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VCell Published Models

Go here for a complete, searchable listing of Published VCell Models (1999 – present)

Access Published VCell Models

VCell models are used in many publications and authors are encouraged to make these models available to the community by making the models public. You can install VCell and open, save all public models using the instructions provided below.

Publish VCell Models

Provide your readers with a pointer.
In the paper, direct users to the Virtual Cell database accessible via the software, then refer to your username and the name of the archived biomodel. Users will find the model in your username folder. e.g. The Virtual Cell Model, providemodelname, is available in the public domain at http://vcell.org/ under the shared username, provideusername.
See below to Publish a VCell Model

Access the Published Models

VCell Model Directory

How to Access the Published Models

The Virtual Cell is being referenced in published articles since it was used to create the experimental models discussed in these articles. The models have been made public so that other Virtual Cell users may access them and view the results. To access a public model proceed as follows:

BioModels

  1. log on to the Virtual Cell software.
  2. In the Database pane (lower left), Select the BioModels tab from within the VCell Database.
  3. Published models are within the Public Biomodels folder; models are organized by “user name: model name”. Open the Search box to search by user name or model name.
  4. Double click the model to open.
  5. If you wish to modify the model or run new simulations, copy it into your VC Workspace under your own User account.

MathModels

  1. log on to the Virtual Cell software.
  2. In the Database pane (lower left), Select the MathModels tab from within the VCell Database.
  3. Published models are within the Public Mathmodels folder; models are organized by “user name: model name”. Open the Search box to search by user name or model name.
  4. Double click the model to open.
  5. If you wish to modify the model or run new simulations, copy it into your VC Workspace under your own User account.

Provide

Publish A VCell Model

  1. Provide readers with a pointer.
    In the paper, direct users to the Virtual Cell database accessible via the software, then refer to your username and the name of the archived biomodel. Users will find the model in your username folder. e.g. The Virtual Cell Model, “modelname”, is available in the public domain at http://vcell.org/ under the shared username “username”.
  2. Acknowledge the Virtual Cell resource.
    The Virtual Cell is supported by NIH Grant Number P41 GM103313 from the National Institute for General Medical Sciences.
  3. Let readers view your model.
    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. There are two options.
    At a minimum, change your model to a Public model. File>Manage Database – Right click on your model and choose Permission; check “Public” and then OK.
    Ideally, Publish and Archive your model. This saves your model in an unmodifiable state, presumably the same state as that used for the published simulations.
  4. Let us know
    We will add your publication to the list of published models associated with the Virtual Cell. Simply fill out the form below.

Virtual Cell Publication Submission Form

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