I am a systems biology PhD student with background in molecular biology. My doctoral research at the University of Oxford aims at improving our mechanistic understanding of cell cycle dynamics with mathematical models. This involves (1) casting chemical reaction networks into executable models, (2) obtaining highly multiplexed snapshot measurements of cell cycle regulators, from which we reconstruct their time-courses, and (3) developing parameter optimisation and model reduction/selection toolboxes.
Systems Biology Markup Language (SBML) and CellML are extensible markup languages (XML) widely used throughout the biological modeling community. In this talk we showcase new packages (SBML.jl and CellMLToolkit.jl) for importing models from these languages to the ModelingToolkit.jl format for the full suite of SciML tools to simulate and analyze!