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WIREs Syst Biol Med
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Model‐based design of experiments for cellular processes

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Abstract Model‐based design of experiments (MBDOE) assists in the planning of highly effective and efficient experiments. Although the foundations of this field are well‐established, the application of these techniques to understand cellular processes is a fertile and rapidly advancing area as the community seeks to understand ever more complex cellular processes and systems. This review discusses the MBDOE paradigm along with applications and challenges within the context of cellular processes and systems. It also provides a brief tutorial on Fisher information matrix (FIM)‐based and Bayesian experiment design methods along with an overview of existing software packages and computational advances that support MBDOE application and adoption within the Systems Biology community. As cell‐based products and biologics progress into the commercial sector, it is anticipated that MBDOE will become an essential practice for design, quality control, and production. WIREs Syst Biol Med 2013, 5:181–203. doi: 10.1002/wsbm.1204 This article is categorized under: Models of Systems Properties and Processes > Cellular Models Biological Mechanisms > Cell Signaling Analytical and Computational Methods > Computational Methods

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The MBDOE paradigm is an iterative process that incorporates a priori knowledge, existing datasets, and relevant models to plan feasibility constrained experiments. Implementation of these experiments results in new data that directs the model development and revision in a maximally informative manner.

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Box‐and‐Whisker plots of the MBDOE supporting mathematical models based upon the categorized literature. The whiskers extend from the minimum to the maximum in the sample. The median is indicated by the horizontal black line within the green boxes, which extend from the lower to upper quartiles. (a) Model order (number of equations); (b) Total number of model parameters; (c) Number of model parameters considered uncertain. Note: A single paper may be counted more than once in these plots if they addressed more than one application or case study.

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Analysis of the applied MBDOE based upon the categorized literature. (a) Objective of the experiment. (b) MBDOE technique. Note: A single paper may be counted more than once in these plots if they addressed more than one objective or type of design strategy.

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Models of Systems Properties and Processes > Cellular Models
Biological Mechanisms > Cell Signaling
Analytical and Computational Methods > Computational Methods

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