Related Experiment Video
Updated: May 29, 2026
10:41
Tracking and Quantifying Developmental Processes in C. elegans Using Open-source Tools
Published on: December 16, 2015
Developing models in virtual cell
1Department of Pharmacology and Systems Therapeutics and Systems Biology Center New York, Mount Sinai School of Medicine, New York, NY 10029, USA. susana.neves@mssm.edu
Science Signaling
|September 29, 2011
Summary
This resource teaches mathematical modeling using Virtual Cell software. Learn to build ordinary and partial differential equation models for cellular simulations and spatial analysis.
Area of Science:
- Computational Biology
- Biophysics
- Mathematical Biology
Background:
- Mathematical modeling is crucial for understanding complex cellular processes.
- Spatial organization significantly impacts cellular signaling and regulation.
- The Virtual Cell environment offers tools for simulating biological systems.
Purpose of the Study:
- To provide a teaching resource for mathematical modeling in the Virtual Cell environment.
- To guide users in constructing ordinary differential equation (ODE) and partial differential equation (PDE) models.
- To highlight the application of spatial PDE models for analyzing cellular signaling.
Main Methods:
- Developing and running simulations within the Virtual Cell environment.
- Constructing ODE models for well-mixed cellular compartments.
- Implementing PDE models to analyze spatio-temporal dynamics of chemical species.
Main Results:
- Demonstration of how to build both ODE and PDE models in Virtual Cell.
- Explanation of how PDE models capture spatial variations in cellular reactions.
- Examples of using Virtual Cell for spatial modeling of cellular signaling pathways.
Conclusions:
- The Virtual Cell environment facilitates the creation of spatial models for biological systems.
- Spatial modeling in Virtual Cell aids in understanding the regulatory role of cellular organization.
- This resource equips educators and students with practical skills in computational cell biology.
Related Concept Videos
01:21Cell Culture
Most vertebrate cells grow in vitro attached to a substrate as a monolayer, called adherent cultures. The flasks and plates used to grow cells are chemically treated to facilitate cell attachment. However, a few cell types, such as hematopoietic cells, can grow in a suspension. In contrast to adherent cultures, suspension cultures can grow in non-treated cultureware using magnetic stirrers or spinner flasks to agitate the culture media
02:00Molecular 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.