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Updated: Sep 9, 2025

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline
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Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline

Published on: December 7, 2021

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SBMLtoOdinとmenelmacar:専門家と非専門家向けのシステム生物学モデルのインタラクティブビジュアライゼーション

Leonie J Lorenz1, Antoine Andréoletti1,2,3, Tung V N Nguyen1

  • 1European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom.

Bioinformatics (Oxford, England)
|September 2, 2025
PubMed
まとめ

SBMLtoOdinとMenelmacarは生物学的モデルのアクセシビリティを強化しています. これらのツールは 計算モデルを実行可能なコードに変換し インタラクティブなビジュアライゼーションを提供し プログラミングの専門知識のない研究者に力を貸します

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Two-Compartment Open Model: Overview01:05

Two-Compartment Open Model: Overview

Multicompartmental models are crucial tools in pharmacokinetics, providing a framework to understand how drugs move within the body. The two-compartment model is a crucial subtype, segmenting the body into central and peripheral compartments. The central compartment represents areas with high blood flow, such as plasma and highly perfused organs like the kidneys and liver, while the peripheral compartment signifies tissues with lower blood flow, like adipose tissue and muscle tissue.
The...
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pV-Diagrams01:18

pV-Diagrams

The pV diagram, which is a graph of pressure versus volume of the gas under study, is helpful in describing certain aspects of the substance. When the substance behaves like an ideal gas, the ideal gas equation describes the relationship between its pressure and volume. On a pV diagram, it is common to plot an isotherm, which is a curve showing p as a function of V with the number of molecules and the temperature fixed. Then, for an ideal gas, the product of the pressure of the gas and its...
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Molecular Models02:00

Molecular Models

Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
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Multi-input and Multi-variable systems

Cruise control systems in cars are designed as multi-input systems to maintain a driver's desired speed while compensating for external disturbances such as changes in terrain. The block diagram for a cruise control system typically includes two main inputs: the desired speed set by the driver and any external disturbances, such as the incline of the road. By adjusting the engine throttle, the system maintains the vehicle's speed as close to the desired value as possible.
In the absence...
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Multicompartment Models: Overview01:14

Multicompartment Models: Overview

Multicompartment models are mathematical constructs that depict how drugs are distributed and eliminated within the body. They segment the body into several compartments, symbolizing various physiological or anatomical areas connected through drug transfer processes such as absorption, metabolism, distribution, and elimination.
These models offer a more comprehensive representation of drug behavior in the body than one-compartment models. They accommodate the complexity of drug distribution,...
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Mechanistic Models: Overview of Compartment Models01:21

Mechanistic Models: Overview of Compartment Models

Mechanistic models, a category encompassing both physiological and compartmental modeling, differ from empirical models' approaches to incorporating known factors about the systems being modeled. Empirical models describe data with minimal assumptions, while mechanistic models aim to provide a robust description of available data by specifying assumptions and integrating known factors about the system. Compartmental analysis is a key example of a mechanistic model in pharmacokinetics and...
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