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

C4 Pathway and CAM01:27

C4 Pathway and CAM

Most plants use the C3 pathway for carbon fixation. However, some plants, such as sugar cane, corn, and cacti that grow in hot conditions, use alternative pathways to fix carbon and conserve energy loss due to photorespiration. Photorespiration is the process that occurs when the oxygen concentration is high. Under such conditions, the rubisco enzyme in the Calvin cycle binds O2 instead of CO2, which halts photosynthesis and consumes energy.
C4 Pathway
The C4 pathway is used by plants such as...
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...
The JAK-STAT Signaling Pathway01:20

The JAK-STAT Signaling Pathway

Several cytokine receptors have tightly bound Janus kinase or JAK proteins attached at their cytosolic tail. Small signaling molecules such as cytokines, growth hormones, or prolactins bind to the cytokine receptors and initiate their dimerization. The dimerization brings the cytosolic JAKs together that trans-phosphorylate and activates each other. The activated JAKs now phosphorylate cytosolic tails of the cytokine receptors, which serve as binding sites for adaptor proteins such as  SH2...
Interactions Between Signaling Pathways01:19

Interactions Between Signaling Pathways

Signaling cascades usually lack linearity. Multiple pathways interact and regulate one another, allowing cells to integrate and respond to diverse environmental stimuli.
Convergence and divergence, and cross-talk between signaling pathways
Two distinct signaling pathways can converge on a single functional unit, which may either be a single protein or a complex of proteins. The response is either functionally distinct or synergistic between the two pathways but different from the response...
Biostatistics: Overview01:20

Biostatistics: Overview

Biostatistics plays a crucial role in understanding and analyzing data in healthcare and biology. Biostatisticians conduct experiments, gather evidence, and draw meaningful conclusions using statistical methods and techniques. Different variables form the foundation of biostatistical analysis, allowing researchers to understand and interpret data effectively. These variables are classified into different types, each serving a specific purpose in statistical analysis.
Discrete variables are...
Pedigree Analysis01:35

Pedigree Analysis

Overview

You might also read

Related Articles

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

Sort by
Same author

Indoor air quality and its effects on lung function and respiratory symptoms among textile spinning mill workers in India.

Work (Reading, Mass.)·2026
Same author

Deep Learning in Cytopathology: The Potential for Multimodal Synergy of Clinical and Cytological Input Data.

Journal of cytology·2026
Same author

Brain Organoids, Lessons from Fetal Neocortex Formation, and Rational Design for Quality Control.

bioRxiv : the preprint server for biology·2026
Same author

Oncogenic cell fate decision in breast epithelial cells I: growth factors and mechanisms.

Research square·2026
Same author

Screen Time Patterns and Cognitive Development Among Preschool Children.

American journal of preventive medicine·2026
Same author

Performance evaluation of an EEG-guided robotic glove with machine learning models for hand rehabilitation in injured athletes.

Journal of back and musculoskeletal rehabilitation·2026

Related Experiment Video

Updated: Jun 19, 2026

A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

An editor for pathway drawing and data visualization in the Biopathways Workbench.

Robert W Byrnes1, Dawn Cotter, Andreia Maer

  • 1San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093-0505, USA. rbyrnes@sdsc.edu

BMC Systems Biology
|October 6, 2009
PubMed
Summary
This summary is machine-generated.

Pathway Editor software integrates diverse experimental data and pathway diagrams for systems biology. This tool facilitates de novo pathway creation and annotation, enhancing biological pathway modeling capabilities.

More Related Videos

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information
05:01

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information

Published on: July 1, 2020

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline
10:44

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

Published on: December 7, 2021

Related Experiment Videos

Last Updated: Jun 19, 2026

A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information
05:01

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information

Published on: July 1, 2020

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline
10:44

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

Published on: December 7, 2021

Area of Science:

  • Systems Biology
  • Bioinformatics
  • Computational Biology

Background:

  • Pathway models are fundamental to systems biology research.
  • Current software often lacks integrated access to diverse experimental data, compound databases, and reference pathways.
  • This limitation hinders comprehensive pathway model construction.

Purpose of the Study:

  • To develop a unified software application for pathway model creation and analysis.
  • To integrate diverse experimental data types and pathway databases within a single interface.
  • To enhance the capabilities of existing pathway modeling tools.

Main Methods:

  • Developed the Pathway Editor using Java programming language.
  • Integrated LIPID MAPS and KEGG lipid metabolic pathways.
  • Enabled de novo pathway creation with access to metabolomic, microarray, and protein array data.
  • Implemented features for node and interaction annotation, layout configuration, and data display.
  • Built upon the Biopathways Workbench library for file format and database object conversion, including SBML support.

Main Results:

  • The Pathway Editor allows de novo pathway creation and downloading of curated pathways.
  • Users can integrate and visualize time-dependent changes in lipid metabolism from various experimental data types.
  • The software supports annotation with standardized nomenclature and common lipid names.
  • Pathway diagrams can be saved in XML format, referencing specific compounds and experiments.

Conclusions:

  • The Pathway Editor offers a significant advancement in pathway modeling tools.
  • Its integrated approach to data, databases, and visualization streamlines systems biology research.
  • Automatic updates via online database connectivity and focus on annotation improve usability and accuracy.