Previous chapters have focused on metabolic pathway and their genetic parts modeling and selection. In this chapter, we direct our interest towards pathway design in order to move into the engineering aspects of metabolic pathway design. Our focus from now on will not be on reproducing through simulation some biological behavior or trying to understand its mechanism but in determining the possible biological interventions and modifications to be engineered in the cell in order to achieve the desired behavior. Genetic parts selection and experimental design will be essential at this stage. Since this book is about metabolic pathway design, metabolism will continue as our central topic. However, we will also consider solutions that go beyond metabolism and will take advantage of the advanced capabilities that synthetic biology provides to metabolic engineering.
- 1.Cox, R.S., Madsen, C., McLaughlin, J.A., Nguyen, T., Roehner, N., Bartley, B., Beal, J., Bissell, M., Choi, K., Clancy, K., Grünberg, R., Macklin, C., Misirli, G., Oberortner, E., Pocock, M., Samineni, M., Zhang, M., Zhang, Z., Zundel, Z., Gennari, J.H., Myers, C., Sauro, H., Wipat, A.: Synthetic Biology Open Language (SBOL) version 2.2.0. J. Integr. Bioinform. 15(1) (2018). https://doi.org/10.1515/jib-2018-0001
- 5.Quinn, J.Y., Cox, R.S., Adler, A., Beal, J., Bhatia, S., Cai, Y., Chen, J., Clancy, K., Galdzicki, M., Hillson, N.J., Le Novère, N., Maheshwari, A.J., McLaughlin, J.A., Myers, C.J., P, U., Pocock, M., Rodriguez, C., Soldatova, L., Stan, G.B.V., Swainston, N., Wipat, A., Sauro, H.M.: SBOL visual: a graphical language for genetic designs. PLOS Biol. 13(12), e1002,310 (2015). https://doi.org/10.1371/journal.pbio.1002310 CrossRefGoogle Scholar
- 6.Salis, H.M.: The ribosome binding site calculator. In: Methods in Enzymology, vol. 498, pp. 19–42. Elsevier (2011). https://doi.org/10.1016/B978-0-12-385120-8.00002-4 Google Scholar
- A more detailed discussion focused on parameter tuning in genetic designs:Google Scholar
- An excellent and comprehensive reference for statistical design of experiments:Google Scholar
- Montgomery, D.C.: Design and analysis of experiments. John Wiley & Sons (2017).Google Scholar
- The Design of Experiments Guide of the JMP software (https://www.jmp.com/) is also a useful source of information about DoE, illustrated with multiple examples based on the use of the software.