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Preface: Petri nets for systems and synthetic biology. (English) Zbl 1217.68151
MSC:
68Q85 Models and methods for concurrent and distributed computing (process algebras, bisimulation, transition nets, etc.)
92C42 Systems biology, networks
Software:
DSSZ-MC
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References:
[1] 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, Newyork · Zbl 0843.68080
[2] Baldan P, Cocco N, Marin A, Simeoni M (2010) Petri nets for modelling metabolic pathways: a survey. J Nat Comput 9:955–989 · Zbl 1206.68209
[3] Chaouiya C (2007) Petri net modelling of biological networks. Brief in Bioinform 8(4):210–219
[4] David R, Alla H (2005) Discrete, continuous, and hybrid Petri nets. Springer, Berlin · Zbl 1074.93002
[5] Doi A, Drath R, Nagaska M, Matsuno H, Miyano S (1999) Protein dynamics observations of Lambda-Phage by hybrid Petri net. Genome Inform 10:217–218
[6] 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 215–264
[7] Heiner M, Lehrack S, Gilbert D, Marwan W (2009a) Extended stochastic Petri nets for model-based design of Wetlab experiments. transactions on computational systems biology XI. Springer, Heidelberg, pp 138–163 · Zbl 1260.68268
[8] 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, pp 323–332, June
[9] 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, pp 66–79. CEUR-WS.org, October
[10] Merlin PM (1974) A study of the recoverability of computing systems. PhD Thesis, University of California, Irvine 1974. Available from University Microfilms, Ann Arbor, No. 75–11026
[11] Valk R (1978) Self-modifying nets, a natural extension of Petri nets. In: LNCS, automata, languages and programming, vol 62, pp 464–476 · Zbl 0415.68025
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