Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Synthetic Biology

Synthetic Biology

Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
Golden rice
Golden rice is a genetically modified...

Applications of Molecular Taxonomy

Applications of Molecular Taxonomy

Molecular taxonomy has revolutionized the understanding and classification of bacteria, providing precise insights into their diversity, evolutionary relationships, and ecological roles. By utilizing molecular techniques such as DNA sequencing and fingerprinting, researchers have made significant strides in various fields related to bacterial studies.Resolving Taxonomic AmbiguitiesMolecular taxonomy has been instrumental in distinguishing closely related bacterial species initially thought to...

Molecular Models

Molecular Models

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.

Control Systems: Applications

Control Systems: Applications

Electrical engineering plays a pivotal role in our daily lives, with control systems at the heart of many applications, from home appliances to sophisticated space shuttles. Control systems manage and regulate the behavior of devices and processes, ensuring they function safely, correctly, and efficiently.
In modern vehicles, control systems manage various functions to enhance performance and safety. The steering wheel and accelerator are primary inputs in a car's control system. The direction...

Applications of Integration to Find Blood Flow

Applications of Integration to Find Blood Flow

Blood flow through a cylindrical blood vessel can be mathematically described using the principles of laminar flow, a regime in which fluid moves smoothly in parallel layers. In this model, the velocity of the blood is not uniform across the cross-section of the vessel; rather, it varies with the radial distance from the center. The maximum velocity occurs along the central axis, decreasing progressively toward the vessel walls, where it reaches zero due to viscous drag.Approximating Blood...

Statistical Software for Data Analysis and Clinical Trials

Statistical Software for Data Analysis and Clinical Trials

Statistical software is pivotal in data analysis and clinical trials by providing tools to analyze data, draw conclusions, and make predictions. These software packages range from simple data management applications to complex analytical platforms, supporting various statistical tests, models, and simulation techniques. Their significance lies in their ability to handle vast amounts of data with precision and efficiency, enabling researchers to validate hypotheses, identify trends, and make...

You might also read

Related Articles

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

Sort by

Same author

stana: an R package for metagenotyping analysis and interactive application based on clinical data.

NAR genomics and bioinformatics·2025

Same author

Cross-Border Transmissions of the Delta Substrain AY.29 During Tokyo Olympic and Paralympic Games.

Frontiers in microbiology·2022

Same author

Targeting Tyro3 ameliorates a model of PGRN-mutant FTLD-TDP via tau-mediated synaptic pathology.

Nature communications·2018

Same author

Comprehensive phosphoproteome analysis unravels the core signaling network that initiates the earliest synapse pathology in preclinical Alzheimer's disease brain.

Human molecular genetics·2014

Same author

Enhancement of osteoinduction by continual simvastatin release from poly(lactic-co-glycolic acid)-hydroxyapatite-simvastatin nano-fibrous scaffold.

Journal of biomedical nanotechnology·2013

Same author

[Value of three-dimensional speckle-tracking echocardiography and the novel area strain in detecting wall motion abnormalities of coronary artery diseases].

Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition·2013

Search research articles

Related Experiment Video

Updated: May 23, 2026

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

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

Published on: December 7, 2021

Cell Illustrator 4.0: a computational platform for systems biology.

Masao Nagasaki¹, Ayumu Saito, Euna Jeong

¹Human Genome Center, Institute of Medical Science, University of Tokyo, Japan. masao@ims.u-tokyo.ac.jp

In Silico Biology

|March 21, 2012

Summary

Cell Illustrator 4.0 is a Systems Biology software for modeling and simulating biological pathways using Petri nets. This enhanced version offers advanced features for bench scientists, improving biopathway analysis.

More Related Videos

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

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

Published on: February 8, 2017

ExCYT: A Graphical User Interface for Streamlining Analysis of High-Dimensional Cytometry Data

ExCYT: A Graphical User Interface for Streamlining Analysis of High-Dimensional Cytometry Data

Published on: January 16, 2019

Related Experiment Videos

Last Updated: May 23, 2026

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

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

Published on: December 7, 2021

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

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

Published on: February 8, 2017

ExCYT: A Graphical User Interface for Streamlining Analysis of High-Dimensional Cytometry Data

ExCYT: A Graphical User Interface for Streamlining Analysis of High-Dimensional Cytometry Data

Published on: January 16, 2019

Area of Science:

Systems Biology
Computational Biology
Bioinformatics

Background:

Biological pathway modeling is crucial for understanding cellular processes.
Existing tools may lack comprehensive features for complex biopathway analysis.

Purpose of the Study:

To introduce Cell Illustrator 4.0, an advanced software platform for Systems Biology.
To enhance biopathway modeling and simulation capabilities for biological scientists.

Main Methods:

Utilizes an extension of hybrid Petri nets in an object-oriented style.
Incorporates Cell System Markup Language (CSML) 3.0 and Cell System Ontology 3.0.
Features automatic graph layout, parameter search, and high-performance simulation modules.

Main Results:

Cell Illustrator 4.0 supports detailed biopathway models including DNA sequence, molecular density, and 3D localization.
Enables conversion of models to multiple programming languages (FORTRAN, C, C++, Java, Python, Perl).
Facilitates import from SBML, CellML, and BioPAX, and export to SVG and HTML.

Conclusions:

Cell Illustrator 4.0 provides a powerful and versatile platform for Systems Biology research.
The software empowers bench scientists with advanced tools for in-depth biopathway analysis and simulation.