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VCell Publications and Model Curation

What is a Publication in VCell?

A VCell publication links a scientific paper to the computational models (BioModels and MathModels) that support it. Publications serve two purposes:

  1. Discovery - Users can browse publications to find curated, peer-reviewed models relevant to their research.
  2. Curation - Publications drive the process of reviewing, approving, and permanently preserving models in the VCell database.

How Users Find Published Models

In the VCell desktop client, the Database panel (lower left of any document window) organizes public models into three folders:

  • Published - Models created by users and linked to a scientific publication. Grouped by publication citation.
  • Curated - Models created by the VCell team or collaborators to reproduce results described in a publication.
  • Uncurated - Public models that have not been peer-reviewed or linked to a publication.

Published and Curated models represent the highest quality tier - they have been reviewed, are permanently preserved, and are linked to their corresponding papers.

How to Publish a VCell Model (Author Instructions)

When your paper is accepted and you want to associate your VCell model with the publication, follow these steps:

1. Make Your Model Public

Change your model's permissions in the VCell Database:

  • Navigate to File > Permissions...
  • Select Public
  • Click OK

The model will initially appear in the Uncurated public models folder. You can also share with specific users by selecting Grant Access to Specific Users and adding their VCell usernames.

2. Reference VCell in Your Publication

Include your username and model name so readers can find your model:

"The Virtual Cell Model, [modelname] by user [username], can be accessed within the VCell software (available at https://vcell.org)."

3. Acknowledge the Funding Source

Include this acknowledgment in your manuscript:

"The Virtual Cell is supported by NIH Grant R24 GM137787 from the National Institute for General Medical Sciences."

4. Cite the Required VCell Papers

All publications using VCell must cite:

  • 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

Additional citations for specialized model types:

  • Rule-Based models:
    • 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
  • Spatial Hybrid Deterministic-Stochastic models:
    • 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

5. Submit Your Publication Information

Complete the VCell Publication Submission Form with:

  • Your name, email, and VCell username
  • Article title, authors, and journal citation
  • Publication date
  • Model type (BioModel or MathModel) and model name

Upon approval by the VCell team, your model will be archived, listed on the VCell website, and protected from modification or deletion.

Archiving Without Publishing (Deprecated)

Previously, authors could archive models independently through the VCell desktop client by right-clicking a model in the Database panel and selecting Archive. Archiving protected a model from deletion or alteration but did not link it to a publication. This option was removed because it caused confusion among users about the distinction between archiving and publishing.

Model Lifecycle

Every model in VCell has a curation status (VersionFlag) that tracks where it is in the curation lifecycle:

  Current (0)  -->  Archived (1)  -->  Published (3)
   (default)       (protected)        (protected + public)
Status Who can see it Can it be deleted? Typical meaning
Current Depends on access settings Yes Work in progress or uncurated model
Archived Depends on access settings No (admin only) Preserved for reference, may or may not be linked to a publication
Published Everyone (public) No (admin only) Curated, peer-reviewed, linked to a publication

Curation status is independent from access control. A model can be publicly visible but still in "Current" status (not yet curated), or it could be archived but only visible to certain users.

Access Control (GroupAccess)

Access control determines who can view a model. It is a separate concept from curation status.

Level Description
Private Only the model owner can see it (default)
Shared The owner and specific named users can see it
Public Everyone can see it

When a model is published through the curation workflow, its access is automatically set to Public. However, a model author can independently make their model public at any time without it being "published" in the curation sense.

Curator Workflow

Curators are VCell team members with the publicationEditors role. Curation is performed through the Angular webapp at vcell.cam.uchc.edu. Curators are responsible for:

  • Creating and editing publication records (title, authors, DOI, PubMed ID, etc.)
  • Linking the correct model versions to each publication
  • Reviewing models for correctness and completeness
  • Publishing models - the act that makes them permanently public and protected from deletion

What Happens When a Curator Publishes Models

When a curator clicks "Publish Selected Models" in the webapp (or calls the publish API), two things happen atomically for each selected model:

  1. Access becomes public - The model's access control is set to GroupAccessAll, making it visible to all VCell users.
  2. Status becomes Published - The model's VersionFlag is set to Published, protecting it from deletion.

This is an intentionally irreversible operation through normal means. Published models are part of the scientific record and should not be casually removed.

Selective Publishing

Curators can choose to publish all models linked to a publication at once, or selectively publish individual models. This is useful when a publication links to multiple models but only some are ready for curation.

For Developers

See publications-api.md for the REST API reference, data models, and source file locations.