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FLUENT Verification Project Regular Team Meeting
Attending: Chris W, Hao, Zhen, Trent, Lukas, Nisa, Laureano, Payton, Mohammad,
Agenda
Discussion on importance sampling and Monte Carlo Discussion of IWBDA -- interesting paper on Monte Carlo simulation of genetic circuits. Zhen joined some short talk sessions. Zhen pointed us to the SubSBML project: https://github.com/BuildACell/subsbml
Sub-SBML is a Python based toolbox to create, edit, combine, and model interactions among multiple Systems Biology Markup Language (SBML) models. Sub-SBML works with a “subsystem” architecture of modeling where a single SBML model can be contained within a subsystem. Three major functionalities are developed in Sub-SBML that take advantage of this subsystem framework of modeling –
creating subsystems, combining multiple subsystems, and modeling interactions such as transport of molecules and input-output relationships among multiple subsystems.
Payton -- discussed about how SBOL models do not have unique mappings to SBML. Lukas: Can you annotate SBOL with SBML? Erik Winfree's group requested a tutorial on iBioSim. Python library to make genetic circuit figures DNAplotlib https://github.com/VoigtLab/dnaplotlib Trent is joining Sarcos, this is his last day. Zhen will take over his code, most likely will be carried forward by Riley in the fall.
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