Theory in Biosciences

, Volume 135, Issue 4, pp 231–240 | Cite as

Design specifications for cellular regulation

  • David C. Krakauer
  • Lydia Müller
  • Sonja J. Prohaska
  • Peter F. StadlerEmail author
Original Paper


A critical feature of all cellular processes is the ability to control the rate of gene or protein expression and metabolic flux in changing environments through regulatory feedback. We review the many ways that regulation is represented through causal, logical, and dynamical components. Formalizing the nature of these components promotes effective comparison among distinct regulatory networks and provides a common framework for the potential design and control of regulatory systems in synthetic biology.


Typed I/O maps Feedback Memory Codes 



The authors thank the John Templeton Foundation for funding this research with the Grant “Origins and Evolution of Regulation in Biological Systems”—ID: 24332. The opinions expressed in this publication are those of the author(s) and do not necessarily reflect the views of the John Templeton Foundation. This work was partially funded by the the German Federal Ministry of Science (0316165C) as part of the e:Bio initiative.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  1. 1.Santa Fe InstituteSanta FeUSA
  2. 2.Natural Language Processing Group, Department of Computer Science, and Interdisciplinary Center for BioinformaticsUniversity LeipzigLeipzigGermany
  3. 3.Computational EvoDevo Group, Department of Computer Science and Interdisciplinary Center for BioinformaticsUniversity LeipzigLeipzigGermany
  4. 4.Bioinformatics Group at the Department of Computer Science, Interdisciplinary Center for Bioinformatics, ScaDS, Competence Center for Scalable Data services and Solutions, and German Center for Integrative Biodiversity ResearchUniversity LeipzigLeipzigGermany
  5. 5.Max-Planck Institute for Mathematics in the SciencesLeipzigGermany
  6. 6.Fraunhofer Institut für Zelltherapie und Immunologie–IZILeipzigGermany
  7. 7.Department of Theoretical ChemistryUniversity of ViennaWienAustria
  8. 8.Center for Non-Coding RNA in Technology and HealthUniversity of CopenhagenFrederiksberg CDenmark

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