(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
(Advanced)
** F Liu, M Heiner and C Rohr (2012):
Manual
for Colored Petri Nets in Snoopy,
Technical report 02-12, Brandenburg University of Technology Cottbus, Department of Computer Science
(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]
(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].
(More detailed treatment)
** 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]
(Case study)
** Zujian Wu, Shengxian Wang and David Gilbert. (2012).
A Hybrid Approach to Piece-wise Modelling of Biochemical Systems
PPSN 2012
(12th International Conference on Parallel Problem Solving From Nature - September 1-5, 2012 Taormina, Italy)
[Preprint]
(Case study)
** Robin Donaldson and David Gilbert (2008).
A Model Checking Approach to the
Parameter Estimation of Biochemical Pathways. In proceedings
CMSB 2008
(Computational Methods in Systems Biology).
Heiner, Monika; Uhrmacher, Adelinde M. (Eds.)
LNCS 5307/2008, pp269-287.
ISBN: 978-3-540-88561-0.
[Preprint]
(Overview)
* David Gilbert and Monika Heiner (2011),
Petri nets for multiscale Systems Biology.
Project summary (website).
(Case study)
** Q. Gao, D. Gilbert, M. Heiner, F. Liu, D. Maccagnola and D. Tree,
Multiscale Modelling and Analysis of Planar Cell Polarity in the Drosophila Wing,
IEEE/ACM Transactions on Computational Biology and Bioinformatics,
to appear.
[Preprint]
(iGEM example, simple treatment)
* X.Gu, M.Trybiło, S.Ramsay, M.Jensen, R.Fulton, S.
Rosser and D. Gilbert (2010),
Engineering a novel self-powering
electrochemical biosensor,
in Journal for Systems and Synthetic Biology, Springer,
Special Issue:Top-down and bottom-up
approaches to the design of biological systems - papers
arising from the Second European Conference on Synthetic Biology
1:4, 203-214, DOI: 10.1007/s11693-010-9063.
(iGEM example, detailed treatment)
** David Gilbert, Monika Heiner, Susan Rosser, Rachael Fulton, Xu Gu and Maciej
Trybiło (2008),
A
Case Study in Model-driven Synthetic Biology.
In
Biologically
Inspired Cooperative Computing: BICC 2008. IFIP Springer
ISSN 1571-5736 (Print) 1861-2288 (Online).
Volume 268/2008.
DOI 10.1007/978-0-387-09655-1.
ISBN 978-0-387-09654-4.
pp 163-175.
[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]
*** 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]
(Overview)
* David Gilbert, Alfonso Jaramillo, Natalio Krasnogor and Victor de Lorenzo (2010),
Synthetic
biology gains momentum in Europe,
in Journal for Systems and Synthetic Biology, Springer,
Special Issue:Top-down and bottom-up
approaches to the design of biological systems - papers
arising from the Second European Conference on Synthetic Biology
1:4, pp 145-147, DOI: 10.1007/s11693-010-9065-0
(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).