amorphys
stable
Table of contents:
Why amorphys?
Overview
Background
What is amorphys?
Structure
How is it going to work?
Editor UI
Designer UI
Experiment runner
Core objects
Entity
Entity class
Types of entities
Spatial entity
Temporal entity
Signals
Programs and Routines
Relationship
How Relationship works
Pre-defined relationship keys
Spatial relationships
Temporal relationships
Relationships between signals
Defining your own relationship key(s)
Context
Context class
Classes for measurements
Date
Time
Subject-related
Age
Sex
Death
Space
Quantity
Notes on unit usages
URI-based reference
Referrable class
Individual class
Person class
License class
Citation class
Description of protocol control
Overview
Unitary stimulus control
StimulusState
ApparatusState
Sequence-type stimulus description
Sequencer
StimulusBlock
StimulusGeneration
Context-dependent stimulus sequence
StateMachine
MachineState
MachineStateTransition
Behavioral model for a subject
Variables and expressions
Use of variables
Use of conditions
Expressions and formatters
Use of templates
Supplementary documents
Predefined subclasses for Spatial
Subject entity
Component entity
Predefined subclasses for Temporal
Procedure
Action and Block
Phase
Specific types of actions
Predefined subclasses for Signal
Sampled and its subclasses
Event and its subclasses
State
Definition of your own entity class
Metadata structure
Overview
Sections
A recommended way of annotation
“section” class
Formatting options
Single-file format
Multi-file format
Project organization
“organization” section
Dataset class
Contributor class
Institution class
Funding class
Subject description
“subjects” section
Setups
“setups” section
Setup class
Acquisition
“acquisition” section
Procedures
“procedures” section
Task/Sweep control
“tasks” section
Experimental variables
An example
Scopes
Structure of scopes
Basic properties
Subsection for description of lower scope(s)
amorphys
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Core objects
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Behavioral model for a subject
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Behavioral model for a subject
¶
TODO
cues: driven-by
actions: monitored-by
types are defined ontologically