(Basic)
* W Marwan, C Rohr and M Heiner:
Petri nets in Snoopy: A unifying framework for the graphical display, computational modelling, and simulation of
bacterial regulatory networks.
In Methods in Molecular Biology - Bacterial Molecular Networks, (Jv Helden, A Toussaint and D Thieffry, Eds.),
Humana Press, pages 409-437, 2012
(Advanced)
** MA Blätke, M Heiner, and W Marwan (2011),
Tutorial
- Petri Nets in Systems Biology.
Otto von Guericke University Magdeburg, Magdeburg Centre for Systems Biology
(For a beginner:)
* Monika Heiner, Robin Donaldson and David Gilbert (2010):
Petri Nets for Systems Biology;
In
Symbolic Systems
Biology: Theory and Methods, (MS Iyengar, Ed.), Jones &
Bartlett Learning, LCC, pages 61-97.
[Preprint]
(Formal definitions, more advanced examples:)
** Monika Heiner, David Gilbert, and Robin Donaldson (2008),
Petri Nets for Systems and Synthetic Biology.
In
M Bernardo, P Degano, and G Zavattaro (Eds.):
Formal Methods for
Systems Biology SFM 2008, Springer LNCS
5016, pp. 215-264, 2008.
[Preprint]
(Application to biological assays)
*** Monika Heiner, Sebastian Lehrack, David Gilbert and Wolfgang Marwan (2009),
Extended Stochastic Petri Nets
for Model-Based Design of Wetlab Experiments
in C Priami, RJ Back, I Petre (eds.): Computational models for cell processes;
Trans. on Computational Systems Biology XI, Springer LNCS 5750, pp. 138-163.
[Preprint]
** Rainer Breitling, David Gilbert, Monika Heiner, Richard Orton (2008). A structured approach for the engineering of biochemical network models, illustrated for signalling pathways. Briefings in Bioinformatics, 2008 9(5):404-42, doi:10.1093/bib/bbn026 [preprint]
*** D. Gilbert, M. Heiner, R. Breitling, R. Orton (2010). Computational modelling of kinase signalling cascades in MAP Kinase Signaling Protocols, Rony Seger (Ed), Methods in Molecular Biology, 2010, Volume 661, Part 4, 369-384, DOI: 10.1007/978-1-60761-795-2_22. [PubMed]
(Simple introduction)
* Rainer Breitling, Robin Donaldson, David Gilbert, Monika Heiner (2010):
Biomodel
Engineering - From Structure to Behavior; (position paper)
in C Priami et al. (eds.):
Trans. on
Computational Systems Biology XII,
Springer LNCS 5945, pp. 1-12.
[Preprint].
*** M Heiner and D Gilbert: How Might Petri Nets Enhance Your Systems Biology Toolkit; In Proc. PETRI NETS 2011, LNCS 6709/2011, Springer, pages 17-37, DOI: 10.1007/978-3-642-21834-7_2. [Preprint]
(Link to volume with many examples of different modelling methodologies / examples)
*** Corrado Priami, Rainer Breitling, David Gilbert, Monika Heiner, Adelinde M.
Uhrmacher (Eds.) (2010).
Transactions on Computational Systems Biology XII:
Special Issue on Modeling Methodologies.
Springer LNCS 5945, ISSN 0302-9743 (Print), 1611-3349 (Online).
Rainer Breitling, Robin Donaldson, David Gilbert, Monika Heiner (2010): Biomodel Engineering - From Structure to Behavior; (position paper) in C Priami et al. (eds.): Trans. on Computational Systems Biology XII, Springer LNCS 5945, pp. 1-12. [Preprint].
David Gilbert, Rainer Breitling, Monika Heiner, and Robin Donaldson (2009). An introduction to BioModel Engineering, illustrated for signal transduction pathways, 9th International Workshop, WMC 2008, Edinburgh, UK, July 28-31, 2008, Revised Selected and Invited Papers, Corne, D.; Frisco, P.; Paun, G.; Rozenberg, G.; Salomaa, A. (Eds.) LNCS Volume 5391, pp13-28 ISBN: 978-3-540-95884-0. [Preprint].
David Gilbert, Monika Heiner and Sebastian Lehrack (2007). A Unifying Framework for Modelling and Analysing Biochemical Pathways Using Petri Nets In proceedings CMSB 2007 (Computational Methods in Systems Biology), Editors: M.Calder and S.Gilmore, Springer LNCS/LNBI 4695, pp. 200-216.
David Gilbert and Monika Heiner, (2006). From Petri Nets to Differential Equations - an Integrative Approach for Biochemical Network Analysis, 27th International Conference on Application and Theory of Petri Nets and other models of concurrency (ATPN06), Turku, Finland, June 26-30, 2006. Proceedings; Editors: Susanna Donatelli, P. S. Thiagarajan; LNCS 4024 / 2006, pp. 181-200, ISBN: 3-540-34699-6 DOI: 10.1007/11767589 -->