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=== Blue Brain NEXUS ===
=== Blue Brain NEXUS ===
Blue Brain NEXUS<ref>{{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}}</ref><ref>{{Cite web|title=The Nexus Ecosystem: Better (Research) Data Management|url=https://bluebrainnexus.io|access-date=2021-06-04|website=bluebrainnexus.io}}</ref> is a data integration platform which allows users to search, deposit, and organise data. It stands on the [[FAIR data]] principle to provide flexible data management solutions beyond neuroscience studies. It is an [[Open-source software|open source software]] and available for everyone on [[GitHub]].<ref>{{Citation|title=BlueBrain/nexus|date=2021-06-03|url=https://github.com/BlueBrain/nexus|publisher=The Blue Brain Project|access-date=2021-06-04}}</ref>
Blue Brain NEXUS<ref>{{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}}</ref><ref>{{Cite web|title=The Nexus Ecosystem: Better (Research) Data Management|url=https://bluebrainnexus.io|access-date=2021-06-04|website=bluebrainnexus.io}}</ref> 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]] principle to provide flexible data management solutions beyond neuroscience studies. It is an [[Open-source software|open source software]] and available for everyone on [[GitHub]].<ref>{{Citation|title=BlueBrain/nexus|date=2021-06-03|url=https://github.com/BlueBrain/nexus|publisher=The Blue Brain Project|access-date=2021-06-04}}</ref>


=== BluePyOpt ===
=== BluePyOpt ===

Revision as of 16:05, 3 October 2022

The Blue Brain Project is a Swiss brain research initiative that aims to create a digital reconstruction of the mouse brain. 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, Adriana Salvatore and Sean Hill. Using a Blue Gene supercomputer running Michael Hines's NEURON, the simulation involves a biologically realistic model of neurons[1][2][3] and an empirically reconstructed model connectome.

There are a number of collaborations, 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 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]

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.[14]

Software

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

Blue Brain NEXUS

Blue Brain NEXUS[15][16] 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 principle to provide flexible data management solutions beyond neuroscience studies. It is an open source software and available for everyone on GitHub.[17]

BluePyOpt

BluePyOpt[18] 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,[19] and Stefano Masori.[20] It is an open source software and available for everyone on GitHub.[21]

CoreNEURON

CoreNEURON[22] 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.[23]

NeuroMorphoVis

NeuroMorphoVis[24] is a visualisation tool for morphologies of neurons. It is an open source software and available for everyone on GitHub.[25]

SONATA

SONATA[26] 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. It is an open source software and available for everyone on GitHub.[27][28]

Funding

The project is funded primarily by the Swiss government and the Future and Emerging Technologies (FET) Flagship grant from the European Commission,[29] 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.[30]

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.[31] 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.[32]

Documentary

Noah Hutton created the documentary film In Silico over a 10-year period. The film was released in April 2021.[33]The film covers the "shifting goals and landmarks"[34] 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."[35]

See also

References

  1. ^ Graham-Rowe D (June 2005). "Mission to build a simulated brain begins". NewScientist.
  2. ^ Palmer, Jason. Simulated brain closer to thought, BBC News.
  3. ^ Segev I. "ASC 2012: Prof. Idan Segev - The blue brain". The Hebrew University of Jerusalem. Archived from the original on 2021-12-21. Retrieved 31 May 2013.
  4. ^ "Project Milestones". Blue Brain. Retrieved 2008-08-11.
  5. ^ Horton JC, Adams DL (April 2005). "The cortical column: a structure without a function". Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 360 (1456): 837–62. doi:10.1098/rstb.2005.1623. PMC 1569491. PMID 15937015.
  6. ^ Rakic P (August 2008). "Confusing cortical columns". Proceedings of the National Academy of Sciences of the United States of America. 105 (34): 12099–100. Bibcode:2008PNAS..10512099R. doi:10.1073/pnas.0807271105. PMC 2527871. PMID 18715998.
  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". YouTube. Retrieved 2011-08-29.[dead YouTube link]
  9. ^ "News and Media information". Blue Brain. Archived from the original on 2008-09-19. Retrieved 2008-08-11.
  10. ^ Jolivet R, Coggan JS, Allaman I, Magistretti PJ (February 2015). "Multi-timescale modeling of activity-dependent metabolic coupling in the neuron-glia-vasculature ensemble". PLOS Computational Biology. 11 (2): e1004036. Bibcode:2015PLSCB..11E4036J. doi:10.1371/journal.pcbi.1004036. PMC 4342167. PMID 25719367.
  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. ^ "Brain in the computer: What did I learn from simulating the brain - Idan Segev". YouTube.
  14. ^ Blue Brain builds neurons with mathematics Kate Mullins, EPFL news. June 4th, 2022
  15. ^ "Building the Blue Brain Nexus". Informatics from Technology Networks. Retrieved 2021-06-04.
  16. ^ "The Nexus Ecosystem: Better (Research) Data Management". bluebrainnexus.io. Retrieved 2021-06-04.
  17. ^ BlueBrain/nexus, The Blue Brain Project, 2021-06-03, retrieved 2021-06-04
  18. ^ Van Geit W, Gevaert M, Chindemi G, Rössert C, Courcol JD, Muller EB, et al. (2016). "BluePyOpt: Leveraging Open Source Software and Cloud Infrastructure to Optimise Model Parameters in Neuroscience". Frontiers in Neuroinformatics. 10: 17. arXiv:1603.00500. doi:10.3389/fninf.2016.00017. PMC 4896051. PMID 27375471.
  19. ^ Migliore R, Lupascu CA, Bologna LL, Romani A, Courcol JD, Antonel S, et al. (September 2018). "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. Bibcode:2018PLSCB..14E6423M. doi:10.1371/journal.pcbi.1006423. PMC 6160220. PMID 30222740.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  20. ^ Masoli S, Rizza MF, Sgritta M, Van Geit W, Schürmann F, D'Angelo E (2017). "Single Neuron Optimization as a Basis for Accurate Biophysical Modeling: The Case of Cerebellar Granule Cells". Frontiers in Cellular Neuroscience. 11: 71. doi:10.3389/fncel.2017.00071. PMC 5350144. PMID 28360841.
  21. ^ BlueBrain/BluePyOpt, The Blue Brain Project, 2020-12-16, retrieved 2020-12-16
  22. ^ Kumbhar P, Hines M, Fouriaux J, Ovcharenko A, King J, Delalondre F, Schürmann F (2019). "CoreNEURON : An Optimized Compute Engine for the NEURON Simulator". Frontiers in Neuroinformatics. 13: 63. arXiv:1901.10975. doi:10.3389/fninf.2019.00063. PMC 6763692. PMID 31616273.
  23. ^ BlueBrain/CoreNeuron, The Blue Brain Project, 2020-12-15, retrieved 2020-12-16
  24. ^ Abdellah M, Hernando J, Eilemann S, Lapere S, Antille N, Markram H, Schürmann F (July 2018). "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. PMC 6022592. PMID 29949998.
  25. ^ BlueBrain/NeuroMorphoVis, The Blue Brain Project, 2020-12-15, retrieved 2020-12-16
  26. ^ Dai K, Hernando J, Billeh YN, Gratiy SL, Planas J, Davison AP, et al. (February 2020). "The SONATA data format for efficient description of large-scale network models". PLOS Computational Biology. 16 (2): e1007696. Bibcode:2020PLSCB..16E7696D. doi:10.1371/journal.pcbi.1007696. PMC 7058350. PMID 32092054.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  27. ^ BlueBrain/sonata, The Blue Brain Project, 2018-04-28, retrieved 2020-12-24
  28. ^ AllenInstitute/sonata, Allen Institute, 2020-12-02, retrieved 2020-12-24
  29. ^ Abbott A (23 January 2013). "Brain-simulation and graphene projects win billion-euro competition". Nature. doi:10.1038/nature.2013.12291. S2CID 61977896.
  30. ^ "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.
  31. ^ "Cajal Blue Brain Project". Archived from the original on 2011-03-19. Retrieved 2011-01-07.
  32. ^ "Nanotechnology Microscope for Brain Studies". 21 May 2009. Retrieved 2011-01-07.
  33. ^ "Allowing Room for Shifts to Happen: Noah Hutton on the Decade-Long Making of His Brain Science Doc In Silico". 21 June 2021.
  34. ^ "In Silico". 30 April 2021.
  35. ^ ""In Silico" – the future is now, or is it?". 11 November 2020.

Further reading

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