Seminář UPSY - Šafránek D.: Formal Biochemical Space to Bridge the Gap Between Mathematical Modelling and Biology


The concept of Biochemical Space (BCS) makes a crucial methodological part of Comprehensive Modelling Platform, a general platform for computational modelling and analysis of biological processes, introduced as a concept for unambiguous representation of internally consistent reduced mathematical models of oxygenic photosynthesis and further refined to a general online modelling platform for complex biophysical processes.  BCS provides a concise mapping of mathematical models to their biological description established at a desired level of abstraction. On theoretical end, we present BCS as a completely formal language with rigorously defined semantics by means of a simplified Kappa calculus. On the practical end, we show BCS models defined for metabolic, photosynthetic and circadian clock processes to demonstrate the usability of the language.

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