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Open Source Brain specifications

Information


Unique identifier OMICS_26286
Name Open Source Brain
Restrictions to use None
Community driven No
Data access Browse
User data submission Allowed
Registration required Yes
Maintained Yes

Documentation


Maintainer


  • person_outline Angus Silver

Additional information


http://www.opensourcebrain.org/docs#Getting_Started

Publication for Open Source Brain

Open Source Brain citations

 (11)
library_books

Credibility, Replicability, and Reproducibility in Simulation for Biomedicine and Clinical Applications in Neuroscience

2018
Front Neuroinform
PMCID: 5911506
PMID: 29713272
DOI: 10.3389/fninf.2018.00018

[…] es include the NeuroMorpho.Org database of neuronal morphologies, the ModelDB database of computational neuroscience models (see this issue) in a variety of simulation packages and languages, and the Open Source Brain database for collaborative research (, ; Gleeson et al., unpublished). We discuss these resources further in the section discussing the “Role of the Community.”A recent initiative to […]

library_books

Active contours driven by local and global fitted image models for image segmentation robust to intensity inhomogeneity

2017
PLoS One
PMCID: 5380353
PMID: 28376124
DOI: 10.1371/journal.pone.0174813

[…] In this section, the segmentation results of the proposed method are compared with three alternative open source brain MR image segmentation softwares: SPM [, ], LSF [, ] and BrainSuite [, ] using the Brain Web database. In order to compare the segmentation results, the brain region was extracted by […]

library_books

Mindboggling morphometry of human brains

2017
PLoS Comput Biol
PMCID: 5322885
PMID: 28231282
DOI: 10.1371/journal.pcbi.1005350

[…] In this article, we have documented the Mindboggle open source brain morphometry platform and demonstrated its use in studies of shape variation in healthy and diseased humans. There are many ways in which the open source software community can extend […]

library_books

Distal Spike Initiation Zone Location Estimation by Morphological Simulation of Ionic Current Filtering Demonstrated in a Novel Model of an Identified Drosophila Motoneuron

2015
PLoS Comput Biol
PMCID: 4433181
PMID: 25978332
DOI: 10.1371/journal.pcbi.1004189

[…] ributions, potential averages from spiking traces were calculated without removing individual spikes. The model neuron is available both in the ModelDB repository (accession number 152028) and in the Open Source Brain (OSB) initiative (identified as drosophila-acc-l3-motoneuron-gunay-et-al-2014).To measure distal currents in the morphology, voltage differences between nearby compartments were reco […]

library_books

BrainSignals Revisited: Simplifying a Computational Model of Cerebral Physiology

2015
PLoS One
PMCID: 4427507
PMID: 25961297
DOI: 10.1371/journal.pone.0126695

[…] Models were implemented in the open source Brain/Circulation Model Developer (BCMD) environment, a replacement for the BRAINCIRC interface with which BrainSignals was originally developed []. Like its predecessor, BCMD employs the […]

library_books

Bulbar Microcircuit Model Predicts Connectivity and Roles of Interneurons in Odor Coding

2015
PLoS One
PMCID: 4420273
PMID: 25942312
DOI: 10.1371/journal.pone.0098045

[…] ode was in Python (python.org, scipy.org, mpi4py.scipy.org). Our model and related scripts can be downloaded from Senselab ModelDB (http://senselab.med.yale.edu/ModelDB/ accession number: 153574) and Open Source Brain (http://www.opensourcebrain.org/projects/olfactory-bulb). […]

Citations

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Open Source Brain institution(s)
Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK; MetaCell Limited, Oxford, UK; Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil; Computational Neuroscience Initiative and Department of Physics and Astronomy, University of Pennsylvania, Philadelphia , PA, USA; School of Life Sciences, Arizona State University, Tempe, AZ, USA; Annotate Software Limited, Edinburgh, UK; School of Mathematical and Statistical Sciences, Arizona State University, Tempe, AZ, USA; Unité de Neuroscience, Information et Complexité, Centre National de la Recherche Scientifique, Gif-sur-Yvette, France; Kings County Hospital and Downstate Medical Center, Brooklyn, NY, USA; School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland; Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA; OpenWorm Foundation, DE, USA; University of California San Diego, La Jolla, CA, USA; Center for Medical Informatics, Yale University, New Haven, CT, USA; Department of Biomedical Science, University of Sassari, Sassari, Italy; Institute of Neuroinformatics, University of Zurich and ETH Zurich, Zurich, Switzerland; Institute of Neuroscience and Medicine (INM-6), Institute for Advanced Simulation (IAS-6) and JARA Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Germany; Blue Brain Project, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
Open Source Brain funding source(s)
Supported by the Wellcome Trust (086699, 101445, 095667), a WT PRF (203048) and an ERC advanced grant (294667), the BBSRC-NSF/BIO program (BB/N005236/1 & NSF #1458840) and NSF #1458495, the EU Marie Curie Initial Training Network CEREBNET (FP7-ITN-PEOPLE-2008; 238686), NIBIB U01EB017695, DOH01-C32250GG-3450000 and NIH R01EB022903, NIH grant DC009977 and NIH NS11613, Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP), proc. 2017/04748-0, NIH R01MH106674 and NIH R01EB021711, EU 7th Framework Program (FP7/2007-2013) under grant agreement n° 604102 (Human Brain Project, Ramp up phase) and EU Horizon 2020 research and innovation program under grant agreement n° 720270 (HBP, SGA1), and partially by the Google Summer of Code program, coordinated through the INCF.

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