/fninf.2019.00063/full|journal=Frontiers in Neuroinformatics|language=English|volume=13|doi=10.3389/fninf.2019.00063|issn=1662-5196}}</ref> is a supplemental tool to [[Neuron (software)|NEURON]], which allows large scale simulation by boosting memory usage and computational speed. It is open source and is available to everyone through [[GitHub]] <ref>{{Citation|title=BlueBrain/CoreNeuron|date=2020-12-15|url=https://github.com/BlueBrain/CoreNeuron|publisher=The Blue Brain Project|access-date=2020-12-16}}</ref>.
CoreNEURON<ref>{{Cite journal|last=Kumbhar|first=Pramod|last2=Hines|first2=Michael|last3=Fouriaux|first3=Jeremy|last4=Ovcharenko|first4=Aleksandr|last5=King|first5=James|last6=Delalondre|first6=Fabien|last7=Schürmann|first7=Felix|date=2019|title=CoreNEURON : An Optimized Compute Engine for the NEURON Simulator|url=https://www.frontiersin.org/articles/10.3389/fninf.2019.00063/full|journal=Frontiers in Neuroinformatics|language=English|volume=13|doi=10.3389/fninf.2019.00063|issn=1662-5196}}</ref> is a supplemental tool to [[Neuron (software)|NEURON]], which allows large scale simulation by boosting memory usage and computational speed. It is an [[Open-source software|open source software]] and available for everyone on [[GitHub]] <ref>{{Citation|title=BlueBrain/CoreNeuron|date=2020-12-15|url=https://github.com/BlueBrain/CoreNeuron|publisher=The Blue Brain Project|access-date=2020-12-16}}</ref>.


=== NeuroMorphoVis ===
=== NeuroMorphoVis ===
NeuroMorphoVis<ref>{{Cite journal|last=Abdellah|first=Marwan|last2=Hernando|first2=Juan|last3=Eilemann|first3=Stefan|last4=Lapere|first4=Samuel|last5=Antille|first5=Nicolas|last6=Markram|first6=Henry|last7=Schürmann|first7=Felix|date=2018-07-01|title=NeuroMorphoVis: a collaborative framework for analysis and visualization of neuronal morphology skeletons reconstructed from microscopy stacks|url=https://academic.oup.com/bioinformatics/article/34/13/i574/5045775|journal=Bioinformatics|language=en|volume=34|issue=13|pages=i574–i582|doi=10.1093/bioinformatics/bty231|issn=1367-4803}}</ref> is a visualisation tool for morphologies of neurons. It is open source and available for everyone on [[GitHub]]<ref>{{Citation|title=BlueBrain/NeuroMorphoVis|date=2020-12-15|url=https://github.com/BlueBrain/NeuroMorphoVis|publisher=The Blue Brain Project|access-date=2020-12-16}}</ref>
NeuroMorphoVis<ref>{{Cite journal|last=Abdellah|first=Marwan|last2=Hernando|first2=Juan|last3=Eilemann|first3=Stefan|last4=Lapere|first4=Samuel|last5=Antille|first5=Nicolas|last6=Markram|first6=Henry|last7=Schürmann|first7=Felix|date=2018-07-01|title=NeuroMorphoVis: a collaborative framework for analysis and visualization of neuronal morphology skeletons reconstructed from microscopy stacks|url=https://academic.oup.com/bioinformatics/article/34/13/i574/5045775|journal=Bioinformatics|language=en|volume=34|issue=13|pages=i574–i582|doi=10.1093/bioinformatics/bty231|issn=1367-4803}}</ref> is a visualisation tool for morphologies of neurons. It is an [[Open-source software|open source software]] and available for everyone on[[GitHub]]<ref>{{Citation|title=BlueBrain/NeuroMorphoVis|date=2020-12-15|url=https://github.com/BlueBrain/NeuroMorphoVis|publisher=The Blue Brain Project|access-date=2020-12-16}}</ref>


== Funding ==
== Funding ==

Revision as of 15:57, 16 December 2020

The Blue Brain Project is a Swiss brain research initiative that aims to create a digital reconstruction of rodent and eventually human brains by reverse-engineering mammalian brain circuitry. The project was founded in May 2005 by the Brain and Mind Institute of École Polytechnique Fédérale de Lausanne (EPFL) in Switzerland. Its mission is to use biologically-detailed digital reconstructions and simulations of the mammalian brain to identify the fundamental principles of brain structure and function.

The project is headed by the founding director Henry Markram—who also launched the European Human Brain Project—and is co-directed by Felix Schürmann and Sean Hill. Using a Blue Gene supercomputer running Michael Hines's NEURON software, the simulation involves a biologically realistic model of neurons[1][2][3] and an empirically reconstructed model connectome. It is hoped that it will eventually shed light on the nature of consciousness.[3]

There are a number of sub-projects, including the Cajal Blue Brain, which is coordinated by the Supercomputing and Visualization Center of Madrid (CeSViMa), and others run by universities and independent laboratories.

Goal

The initial goal of the project, which was completed in December 2006,[4] was the creation of a simulated rat neocortical column, which is considered by some researchers to be the smallest functional unit of the neocortex,[5][6] which is thought to be responsible for higher functions such as conscious thought. In humans, each column is about 2 mm (0.079 in) in length, has a diameter of 0.5 mm (0.020 in) and contains about 60,000 neurons. Rat neocortical columns are very similar in structure but contain only 10,000 neurons and 108 synapses. Between 1995 and 2005, Markram mapped the types of neurons and their connections in such a column.

Progress

By 2005, the first cellular model was completed. The first artificial cellular neocortical column of 10,000 cells was built by 2008. By July 2011, a cellular mesocircuit of 100 neocortical columns with a million cells in total was built. A cellular rat brain had been planned[needs update] for 2014 with 100 mesocircuits totalling a hundred million cells. A cellular human brain equivalent to 1,000 rat brains with a total of a hundred billion cells has been predicted to be possible by 2023.[7][8]

In 2005, the project was publishing its initial results in scientific literature and aiming to construct a simulation on the molecular level,[1] which will allow studying the effects of gene expression. It also aimed to simplify the column simulation to allow parallel simulation of large numbers of connected columns with the ultimate goal of simulating a whole neocortex, which in humans consists of about a million cortical columns.[citation needed]

In November 2007,[9] the project reported the end of the first phase, delivering a data-driven process for creating, validating, and researching the neocortical column.

In 2015, scientists at École Polytechnique Fédérale de Lausanne (EPFL) developed a quantitative model of the previously unknown relationship between the glial cell astrocytes and neurons. This model describes the energy management of the brain through the function of the neuro-glial vascular unit (NGV). The additional layer of neuron-glial cells is being added to Blue Brain Project models to improve functionality of the system.[10]

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 networks cannot detect that many dimensions. The Blue Brain Project was able to model these networks using algebraic topology.[11]

In 2018, Blue Brain Project released its first digital 3D brain cell atlas 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.[12]

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).[13]

Software

The Blue Brain Project has developed a number of software to reconstruct and to simulate brain.

BluePyOpt

BluePyOpt[14] 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. It is an open source software and available for everyone on GitHub[15]. Attempts to reconstruct single neutrons using BluePyOpt are reported by Rosanna Migliore[16], and Stephano Masori[17].

CoreNEURON

CoreNEURON[18] is a supplemental tool to NEURON, which allows large scale simulation by boosting memory usage and computational speed. It is an open source software and available for everyone on GitHub [19].

NeuroMorphoVis

NeuroMorphoVis[20] is a visualisation tool for morphologies of neurons. It is an open source software and available for everyone onGitHub[21]

Funding

The project is funded primarily by the Swiss government and the Future and Emerging Technologies (FET) Flagship grant from the European Commission,[22] 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.[23]

Related projects

Cajal Blue Brain

Cajal Blue Brain used the Magerit supercomputer (CeSViMa)

The Cajal Blue Brain Project is coordinated by the Technical University of Madrid and uses the facilities of the Supercomputing and Visualization Center of Madrid and its supercomputer Magerit.[24] 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. Nanotechnology, in the form of a newly designed brain microscope, plays an important role in its research plans.[25]

Documentary

A 10-part documentary is being made by Noah Hutton; each installment will explore the year-long workings of the project at the EPFL. Filming began in 2009, and the documentary is planned to be released in 2020. Other similar research projects are also mentioned.[26]

See also

References

  1. ^ a b Graham-Rowe, Duncan. "Mission to build a simulated brain begins", NewScientist, June 2005.
  2. ^ Palmer, Jason. Simulated brain closer to thought, BBC News.
  3. ^ a b Segev, Idan. "ASC 2012: Prof. Idan Segev - The blue brain". The Hebrew University of Jerusalem. Retrieved 31 May 2013.
  4. ^ "Project Milestones". Blue Brain. Retrieved 2008-08-11.
  5. ^ Horton, Jonathan C; Adams, Daniel L (29 April 2005). "The cortical column: a structure without a function". Philosophical Transactions of the Royal Society B: Biological Sciences. 360 (1456): 837–862. doi:10.1098/rstb.2005.1623. PMC 1569491. PMID 15937015.
  6. ^ Rakic, P. (20 August 2008). "Confusing cortical columns". Proceedings of the National Academy of Sciences. 105 (34): 12099–12100. doi:10.1073/pnas.0807271105.
  7. ^ "Henry Markram: Simulating the brain; the next decisive years, video [3/3] 07:00". Retrieved 2011-08-29.
  8. ^ "Henry Markram: Simulating the brain; the next decisive years - 07:00". Retrieved 2011-08-29.
  9. ^ "News and Media information". Blue Brain. Archived from the original on 2008-09-19. Retrieved 2008-08-11.
  10. ^ Jolivet, Renaud; Coggan, Jay S.; Allaman, Igor; Magistretti, Pierre J.; Graham, Lyle (26 February 2015). "Multi-timescale Modeling of Activity-Dependent Metabolic Coupling in the Neuron-Glia-Vasculature Ensemble". PLOS Computational Biology. 11 (2): e1004036. doi:10.1371/journal.pcbi.1004036.
  11. ^ "Blue Brain Team Discovers a Multi-Dimensional Universe in Brain Networks". Frontiers Science News, June 12, 2017.
  12. ^ "Blue Brain Project releases first-ever digital 3D brain cell atlas". ScienceDaily. November 28, 2018. Retrieved 18 April 2019.
  13. ^ https://www.youtube.com/watch?v=sEiDxti0opE
  14. ^ Van Geit, Werner; Gevaert, Michael; Chindemi, Giuseppe; Rössert, Christian; Courcol, Jean-Denis; Muller, Eilif B.; Schürmann, Felix; Segev, Idan; Markram, Henry (2016). "BluePyOpt: Leveraging Open Source Software and Cloud Infrastructure to Optimise Model Parameters in Neuroscience". Frontiers in Neuroinformatics. 10. doi:10.3389/fninf.2016.00017. ISSN 1662-5196.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  15. ^ BlueBrain/BluePyOpt, The Blue Brain Project, 2020-12-16, retrieved 2020-12-16
  16. ^ Migliore, Rosanna; Lupascu, Carmen A.; Bologna, Luca L.; Romani, Armando; Courcol, Jean-Denis; Antonel, Stefano; Van Geit, Werner A. H.; Thomson, Alex M.; Mercer, Audrey; Lange, Sigrun; Falck, Joanne (2018-09-17). "The physiological variability of channel density in hippocampal CA1 pyramidal cells and interneurons explored using a unified data-driven modeling workflow". PLOS Computational Biology. 14 (9): e1006423. doi:10.1371/journal.pcbi.1006423. ISSN 1553-7358. PMC 6160220. PMID 30222740.{{cite journal}}: CS1 maint: PMC format (link) CS1 maint: unflagged free DOI (link)
  17. ^ Masoli, Stefano; Rizza, Martina F.; Sgritta, Martina; Van Geit, Werner; Schürmann, Felix; D'Angelo, Egidio (2017). "Single Neuron Optimization as a Basis for Accurate Biophysical Modeling: The Case of Cerebellar Granule Cells". Frontiers in Cellular Neuroscience. 11. doi:10.3389/fncel.2017.00071. ISSN 1662-5102.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  18. ^ Kumbhar, Pramod; Hines, Michael; Fouriaux, Jeremy; Ovcharenko, Aleksandr; King, James; Delalondre, Fabien; Schürmann, Felix (2019). "CoreNEURON : An Optimized Compute Engine for the NEURON Simulator". Frontiers in Neuroinformatics. 13. doi:10.3389/fninf.2019.00063. ISSN 1662-5196.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  19. ^ BlueBrain/CoreNeuron, The Blue Brain Project, 2020-12-15, retrieved 2020-12-16
  20. ^ Abdellah, Marwan; Hernando, Juan; Eilemann, Stefan; Lapere, Samuel; Antille, Nicolas; Markram, Henry; Schürmann, Felix (2018-07-01). "NeuroMorphoVis: a collaborative framework for analysis and visualization of neuronal morphology skeletons reconstructed from microscopy stacks". Bioinformatics. 34 (13): i574–i582. doi:10.1093/bioinformatics/bty231. ISSN 1367-4803.
  21. ^ BlueBrain/NeuroMorphoVis, The Blue Brain Project, 2020-12-15, retrieved 2020-12-16
  22. ^ Abbott, Alison (23 January 2013). "Brain-simulation and graphene projects win billion-euro competition". Nature. doi:10.1038/nature.2013.12291.
  23. ^ "Blue Brain Project - IBM has not withdrawn support". Henry Markram, Project Director as quoted by IBM Switzerland to Technology Report on January 19, 2009. Retrieved 2009-04-14.
  24. ^ "Cajal Blue Brain Project". Archived from the original on 2011-03-19. Retrieved 2011-01-07.
  25. ^ "Nanotechnology Microscope for Brain Studies". Retrieved 2011-01-07.
  26. ^ "Blue Brain Film Information".

Further reading

Wikimedia Commons has media related to Blue Brain Project.

External links

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