Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Modeling and Similitude

Modeling and Similitude

Scaled modeling is a fundamental technique in engineering, enabling the study of large and complex systems by creating smaller, manageable replicas that recreate critical characteristics of the original. In hydrology and civil infrastructure, for example, scaled models of dams help analyze water flow, turbulence, and pressure. This method allows for accurate predictions of real-world behavior within a controlled environment, significantly reducing the cost and time involved in full-scale...

Typical Model Studies

Typical Model Studies

Fluid mechanics model studies often utilize scaled-down systems to predict fluid behavior in full-scale environments, such as river flows, dam spillways, and structures interacting with open surfaces. Maintaining Froude number similarity in river models is crucial, as it replicates surface flow features like wave patterns and velocities.

Design Example: Creating a Hydraulic Model of a Dam Spillway

Design Example: Creating a Hydraulic Model of a Dam Spillway

Scaled hydraulic models of dam spillways provide a practical way to replicate and study the intricate flow dynamics of these structures. Often built to a 1:15 ratio, these models allow for observing critical water behavior, such as velocity distribution, flow patterns, and energy dissipation.

Modeling with Differential Equations

Modeling with Differential Equations

Population dynamics can be described mathematically by considering the population size P(t) as a function of time. The rate of change of the population is then represented by the derivative of P(t). A simple assumption is that the rate of growth is proportional to the size of the population itself. This leads to an exponential growth model, where the population increases rapidly without bound. While this is a useful first approximation, it does not reflect realistic long-term...

Steps in the Modeling Process

Steps in the Modeling Process

Albert Bandura's theory of observational learning identifies four critical processes: attention, retention, motor reproduction, and reinforcement or motivation.
Attention is the first necessary component for observational learning. It involves focusing on what the model is doing and saying. For example, if you decide to take a drawing class to enhance your skills, you need to pay close attention to the instructor's words and hand movements. The characteristics of the model significantly...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Profiling cell proliferation after whole-genome duplication in human cells.

Biology open·2026

Same author

Odor-specific olfactory stimulation is associated with selective transcriptional changes and partial improvement of stress-evoked bladder overactivity in mice.

Frontiers in neuroscience·2026

Same author

Creating an engine of scientific discovery, an Indo-Japan perspective: learnings from IJNTC 2025 workshop.

NPJ systems biology and applications·2026

Same author

Outplaying elite table tennis players with an autonomous robot.

Nature·2026

Same author

Mixing features of transcription factors and genes enable accurate prediction of gene regulation relationships for unknown transcription factors.

NAR genomics and bioinformatics·2026

Same author

The future of fundamental science led by generative closed-loop artificial intelligence.

Frontiers in artificial intelligence·2026

Same journal

Mapping the 3D Chromosome Organization of a Biosynthetic Gene Cluster by Capture Hi-C (CHi-C).

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Mapping the 3D Chromosome Organization of Streptomyces by Hi-C.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

CUT&Tag Epigenomic Profiling of Biosynthetic Gene Clusters in Arabidopsis thaliana.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Rhizobium rhizogenes-Mediated Hairy Root Transformation Protocol for Lotus japonicus and Other Legumes.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Characterization of Bioactive Saponins from Sea Cucumbers.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Methods for Functional Validation of Terpenoid Metabolic Clusters in Nicotiana benthamiana and Aspergillus oryzae.

Methods in molecular biology (Clifton, N.J.)·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Apr 28, 2026

Structural Design and Manufacturing of a Cruiser Class Solar Vehicle

Structural Design and Manufacturing of a Cruiser Class Solar Vehicle

Published on: January 30, 2019

Modeling and simulation using CellDesigner.

Yukiko Matsuoka¹, Akira Funahashi, Samik Ghosh

¹The Systems Biology Institute, 5-6-9 Shirokanedai, Minato-ku, Tokyo, 108-0071, Japan.

Methods in Molecular Biology (Clifton, N.J.)

|June 15, 2014

Summary

This summary is machine-generated.

Learn how to build and simulate biological regulatory systems using in silico modeling. This chapter guides you through CellDesigner software, utilizing standards like Systems Biology Markup Language (SBML) and Systems Biology Graphical Notation (SBGN).

More Related Videos

Finite Element Modelling of a Cellular Electric Microenvironment

Finite Element Modelling of a Cellular Electric Microenvironment

Published on: May 18, 2021

Design and Optimization Strategies of a High-Performance Vented Box

Design and Optimization Strategies of a High-Performance Vented Box

Published on: June 9, 2023

Related Experiment Videos

Last Updated: Apr 28, 2026

Structural Design and Manufacturing of a Cruiser Class Solar Vehicle

Structural Design and Manufacturing of a Cruiser Class Solar Vehicle

Published on: January 30, 2019

Finite Element Modelling of a Cellular Electric Microenvironment

Finite Element Modelling of a Cellular Electric Microenvironment

Published on: May 18, 2021

Design and Optimization Strategies of a High-Performance Vented Box

Design and Optimization Strategies of a High-Performance Vented Box

Published on: June 9, 2023

Area of Science:

Systems biology
Computational biology
Bioinformatics

Background:

Understanding complex biological regulatory systems is crucial in life sciences.
In silico modeling and simulation offer powerful approaches for this understanding.

Purpose of the Study:

To provide a guide on building and simulating biological models.
To demonstrate the use of CellDesigner software for systems biology analysis.
To highlight the importance of adopting standards like SBML and SBGN.

Main Methods:

Utilizing CellDesigner, a graphical modeling tool.
Implementing the Systems Biology Markup Language (SBML) for model representation.
Adopting Systems Biology Graphical Notation (SBGN) for pathway visualization.
Performing in silico simulations to analyze system behavior.

Main Results:

Demonstration of a practical workflow for creating and simulating biological models.
Successful application of CellDesigner with SBML and SBGN standards.
Generation of simulation results that aid in understanding regulatory system dynamics.

Conclusions:

CellDesigner, combined with SBML and SBGN, provides an effective platform for in silico modeling and simulation.
This approach facilitates a deeper comprehension of biological regulatory systems.
Adherence to standards ensures model interoperability and reproducibility.