Related Experiment Video
Updated: Aug 24, 2026
08:01
A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
Genomic Object Net: II. Modelling biopathways by hybrid functional Petri net with extension
Atsushi Doi1, Masao Nagasaki, Sachie Fujita
1Graduate School of Science and Engineering, Yamaguchi University, Yoshida, Yamaguchi, Japan.
Applied Bioinformatics
|May 8, 2004
Abstract:
This paper demonstrates how to create an HFPNe (hybrid functional Petri net with extension) model, using the lac operon gene regulatory mechanism and glycolytic pathway as an example. Using this example, readers can then model other biopathways of interest. Simulations of the HFPNe model were performed using the software package Genomic Object Net.
Related Concept Videos
02:26Protein Networks
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
02:26Protein Networks
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
03:36Genome Annotation and Assembly
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
01:23Operon Model
The operon model represents a fundamental mechanism of gene regulation in prokaryotes, enabling coordinated expression of genes involved in related metabolic or functional pathways. Operons consist of structural genes, a promoter, and an operator, with transcription regulated by repressors, activators, and small effector molecules.Structure and Function of OperonsAn operon is a cluster of structural genes transcribed together under the control of a single promoter. The promoter region...