The Virtual Cell: a software environment for computational cell biology
- PMID: 11587765
- DOI: 10.1016/S0167-7799(01)01740-1
The Virtual Cell: a software environment for computational cell biology
Abstract
The newly emerging field of computational cell biology requires software tools that address the needs of a broad community of scientists. Cell biological processes are controlled by an interacting set of biochemical and electrophysiological events that are distributed within complex cellular structures. Computational modeling is familiar to researchers in fields such as molecular structure, neurobiology and metabolic pathway engineering, and is rapidly emerging in the area of gene expression. Although some of these established modeling approaches can be adapted to address problems of interest to cell biologists, relatively few software development efforts have been directed at the field as a whole. The Virtual Cell is a computational environment designed for cell biologists as well as for mathematical biologists and bioengineers. It serves to aid the construction of cell biological models and the generation of simulations from them. The system enables the formulation of both compartmental and spatial models, the latter with either idealized or experimentally derived geometries of one, two or three dimensions.
Similar articles
-
The Virtual Cell project.Novartis Found Symp. 2002;247:151-60; discussion 160-1, 198-206, 244-52. Novartis Found Symp. 2002. PMID: 12539954 Review.
-
UML as a cell and biochemistry modeling language.Biosystems. 2005 Jun;80(3):283-302. doi: 10.1016/j.biosystems.2004.12.003. Epub 2005 Feb 17. Biosystems. 2005. PMID: 15888343
-
Computational cell biology: spatiotemporal simulation of cellular events.Annu Rev Biophys Biomol Struct. 2002;31:423-41. doi: 10.1146/annurev.biophys.31.101101.140930. Epub 2001 Oct 25. Annu Rev Biophys Biomol Struct. 2002. PMID: 11988477 Review.
-
Quantitative cell biology with the Virtual Cell.Trends Cell Biol. 2003 Nov;13(11):570-6. doi: 10.1016/j.tcb.2003.09.002. Trends Cell Biol. 2003. PMID: 14573350 Review.
-
A reductionist's systems biology: opinion.Curr Opin Cell Biol. 2005 Feb;17(1):9-11. doi: 10.1016/j.ceb.2004.12.012. Curr Opin Cell Biol. 2005. PMID: 15661513
Cited by
-
bnglViz: online visualization of rule-based models.Bioinformatics. 2024 Jun 3;40(6):btae351. doi: 10.1093/bioinformatics/btae351. Bioinformatics. 2024. PMID: 38814806 Free PMC article.
-
Cell4D: a general purpose spatial stochastic simulator for cellular pathways.BMC Bioinformatics. 2024 Mar 21;25(1):121. doi: 10.1186/s12859-024-05739-0. BMC Bioinformatics. 2024. PMID: 38515063 Free PMC article.
-
Applications and Challenges of Machine Learning to Enable Realistic Cellular Simulations.Front Phys. 2020 Jan;7:247. doi: 10.3389/fphy.2019.00247. Epub 2020 Jan 21. Front Phys. 2020. PMID: 36188416 Free PMC article.
-
A scalable, open-source implementation of a large-scale mechanistic model for single cell proliferation and death signaling.Nat Commun. 2022 Jun 21;13(1):3555. doi: 10.1038/s41467-022-31138-1. Nat Commun. 2022. PMID: 35729113 Free PMC article.
-
Data Management Schema Design for Effective Nanoparticle Formulation for Neurotherapeutics.AIChE J. 2021 Dec;67(12):e17459. doi: 10.1002/aic.17459. Epub 2021 Sep 22. AIChE J. 2021. PMID: 35399334 Free PMC article.
Publication types
MeSH terms
Grants and funding
LinkOut - more resources
Full Text Sources
Other Literature Sources
