BioModel Engineering for Systems and Synthetic Biology: Reading List

Basic introduction

(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

Basic framework

(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]

BioModel engineering

(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]

Multiscale modelling

(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]

Synthetic biology

(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]

Further reading

*** 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]

Wider reading

(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).