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WebCM: A Web-Based Platform for Multiuser Individual-Based Modeling of Multicellular Microbial Populations and

Jason Philippou1, Guillermo Yáñez Feliú1, Timothy J Rudge1

  • 1Interdisciplinary Computing and Complex Biosystems, School of Computing, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K.

ACS Synthetic Biology
|May 14, 2024
PubMed
Summary
This summary is machine-generated.

WebCM is a web platform for creating and running microbial population simulations. It offers 3D visualization and supports collaborative research through cloud or local server deployment.

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Area of Science:

  • Microbiology
  • Computational Biology
  • Bioinformatics

Background:

  • Microbial population dynamics are complex and require advanced simulation tools.
  • Existing simulation software often lacks user-friendly interfaces and collaborative features.
  • Web-based platforms can enhance accessibility and collaboration in computational biology.

Purpose of the Study:

  • To introduce WebCM, a novel web platform for individual-based simulations of microbial populations.
  • To provide a user-friendly, browser-based interface for creating, editing, running, and visualizing simulations.
  • To leverage existing simulation software (CellModeller) for efficient computation on remote servers.

Main Methods:

  • WebCM utilizes the CellModeller software for backend simulations.
  • It employs a web-browser interface for model editing, execution, and playback.
  • The platform supports simultaneous multi-user access and management of multiple simulations.
  • It leverages GPU and CPU parallelization for computational efficiency.

Main Results:

  • WebCM enables real-time, interactive 3D graphical representations of simulations.
  • Users can inspect simulations at all time points and download results for offline analysis.
  • The platform facilitates collaborative research by allowing shared access to computational resources.
  • WebCM can be deployed on cloud services or local servers.

Conclusions:

  • WebCM provides an accessible and powerful platform for microbial population and community simulations.
  • The web-based interface and collaborative features enhance the usability and impact of computational modeling.
  • WebCM, by integrating CellModeller, offers efficient simulation capabilities with parallel processing.
  • The platform supports both individual laboratory use and inter-laboratory collaboration.