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

Developing complex signaling models using GENESIS/Kinetikit.

Sharat Jacob Vayttaden1, Upinder Singh Bhalla

  • 1National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore 560065, India. sharat@ncbs.res.in

Science'S STKE : Signal Transduction Knowledge Environment
|February 12, 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

Mechanisms and implications of high depolarization baseline offsets in conductance-based neuronal models.

Journal of neurophysiology·2025
Same author

Discriminating neural ensemble patterns through dendritic computations in randomly connected feedforward networks.

eLife·2025
Same author

Understanding molecular signaling cascades in neural disease using multi-resolution models.

Current opinion in neurobiology·2023
Same author

Combining hypothesis- and data-driven neuroscience modeling in FAIR workflows.

eLife·2022
Same author

Adult brain neurons require continual expression of the schizophrenia-risk gene Tcf4 for structural and functional integrity.

Translational psychiatry·2021
Same author

Correction: Precise excitation-inhibition balance controls gain and timing in the hippocampus.

eLife·2021
Same journal

Identification of redox-active cell-surface proteins by mechanism-based kinetic trapping.

Science's STKE : signal transduction knowledge environment·2007
Same journal

Image correlation spectroscopy.

Science's STKE : signal transduction knowledge environment·2007
Same journal

Studies of SARM1 uncover similarities between immune and neuronal responses to danger.

Science's STKE : signal transduction knowledge environment·2007
Same journal

A discrete signaling function for an inositol pyrophosphate.

Science's STKE : signal transduction knowledge environment·2007
Same journal

Putting on the RITz.

Science's STKE : signal transduction knowledge environment·2007
Same journal

Type I interferons as anti-inflammatory mediators.

Science's STKE : signal transduction knowledge environment·2007
See all related articles

We developed GENESIS/Kinetikit, a graphical simulation environment for building biologically realistic models of biochemical signaling pathways. This tool aids in understanding complex signaling networks by combining computational engines, modeling tools, and a curated model library.

Area of Science:

  • Computational biology
  • Systems biology
  • Biochemical modeling

Background:

  • Developing biologically realistic models of signaling pathways presents significant computational and complexity challenges.
  • Existing methods often struggle with the intricate nature of detailed pathway models.

Purpose of the Study:

  • To introduce the General Neural Simulation System (GENESIS) and Kinetikit (GENESIS/Kinetikit) as a graphical simulation environment for modeling biochemical signaling pathways.
  • To provide a comprehensive toolset that includes numerical computation engines, graphical modeling tools, and a library of pre-existing pathway models.

Main Methods:

  • Utilized deterministic and stochastic methods for simulating biochemical signaling pathways.
  • Developed a graphical simulation environment (GENESIS/Kinetikit) integrating computational engines and modeling tools.

Related Experiment Videos

  • Curated a library of signaling pathway models based on published studies, ensuring simulation outcomes match experimental results.

    • Main Results:

    • The GENESIS/Kinetikit environment facilitates the creation of complex signaling network simulations by combining individual pathway models.
    • A database maintains the library of signaling pathway models, ensuring consistency and reliability.
    • The developed system aims to achieve biological realism for direct comparison with experimental data.

    Conclusions:

    • GENESIS/Kinetikit offers a robust platform for building and simulating complex, biologically realistic signaling pathways.
    • The integrated approach, combining software, tools, and a curated model library, supports cumulative development and enhances understanding of cellular signaling.
    • The system is accessible online, promoting collaborative research in systems biology and computational neuroscience.