Tools

The Tools menu bar provides tools that can be used to assist with model development and analysis in VCell.

• Launch BioNetGen - opens BioNetGen software within VCell. Rule-based modeling is fully integrated within VCell, but BioNetGen software can be useful for model analysis and scripting. More information about BioNetGen can be found at http://bionetgen.org.
• Launch Virtual FRAP - opens VirtualFRAP, a tool to analyze fluorescence photobleaching experiments using VCell spatial modeling technology.
• Launch Visit-based Visualization Tool - opens locally installed VisIT software for visualizing complex VCell geometries and simulation results. VisIT is an open source visualization, animation and analysis tool available from Lawrence LIvermore National Laboratory at https://wci.llnl.gov/simulation/computer-codes/visit/
• Transform to Stochastic Capable - launches a tool to convert a deterministic model to a stochastic-capable model, where possible.