Biophysically based models of physiological processes capture physiological phenotype in a quantitative and predictive form. They underpin research in physiology in the same way that nucleotide sequence underpins research in genetics, since there is no other way to deal with the complexity of physiological systems in a quantitative fashion. Most importantly, biophysical models bring with them the constraints on physiological behaviour imposed by the conservation laws of physics. Physiological function depends on these laws of nature as much as it depends on molecular biology. To ensure that biophysically based models and data are encoded in a reproducible fashion, we are developing three XML standards: CellML (for biophysical models based on ordinary differential and algebraic equations), FieldML (for partial differential equations and spatially varying models) and BiosignalML (for time-varying signals). Another standard (SED-ML) is being developed in collaboration with the molecular systems biology community to encode the simulation protocols – again to ensure reproducibility of stated results. A website has been developed to support the modelling community using these standards.
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