Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Mechanistic Models: Overview of Compartment Models01:21

Mechanistic Models: Overview of Compartment Models

587
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...
587
Molecular Models02:00

Molecular Models

37.5K
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.
37.5K
Multicompartment Models: Overview01:14

Multicompartment Models: Overview

712
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,...
712
Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving01:29

Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving

438
Mechanistic models play a crucial role in algorithms for numerical problem-solving, particularly in nonlinear mixed effects modeling (NMEM). These models aim to minimize specific objective functions by evaluating various parameter estimates, leading to the development of systematic algorithms. In some cases, linearization techniques approximate the model using linear equations.
In individual population analyses, different algorithms are employed, such as Cauchy's method, which uses a...
438
Mechanistic Models: Compartment Models in Individual and Population Analysis01:23

Mechanistic Models: Compartment Models in Individual and Population Analysis

359
Mechanistic models are utilized in individual analysis using single-source data, but imperfections arise due to data collection errors, preventing perfect prediction of observed data. The mathematical equation involves known values (Xi), observed concentrations (Ci), measurement errors (εi), model parameters (ϕj), and the related function (ƒi) for i number of values. Different least-squares metrics quantify differences between predicted and observed values. The ordinary least...
359
Induced-fit Model01:13

Induced-fit Model

77.0K
Most chemical reactions in cells require enzymes—biological catalysts that speed up the reaction without being consumed or permanently changed. They reduce the activation energy needed to convert the reactants into products. Enzymes are proteins, that usually work by binding to a substrate—a reactant molecule that they act upon.
Enzymes exhibit substrate specificity, meaning that they can only bind to certain substrates. This is mainly determined by the shape and chemical...
77.0K

You might also read

Related Articles

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

Sort by
Same author

Correction: Revisiting Turing's Chemical Basis of Morphogenesis.

Bulletin of mathematical biology·2026
Same author

Revisiting Turing's Chemical Basis of Morphogenesis.

Bulletin of mathematical biology·2026
Same author

From FAIR to CURE: guidelines for computational models of biological systems.

NPJ systems biology and applications·2026
Same author

Optogenetic control of transition to metamorphosis.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same author

Béla Novák (1956-2025) - a legacy of scientific discovery and personal charm.

Journal of cell science·2025
Same author

Preclinical NCI-MPACT: prospective modeling of the mutation-based NCI-MPACT clinical trial therapeutic strategy in patient-derived xenograft models.

Frontiers in oncology·2025

Related Experiment Video

Updated: May 1, 2026

Modeling an Enzyme Active Site using Molecular Visualization Freeware
14:37

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Published on: December 25, 2021

11.6K

Multistate Model Builder (MSMB): a flexible editor for compact biochemical models.

Alida Palmisano1, Stefan Hoops, Layne T Watson

  • 1Department of Computer Science, Virginia Polytechnic and State University, 2202 Kraft Drive, Blacksburg, VA 24060, USA. alida.palmisano@vt.edu.

BMC Systems Biology
|April 9, 2014
PubMed
Summary
This summary is machine-generated.

MSMB (Multistate Model Builder) simplifies molecular network modeling with a novel multistate syntax and interactive feedback, reducing complexity and speeding up the creation of accurate biological models.

More Related Videos

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
09:17

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

2.5K
Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches
07:31

Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches

Published on: September 1, 2023

3.3K

Related Experiment Videos

Last Updated: May 1, 2026

Modeling an Enzyme Active Site using Molecular Visualization Freeware
14:37

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Published on: December 25, 2021

11.6K
Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
09:17

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

2.5K
Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches
07:31

Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches

Published on: September 1, 2023

3.3K

Area of Science:

  • Systems Biology
  • Computational Biology
  • Molecular Modeling

Background:

  • Modeling molecular regulatory networks is complex due to intricate biological processes.
  • Existing biochemical model editors lack the flexibility and interactive support needed for creative model building.

Purpose of the Study:

  • To introduce MSMB (Multistate Model Builder), a novel model editor designed to enhance the creation of molecular regulatory network models.
  • To provide a more flexible and interactive environment for modelers.

Main Methods:

  • Developed MSMB with a simple yet powerful syntax for describing multistate species.
  • Integrated extensive, on-the-fly feedback mechanisms, including adjustable error notifications.
  • Implemented adaptable default values and behaviors for user-centric model manipulation.

Main Results:

  • The multistate syntax reduces the number of reactions required for complex molecular systems, simplifying model creation.
  • Interactive feedback guides users toward syntactically correct and consistent models.
  • Models can be exported to standard formats like SBML and COPASI.

Conclusions:

  • Multistate reactions decrease the reaction count in biochemical models, reducing cognitive load and enabling the construction of more complex networks.
  • MSMB's interactive features accelerate model creation by facilitating the development of syntactically valid models.
  • The software supports creative modeling by adapting to user preferences.