Preface: Petri nets for Systems and Synthetic Biology
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This special issue Petri Nets for Systems and Synthetic Biology presents selected highlights of a challenging and highly active research field. It consists of two parts, the former “Part 1: Bridging Gaps” and the current “Part 2: Unifying Diversity”.
Systems Biology is the biology-based interdisciplinary research area that focuses on complex interactions between the components of biological systems, and how these interactions give rise to function and behavior of these systems. One of the ambitions of Systems Biology is to discover the outcome of organic evolution and to describe this acquired knowledge in models, which are explanatory of the biological mechanisms as well as suitable for reliable prediction of behaviour when the system is perturbed by, e.g., mutations, chemical interventions or changes in the environment.
In the emerging discipline Synthetic Biology, the very same kind of models are taken as design templates for novel synthetic biological systems, i.e.,...
KeywordsSynthetic Biology Label Transition System Stochastic Activity Network Large Scale Biological Network Gene Clock System
- Ajmone Marsan M, Balbo G, Conte G, Donatelli S, Franceschinis G (1995) Modelling with generalized stochastic Petri nets. Wiley series in parallel computing, 2nd edn. Wiley, New YorkGoogle Scholar
- Baldan P, Cocco N, Marin A, Simeoni M (2010) Petri nets for modelling metabolic pathways: a survey. J Nat Comput 9(4):955–989Google Scholar
- Doi A, Drath R, Nagaska M, Matsuno H, Miyano S (1999) Protein dynamics observations of lambda-phage by hybrid Petri net. Genome Inform 10:217–218Google Scholar
- Gilbert D, Heiner M, Lehrack S (2007) A unifying framework for modelling and analysing biochemical pathways using Petri nets. In: Proceedings of the CMSB. LNCS/LNBI 4695, Springer, Heidelberg, pp 200–216Google Scholar
- Heiner M, Gilbert D (2011) How Might Petri Nets Enhance Your Systems Biology Toolkit. In: Proceedings of the PETRI NETS 2011. LNCS, vol 6709 . Springer, Heidelberg, pp 17–37Google Scholar
- Heiner M, Gilbert D, Donaldson R (2008) Petri nets in systems and synthetic biology. In: Schools on formal methods (SFM). LNCS, vol 5016, Springer, Heidelberg, pp 215–264Google Scholar
- Heiner M, Lehrack S, Gilbert D, Marwan W (2009a) Extended stochastic Petri nets for model-based design of wetlab experiments. In: Transactions on computational systems biology XI, LNCS. Springer, Heidelberg, pp 138–163Google Scholar
- Heiner M, Schwarick M, Tovchigrechko A (2009b) DSSZ-MC—a tool for symbolic analysis of extended Petri nets. In: Proceedings of the PETRI NETS 2009. LNCS, vol 5606. Springer, Heidelberg, pp 323–332Google Scholar
- Herajy M, Heiner M (2010) Hybrid Petri nets for modelling of hybrid biochemical interactions. In: Proceedings of the 17th German workshop on algorithms and tools for Petri nets (AWPN 2010). CEUR workshop proceedings, vol 643. http://www.CEUR-WS.org, pp 66–79
- Merlin PM (1974) A study of the recoverability of computing systems. University of California, Irvine. PhD Thesis, 1974. Available from University Microfilms, Ann Arbor, No. 75–11026Google Scholar
- Valk R (1978) Self-modifying nets, a natural extension of Petri nets. In: Automata, languages and programming. LNCS, vol 62. Springer, Heidelberg, pp 464–476Google Scholar