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 Experiment Videos

Simulating genetic networks made easy: network construction with simple building blocks.

Steven Vercruysse1, Martin Kuiper

  • 1Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB), Ghent University Technologiepark 927, B-9052, Gent, Belgium.

Bioinformatics (Oxford, England)
|August 21, 2004
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

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

Sort by
Same author

Fine tuning a logical model of cancer cells to predict drug synergies: combining manual curation and automated parameterization.

Frontiers in systems biology·2025
Same author

Integration of chromosome locations and functional aspects of enhancers and topologically associating domains in knowledge graphs enables versatile queries about gene regulation.

Nucleic acids research·2024
Same author

Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches.

Frontiers in immunology·2024
Same author

Dynamic Boolean modeling of molecular and cellular interactions in psoriasis predicts drug target candidates.

iScience·2024
Same author

TFCheckpoint database update, a cross-referencing system for transcription factors from human, mouse and rat.

Nucleic acids research·2023
Same author

Characterisation of Colorectal Cancer Cell Lines through Proteomic Profiling of Their Extracellular Vesicles.

Proteomes·2023

SIM-plex is a new genetic network simulator. It uses Piecewise Linear Differential Equations (PLDEs) for switch-like interaction modeling, offering an intuitive user interface.

Area of Science:

  • Computational Biology
  • Systems Biology
  • Bioinformatics

Background:

  • Genetic networks are complex systems.
  • Modeling these networks aids understanding of cellular processes.
  • Existing simulation tools may lack user-friendliness or specific modeling capabilities.

Purpose of the Study:

  • To introduce SIM-plex, a novel genetic network simulator.
  • To provide an intuitive platform for specifying and simulating genetic interactions.
  • To leverage Piecewise Linear Differential Equations (PLDEs) for modeling genetic network dynamics.

Main Methods:

  • Developed SIM-plex, a software tool based on Java.
  • Implemented a mathematical model using Piecewise Linear Differential Equations (PLDEs).

Related Experiment Videos

  • Designed an intuitive user interface for defining genetic interactions via 'if-then' statements.

    • Main Results:

    • SIM-plex enables straightforward specification of genetic interactions.
    • The simulator effectively models genetic interactions using a switch-like approximation via PLDEs.
    • The software provides a user-friendly approach to genetic network simulation.

    Conclusions:

    • SIM-plex offers an accessible tool for researchers studying genetic networks.
    • The use of PLDEs provides a robust mathematical foundation for the simulator.
    • This simulator can facilitate research in systems biology and computational biology.