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

Reaction Mechanisms03:06

Reaction Mechanisms

26.0K
Chemical reactions often occur in a stepwise fashion, involving two or more distinct reactions taking place in a sequence. A balanced equation indicates the reacting species and the product species, but it reveals no details about how the reaction occurs at the molecular level. The reaction mechanism (or reaction path) provides details regarding the precise, step-by-step process by which a reaction occurs.
For instance, the decomposition of ozone appears to follow a mechanism with two steps:
26.0K
Coupled Reactions01:17

Coupled Reactions

7.8K
Cellular processes such as building and breaking down complex molecules occur through stepwise chemical reactions. Some of these chemical reactions are spontaneous and release energy, whereas others require energy to proceed. Cells often couple the energy-releasing reaction with the energy-requiring one to carry out important cell functions. 
Energy in adenosine triphosphate or ATP molecules is easily accessible to do work. ATP powers the majority of energy-requiring cellular reactions....
7.8K
Reaction Rate02:53

Reaction Rate

52.7K
The rate of reaction is the change in the amount of a reactant or product per unit time. Reaction rates are therefore determined by measuring the time dependence of some property that can be related to reactant or product amounts. Rates of reactions that consume or produce gaseous substances, for example, are conveniently determined by measuring changes in volume or pressure.
The mathematical representation of the change in the concentration of reactants and products, over time, is the rate...
52.7K
Reaction Quotient02:35

Reaction Quotient

48.6K
The status of a reversible reaction is conveniently assessed by evaluating its reaction quotient (Q). For a reversible reaction described by m A + n B ⇌ x C + y D, the reaction quotient is derived directly from the stoichiometry of the balanced equation as
48.6K
Support Reactions in Three Dimensions01:27

Support Reactions in Three Dimensions

991
Support reactions in three dimensions help maintain the stability and equilibrium of various structures and systems. These reactions prevent the system from translating and rotating, ensuring the design can withstand external forces and perform its intended function efficiently and safely. Some of the supports providing support reactions in three dimensions are discussed below:
Ball and Socket Joint is one of the supports allowing free rotation about any axis. This freedom of rotation is...
991
Support Reactions01:30

Support Reactions

459
A coplanar force system refers to a set of forces that all lie in the same plane and are subject to different reactions between the point of contact and the supports. Understanding how different types of supports affect coplanar forces is crucial for designing safe and reliable structures that can withstand external loads.
The purpose of the supports is to prevent the translational motion of the system by applying an equal and opposite force and to prevent the system's rotation by applying...
459

You might also read

Related Articles

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

Sort by
Same author

A standardized workflow for kinetic metabolic model curation and dissemination.

PLoS computational biology·2026
Same author

Antimony 3: Extending human-readable model definitions for SBML Level 3 Core and Packages.

bioRxiv : the preprint server for biology·2026
Same author

Evaluating the limitations of Bayesian metabolic control analysis.

PLoS computational biology·2026
Same author

Verification and reproducible curation of the BioModels repository.

PLoS computational biology·2025
Same author

A Roadmap for the Future of Systems Biology in Cancer Research.

Cancer research·2025
Same author

SBMLNetwork: A framework for standards-based visualization of biochemical models.

PLoS computational biology·2025
Same journal

Poisoning the Genome: Targeted Backdoor Attacks on DNA Foundation Models.

ArXiv·2026
Same journal

Mechanistic mathematical model of the in vitro infection dynamics of Bunyamwera and Batai viruses including MOI-dependent shortening of the eclipse phase.

ArXiv·2026
Same journal

AI-Driven Lumped-Element Modeling of Human Respiratory System for Studying Voice Mechanics.

ArXiv·2026
Same journal

Beyond Algorithms: Conceptual Innovation in Medical Imaging AI.

ArXiv·2026
Same journal

Feynman Kac Reweighted Schrödinger Bridge Matching for Surface-Based Tau PET Harmonization.

ArXiv·2026
Same journal

Agentic Discovery of Non-Canonical Antimicrobial Peptides with AMPGAN v3.

ArXiv·2026
See all related articles

Related Experiment Video

Updated: Jul 17, 2025

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

9.9K

SBcoyote: An Extensible Python-Based Reaction Editor and Viewer.

Jin Xu1, Gary Geng2, Nhan D Nguyen3

  • 1Department of Bioengineering, University of Washington, Seattle 98195, WA, USA.

Arxiv
|August 30, 2023
PubMed
Summary
This summary is machine-generated.

SBcoyote is an open-source biochemical viewer and editor for visualizing and editing biological pathways. Its extensive Python plugin API and SBML support facilitate custom functionality and data exchange.

More Related Videos

An Open-Source, Fully Customizable 5-Choice Serial Reaction Time Task Toolbox for Automated Behavioral Training of Rodents
09:39

An Open-Source, Fully Customizable 5-Choice Serial Reaction Time Task Toolbox for Automated Behavioral Training of Rodents

Published on: January 19, 2022

4.2K
Automated Interactive Video Playback for Studies of Animal Communication
07:21

Automated Interactive Video Playback for Studies of Animal Communication

Published on: February 9, 2011

13.6K

Related Experiment Videos

Last Updated: Jul 17, 2025

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

9.9K
An Open-Source, Fully Customizable 5-Choice Serial Reaction Time Task Toolbox for Automated Behavioral Training of Rodents
09:39

An Open-Source, Fully Customizable 5-Choice Serial Reaction Time Task Toolbox for Automated Behavioral Training of Rodents

Published on: January 19, 2022

4.2K
Automated Interactive Video Playback for Studies of Animal Communication
07:21

Automated Interactive Video Playback for Studies of Animal Communication

Published on: February 9, 2011

13.6K

Area of Science:

  • Systems biology
  • Computational biology
  • Biochemical modeling

Background:

  • Biochemical reaction networks are fundamental to understanding cellular processes.
  • Efficient visualization and editing tools are crucial for systems biology research.
  • Interoperability between different modeling software is a significant challenge.

Approach:

  • SBcoyote is an open-source, cross-platform biochemical reaction viewer and editor.
  • It features a Python-based GUI using wxPython for visualization and editing of compartments, species, and reactions.
  • The tool supports extensive stylization options, network navigation features, and a Python plugin API.

Key Points:

  • SBcoyote allows detailed visualization and editing of biochemical networks with customizable elements.
  • A unique Python plugin API enables third-party developers to extend functionality.
  • Support for SBML level 3 layout and render standards ensures data exchange with other software.

Conclusions:

  • SBcoyote provides a flexible and extensible platform for biochemical network analysis.
  • Its plugin architecture and interoperability features enhance its utility for systems biology research.
  • The tool is available under the MIT license with a plugin manager for easy installation and updates.