Bringing Together Models from Bottom-Up and Top-Down Approaches: An Application for Growth of Escherichia coli on Different Carbohydrates
Modeling in systems biology follows two lines: a data driven top-down approach that integrates experimental data from various “omics” technologies and a model based bottom-up approach where the model structure is given and kinetic parameters are chosen in such a way that an experimental observation can be reproduced quantitatively or qualitatively. Mathematical models are frequently used to elucidate cellular design principles in order to understand complex biochemical networks better. To show that both approaches lead to a consistent description of cellular dynamics, mathematical models from both approaches are explored. On the level of transcription factor activities a sufficient qualitative agreement is observed. Experimental data for the classical growth experiment of Escherichia coli on two carbon sources, glucose and lactose is available to set up the data driven model and to support the theoretical findings from the bottom-up approach.
KeywordsSpecific Growth Rate Singular Value Decomposition Transcription Factor Activity Stringent Response High Specific Growth Rate
Funding in part by the German BMBF during the FORSYS initiative is acknowledged.
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