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Virtual Cell modelling and simulation software environment
Open accessAbstract
The Virtual Cell (VCell; http://vcell.org/) is a problem solving environment, built on a central database, for analysis, modelling and simulation of cell biological processes. VCell integrates a growing range of molecular mechanisms, including reaction kinetics, diffusion, flow, membrane transport, lateral membrane diffusion and electrophysiology, and can associate these with geometries derived from experimental microscope images. It has been developed and deployed as a web-based, distributed, client-server system, with more than a thousand world-wide users. VCell provides a separation of layers (core technologies and abstractions) representing biological models, physical mechanisms, geometry, mathematical models and numerical methods. This separation clarifies the impact of modelling decisions, assumptions and approximations. The result is a physically consistent, mathematically rigorous, spatial modelling and simulation framework. Users create biological models and VCell will automatically (i) generate the appropriate mathematical encoding for running a simulation and (ii) generate and compile the appropriate computer code. Both deterministic and stochastic algorithms are supported for describing and running non-spatial simulations; a full partial differential equation solver using the finite volume numerical algorithm is available for reaction-diffusion-advection simulations in complex cell geometries including 3D geometries derived from microscope images. Using the VCell database, models and model components can be reused and updated, as well as privately shared among collaborating groups, or published. Exchange of models with other tools is possible via import/export of SBML, CellML and MatLab formats. Furthermore, curation of models is facilitated by external database binding mechanisms for unique identification of components and by standardised annotations compliant with the MIRIAM standard. VCell is now open source, with its native model encoding language (VCML) being a public specification, which stands as the basis for a new generation of more customised, experiment-centric modelling tools using a new plug-in based platform.
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“BioPAX pathway data can also be converted into simulation models, for instance using differential equations51 or rule-based modeling languages52, to predict how a biological system may function after a gene is knocked-out.”
From The BioPAX community standard for pathway data sharing (2010) · cites this paper as [51]
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Hernández, J. A. (2013) · Journal of Biophysics · doi:10.1155/2013/654543 · Cited by 1
Jiang, H., Manzella, M., Djapic, L., & Ganesan, N. (2016) · ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB) · doi:10.1145/2975167.2975207 · Cited by 1
SEML: A Simplified English Modeling Language for Constructing Biological Models in Julia
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DeWoskin, R. S., Knudsen, T. B., & Shah, I. (2014) · Elsevier eBooks · doi:10.1016/b978-0-12-386454-3.01059-9 · Cited by 1
de Lomana, A. L. G. (2010) · Repositori digital de la UPF (Universitat Pompeu Fabra) · Cited by 1
Metadata
- Authors
- Moraru, I. I., Schaff, J. C., Slepchenko, B. M., Blinov, M. L., Morgan, F., Lakshminarayana, A., Gao, F., Li, Y., & Loew, L. M.
- Affiliations
- UConn Health (US)
- Venue
- IET Systems Biology
- Published
- 2008-09-15
- Volume
- 2
- Issue
- 5
- Pages
- 352-362
- ISSN
- 1751-8849 (ISSN-L)
- 1751-8857
- PMC
- PMC2711391
- OpenAlex
- W2097319997
- Cited by
- 236
- References
- 20
- Citations by year
- 2026: 6 · 2025: 7 · 2024: 7 · 2023: 5 · 2022: 11 · 2021: 17 · 2020: 12 · 2019: 12 · 2018: 11 · 2017: 8 · 2016: 14 · 2015: 22 · 2014: 16 · 2013: 24 · 2012: 16
- FWCI
- 6.59
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- IET Systems Biology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institutes of Health (5u54gm064346-10, 5u54rr022232-05)
- National Institute of General Medical Sciences (U54-GM064346)
- National Center for Research Resources (U54-RR022232, P41RR013186)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Physical Sciences › Mathematics › Modeling and Simulation › Modeling and Simulation Systems
- Social Sciences › Decision Sciences › Information Systems and Management › Scientific Computing and Data Management
- Keywords
- Virtual Cell, computational cell biology, reaction kinetics, advection-diffusion-reaction, membrane transport, electrophysiology, stochastic simulation, partial differential equation solvers, finite volume method, SBML, CellML, model exchange, model reuse, open source software
- MeSH terms
- Computer Simulation, Models, Biological, Programming Languages, Software, User-Computer Interface, Signal Transduction, Databases, Factual, Information Storage and Retrieval, Proteome
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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