Mikes Notes
WholeCellViz is a web-based software program for visually analysing whole-cell simulations. PIPI internal architecture uses many of the same techniques.
From its website
WholeCellViz is a web-based software program for visually analyzing whole-cell simulations.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.
Features
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.
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