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: Compartment Models in Individual and Population Analysis01:23

Mechanistic Models: Compartment Models in Individual and Population Analysis

173
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...
173
Methods of Documentation VI: Case Management Model01:15

Methods of Documentation VI: Case Management Model

762
The case management model is a multidisciplinary approach that involves healthcare professionals from diverse disciplines, such as physicians, nurses, therapists, social workers, and pharmacists, working collaboratively to address the various needs of patients. Each healthcare professional brings unique expertise and perspectives, contributing to a more comprehensive understanding of the patient's condition and tailoring treatment plans accordingly.
For example, a patient with a chronic...
762
Compartment Models: Single-Compartment Model01:14

Compartment Models: Single-Compartment Model

2.9K
The single-compartment model serves as a simplified representation of the human body. This model assumes that the body functions as a single, well-mixed open compartment. When a drug is administered intravenously, it enters the body and quickly distributes uniformly. The drug then undergoes biotransformation and elimination, ultimately leaving the body. The volume of this compartment is referred to as the apparent volume of distribution into which the drug can uniformly distribute. In this...
2.9K
Molecular Models02:00

Molecular Models

43.0K
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.
43.0K
Models, Theories, and Laws01:16

Models, Theories, and Laws

8.1K
Scientists frequently use models to help them comprehend a specific collection of phenomena. In physics, a model is a condensed version of a physical system that is too complex to study thoroughly. One such example is the light wave model; unlike water waves, light waves are typically invisible to us. Nonetheless, it is helpful to think of light as being composed of waves, since investigations show that light behaves like water waves. Since it is impossible to visually see what is genuinely...
8.1K
Mechanistic Models: Overview of Compartment Models01:21

Mechanistic Models: Overview of Compartment Models

276
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...
276

You might also read

Related Articles

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

Sort by
Same author

A Randomized Trial of Rifaximin vs Low Fermentable Oligosaccharides, Disaccharides, Monosaccharides, and Polyols Diet for Symptom Outcomes and Microbiome Changes in Irritable Bowel Syndrome.

Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association·2026
Same author

Fermentable Oligosaccharides, Disaccharides, Monosaccharides, and Polyols Reintroduction in Clinical Practice: Surveying the Gaps and Opportunities.

Gastro hep advances·2026
Same author

ORP-101 in Irritable Bowel Syndrome With Diarrhea: A Phase II Randomized, Controlled Trial.

Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association·2026
Same author

Chronic, Noninfectious Diarrhea: A Review.

JAMA·2026
Same author

Nociplastic Pain is Associated With Increased Healthcare Utilization and Lower Quality of Life in Patients With Inflammatory Bowel Disease.

The American journal of gastroenterology·2026
Same author

Public Health.

Alzheimer's & dementia : the journal of the Alzheimer's Association·2025
Same journal

SENTINEL: A Shiny App for Processing and Analysis of Fenceline Sensor Data.

Environmental modelling & software : with environment data news·2025
Same journal

Enhancing Hydrological Modeling of Ungauged Watersheds through Machine Learning and Physical Similarity-based Regionalization of Calibration Parameters.

Environmental modelling & software : with environment data news·2025
Same journal

Streamlining land surface model Initialization: Automated data retrieval for VELMA using HMS REST API and GDAL.

Environmental modelling & software : with environment data news·2025
Same journal

Intelligent control of combined sewer systems using PySWMM-A Python wrapper for EPA's Stormwater Management Model.

Environmental modelling & software : with environment data news·2025
Same journal

Impact of model structure on radionuclide transport in urban stormwater.

Environmental modelling & software : with environment data news·2025
Same journal

Bridging Existing Energy and Chemical Transport Models to Enhance Air Quality Policy Assessment.

Environmental modelling & software : with environment data news·2025
See all related articles

Related Experiment Video

Updated: Dec 8, 2025

Constructing and Visualizing Models using Mime-based Machine-learning Framework
06:19

Constructing and Visualizing Models using Mime-based Machine-learning Framework

Published on: July 22, 2025

1.8K

On code sharing and model documentation of published individual and agent-based models.

Marco A Janssen1, Calvin Pritchard2, Allen Lee2

  • 1School of Sustainability and Center for Behavior, Institutions and Environment, Arizona State University, USA.

Environmental Modelling & Software : with Environment Data News
|September 22, 2020
PubMed
Summary
This summary is machine-generated.

Replication in computational modeling is improving slowly. While code sharing is increasing, comprehensive model documentation is still lacking, hindering reproducible science.

Keywords:
Agent-based modelingIndividual-based modelingOpen scienceReplicabilityReuse

More Related Videos

3D Printing of Biomolecular Models for Research and Pedagogy
09:17

3D Printing of Biomolecular Models for Research and Pedagogy

Published on: March 13, 2017

24.7K
Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
09:37

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

Published on: August 15, 2019

10.2K

Related Experiment Videos

Last Updated: Dec 8, 2025

Constructing and Visualizing Models using Mime-based Machine-learning Framework
06:19

Constructing and Visualizing Models using Mime-based Machine-learning Framework

Published on: July 22, 2025

1.8K
3D Printing of Biomolecular Models for Research and Pedagogy
09:17

3D Printing of Biomolecular Models for Research and Pedagogy

Published on: March 13, 2017

24.7K
Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
09:37

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

Published on: August 15, 2019

10.2K

Area of Science:

  • Computational modeling
  • Scientific reproducibility
  • Agent-based modeling

Background:

  • Replication is fundamental to scientific validity.
  • Computational models are increasingly used in research.
  • Reproducibility of computational models is a growing concern.

Purpose of the Study:

  • To assess code sharing and model documentation practices in computational modeling publications.
  • To identify factors influencing the transparency and reproducibility of individual-based and agent-based models.

Main Methods:

  • Analysis of 7500 publications on individual-based and agent-based models.
  • Evaluation of code availability and documentation completeness.
  • Correlation analysis between documentation elements and citation rates.

Main Results:

  • Code availability increased to 18% by 2018.
  • Model documentation often lacks crucial elements like equations, flow charts, and pseudocode.
  • Publications with detailed documentation (equations, flow charts) receive more citations.

Conclusions:

  • Code sharing practices are improving but slowly.
  • Enhanced model documentation is linked to higher impact and transparency.
  • Significant shifts in norms are needed for computational modeling to achieve true reproducibility.