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An Introduction to BioModel Engineering, Illustrated for Signal Transduction Pathways [chapter]

David Gilbert, Rainer Breitling, Monika Heiner, Robin Donaldson
2009 Lecture Notes in Computer Science  
We illustrate this with an example in the area of intracellular signalling pathways.  ...  This paper illustrates a major theme in BioModel Engineering, namely that identifying a quantitative model of a dynamic system means building the structure, finding an initial state, and parameter fitting  ...  Acknowledgments DR was supported for his work on model checking by the SIMAP project which is funded by the European Commission framework 6 STREP programme.  ... 
doi:10.1007/978-3-540-95885-7_2 fatcat:5ifoq5cfobaunisn2w3k5mbwee

Computational Modelling of Kinase Signalling Cascades [chapter]

David Gilbert, Monika Heiner, Rainer Breitling, Richard Orton
2010 Msphere  
In this chapter, we describe general methods used to create dynamic computational models of kinase signalling cascades, and tools to support this activity.  ...  BioModel Engineering does not aim at engineering biological systems per se (in contrast to synthetic biology), but rather aims at describing their structure and behaviour, in particular at the level of  ...  This is part of a larger process of BioModel Engineering -see (1) and Note 2.  ... 
doi:10.1007/978-1-60761-795-2_22 pmid:20811995 fatcat:oem7vh54sreatggrrdupxotgkq

How Might Petri Nets Enhance Your Systems Biology Toolkit [chapter]

Monika Heiner, David Gilbert
2011 Lecture Notes in Computer Science  
We discuss the extent to which the Petri net approach can be used as an umbrella formalism to support the process of BioModel Engineering.  ...  -this is one of the questions that we get on a regular basis, which motivated us to write an answer in the form of this paper.  ...  We assume a basic understanding of Petri nets; a gentle introduction within the given context of BioModel Engineering can be found in [28, 48] , for related formal definitions see [29] . 2 Representation  ... 
doi:10.1007/978-3-642-21834-7_2 fatcat:jhckua5qhvc3xohjwrrfqswxpq

Computational methodologies for modelling, analysis and simulation of signalling networks

D. Gilbert, H. Fuss, X. Gu, R. Orton, S. Robinson, V. Vyshemirsky, M. J. Kurth, C. S. Downes, W. Dubitzky
2006 Briefings in Bioinformatics  
We propose a conceptual framework, and discuss the role of signalling networks in three major areas: signal transduction, cellular rhythms and cell-to-cell communication.  ...  In order to avoid an overly abstract and general discussion, we focus on three case studies in the areas of receptor signalling and kinase cascades, cell-cycle regulation and wound healing.  ...  The authors would like to thank Monika Heiner and Sebastian Lehrack of the University of Cottbus, Germany, for their helpful comments.  ... 
doi:10.1093/bib/bbl043 pmid:17116646 fatcat:cf42u6jo6fgq5lp63c22gh4xqe

Modular assembly of dynamic models in systems biology

Michael Pan, Peter J. Gawthrop, Joseph Cursons, Edmund J. Crampin, Anders Wallqvist
2021 PLoS Computational Biology  
to illustrate the ability to modify the model granularity.  ...  We use two examples to illustrate the utility of bond graphs in this context: a model of a mitogen-activated protein kinase (MAPK) cascade to illustrate the reusability of modules and a model of glycolysis  ...  We illustrate the utility of this approach in streamlining the development of models for a signalling network (the MAPK cascade) and a metabolic network (the Introduction Over the past few decades, advances  ... 
doi:10.1371/journal.pcbi.1009513 pmid:34644304 pmcid:PMC8544865 fatcat:mb42nil43bfzlk4djyhtp5hak4

BioModel engineering for multiscale Systems Biology

Monika Heiner, David Gilbert
2013 Progress in Biophysics and Molecular Biology  
Furthermore, models can be used to help make genetic engineering easier and more reliable, serving as design templates for novel synthetic biological systems e an emerging discipline known as Synthetic  ...  We illustrate our approach with case studies demonstrating hierarchical flattening, treatment of space, and hierarchical organisation of space. Ó 2012 Elsevier Ltd. Motivation BioModel Engineering.  ...  Currently we wish to focus on modelling the dynamic behaviour of biological systems, with an emphasis on the underlying mechanisms, for example gene transcription networks, metabolic pathways and signal  ... 
doi:10.1016/j.pbiomolbio.2012.10.001 pmid:23067820 fatcat:mf4cq3jawbbfrgqb6kut5b4equ

JAK/STAT signalling – an executable model assembled from molecule-centred modules demonstrating a module-oriented database concept for systems and synthetic biology

Mary Ann Blätke, Anna Dittrich, Christian Rohr, Monika Heiner, Fred Schaper, Wolfgang Marwan
2013 Molecular Biosystems  
The JAK/STAT signalling pathway with the extensive crosstalk of its components is selected as case study.  ...  Each module contains metadata for documentation purposes and can be extended to a wiki-like minireview. The database can manage multiple versions of each module.  ...  Acknowledgemnts We thank Professor David Gilbert for critical reading of the manuscript and for suggesting module based automatic biomodel engineering and its application to  ... 
doi:10.1039/c3mb25593j pmid:23443149 fatcat:6c2ttcuimffd3d5aezzpapg4ce

Mathematical modeling of intracellular signaling pathways

Edda Klipp, Wolfram Liebermeister
2006 BMC Neuroscience  
Dynamic modeling and simulation of signal transduction pathways is an important topic in systems biology and is obtaining growing attention from researchers with experimental or theoretical background.  ...  The variety of mechanisms found and modeling techniques used are illustrated with models of different signaling pathways.  ...  To illustrate these points, we will review a number of models that have been established for signaling systems in eukaryotic cells, with an emphasis on neuron cells.  ... 
doi:10.1186/1471-2202-7-s1-s10 pmid:17118154 pmcid:PMC1775040 fatcat:g52sggzgmvgufdd43l3onpjnwi

VERIFICATION AND TESTING OF BIOLOGICAL MODELS

Allan Clark, Jane Hillston, Stephen Gilmore, Peter Kemper
2010 Proceedings of the 2010 Winter Simulation Conference  
In this paper, we describe relevant steps in the verification and testing of a TNFa-mediated NF-kB signal transduction pathway model and discuss to what extent automated techniques help a practitioner  ...  to derive a suitable model. 620 978-1-4244-9865-9/10/$26.00 ©2010 IEEE  ...  Signalling Pathway Analysis".  ... 
doi:10.1109/wsc.2010.5679126 dblp:conf/wsc/ClarkHGK10 fatcat:ljexuf6wfzcjdjswczjla3vn24

Systems Biology and Physiome Projects

Aleksander S. Popel, Peter J. Hunter
2009 Wiley Interdisciplinary Reviews: Systems Biology and Medicine  
, introduction of novel diagnostic and surgical procedures, design and use of medical devices, and education and training.  ...  The systems approaches are poised to revolutionize medicine as they have been revolutionizing biology, through their application to drug discovery and therapeutic applications including personalized medicine  ...  The signal transduction pathways that control smooth muscle cells and fibroblasts are modeled in CellML as systems of ordinary differential equations and nonlinear algebraic equations describing the signaling  ... 
doi:10.1002/wsbm.67 pmid:20835988 pmcid:PMC2941734 fatcat:mqluulm6anaopfuqz3hh542d7e

Genome Scale Modeling in Systems Biology: Algorithms and Resources

Ali Najafi, Gholamreza Bidkhori, Joseph Bozorgmehr, Ina Koch, Ali Masoudi-Nejad
2014 Current Genomics  
In fact, biological networks have been developed as a platform for integrating information from high to low-throughput experiments for the analysis of biological systems.  ...  Overall, systems biology aims for a holistic description and understanding of biological processes by an integration of analytical experimental approaches along with synthetic computational models.  ...  ACKNOWLEDGEMENTS We would like to thank all members of the laboratory of systems biology and bioinformatics (LBB) for their help during course of this study.  ... 
doi:10.2174/1389202915666140319002221 pmid:24822031 pmcid:PMC4009841 fatcat:xh7tgip2yfdq3fe2typ74jlfkq

Logical Modeling and Dynamical Analysis of Cellular Networks

Wassim Abou-Jaoudé, Pauline Traynard, Pedro T. Monteiro, Julio Saez-Rodriguez, Tomáš Helikar, Denis Thieffry, Claudine Chaouiya
2016 Frontiers in Genetics  
After an introduction to the logical modeling framework and to several of its variants, we review here a number of recent methodological advances to ease the analysis of large and intricate networks.  ...  To illustrate these developments, we further consider several published logical models for two important biological processes, namely the differentiation of T helper cells and the control of mammalian  ...  ACKNOWLEDGMENTS The authors would like to thank all members of the CoLoMoTo consortium for inspiring discussions and fruitful collaborations.  ... 
doi:10.3389/fgene.2016.00094 pmid:27303434 pmcid:PMC4885885 fatcat:pzlnaxxfibdd5ewc7gcabqfyqq

Speeding up systems biology simulations of biochemical pathways using condor

Xuan Liu, Simon J. E. Taylor, Navonil Mustafee, Jun Wang, Qian Gao, David Gilbert
2013 Concurrency and Computation  
We present our results based on a case study with a model of the mammalian ErbB signaling pathway, a pathway strongly linked to cancer.  ...  Following on from this work, we have created the SIMAP Utility, a standalone simulation tool dedicated to the modelling and analysis of the EGFR-MAP kinase pathway.  ...  ACKNOWLEDGEMENTS This work has been partially supported by the Simulation Modelling of the EGFR-MAP Kinase Pathway (SIMAP) project which was funded by the European Commission under the FP6 -Information  ... 
doi:10.1002/cpe.3161 fatcat:nuyelcr7krgf5lvc4uyicnxida

Postsynaptic Signal Transduction Models for Long-Term Potentiation and Depression

Tiina Manninen, Katri Hituri, Jeanette Hellgren Kotaleski, Kim T. Blackwell, Marja-Leena Linne
2010 Frontiers in Computational Neuroscience  
To investigate which species and interactions are critical for synaptic plasticity, many computational postsynaptic signal transduction models have been developed.  ...  model databases, and (3) comparison to previous models is lacking.  ...  In order to predict the future direction of the field, trends regarding the development of models of postsynaptic signal transduction pathways underlying LTP and LTD are illustrated (Figures 2 and 3 )  ... 
doi:10.3389/fncom.2010.00152 pmid:21188161 pmcid:PMC3006457 fatcat:km3tmd5k5je3liym2qikyr3r3q

Empirical Study of Computational Intelligence Strategies for Biochemical Systems Modelling [chapter]

Zujian Wu, Crina Grosan, David Gilbert
2014 Studies in Computational Intelligence  
Simulation results of different variants of those computational methods on a standard signaling pathway show that it is feasible to obtain a tradeoff between the generation of desired behaviour and similar  ...  It is feasible to piece-wise model the biochemical networks from scratch by employing strategies able to assemble reusable components.  ...  Part of this work has been supported by the Romanian National Authority for Scientific Research PN-II-PT-PCCA-2011-3.2-0917.  ... 
doi:10.1007/978-3-319-01692-4_19 fatcat:yomjczpur5d4tpdvjt72354szi
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