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An Introduction to BioModel Engineering, Illustrated for Signal Transduction Pathways
[chapter]
2009
Lecture Notes in Computer Science
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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]
2010
Msphere
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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]
2011
Lecture Notes in Computer Science
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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
2006
Briefings in Bioinformatics
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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
2021
PLoS Computational Biology
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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
2013
Progress in Biophysics and Molecular Biology
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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
2013
Molecular Biosystems
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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
2006
BMC Neuroscience
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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
2010
Proceedings of the 2010 Winter Simulation Conference
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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
2009
Wiley Interdisciplinary Reviews: Systems Biology and Medicine
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, 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
2014
Current Genomics
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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
2016
Frontiers in Genetics
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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
2013
Concurrency and Computation
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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
2010
Frontiers in Computational Neuroscience
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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]
2014
Studies in Computational Intelligence
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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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