vcell_support@uchc.edu

Publish A VCell Model

Publish A VCell Model 2024-04-15T17:05:14+00:00
      1. Make your model available to the public.
        All models in Virtual Cell begin as private models. To let others see your model, you must change the permissions for the model in the Virtual Cell Database. First, change your model to a Public model. File>Manage Database – Right-click on your model and choose Permission; check “Public” and then OK. Once your model has been made public, it will initially appear in the “Uncurated” Public models folder in the VCell Database.
      2. Provide your username and model name within your publication.
        In the paper, direct users to the Virtual Cell software, and refer to your username and the name of the public model, e.g. The Virtual Cell Model, “modelname” by user “username”, can be accessed within the VCell software (available at https://vcell.org).
      3. Acknowledge the Virtual Cell resource in the Acknowledgement section of your manuscript.
        The Virtual Cell is supported by NIH Grant R24 GM137787 from the National Institute for General Medical Sciences.
      4. Always Cite the VCell via the following publications:
        • Schaff, J., C. C. Fink, B. Slepchenko, J. H. Carson, and L. M. Loew. 1997. A general computational framework for modeling cellular structure and function. Biophysical journal 73:1135-1146. PMC1181013 PMID: 9284281 DOI: 10.1016/S0006-3495(97)78146-3
        • Cowan, A. E., Moraru, II, J. C. Schaff, B. M. Slepchenko, and L. M. Loew. 2012. Spatial modeling of cell signaling networks. Methods Cell Biol 110:195-221. PMC3519356 PMID: 22482950 DOI: 10.1016/B978-0-12-388403-9.00008-4
      5. In addition, for Rule-Based models please cite:
        • Blinov, M. L., J. C. Schaff, D. Vasilescu, Moraru, II, J. E. Bloom, and L. M. Loew. 2017. Compartmental and Spatial Rule-Based Modeling with Virtual Cell. Biophysical journal 113:1365-1372. PMC5627391 PMID: 28978431 DOI: 10.1016/j.bpj.2017.08.022
      6. In addition, for Spatial Hybrid Deterministic-Stochastic Models please cite: 
        • Schaff, J. C., F. Gao, Y. Li, I. L. Novak, and B. M. Slepchenko. 2016. Numerical Approach to Spatial Deterministic-Stochastic Models Arising in Cell Biology. PLoS Comput Biol 12:e1005236. PMC5154471 PMID: 27959915 DOI: 10.1371/journal.pcbi.1005236
      7. And lastly, please let us know
        Your model will be added to the Published Models folder in the VCell Database and listed on our website, along with the cited publication. Simply fill out the form below. Once we associate the model with a publication, the public model will be archived so it cannot be changed, and the model will be annotated with the publication information. An archived model can be copied and saved as a new editable version.

    Virtual Cell Publication Submission Form

    Submit your publication reference information and the VCell model cited in your publication.
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