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Glossary

Core concepts

Mathematical or computational model (e.g., BNGL, CellML, SBML)

A specification of a mathematical or computational description of a system, such as a set of ODEs. Models are captured using formats such as BNGL, CellML, and SBML. Model formats are specified using the EDAM ontology.

Simulation or simulation experiment (SED-ML)

A specification of how to execute a model, such as the interval over which to integrate a set of ODEs and which algorithm to integrate the ODEs. Simulations are captured using the SED-ML format.

Simulation algorithm

A method for executing a simulation, such as a method for integrating a set of ODEs such as Euler's method. Algorithms are specified using the KiSAO ontology.

Simulator or simulation tool

A software application for executing a simulation project (COMBINE/OMEX archive) and exporting its outputs (HDF5 file).

Simulation run

An execution of a simulation project (COMBINE/OMEX archive).

Simulation output or results (HDF5)

The outcome of a simulation, such as the predicted trajectory of the value of one or more variables. Simulation results are captured using the HDF5 format. The dimensions of simulation outputs are specified using the SIO ontology.

Data visualization of simulation results (Vega)

A specification of a diagram for depicting the results of a simulation. Data visualizations are captured using the Vega format.

Metadata (OMEX Metadata)

A specification of the semantic meaning and/or provenance of a modeling project or a component of a modeling project. Metadata is captured using the OMEX Metadata format.

Modeling or simulation project or study (COMBINE/OMEX archive)

A collection of one or more models (e.g., BNGL, CellML, SBML files) and one or more simulations (SED-ML files), as well as visualizations for the results of the simulations (Vega files), and metadata about these files (OMEX Metadata files). Projects are captured using the COMBINE/OMEX archive format.

Modeling and simulation formats

COMBINE/OMEX archive

Format used to capture the specifications of simulation projects including * Models (e.g., SBML files) * Simulations (e.g., SED-ML files) * Visualizations of simulation results (e.g., Vega files) * Metadata (e.g., OMEX metadata files) * Other associated information.

More info: combinearchive.org

Hierarchical Data Format version 5 (HDF5)

Format used to store simulation results. Stores simulation results as sets of multidimensional matrices.

More info: HDF Group

Simulation Experiment Description Markup Language (SED-ML)

Format used to capture the specifications of simulations such as * Which models to simulate * How to create variants of those models * What types of simulation to run (e.g., steady-state, time course) * When to start simulation and how long to run them * Which algorithms to use to run simulations * The parameters that algorithms should be executed with

More info: sed-ml.org

OMEX Manifest

Format used to capture the formats of the contents of COMBINE/OMEX archives.

More info: combinearchive.org

OMEX Metadata

Format used to capture metadata about simulation projects.

More info: sys-bio.github.io

Vega

Declarative grammar used to describe diagrams for interactively visualizing the results of simulations.

More info: vega.github.io

Modeling frameworks and simulation algorithms

Differential Algebraic Equations (DAE)

Modeling framework for describing a system as a set of differential and algebraic equations.

More info: Wikipedia

Flux Balance Analysis (FBA)

Modeling framework for analyzing the optimal steady state flux distribution of a system, such as metabolic network.

More info: Wikipedia

Ordinary Differential Equations (ODE)

Modeling framework for describing a system in terms of the rate of each variable.

More info: Wikipedia

Resource Balance Analysis (RBA)

Modeling framework analyzing the optimal steady state resource allocation of a system, such as metabolic network.

More info: INRAE

Stochastic Simulation Algorithm (SSA)

Simulation algorithm for generating a statistically correct trajectory of a system of stochastic equations.

More info: Wikipedia

Ontologies

EMBRACE Data and Methods (EDAM)

Ontology used to specify model and simulation formats such as SBML and SED-ML.

More info: edamontology.org

Kinetic Simulation and Algorithms Ontology (KiSAO)

Ontology used to specify simulation algorithms and their parameters.

More info: github.com/SED-ML

Linguist

Dataset used to specify programming languages.

More info: GitHub

Semanticscience Integrated Ontology (SIO)

Ontology used to specify the dimensions of the outputs of simulations.

More info: github.com/MaastrichtU-IDS

Software Package Data Exchange (SPDX)

Ontology used to specify licenses.

More info: spdx.org

Systems Biology Ontology (SBO)

Ontology used to specify modeling frameworks.

More info: github.com/EBI-BioModels


Last update: 2022-05-18
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