TVB-O Documentation

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SIMULATION EXPERIMENTS WITH TVB-O
① EXPLORE
- The platform, feature by feature
- Ontology
  - Specification (Widoco)
  - WebVOWL visualisation
② SPECIFY
③ GENERATE
④ RUN
- Run on a backend
- The experiment result
⑤ SHARE
EXAMPLES & USE-CASES
Quick examples
Worked experiments
Bifurcation track
Replication Studies
- The replication pipeline
AGENTIC CODING
Overview
For beginners
Installing & tuning skills
Skill reference
AGENTS.md
INTEROPERABILITY
Overview
The Virtual Brain (TVB)
- Connectome
- Monitors
Coming from tvboptim
PyRates
NetworkDynamics.jl
BifurcationKit.jl
- Tsodyks-Markram model
- CO oxidation model
ModelingToolkit.jl
- Higher-order ODE lowering
NeuroML / LEMS
REFERENCE
Quick reference
Command-line interface
Data Model
- Schemas
  - Common
  - figure
  - SANDS
  - Software
  - TVB Datamodel
  - TVB Databases
  - TVB-O Study
  - TVB-O Units
  - Types
- Classes
- Slots
  - abbreviation
  - abs_tol
  - absolute_value
  - accelerator
  - account
  - acquisition
  - acronym
  - acted_on_behalf_of
  - active_contacts
  - activities
  - add
  - additional_equations
  - additive
  - affect
  - affect_negative
  - affect_parameters
  - affect_states
  - age
  - aggregate
  - aggregation
  - algorithm
  - algorithms
  - allow_self_connections
  - alternate Name
  - alternative_identifier
  - amplitude
  - analyses
  - analysis
  - anatomical Axes Orientation
  - animation
  - annotations
  - application_category
  - apply_every
  - apply_on_dimension
  - archive
  - args
  - arguments
  - array_chunk
  - arrow
  - aspect
  - associated_with
  - at
  - atlas
  - author
  - authors
  - auto_format
  - autonomous
  - aux_data
  - average
  - axes Origin
  - axis
  - axis_width
  - azimuth
  - backend
  - backends
  - background
  - base
  - baseline_value
  - batch_mode
  - batch_size
  - bc_type
  - between
  - bids
  - bids_dir
  - bids_root
  - bids_version
  - bindings
  - block_size
  - bothside
  - bottom
  - boundaries
  - boundary_conditions
  - bounds
  - box_aspect
  - branches
  - build_hash
  - builder
  - bundle
  - by
  - call_args
  - callable
  - camera
  - capture
  - cases
  - category
  - cell
  - cells
  - center
  - checkpoint_interval
  - chunk
  - citation
  - citekey
  - class_call
  - class_reference
  - clinical_improvement
  - clinical_scores
  - clip
  - code_modules
  - code_source
  - codegen_format
  - coefficient
  - cohort
  - col_label_pad
  - col_label_size
  - col_labels
  - color
  - colorbar
  - colormap
  - colormaps
  - colors
  - columns
  - command
  - comment
  - comparison
  - compile
  - concept_iri
  - condition
  - condition_parameters
  - condition_states
  - conditional
  - conditionals
  - conditions
  - connectivity
  - connectivity_ref
  - connectome
  - constructor_args
  - contact_id
  - contacts
  - container
  - container_args
  - container_binds
  - container_image
  - continuation
  - continuations
  - coordinate
  - coordinate_space
  - coordinates
  - coordinate Space
  - cores
  - correlated
  - correlated_over
  - correlation
  - count
  - coupling
  - coupling_evaluation
  - coupling_function
  - coupling_inputs
  - coupling_terms
  - coupling_variable
  - covariance
  - cpus_per_task
  - cse
  - curvature
  - dash
  - data
  - data_file
  - data_source
  - data Location
  - dataset
  - dataset_id
  - dataset_path
  - dataset_type
  - datatype
  - date_created
  - date_modified
  - decimals
  - default
  - default Image
  - definition
  - degree
  - delay
  - delayed
  - delta_p
  - density
  - depends_on
  - derivative_initial_value
  - derived_from
  - derived_from_model
  - derived_observations
  - derived_parameters
  - derived_variables
  - desc
  - description
  - descriptor
  - detail
  - detect_bifurcation
  - detect_fold
  - development_status
  - device_scale_factor
  - diagnosis
  - diagonal
  - differentiation
  - digest
  - digital Identifier
  - dimension
  - dimension_labels
  - dims
  - directed
  - direction
  - discretization
  - distance
  - distance_unit
  - distribute
  - distribution
  - diverging
  - doi
  - domain
  - downsample_period
  - dpi
  - ds
  - ds_max
  - ds_min
  - dtype
  - duration
  - dynamics
  - ecosystem
  - edge_alpha
  - edge_color
  - edge_matrix_files
  - edge_percentile
  - edge_template
  - edge_width
  - edges
  - efield
  - electrode_id
  - electrode_reference
  - electrodes
  - element
  - element_domains
  - element_type
  - elements
  - elevation
  - emit
  - emit_kind
  - emit_provenance
  - empirical_data
  - encoding
  - ended_at
  - enforce
  - engine
  - entities
  - env
  - environment
  - environment_type
  - equation
  - equation_order
  - equation_type
  - evaluate
  - evaluator
  - event_type
  - events
  - evict
  - evict_equation
  - execution
  - executor
  - experiment
  - experiment_yaml_hash
  - expires_with
  - explorations
  - explored_values
  - expression
  - extension
  - family_wise
  - field
  - field_dynamics
  - figures
  - file
  - files
  - fill
  - fill_cell
  - find_fixpoint
  - font_family
  - font_size
  - format
  - fps
  - fraction
  - frame
  - frames
  - free
  - free_parameters
  - freeze_parameters
  - frequency
  - function
  - functions
  - funder
  - gather
  - gaussian
  - generated
  - generated_at
  - generated_by
  - geometry
  - git
  - graph_generator
  - graph_representation
  - gres
  - grid
  - grid_lines
  - grounding
  - group
  - groups
  - ha
  - handedness
  - handle_length
  - has_reference
  - hash
  - has Parent
  - head
  - height
  - height_ratios
  - hemi
  - hemisphere
  - heterogeneous
  - hi
  - hide_xticklabels
  - hide_yticklabels
  - highlight
  - histogram
  - history
  - homepage
  - hspace
  - hyperparameters
  - id
  - ifabsent
  - image
  - imaging_modality
  - in_templates
  - include
  - includes
  - incoming_states
  - inferences
  - initial_expression
  - initial_state
  - initial_value
  - ink
  - inner_coupling
  - inner_iterations
  - input
  - inputs
  - insets
  - integration
  - intensity
  - intensity_projection
  - intermediate_expressions
  - interoperates_with
  - interpolate_delays
  - interpolation
  - invert_x
  - invert_y
  - invert_z
  - iri
  - is_accessible_for_free
  - issue_tracker
  - is Version Of
  - jobs
  - key
  - keys
  - keywords
  - kind
  - label
  - label_pad
  - labels
  - labels_dimensions
  - labels_ordering
  - latex
  - layers
  - layout
  - layout_engine
  - learning_rate
  - learning_rate_schedule
  - learning_rate_warmup
  - left
  - lefthandside
  - legend
  - legend_frame
  - legend_handle_length
  - legend_pad
  - level
  - lhs
  - library
  - license
  - likelihood
  - line_width
  - linear_solver
  - linestyles
  - lo
  - loader
  - loc
  - local
  - local_coupling_term
  - local_states
  - location
  - log_scale
  - lookup Label
  - loss
  - mail_type
  - mail_user
  - maintainer
  - manufacturer
  - mark
  - marker_size
  - markers
  - mask
  - max_bisection_steps
  - max_iterations
  - max_steps
  - measure
  - measure_specs
  - measure_type
  - measures
  - mem
  - members
  - mesh
  - mesh_file
  - mesh_format
  - mesh_intervals
  - metadata
  - method
  - metric
  - min_coverage
  - minor_tick_length
  - minor_tick_width
  - minor_ticks
  - modality
  - mode
  - model
  - model_equation_ref
  - model_paradigm
  - model_param_ref
  - model_type
  - modes
  - modified
  - module
  - modules
  - mtime
  - muted
  - n
  - n_inversion
  - n_iterations
  - n_parallel
  - n_regions
  - n_sections
  - n_threads
  - n_trials
  - n_vertices
  - n_workers
  - name
  - native Unit
  - nbins
  - ncols
  - network
  - nev
  - newton_max_iterations
  - newton_tol
  - nextflow
  - node_edge_color
  - node_edge_width
  - node_mapping
  - node_size
  - node_template
  - nodes
  - noise
  - noise_draw
  - noise_type
  - non_negative
  - normals
  - not_in_templates
  - notes
  - nrows
  - num_chains
  - num_samples
  - num_warmup
  - number
  - number_loc
  - number_of_elements
  - number_of_modes
  - number_of_nodes
  - number_of_stages
  - number_of_subjects
  - number_of_vertices
  - objective
  - objectives
  - observable
  - observational_measures
  - observations
  - observed
  - ode_solver
  - of
  - on_region
  - ontology Identifier
  - opacity
  - opaque
  - operating_system
  - operator_type
  - operators
  - optimizations
  - optional
  - options
  - opts
  - orientation
  - original Lookup Label
  - out_dir
  - output
  - output_equation
  - outputs
  - outsym
  - over
  - package
  - pad
  - palette
  - panel_key
  - panel_number_format
  - panel_number_loc
  - panel_number_offset
  - panel_number_size
  - panel_numbers
  - panels
  - parallel_batch_size
  - parallel_mode
  - parameter
  - parameters
  - parcel_map_field
  - parcellation
  - parent_network
  - parent_score
  - part
  - partition
  - path
  - percent_change
  - percentile
  - period
  - permutations
  - permute
  - pipeline
  - placeholder
  - platform
  - position
  - post_expression
  - pre_expression
  - precision
  - preconditioner
  - predicted
  - preprocessing
  - primary_weight
  - priors
  - procedure
  - processing_pipeline
  - produced_by
  - producer
  - programming_language
  - projection
  - protocols
  - provenance
  - provenance_format
  - pulse_width
  - pycode
  - quantity_kind
  - query
  - queue
  - ramp
  - random_seed
  - random_state
  - range
  - recipe
  - recon_path
  - reconcile
  - reconstruction
  - record
  - reduce
  - ref
  - reference
  - reference_image
  - reference_publication
  - references
  - region
  - region_mapping
  - regional_connectivity
  - regions
  - rel_tol
  - related UBERONTerm
  - render
  - replaces
  - reported_optimum
  - repository
  - required
  - requirements
  - requires
  - reset_state
  - results
  - resync
  - resync_masked
  - retries
  - rhs
  - right
  - righthandside
  - rng
  - role
  - rotation
  - row_label_rotation
  - row_labels
  - rules
  - run_id
  - runtime_platform
  - same_as
  - sample
  - sampler
  - sampling_period
  - sampling_period_unit
  - sampling_rate
  - scale
  - scipy_ode_base
  - score
  - seed
  - seed_offset
  - segmentation
  - sel
  - sequential
  - session_id
  - sessions
  - settings
  - settle_seed
  - setup
  - sex
  - shape
  - share_x
  - share_y
  - show
  - sigma
  - simulation_experiments
  - simulation_period
  - size
  - skip_t
  - slurm
  - snakemake
  - software
  - software_environment
  - solver
  - source
  - source_branch
  - source_code
  - source_experiment
  - source_network
  - source_observations
  - source_point
  - source_url
  - source_var
  - sources
  - space
  - sparse
  - spine_offset
  - spines
  - stages
  - started_at
  - state
  - state_variables
  - state_wise_sigma
  - statistic
  - step
  - step_size
  - steps
  - still
  - stimulation
  - stimulation_variable
  - stimulus
  - strategy
  - structural_measures
  - studies
  - style
  - subdir
  - subdirs
  - subject_id
  - subjects
  - subnetwork
  - suffix
  - surface
  - surface_atlas
  - surrogate
  - sweep_direction
  - sweep_seeding
  - symbol
  - symmetric
  - symmetry
  - system_size
  - system_type
  - tail
  - tail_duration
  - tail_samples
  - tail_used
  - tail_x
  - target
  - target_component
  - target_data
  - target_network
  - target_parameter
  - target_range
  - target_regions
  - target_structure
  - target_value
  - target_var
  - target_variable
  - targets
  - task_iri
  - task_name
  - template
  - template_variants
  - templates
  - tensor_coefficient
  - terminology
  - text
  - theme
  - threshold_applied
  - tick_direction
  - tick_length
  - tick_pad
  - tick_prune
  - tick_size
  - tick_width
  - ticklabels
  - ticks
  - time
  - time_dependent
  - time_post_surgery
  - time_range
  - time_scale
  - time_unit
  - timepoint
  - timing_info
  - title
  - title_pad
  - tol_stability
  - tool_role
  - top
  - traceable
  - tracked
  - tractogram
  - trailing
  - trajectory
  - transform
  - transforms
  - transient_time
  - triangle
  - triangle_gap
  - trigger_times
  - trim_margins
  - truncation_window
  - type
  - unit
  - units
  - update_expression
  - update_rules
  - url
  - used
  - va
  - valid_diagonal
  - value
  - values
  - variable_of_interest
  - variant
  - vectorize
  - vectorized
  - venv
  - version
  - version_spec
  - version Identifier
  - vertex_to_region
  - vertices_field
  - view
  - vmax
  - vmin
  - voi
  - volume
  - volume_data
  - wait_selector
  - warmup
  - warmup_from
  - warmup_source
  - waves
  - weight
  - weight_distribution
  - weight_parameter
  - weighted
  - weighting
  - weights
  - width
  - width_ratios
  - window_size
  - workflow
  - workflow_overrides
  - wrt
  - wspace
  - x
  - xlabel
  - xlabel_pad
  - xlabel_side
  - xlim
  - xscale
  - xtick_format
  - xtick_rotation
  - xtick_side
  - xticks
  - y
  - year
  - ylabel
  - ylabel_pad
  - ylabel_side
  - ylim
  - yscale
  - ytick_format
  - ytick_rotation
  - ytick_side
  - yticks
  - z
  - zlabel
  - zlabel_pad
  - zlim
  - zoom
- Enumerations
API Documentation
- Log
- Multiscale
- Platform
- Adapters
- Analysis
- API
- Hand-written behaviour attached to the generated model classes.
- Classes
  - Atlas
  - Continuation
  - Correlated Noise
  - Coupling
  - Dynamics
  - Equation
  - Experiment
  - Function
  - Network
  - Noise
  - Observation
  - Parcellation
  - Perturbation
  - Phenotype
  - Software
  - Study
- CLI
  - Brain
  - Cache
  - Config
  - Export
  - Figures
  - Formats
  - Import
  - Info
  - Install
  - Network
  - Run
  - Save
  - Skills
  - Study
  - Units
  - Validate
  - Verify
  - Version
  - Workflow
- TVB-O Code Generation
  - Code
  - CUDA
  - Functions
  - LEMS
  - Prune
  - PyRates
  - Reducers
  - Streaming Reducers
  - Style
  - Templater
  - Transforms
- Data
  - Analysis Io
  - Connectome Build
  - Converters
  - Dataref
  - Experiment Result Io
  - Matrix Io
  - Mesh Fem
  - Mesh Io
  - Network Io
  - Param Io
  - Provenance
  - Registry
  - Study Manifest
  - Types
- Data Model
- Export
  - Formats
  - Registry
- Graph Generators
  - Catalog
  - Procedural
- JAX
  - Xarray Pytrees
- TVB-O Ontology
  - Config
  - Constants
  - DB
  - Graph
  - OWL
  - Query
  - Atlas
    - Freesurfer
  - Semantic Web
    - TVB-GO
- Parse
  - Expression
  - Lems Loader
  - Symbols
  - System
- Plot
  - Analysis
  - Animate
  - Capture
  - Dynamics
  - Dynamics Layout
  - Experiment Layout
  - Layout Mosaic
  - Network
  - Network Graph
  - Ontology
  - Palette
  - Phase
  - Schematic
  - Timeseries
  - Utils
- Run
  - Compgraph
  - Graph
  - Julia
- Templates
- Utilities
  - Auto
  - Figure Compare
  - Pydantic Loader
  - Report
  - Study Layout
  - Units
  - Yaml Loader
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