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2014 | OriginalPaper | Buchkapitel

On Industrial Strength Bio-design Automation

verfasst von : Wolf-Ekkehard Matzke, Chris P. Barnes, Eyck Jentzsch, Thorsten Mascher, Michael Stumpf

Erschienen in: Information and Communication Technologies in Education, Research, and Industrial Applications

Verlag: Springer International Publishing

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Abstract

Bio-Design Automation (BDA) denotes the nascent domain-specific Information and Communication Technology (ICT) discipline for synthetic biology, which constitutes the core technology of the Knowledge-Based Bio-Economy (KBBE). Ultimately, the success or failure of synthetic biology and the emerging KBBE equates to the progress or lack of progress in establishing an industrial strength BDA discipline. In this paper, we seek answers to the question “What does it take for BDA to become an industrial strength discipline?” Our goal is to stimulate a broad community discussion including Business Managers, Computer Scientists, ICT professionals, Synthetic Biologists, etc. around this question. To jump-start the debate, we will provide four core hypotheses covering what we believe are the most important aspects to be considered. Given that industrial strength is a composite aggregate of several technical and managerial variables, we have chosen to take a holistic approach and not restrict ourselves a priori to any particular viewpoints. Last, but not least, we will apply our findings and provide a prototypical industrial implementation of a BDA platform.

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Fußnoten
1
THE EUROPEAN BIOECONOMY IN 2030. Delivering Sustainable Growth by addressing the Grand Societal Challenges: http://​www.​epsoweb.​org/​file/​560.
 
8
In silico is a term popular among synthetic biologists. Wikipedia explains (see http://​en.​wikipedia.​org/​wiki/​In_​silico): “In silico is an expression used to mean ‘performed on computer or via computer simulation.’ The phrase was coined in 1989 as an analogy to the Latin phrases in vivo, in vitro, and in situ, which are commonly used in biology … and refer to experiments done in living organisms, outside of living organisms, and where they are found in nature, respectively.”
 
9
The labeling of the business related core hypothesis as The Business Model (, Stupid) hypothesis will be explained in Sect. 5 of this paper.
 
13
Mendel is the registered trademark of the BDA platform of MINRES Technologies GmbH. The name was chosen in honor of Gregor Mendel, the father of genetics.
 
15
Lately, the MVP approach and the lean-start-up methodology became very prominent among high-tech start-ups.
 
16
https://​goblinworks.​com/​, Goblinworks, Inc. is a start-up that develops Pathfinder, a massive-multiplayer online game.
 
18
“Product tiering is a pricing structure that is … used by producers, in which” customers “are segmented by willingness” and ability “to pay for specific (added) product benefits.” See: Breetz C (2014) Product Packaging as Tool to Demand a Price Premium: Does Packaging Enhance Consumers ‘Value Perception to Justify a Price Premium. Anchor Academic Publishing.
 
19
As the intended products are targeted mainly to SMEs, super computers are not a valid attempt for financial reasons.
 
20
SystemC is a set of C++ classes and macros which provide an event-driven simulation interface in C++; http://​en.​wikipedia.​org/​wiki/​SystemC.
 
Literatur
1.
Zurück zum Zitat Barnes, C.P., Silk, D., Sheng, X., et al.: Bayesian design of synthetic biological systems. Proc. Natl. Acad. Sci. USA 108, 15190–15195 (2011)CrossRef Barnes, C.P., Silk, D., Sheng, X., et al.: Bayesian design of synthetic biological systems. Proc. Natl. Acad. Sci. USA 108, 15190–15195 (2011)CrossRef
2.
Zurück zum Zitat Barnes, C.P., Silk, D., Stumpf, M.P.H.: Bayesian design strategies for synthetic biology. Interface Focus 1, 895–908 (2011)CrossRef Barnes, C.P., Silk, D., Stumpf, M.P.H.: Bayesian design strategies for synthetic biology. Interface Focus 1, 895–908 (2011)CrossRef
3.
Zurück zum Zitat Bessani, A., Correia, M., Quaresma, B., et al.: DepSky: dependable and secure storage in a cloud-of-clouds. Trans. Storage 9, 1–33 (2013)CrossRef Bessani, A., Correia, M., Quaresma, B., et al.: DepSky: dependable and secure storage in a cloud-of-clouds. Trans. Storage 9, 1–33 (2013)CrossRef
4.
Zurück zum Zitat Bhatia, S., Densmore, D., Pigeon, A.: Design visualizer for synthetic biology. ACS Synth. Biol. 2, 348–350 (2013)CrossRef Bhatia, S., Densmore, D., Pigeon, A.: Design visualizer for synthetic biology. ACS Synth. Biol. 2, 348–350 (2013)CrossRef
5.
Zurück zum Zitat Blank, S.: Why the lean start-up changes everything. Harvard Bus. Rev. 91, 63–72 (2013) Blank, S.: Why the lean start-up changes everything. Harvard Bus. Rev. 91, 63–72 (2013)
6.
Zurück zum Zitat Buchli, J., Santini, C.C.: Complexity engineering, harnessing emergent phenomena as opportunities for engineering. In: Reports of the Santa Fe Institute’s Complex Systems Summer School (2005) Buchli, J., Santini, C.C.: Complexity engineering, harnessing emergent phenomena as opportunities for engineering. In: Reports of the Santa Fe Institute’s Complex Systems Summer School (2005)
7.
Zurück zum Zitat Cederfeldt, M., Elgh, F.: Design automation in SMEs-current state, potential, need and requirements. In: ICED 05: 15th International Conference on Engineering Design: Engineering Design and the Global Economy, p. 1507. Engineers Australia (2005) Cederfeldt, M., Elgh, F.: Design automation in SMEs-current state, potential, need and requirements. In: ICED 05: 15th International Conference on Engineering Design: Engineering Design and the Global Economy, p. 1507. Engineers Australia (2005)
8.
Zurück zum Zitat Christiansson, P., Svidt, K., Sørensen, K.B.: Future integrated design environments. J. Inf. Technol. Constr. 14, 445–460 (2009) Christiansson, P., Svidt, K., Sørensen, K.B.: Future integrated design environments. J. Inf. Technol. Constr. 14, 445–460 (2009)
9.
Zurück zum Zitat Collins, H.M.: Tacit knowledge, trust and the Q of sapphire. Soc. Stud. Sci. 31, 71–85 (2001)CrossRef Collins, H.M.: Tacit knowledge, trust and the Q of sapphire. Soc. Stud. Sci. 31, 71–85 (2001)CrossRef
10.
Zurück zum Zitat Densmore, D.: Bio-design automation: nobody said it would be easy. ACS Synth. Biol. 1, 296 (2012)CrossRef Densmore, D.: Bio-design automation: nobody said it would be easy. ACS Synth. Biol. 1, 296 (2012)CrossRef
11.
12.
Zurück zum Zitat Ermolayev, V., Keberle, N., Matzke, W.-E.: An upper level ontological model for engineering design performance domain. In: Li, Q., Spaccapietra, S., Yu, E., Olivé, A. (eds.) ER 2008. LNCS, vol. 5231, pp. 98–113. Springer, Heidelberg (2008)CrossRef Ermolayev, V., Keberle, N., Matzke, W.-E.: An upper level ontological model for engineering design performance domain. In: Li, Q., Spaccapietra, S., Yu, E., Olivé, A. (eds.) ER 2008. LNCS, vol. 5231, pp. 98–113. Springer, Heidelberg (2008)CrossRef
13.
Zurück zum Zitat Ermolayev, V., Matzke, W.-E.: Towards industrial strength business performance management. In: Mařík, V., Vyatkin, V., Colombo, A.W. (eds.) HoloMAS 2007. LNCS (LNAI), vol. 4659, pp. 387–400. Springer, Heidelberg (2007)CrossRef Ermolayev, V., Matzke, W.-E.: Towards industrial strength business performance management. In: Mařík, V., Vyatkin, V., Colombo, A.W. (eds.) HoloMAS 2007. LNCS (LNAI), vol. 4659, pp. 387–400. Springer, Heidelberg (2007)CrossRef
14.
Zurück zum Zitat Gardner, T.S.: Synthetic biology: from hype to impact. Trends Biotechnol. 31, 123–125 (2013)CrossRef Gardner, T.S.: Synthetic biology: from hype to impact. Trends Biotechnol. 31, 123–125 (2013)CrossRef
15.
Zurück zum Zitat Gentner, D., Stevens, A.L.: Mental Models. Psychology Press, Hillsdale (1983) Gentner, D., Stevens, A.L.: Mental Models. Psychology Press, Hillsdale (1983)
16.
Zurück zum Zitat Gioia, D.A., Pitre, E.: Multiparadigm perspectives on theory building. Acad. Manag. Rev. 15, 584–602 (1990) Gioia, D.A., Pitre, E.: Multiparadigm perspectives on theory building. Acad. Manag. Rev. 15, 584–602 (1990)
17.
Zurück zum Zitat Gregor, S., Jones, D.: The anatomy of a design theory. J. Assoc. Inf. Syst. 8, 312–335 (2007) Gregor, S., Jones, D.: The anatomy of a design theory. J. Assoc. Inf. Syst. 8, 312–335 (2007)
18.
Zurück zum Zitat Habibi, N., Mohd Hashim, S.Z., Rodriguez, C.A., et al.: A review of CADs, languages and data models for synthetic biology. J. Teknologi 63 (2013) Habibi, N., Mohd Hashim, S.Z., Rodriguez, C.A., et al.: A review of CADs, languages and data models for synthetic biology. J. Teknologi 63 (2013)
19.
Zurück zum Zitat Hassoun, S.: Genetic/bio design automation for (re-)engineering biological systems. In: Design, Automation and Test in Europe Conference & Exhibition (DATE 2012), pp. 242–247 (2012) Hassoun, S.: Genetic/bio design automation for (re-)engineering biological systems. In: Design, Automation and Test in Europe Conference & Exhibition (DATE 2012), pp. 242–247 (2012)
20.
Zurück zum Zitat Huerta, M., Downing, G., Haseltine, F., et al.: NIH Working Definition of Bioinformatics and Computational Biology. US National Institute of Health (2000) Huerta, M., Downing, G., Haseltine, F., et al.: NIH Working Definition of Bioinformatics and Computational Biology. US National Institute of Health (2000)
21.
Zurück zum Zitat Lindgren, P., Rasmusssen, O.H., Poulsen, H., et al.: Open business model innovation in healthcare sector. J. Multi Bus. Model Innov. Technol. 1, 23–52 (2012) Lindgren, P., Rasmusssen, O.H., Poulsen, H., et al.: Open business model innovation in healthcare sector. J. Multi Bus. Model Innov. Technol. 1, 23–52 (2012)
22.
Zurück zum Zitat Lipshtat, A., Loinger, A., Balaban, N.Q., et al.: Genetic toggle switch without cooperative binding. Phys. Rev. Lett. 96, 188101 (2006)CrossRef Lipshtat, A., Loinger, A., Balaban, N.Q., et al.: Genetic toggle switch without cooperative binding. Phys. Rev. Lett. 96, 188101 (2006)CrossRef
23.
Zurück zum Zitat Luscombe, N.M., Greenbaum, D., Gerstein, M.: What is bioinformatics? A proposed definition and overview of the field. Methods Inf. Med. 40, 346–358 (2001) Luscombe, N.M., Greenbaum, D., Gerstein, M.: What is bioinformatics? A proposed definition and overview of the field. Methods Inf. Med. 40, 346–358 (2001)
24.
Zurück zum Zitat Ma, W., Trusina, A., El-Samad, H., et al.: Defining network topologies that can achieve biochemical adaptation. Cell 138, 760–773 (2009)CrossRef Ma, W., Trusina, A., El-Samad, H., et al.: Defining network topologies that can achieve biochemical adaptation. Cell 138, 760–773 (2009)CrossRef
25.
Zurück zum Zitat Martin, J., Odell, J.J.: Object-Oriented Methods: A Foundation, UML edn., 2nd edn. Prentice-Hall, Upper Saddle River (1998) Martin, J., Odell, J.J.: Object-Oriented Methods: A Foundation, UML edn., 2nd edn. Prentice-Hall, Upper Saddle River (1998)
26.
Zurück zum Zitat Matzke, W.-E.: Biotechnology, synthetic biology, and ICT define the emerging knowledge-based bio-economy. In: Ermolayev, V., Mayr, H.C., Nikitchenko, M., Spivakovsky, A., Zholtkevych, G. (eds.) ICTERI 2013. CCIS, vol. 412, pp. 1–19. Springer, Heidelberg (2013)CrossRef Matzke, W.-E.: Biotechnology, synthetic biology, and ICT define the emerging knowledge-based bio-economy. In: Ermolayev, V., Mayr, H.C., Nikitchenko, M., Spivakovsky, A., Zholtkevych, G. (eds.) ICTERI 2013. CCIS, vol. 412, pp. 1–19. Springer, Heidelberg (2013)CrossRef
27.
Zurück zum Zitat Matzke, W.-E.: Engineering design performance management–from alchemy to science through ISTa. In: Proceedings of the 4th International Conference on Information Systems Technology and Its Applications. LNI, GI, pp. 154–179 (2005) Matzke, W.-E.: Engineering design performance management–from alchemy to science through ISTa. In: Proceedings of the 4th International Conference on Information Systems Technology and Its Applications. LNI, GI, pp. 154–179 (2005)
28.
Zurück zum Zitat Matzke, W.-E., Stumpf, M., Mascher, T.: Towards industrial strength BDA - a short essay. In: 5th International Workshop on Bio-Design Automation. Imperial College, London, UK (2013) Matzke, W.-E., Stumpf, M., Mascher, T.: Towards industrial strength BDA - a short essay. In: 5th International Workshop on Bio-Design Automation. Imperial College, London, UK (2013)
29.
Zurück zum Zitat Nonaka, I.: The knowledge-creating company. Harv. Bus. Rev. 85, 162–171 (2007) Nonaka, I.: The knowledge-creating company. Harv. Bus. Rev. 85, 162–171 (2007)
30.
Zurück zum Zitat Noori, N., Weiss, M.: Going open: does it mean giving away control? Technol. Innov. Manag. Rev. (2013) Noori, N., Weiss, M.: Going open: does it mean giving away control? Technol. Innov. Manag. Rev. (2013)
31.
Zurück zum Zitat Otero-Muras, I., Szederkényi, G., Hangos, K.M., et al.: Dynamic analysis and control of biochemical reaction networks. Math. Comput. Simul. 79, 999–1009 (2008)CrossRefMATH Otero-Muras, I., Szederkényi, G., Hangos, K.M., et al.: Dynamic analysis and control of biochemical reaction networks. Math. Comput. Simul. 79, 999–1009 (2008)CrossRefMATH
32.
Zurück zum Zitat Parnas, D.L., Clements, P.C.: A rational design process: how and why to take it. IEEE Trans. Softw. Eng. SE-12, 251–257 (1986) Parnas, D.L., Clements, P.C.: A rational design process: how and why to take it. IEEE Trans. Softw. Eng. SE-12, 251–257 (1986)
33.
Zurück zum Zitat Polanyi, M.: The Tacit Dimension. Routledge & K. Paul, London (1967) Polanyi, M.: The Tacit Dimension. Routledge & K. Paul, London (1967)
34.
Zurück zum Zitat Riehle, D.: Erratum to: The single-vendor commercial open source business model. Inf. Syst. E-Bus. Manag. 10, 427 (2012)CrossRef Riehle, D.: Erratum to: The single-vendor commercial open source business model. Inf. Syst. E-Bus. Manag. 10, 427 (2012)CrossRef
35.
Zurück zum Zitat Riehle, D.: The single-vendor commercial open sourse business model. Inf. Syst. E-Bus. Manag. 10, 5–17 (2012)CrossRef Riehle, D.: The single-vendor commercial open sourse business model. Inf. Syst. E-Bus. Manag. 10, 5–17 (2012)CrossRef
36.
Zurück zum Zitat Rouse, M.: Industrial strength. In: WhatIs.com (2005) Rouse, M.: Industrial strength. In: WhatIs.com (2005)
37.
Zurück zum Zitat Shaw, W.H.: Engineering management in our modern age. In: Proceedings of the Engineering Management Conference. IEMC ‘02, pp. 504–509. IEEE (2002) Shaw, W.H.: Engineering management in our modern age. In: Proceedings of the Engineering Management Conference. IEMC ‘02, pp. 504–509. IEEE (2002)
38.
Zurück zum Zitat Simon, H.A.: The Sciences of the Artificial. MIT Press, Cambridge (1996) Simon, H.A.: The Sciences of the Artificial. MIT Press, Cambridge (1996)
39.
Zurück zum Zitat The Eclipse Foundation. Eclipse Foundation (2014) The Eclipse Foundation. Eclipse Foundation (2014)
40.
Zurück zum Zitat Thiriet, M.: Conclusion. In: Intracellular Signaling Mediators in the Circulatory and Ventilatory Systems, pp. 911–918. Springer, New York (2013) Thiriet, M.: Conclusion. In: Intracellular Signaling Mediators in the Circulatory and Ventilatory Systems, pp. 911–918. Springer, New York (2013)
41.
Zurück zum Zitat van Beuzekom, B., Arundel, A.: OECD Biotechnology Statistics 2009. OECD Publishing, Paris (2009) van Beuzekom, B., Arundel, A.: OECD Biotechnology Statistics 2009. OECD Publishing, Paris (2009)
42.
Zurück zum Zitat Wagner, R.K., Sternberg, R.J.: Practical intelligence in real-world pursuits: the role of tacit knowledge. J. Pers. Soc. Psychol. 49, 436 (1985)CrossRef Wagner, R.K., Sternberg, R.J.: Practical intelligence in real-world pursuits: the role of tacit knowledge. J. Pers. Soc. Psychol. 49, 436 (1985)CrossRef
43.
Zurück zum Zitat Zott, C., Amit, R.: Business model design: an activity system perspective. Long Range Plan. 43, 216–226 (2010)CrossRef Zott, C., Amit, R.: Business model design: an activity system perspective. Long Range Plan. 43, 216–226 (2010)CrossRef
Metadaten
Titel
On Industrial Strength Bio-design Automation
verfasst von
Wolf-Ekkehard Matzke
Chris P. Barnes
Eyck Jentzsch
Thorsten Mascher
Michael Stumpf
Copyright-Jahr
2014
DOI
https://doi.org/10.1007/978-3-319-13206-8_14