Search Results - "standalone python code"

The format of FEM output. We list only those fields which are used by BlueRecording.

Authors: Joseph James Tharayil Jorge Blanco Alonso Silvia Farcito et al.

Subject Terms: Biophysics, Cell Biology, Genetics, Neuroscience, Physiology, Biotechnology, Evolutionary Biology, Developmental Biology, Cancer, Space Science, Biological Sciences not elsewhere classified, Mathematical Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, standalone python code, sonata data format, rat somatosensory cortex, new avenues open, network simulations accessible, coreneuron computation engine, computational neuroscience grows, complex tissue anatomy, permit online calculation, signal information content, e ., non, simulate eeg recordings, enable efficient calculation, div >< p, dipolar current sources

Relation: https://figshare.com/articles/journal_contribution/The_format_of_FEM_output_We_list_only_those_fields_which_are_used_by_BlueRecording_/29138112

Availability: https://doi.org/10.1371/journal.pcbi.1013023.s005
https://figshare.com/articles/journal_contribution/The_format_of_FEM_output_We_list_only_those_fields_which_are_used_by_BlueRecording_/29138112

Methods for the generation of finite element meshes and simulation of electric fields.

Authors: Joseph James Tharayil Jorge Blanco Alonso Silvia Farcito et al.

Subject Terms: Biophysics, Cell Biology, Genetics, Neuroscience, Physiology, Biotechnology, Evolutionary Biology, Developmental Biology, Cancer, Space Science, Biological Sciences not elsewhere classified, Mathematical Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, standalone python code, sonata data format, rat somatosensory cortex, new avenues open, network simulations accessible, coreneuron computation engine, computational neuroscience grows, complex tissue anatomy, permit online calculation, signal information content, e ., non, simulate eeg recordings, enable efficient calculation, div >< p, dipolar current sources

Relation: https://figshare.com/articles/journal_contribution/Methods_for_the_generation_of_finite_element_meshes_and_simulation_of_electric_fields_/29138100

Availability: https://doi.org/10.1371/journal.pcbi.1013023.s001
https://figshare.com/articles/journal_contribution/Methods_for_the_generation_of_finite_element_meshes_and_simulation_of_electric_fields_/29138100

Methods for the input of current or conductance noise to the model.

Authors: Joseph James Tharayil Jorge Blanco Alonso Silvia Farcito et al.

Subject Terms: Biophysics, Cell Biology, Genetics, Neuroscience, Physiology, Biotechnology, Evolutionary Biology, Developmental Biology, Cancer, Space Science, Biological Sciences not elsewhere classified, Mathematical Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, standalone python code, sonata data format, rat somatosensory cortex, new avenues open, network simulations accessible, coreneuron computation engine, computational neuroscience grows, complex tissue anatomy, permit online calculation, signal information content, e ., non, simulate eeg recordings, enable efficient calculation, div >< p, dipolar current sources

Relation: https://figshare.com/articles/journal_contribution/Methods_for_the_input_of_current_or_conductance_noise_to_the_model_/29138103

Availability: https://doi.org/10.1371/journal.pcbi.1013023.s002
https://figshare.com/articles/journal_contribution/Methods_for_the_input_of_current_or_conductance_noise_to_the_model_/29138103

Methods for the generation of finite element meshes and simulation of electric fields.

Authors: Joseph James Tharayil Jorge Blanco Alonso Silvia Farcito et al.

Subject Terms: Biophysics, Cell Biology, Genetics, Neuroscience, Physiology, Biotechnology, Evolutionary Biology, Developmental Biology, Cancer, Space Science, Biological Sciences not elsewhere classified, Mathematical Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, standalone python code, sonata data format, rat somatosensory cortex, new avenues open, network simulations accessible, coreneuron computation engine, computational neuroscience grows, complex tissue anatomy, permit online calculation, signal information content, e ., non, simulate eeg recordings, enable efficient calculation, div >< p, dipolar current sources

Relation: https://figshare.com/articles/journal_contribution/Methods_for_the_generation_of_finite_element_meshes_and_simulation_of_electric_fields_/29138100

Availability: https://doi.org/10.1371/journal.pcbi.1013023.s001
https://figshare.com/articles/journal_contribution/Methods_for_the_generation_of_finite_element_meshes_and_simulation_of_electric_fields_/29138100

The format of FEM output. We list only those fields which are used by BlueRecording.

Authors: Joseph James Tharayil Jorge Blanco Alonso Silvia Farcito et al.

Subject Terms: Biophysics, Cell Biology, Genetics, Neuroscience, Physiology, Biotechnology, Evolutionary Biology, Developmental Biology, Cancer, Space Science, Biological Sciences not elsewhere classified, Mathematical Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, standalone python code, sonata data format, rat somatosensory cortex, new avenues open, network simulations accessible, coreneuron computation engine, computational neuroscience grows, complex tissue anatomy, permit online calculation, signal information content, e ., non, simulate eeg recordings, enable efficient calculation, div >< p, dipolar current sources

Relation: https://figshare.com/articles/journal_contribution/The_format_of_FEM_output_We_list_only_those_fields_which_are_used_by_BlueRecording_/29138112

Availability: https://doi.org/10.1371/journal.pcbi.1013023.s005
https://figshare.com/articles/journal_contribution/The_format_of_FEM_output_We_list_only_those_fields_which_are_used_by_BlueRecording_/29138112

Methods for the input of current or conductance noise to the model.

Authors: Joseph James Tharayil Jorge Blanco Alonso Silvia Farcito et al.

Subject Terms: Biophysics, Cell Biology, Genetics, Neuroscience, Physiology, Biotechnology, Evolutionary Biology, Developmental Biology, Cancer, Space Science, Biological Sciences not elsewhere classified, Mathematical Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, standalone python code, sonata data format, rat somatosensory cortex, new avenues open, network simulations accessible, coreneuron computation engine, computational neuroscience grows, complex tissue anatomy, permit online calculation, signal information content, e ., non, simulate eeg recordings, enable efficient calculation, div >< p, dipolar current sources

Relation: https://figshare.com/articles/journal_contribution/Methods_for_the_input_of_current_or_conductance_noise_to_the_model_/29138103

Availability: https://doi.org/10.1371/journal.pcbi.1013023.s002
https://figshare.com/articles/journal_contribution/Methods_for_the_input_of_current_or_conductance_noise_to_the_model_/29138103

Simplified calculation methods produce inaccurate signals.

Authors: Joseph James Tharayil Jorge Blanco Alonso Silvia Farcito et al.

Subject Terms: Biophysics, Cell Biology, Genetics, Neuroscience, Physiology, Biotechnology, Evolutionary Biology, Developmental Biology, Cancer, Space Science, Biological Sciences not elsewhere classified, Mathematical Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, standalone python code, sonata data format, rat somatosensory cortex, new avenues open, network simulations accessible, coreneuron computation engine, computational neuroscience grows, complex tissue anatomy, permit online calculation, signal information content, e ., non, simulate eeg recordings, enable efficient calculation, div >< p, dipolar current sources

Relation: https://figshare.com/articles/figure/Simplified_calculation_methods_produce_inaccurate_signals_/29138127

Availability: https://doi.org/10.1371/journal.pcbi.1013023.g005
https://figshare.com/articles/figure/Simplified_calculation_methods_produce_inaccurate_signals_/29138127

The format of the simulation reports

Authors: Joseph James Tharayil Jorge Blanco Alonso Silvia Farcito et al.

Subject Terms: Biophysics, Cell Biology, Genetics, Neuroscience, Physiology, Biotechnology, Evolutionary Biology, Developmental Biology, Cancer, Space Science, Biological Sciences not elsewhere classified, Mathematical Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, standalone python code, sonata data format, rat somatosensory cortex, new avenues open, network simulations accessible, coreneuron computation engine, computational neuroscience grows, complex tissue anatomy, permit online calculation, signal information content, e ., non, simulate eeg recordings, enable efficient calculation, div >< p, dipolar current sources

Relation: https://figshare.com/articles/dataset/The_format_of_the_simulation_reports/29138142

Availability: https://doi.org/10.1371/journal.pcbi.1013023.t003
https://figshare.com/articles/dataset/The_format_of_the_simulation_reports/29138142

Comparison of BlueRecording with existing tools

Authors: Joseph James Tharayil Jorge Blanco Alonso Silvia Farcito et al.

Subject Terms: Biophysics, Cell Biology, Genetics, Neuroscience, Physiology, Biotechnology, Evolutionary Biology, Developmental Biology, Cancer, Space Science, Biological Sciences not elsewhere classified, Mathematical Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, standalone python code, sonata data format, rat somatosensory cortex, new avenues open, network simulations accessible, coreneuron computation engine, computational neuroscience grows, complex tissue anatomy, permit online calculation, signal information content, e ., non, simulate eeg recordings, enable efficient calculation, div >< p, dipolar current sources

Relation: https://figshare.com/articles/dataset/Comparison_of_BlueRecording_with_existing_tools/29138145

Availability: https://doi.org/10.1371/journal.pcbi.1013023.t004
https://figshare.com/articles/dataset/Comparison_of_BlueRecording_with_existing_tools/29138145

BlueRecording simulates whisker-flick EEG.

Authors: Joseph James Tharayil Jorge Blanco Alonso Silvia Farcito et al.

Subject Terms: Biophysics, Cell Biology, Genetics, Neuroscience, Physiology, Biotechnology, Evolutionary Biology, Developmental Biology, Cancer, Space Science, Biological Sciences not elsewhere classified, Mathematical Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, standalone python code, sonata data format, rat somatosensory cortex, new avenues open, network simulations accessible, coreneuron computation engine, computational neuroscience grows, complex tissue anatomy, permit online calculation, signal information content, e ., non, simulate eeg recordings, enable efficient calculation, div >< p, dipolar current sources

Availability: https://doi.org/10.1371/journal.pcbi.1013023.g006
https://figshare.com/articles/figure/BlueRecording_simulates_whisker-flick_EEG_/29138130

The format of the weights file

Authors: Joseph James Tharayil Jorge Blanco Alonso Silvia Farcito et al.

Subject Terms: Biophysics, Cell Biology, Genetics, Neuroscience, Physiology, Biotechnology, Evolutionary Biology, Developmental Biology, Cancer, Space Science, Biological Sciences not elsewhere classified, Mathematical Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, standalone python code, sonata data format, rat somatosensory cortex, new avenues open, network simulations accessible, coreneuron computation engine, computational neuroscience grows, complex tissue anatomy, permit online calculation, signal information content, e ., non, simulate eeg recordings, enable efficient calculation, div >< p, dipolar current sources

Relation: https://figshare.com/articles/dataset/The_format_of_the_weights_file/29138136

Availability: https://doi.org/10.1371/journal.pcbi.1013023.t001
https://figshare.com/articles/dataset/The_format_of_the_weights_file/29138136

Differences in compartment weights explain differences between EEG and ECoG.

Authors: Joseph James Tharayil Jorge Blanco Alonso Silvia Farcito et al.

Subject Terms: Biophysics, Cell Biology, Genetics, Neuroscience, Physiology, Biotechnology, Evolutionary Biology, Developmental Biology, Cancer, Space Science, Biological Sciences not elsewhere classified, Mathematical Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, standalone python code, sonata data format, rat somatosensory cortex, new avenues open, network simulations accessible, coreneuron computation engine, computational neuroscience grows, complex tissue anatomy, permit online calculation, signal information content, e ., non, simulate eeg recordings, enable efficient calculation, div >< p, dipolar current sources

Relation: https://figshare.com/articles/figure/Differences_in_compartment_weights_explain_differences_between_EEG_and_ECoG_/29138124

Availability: https://doi.org/10.1371/journal.pcbi.1013023.g004
https://figshare.com/articles/figure/Differences_in_compartment_weights_explain_differences_between_EEG_and_ECoG_/29138124

BlueRecording simulates resting-state EEG in the rat SSCx model.

Authors: Joseph James Tharayil Jorge Blanco Alonso Silvia Farcito et al.

Subject Terms: Biophysics, Cell Biology, Genetics, Neuroscience, Physiology, Biotechnology, Evolutionary Biology, Developmental Biology, Cancer, Space Science, Biological Sciences not elsewhere classified, Mathematical Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, standalone python code, sonata data format, rat somatosensory cortex, new avenues open, network simulations accessible, coreneuron computation engine, computational neuroscience grows, complex tissue anatomy, permit online calculation, signal information content, e ., non, simulate eeg recordings, enable efficient calculation, div >< p, dipolar current sources

Availability: https://doi.org/10.1371/journal.pcbi.1013023.g003
https://figshare.com/articles/figure/BlueRecording_simulates_resting-state_EEG_in_the_rat_SSCx_model_/29138121

The format of the electrode csv file

Authors: Joseph James Tharayil Jorge Blanco Alonso Silvia Farcito et al.

Subject Terms: Biophysics, Cell Biology, Genetics, Neuroscience, Physiology, Biotechnology, Evolutionary Biology, Developmental Biology, Cancer, Space Science, Biological Sciences not elsewhere classified, Mathematical Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, standalone python code, sonata data format, rat somatosensory cortex, new avenues open, network simulations accessible, coreneuron computation engine, computational neuroscience grows, complex tissue anatomy, permit online calculation, signal information content, e ., non, simulate eeg recordings, enable efficient calculation, div >< p, dipolar current sources

Relation: https://figshare.com/articles/dataset/The_format_of_the_electrode_csv_file/29138139

Availability: https://doi.org/10.1371/journal.pcbi.1013023.t002
https://figshare.com/articles/dataset/The_format_of_the_electrode_csv_file/29138139

Workflow for the BlueRecording Pipeline.

Authors: Joseph James Tharayil Jorge Blanco Alonso Silvia Farcito et al.

Subject Terms: Biophysics, Cell Biology, Genetics, Neuroscience, Physiology, Biotechnology, Evolutionary Biology, Developmental Biology, Cancer, Space Science, Biological Sciences not elsewhere classified, Mathematical Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, standalone python code, sonata data format, rat somatosensory cortex, new avenues open, network simulations accessible, coreneuron computation engine, computational neuroscience grows, complex tissue anatomy, permit online calculation, signal information content, e ., non, simulate eeg recordings, enable efficient calculation, div >< p, dipolar current sources

Relation: https://figshare.com/articles/figure/Workflow_for_the_BlueRecording_Pipeline_/29138115

Availability: https://doi.org/10.1371/journal.pcbi.1013023.g001
https://figshare.com/articles/figure/Workflow_for_the_BlueRecording_Pipeline_/29138115

BlueRecording simulates hippocampal LFP.

Authors: Joseph James Tharayil Jorge Blanco Alonso Silvia Farcito et al.

Subject Terms: Biophysics, Cell Biology, Genetics, Neuroscience, Physiology, Biotechnology, Evolutionary Biology, Developmental Biology, Cancer, Space Science, Biological Sciences not elsewhere classified, Mathematical Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, standalone python code, sonata data format, rat somatosensory cortex, new avenues open, network simulations accessible, coreneuron computation engine, computational neuroscience grows, complex tissue anatomy, permit online calculation, signal information content, e ., non, simulate eeg recordings, enable efficient calculation, div >< p, dipolar current sources

Relation: https://figshare.com/articles/figure/BlueRecording_simulates_hippocampal_LFP_/29138133

Availability: https://doi.org/10.1371/journal.pcbi.1013023.g007
https://figshare.com/articles/figure/BlueRecording_simulates_hippocampal_LFP_/29138133

A. E-Field magnitude, in a cross section of the rat head, induced by current applied to an ECoG recording electrode.

Authors: Joseph James Tharayil Jorge Blanco Alonso Silvia Farcito et al.

Subject Terms: Biophysics, Cell Biology, Genetics, Neuroscience, Physiology, Biotechnology, Evolutionary Biology, Developmental Biology, Cancer, Space Science, Biological Sciences not elsewhere classified, Mathematical Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, standalone python code, sonata data format, rat somatosensory cortex, new avenues open, network simulations accessible, coreneuron computation engine, computational neuroscience grows, complex tissue anatomy, permit online calculation, signal information content, e ., non, simulate eeg recordings, enable efficient calculation, div >< p, dipolar current sources

Availability: https://doi.org/10.1371/journal.pcbi.1013023.s004
https://figshare.com/articles/figure/A_E-Field_magnitude_in_a_cross_section_of_the_rat_head_induced_by_current_applied_to_an_ECoG_recording_electrode_/29138109

Extracellular signals recorded in a large homogeneous medium.

Authors: Joseph James Tharayil Jorge Blanco Alonso Silvia Farcito et al.

Subject Terms: Biophysics, Cell Biology, Genetics, Neuroscience, Physiology, Biotechnology, Evolutionary Biology, Developmental Biology, Cancer, Space Science, Biological Sciences not elsewhere classified, Mathematical Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, standalone python code, sonata data format, rat somatosensory cortex, new avenues open, network simulations accessible, coreneuron computation engine, computational neuroscience grows, complex tissue anatomy, permit online calculation, signal information content, e ., non, simulate eeg recordings, enable efficient calculation, div >< p, dipolar current sources

Relation: https://figshare.com/articles/figure/Extracellular_signals_recorded_in_a_large_homogeneous_medium_/29138118

Availability: https://doi.org/10.1371/journal.pcbi.1013023.g002
https://figshare.com/articles/figure/Extracellular_signals_recorded_in_a_large_homogeneous_medium_/29138118

Procedure for aligning the NeuroRat head model underlying the FEM simulations with the BBP circuit model.

Authors: Joseph James Tharayil Jorge Blanco Alonso Silvia Farcito et al.

Subject Terms: Biophysics, Cell Biology, Genetics, Neuroscience, Physiology, Biotechnology, Evolutionary Biology, Developmental Biology, Cancer, Space Science, Biological Sciences not elsewhere classified, Mathematical Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, standalone python code, sonata data format, rat somatosensory cortex, new avenues open, network simulations accessible, coreneuron computation engine, computational neuroscience grows, complex tissue anatomy, permit online calculation, signal information content, e ., non, simulate eeg recordings, enable efficient calculation, div >< p, dipolar current sources

Relation: https://figshare.com/articles/figure/Procedure_for_aligning_the_NeuroRat_head_model_underlying_the_FEM_simulations_with_the_BBP_circuit_model_/29138106

Availability: https://doi.org/10.1371/journal.pcbi.1013023.s003
https://figshare.com/articles/figure/Procedure_for_aligning_the_NeuroRat_head_model_underlying_the_FEM_simulations_with_the_BBP_circuit_model_/29138106

The format of the simulation reports

Authors: Joseph James Tharayil Jorge Blanco Alonso Silvia Farcito et al.

Subject Terms: Biophysics, Cell Biology, Genetics, Neuroscience, Physiology, Biotechnology, Evolutionary Biology, Developmental Biology, Cancer, Space Science, Biological Sciences not elsewhere classified, Mathematical Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, standalone python code, sonata data format, rat somatosensory cortex, new avenues open, network simulations accessible, coreneuron computation engine, computational neuroscience grows, complex tissue anatomy, permit online calculation, signal information content, e ., non, simulate eeg recordings, enable efficient calculation, div >< p, dipolar current sources

Relation: https://figshare.com/articles/dataset/The_format_of_the_simulation_reports/29138142

Availability: https://doi.org/10.1371/journal.pcbi.1013023.t003
https://figshare.com/articles/dataset/The_format_of_the_simulation_reports/29138142