TVB-O logo TVB-O Documentation
  • Home
  • Get Started
  • Examples
  • Reference
  • Platform
  1. Replication Studies
  2. The replication pipeline
  • GET STARTED
  • Home
  • Installation
  • Getting started
  • SIMULATION EXPERIMENTS WITH TVB-O
  • ① EXPLORE
    • The platform, feature by feature
    • Ontology
      • Specification (Widoco)
      • WebVOWL visualisation
  • ② SPECIFY
    • The running example
    • The SimulationExperiment
    • Dynamical systems
      • Defining dynamical systems
      • Initial conditions
      • Noise & stochastic integration
      • Unit-aware computations
      • Beyond the mean field
        • Multi-scale modelling
        • NeuroML component mapping
      • Bifurcation & continuation
        • Run a continuation
        • Numerical continuation
    • Networks & connectomes
      • Network specification
      • Build a connectome from tractography
      • Coupling functions
      • Hierarchical & surface networks
      • Heterogeneous nodes
      • Heterogeneous edges
    • Events & stimulation
    • Observation models
      • Output specification
    • Parameter exploration
    • Fitting, inference & optimization
      • Model fitting
      • Loss functions
      • Algorithms (FIC, EIB)
    • Analyses
    • Calling your own code
    • Figures
      • Styling & colour
      • Custom figure panels
      • Plot a result directly
    • Solving a network of DDEs
      • Cross-backend numerical parity
    • Linked experiments in a SimulationStudy
    • Fan-out over subjects and phenotypes
    • Writing TVB-O YAML
  • ③ GENERATE
    • How code generation works
    • Code generation & export
    • Reproducible workflows
      • Distributed workflows
      • Workflow kits anatomy
      • HPC patterns & containers
    • The study directory
  • ④ RUN
    • Run on a backend
    • The experiment result
  • ⑤ SHARE
    • Share and publish your work
    • Results in BIDS
    • openMINDS
  • EXAMPLES & USE-CASES
  • Quick examples
    • Create a network
    • Dynamics from the database
    • Network from the database
  • Worked experiments
    • Fit functional connectivity (RWW)
    • Fit a MEG frequency gradient (Jansen-Rit)
    • Tune E/I balance
    • Bayesian inference
    • Multi-objective (Hopf-Pareto)
    • Delay & speed synchronization
    • Gradient stability & TBPTT
    • Surface & PDE simulation
  • Bifurcation track
    • 1. Linear stability
    • 2. 2D phase portraits
    • 3. Saddle-node
    • 4. Pitchfork
    • 5. Hysteresis
    • 6. Hopf
  • 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
    • Round-trip demo
    • Analysis
    • Bifurcation
    • Heterogeneous networks
  • NetworkDynamics.jl
    • Network diffusion
    • 2D network diffusion
    • Kuramoto oscillators
    • Heterogeneous Kuramoto
    • FitzHugh-Nagumo
    • Cascading failure
    • Stress on truss
  • BifurcationKit.jl
    • Tsodyks-Markram model
    • CO oxidation model
  • ModelingToolkit.jl
    • Higher-order ODE lowering
  • NeuroML / LEMS
    • LEMS export
    • IRI vs. inline YAML
    • Conformance gallery
  • REFERENCE
  • Quick reference
  • Command-line interface
    • Specs and resolution
    • Verbs
      • tvbo run
      • tvbo export
      • tvbo save
      • tvbo import
      • tvbo info
      • tvbo formats
      • tvbo brain
      • tvbo validate
      • tvbo config
      • tvbo skills
      • tvbo network
    • tvbo workflow
    • Recipes
  • Data Model
    • Schemas
      • Common
      • figure
      • SANDS
      • Software
      • TVB Datamodel
      • TVB Databases
      • TVB-O Study
      • TVB-O Units
      • Types
    • Classes
      • Activity
      • Aggregation
      • Algorithm
      • Algorithm Include
      • Algorithm Stage
      • Analysis
      • Animation
      • Annotation
      • Archive Config
      • Argument
      • Assignment
      • Axis Reduction
      • BIDS Entities
      • Binding
      • Boundary Condition
      • Brain Atlas
      • Brain Region Series
      • Branch Switch
      • Cached Array
      • Callable
      • Camera
      • Case
      • Class Reference
      • Clinical Improvement
      • Clinical Scale
      • Clinical Score
      • Code Source
      • Colorbar
      • Colormaps
      • Color Scale
      • Common Coordinate Space
      • Conditional Block
      • Contact
      • Continuation
      • Coordinate
      • Coupling
      • Coupling Input
      • Data Ref
      • Dataset
      • Data Source
      • DBSDataset
      • DBSProtocol
      • DBSSubject
      • Derived Observation
      • Derived Parameter
      • Derived Variable
      • Differential Operator
      • Differentiation
      • Digest
      • Discretization
      • Distribution
      • Distribution Config
      • Dynamics
      • Edge
      • EField
      • Electrode
      • Encoding
      • Environment Variable
      • Equation
      • Event
      • Execution Config
      • Experiment Result Sidecar
      • Exploration
      • Exploration Axis
      • Field State Variable
      • Figure
      • File
      • Free Parameter
      • Function
      • Function Call
      • Graph
      • Graph Generator
      • Grid
      • Inference
      • Initial State
      • Inset
      • Integrator
      • Layer
      • Layout Template Variant
      • Legend
      • Likelihood
      • Loss Function
      • Matrix
      • Measure Spec
      • Mesh
      • Named Array
      • NDArray
      • Network
      • Node
      • Noise
      • Observation
      • Optimization
      • Optimization Stage
      • Option
      • Palette
      • Panel
      • Parameter
      • Parameter Spec
      • Parcellation
      • Parcellation Entity
      • Parcellation Terminology
      • Partition
      • PDE
      • PDESolver
      • Phenotype
      • Prior
      • Procedure
      • Procedure Step
      • Provenance
      • Random Stream
      • Range
      • Reducer
      • Reference
      • Reference Fingerprint
      • Region
      • Region Mapping
      • Render Spec
      • Result Binding
      • Result Entity
      • Rule
      • Sample
      • Scalar Value
      • Scheduler Directive
      • Session
      • Simulation Experiment
      • Simulation Study
      • Simulation Tool
      • Software Environment
      • Software Package
      • Software Requirement
      • Solver
      • Spatial Domain
      • Spatial Field
      • State Value
      • State Variable
      • Stimulation Setting
      • Stimulus
      • Study
      • Study Collection
      • Study Directory
      • Study File
      • Study Layout
      • Study Member
      • Study Template
      • Style
      • Subject
      • Surface
      • Surrogate
      • Theme
      • Time Series
      • Tool Unit
      • Tractogram
      • Tuning Objective
      • Update Rule
      • Volume
      • Workflow Config
      • Workflow Engine Config
    • 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
      • Aggregation Type
      • Algorithm Composition Mode
      • Axis Reduction Statistic
      • Axis Scale
      • Axis Side
      • Bar Orientation
      • BIDS Dataset Type
      • BIDS Directory Status
      • Boundary Condition Type
      • Comparison Operator
      • Connectivity Rule
      • Continuation Algorithm
      • Corner
      • Coupling Stage Evaluation
      • Development Status
      • Dimension Type
      • Discretization Method
      • Domain Enforcement
      • Ecosystem Enum
      • Element Type
      • Environment Type
      • Event Type
      • Frame Role
      • Graph Representation
      • Hemisphere
      • Imaging Modality
      • Initial State Method
      • Layout Engine
      • Legend Loc
      • Mark Type
      • Model Paradigm
      • Model Type
      • Node Reconciliation
      • Noise Draw
      • Noise Type
      • Numerical Discretization Method
      • Observation Reduction Mode
      • Operator Type
      • Panel Kind
      • Parallel Mode
      • Physical Dimension
      • Procedure Step Type
      • Programming Language Enum
      • Projection
      • Provenance Format
      • Reducer Emit Kind
      • Reduction Type
      • Report Part
      • Requirement Level
      • Requirement Role
      • Rule Orientation
      • Sampling Axis
      • Sex Enum
      • Simulation Scale
      • Sparse Format
      • Specimen Enum
      • Standard Graph Type
      • Study Directory Role
      • Study File Role
      • Subject Batch Mode
      • Surface View
      • Sweep Direction
      • Sweep Seeding
      • System Type
      • Tick Direction
      • Tick Format
      • Tick Prune
      • Tool Role
      • Tracked Content
      • Triangle
      • Unit Enum
      • Volume View
      • Workflow Distribute By
  • API Documentation
    • Log
    • Multiscale
    • Platform
    • Adapters
      • Base
      • BIDS
      • BifurcationKit
      • Brian2
      • Bsplot
      • Colormaps
      • DiffEq
      • Figure Workflow
      • Gillespie
      • Julia
      • Julia Model
      • ModelingToolkit
      • NetworkDynamics
      • NeuroML
      • NumCont
      • Observation Sampling
      • openMINDS
      • PyRates
      • PyRates (Bifurcation)
      • TVB
      • tvboptim
      • Shared small-scale network-lowering core.
        • Lowering
    • Analysis
      • Bifurcation
      • Linear Response
      • Replication
      • Units
    • API
      • Direct Ontology Api
      • Dynamics Api
      • Experiment Api
      • Main
      • Network Api
      • Ontology Api
    • Hand-written behaviour attached to the generated model classes.
      • Continuation
      • Coupling
      • Dynamics
      • Dynamics Runtime
      • Event
      • Integrator
      • Perturbation
    • 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
      • Dialect
      • Dialect Tables
      • Pydantic
      • Schema
    • 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
      • PDE/FEM code-generation templates for TVBO field models.
        • Utils
      • RateML
        • Utils
      • tvboptim
        • Callbacks
        • Observations
        • Utils
    • Utilities
      • Auto
      • Figure Compare
      • Pydantic Loader
      • Report
      • Study Layout
      • Units
      • Yaml Loader
  • DEVELOPER
  • Contributing
  • How this documentation is built
  • Maintainer guide
  1. Replication Studies
  2. The replication pipeline

The replication pipeline

How TVBO turns a published study into generated simulations, figures, and HPC jobs — one declarative spec, provenance-traceable.
Examples & Use-Cases·Replication Studies

TVBO replicates a published study from a single declarative SimulationStudy — its experiments and the figures that read them. The schema below traces the full pipeline: paper → declarative spec → codegen → workflow / HPC → faithful figures, with every plotted number traceable to the run that produced it.

Open the full schema in a new tab

Replication Studies
Overview
 

© Charité - Universitätsmedizin Berlin

  • Edit this page
  • Report an issue