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

A framework for three-dimensional simulation of morphogenesis.

Trevor M Cickovski1, Chenbang Huang, Rajiv Chaturvedi

  • 1Laboratory for Computational Life Sciences, Department of Computer Science and Engineering, University of Notre Dame, 325 Cushing Hall, Notre Dame, IN 46556, USA. tcickovs@nd.edu

IEEE/ACM Transactions on Computational Biology and Bioinformatics
|October 19, 2006
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

Modeling epithelial deformation and cell rearrangement in response to external forces during Zebrafish epiboly.

NPJ systems biology and applications·2026
Same author

Who's afraid of synthetic data? Hybrid approaches to deliver medical digital twins.

Informatics in medicine unlocked·2026
Same author

From FAIR to CURE: guidelines for computational models of biological systems.

NPJ systems biology and applications·2026
Same author

Prediction of Serious Adverse Events Associated With Pediatric Cardiac Catheterizations: External Model Validation of the CRISP Scoring Method.

Journal of the Society for Cardiovascular Angiography & Interventions·2026
Same author

V-Cornea: A computational model of corneal epithelium homeostasis, injury, and recovery.

PLoS computational biology·2025
Same author

Fetal Diagnosis of Hypoplastic Left Heart Syndrome With Restrictive Atrial Septum-Atrial Septal Morphology, Associated Lung Disease and Outcomes.

Prenatal diagnosis·2025
Same journal

circ2DGNN: circRNA-Disease Association Prediction via Transformer-Based Graph Neural Network.

IEEE/ACM transactions on computational biology and bioinformatics·2024
Same journal

Hierarchical Hypergraph Learning in Association- Weighted Heterogeneous Network for miRNA- Disease Association Identification.

IEEE/ACM transactions on computational biology and bioinformatics·2024
Same journal

Discriminative Domain Adaption Network for Simultaneously Removing Batch Effects and Annotating Cell Types in Single-Cell RNA-Seq.

IEEE/ACM transactions on computational biology and bioinformatics·2024
Same journal

MLW-BFECF: A Multi-Weighted Dynamic Cascade Forest Based on Bilinear Feature Extraction for Predicting the Stage of Kidney Renal Clear Cell Carcinoma on Multi-Modal Gene Data.

IEEE/ACM transactions on computational biology and bioinformatics·2024
Same journal

An End-to-End Knowledge Graph Fused Graph Neural Network for Accurate Protein-Protein Interactions Prediction.

IEEE/ACM transactions on computational biology and bioinformatics·2024
Same journal

Generative Biomedical Event Extraction With Constrained Decoding Strategy.

IEEE/ACM transactions on computational biology and bioinformatics·2024
See all related articles

We developed CompuCell3D, a 3D simulation software for organism development. This computational framework models cell behaviors and interactions, enabling diverse biological simulations for developmental biology research.

Area of Science:

  • Computational Biology
  • Developmental Biology
  • Biophysics

Background:

  • Morphogenesis, the biological process of shaping organisms, is complex and involves intricate cell behaviors.
  • Simulating these processes requires robust computational tools capable of handling multi-cellular interactions and spatial dynamics.

Purpose of the Study:

  • To introduce CompuCell3D, a novel software framework for simulating three-dimensional morphogenesis.
  • To provide a flexible and extensible platform for diverse biological simulations.

Main Methods:

  • CompuCell3D utilizes biologically relevant models for cell clustering, growth, and interaction with chemical fields.
  • The software employs design patterns for optimized speed, memory management, extensibility, and flexibility.
  • A model of avian limb bud development was used for verification.

Related Experiment Videos

Main Results:

  • CompuCell3D successfully simulated growth and skeletal pattern formation in the avian limb bud.
  • The framework demonstrated flexibility and efficiency in handling complex biological simulations.

Conclusions:

  • CompuCell3D offers a powerful and versatile tool for researchers studying morphogenesis and developmental biology.
  • The software facilitates the creation of a wide range of biological simulations, advancing our understanding of developmental processes.