WholeCellViz is a web-based software program for visually analyzing whole-cell simulations. This git repository provides the WholeCellViz server and client source code.
WholeCellViz enables users to interactively analyze many aspects of cell physiology including:
- Cell mass, volume, and shape,
- Metabolite, RNA, and protein copy numbers,
- Metabolic reaction fluxes,
- Molecular machine statuses – DNA polymerase, RNA polymerase, ribosome, FtsZ ring, and the
- Chromosome copy number, superhelicity, integrity, and DNA binding status.
Currently, WholeCellViz provides access to cached simulations of the Gram-positive bacterium Mycoplasma genitalium2. See the Advanced usage section below for information about how to install WholeCellViz locally to use the software to run and analyze your own simulations and/or other high-throughput biological data, as well as how to add additional visualizations.
WholeCellViz has several features for visually analyzing whole-cell simulations:
14 structured visualizations encompassing a wide spectrum of cell physiology. These visualizations each provide tooltips and mouse clicks to enable users to obtain further information.
- A time series plot tool to further explore model predictions.
- A layout editor which enables users to configure a grid of structured visualizations and time series plots, enabling users to simultaneously compare multiple model predictions side-by-side.
- A layout history. Simply use your browser's backward/forward buttons to undo/redo layout changes.
- A single animation timeline with play, pause, seek, speed, and repeat controls.
- Data import in JSON format
- Graphical export in SVG format
- Data export in JSON format
WholeCellViz is freely available open-source and can be easily expanded for use with new whole-cell simulations and other high-throughput data. See the Advanced usage section below for information about how to install WholeCellViz locally to use the software to run and analyze your own simulations and/or other high-throughput biological data, as well as how to add additional visualizations.
See the online help at the WholeCellViz website.
Installing WholeCellViz locally
The easiest way to run the WholeCellViz software locally is to download the Whole-cell virtual machine posted at SimTK. Installation and usage instructions are also posted at SimTK. The virtual machine is a virtual Mint Linux machine for use with the free VirtualBox software. The virtual machine includes WholeCellViz as well as the simulation software and WholeCellKB. The virtual machine can be used to run new whole-cell simulations, analyze new simulations using WholeCellViz, and add new structured visualizations to WholeCelLViz.
To install WholeCellViz on your own machine: (1) download the WholeCellViz source code by cloning this repository, and (2) follow the installation instructions in the Developer's Guide.
Copyright (c) 2013 Stanford University
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