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Function of dynamic models in systems biology: linking structure to behaviour

Christian Knüpfer, Clemens Beckstein
2013 Journal of Biomedical Semantics  
Here we focus on how function links the structure and the behaviour of a model.  ...  This description is conceptually embedded in our "meaning facets" framework which systematises the interpretation of dynamic models in structural, functional and behavioural facets.  ...  Conclusion We have applied the notion of function to dynamic models in Systems Biology. Function is the link between the model structure and the model behaviour.  ... 
doi:10.1186/2041-1480-4-24 pmid:24103739 pmcid:PMC3853929 fatcat:wg555nfpvra4jny6iwr5c5u4na

Plant functional types in Earth system models: past experiences and future directions for application of dynamic vegetation models in high-latitude ecosystems

Stan D. Wullschleger, Howard E. Epstein, Elgene O. Box, Eugénie S. Euskirchen, Santonu Goswami, Colleen M. Iversen, Jens Kattge, Richard J. Norby, Peter M. van Bodegom, Xiaofeng Xu
2014 Annals of Botany  
There is much debate, however, as to how plant diversity and function should be represented in these models. † Scope Plant functional types (PFTs) have been adopted by modellers to represent broad groupings  ...  In this review, the PFT concept is traced from its origin in the early 1800s to its current use in regional and global dynamic vegetation models (DVMs).  ...  The Next-Generation Ecosystem Experiments (NGEE Arctic) project is supported by the Office of Biological and Environmental Research in the DOE Office of Science.  ... 
doi:10.1093/aob/mcu077 pmid:24793697 pmcid:PMC4071098 fatcat:6h2z3lku5jemhm6vpsqzretmom

Molecular Biology... What Molecular (systems) Biology?

Miguel Ángel Medina Torres
2012 Molecular Biology  
Acknowledgements The experimental work in my research group is supported by grants PS09/02216 (Spanish Ministry of Science and Innovation, ISCIII and FEDER), and PIE P08-CTS-3759, CVI-6585 and funds from  ...  The knowledge of the structure of this system. 2. The understanding of the dynamics of the system. 3.  ...  the structure and function of modules.  ... 
doi:10.4172/2168-9547.1000e101 fatcat:hsmsi5qbkze35axgr37h25wnuq

Computational systems biology

Hiroaki Kitano
2002 Nature  
A popular notion of complex systems is of very large numbers of simple and identical elements interacting to produce 'complex' behaviours. The reality of biological systems is somewhat different.  ...  Unlike complex systems of simple elements, in which functions emerge from the properties of the networks they form rather than from any specific element, functions in biological systems rely on a combination  ...  In highly robust systems, even damage to their very structure produces only minor alterations in their behaviour.  ... 
doi:10.1038/nature01254 pmid:12432404 fatcat:angnkd6ys5fqpk3a4h6pwytkxa

Systems interface biology

Francis J. Doyle, Jörg Stelling
2006 Journal of the Royal Society Interface  
The field of systems biology has attracted the attention of biologists, engineers, mathematicians, physicists, chemists and others in an endeavour to create systems-level understanding of complex biological  ...  Hence, the interface between systems and biology is of mutual benefit to both disciplines.  ...  We acknowledge the financial support to F.J.D. from the Institute for Collaborative Biotechnologies through grant DAAD19-03-D-0004 from the US Army Research Office.  ... 
doi:10.1098/rsif.2006.0143 pmid:16971329 pmcid:PMC1664650 fatcat:rqtnqq6ulvc5ldya75qha7di5u

Stem cell biology meets systems biology

I. Roeder, F. Radtke
2009 Development  
Here, we review the discussions that took place at a recent EMBO conference in Cambridge, UK, in which these questions were placed in the context of the latest advances in stem cell biology in presentations  ...  that covered stem cell heterogeneity, cell fate decision-making, induced pluripotency, as well as the mathematical modelling of these phenomena.  ...  Acknowledgements We thank our colleagues for sharing information and allowing their work to be described and Nico Scherf from the laboratory of I.R. for help with preparing Fig. 1 .  ... 
doi:10.1242/dev.040758 pmid:19820180 fatcat:czu6an3xmnej7cealb2k5kj2aq

Whither systems biology

A. A. Hyman
2011 Philosophical Transactions of the Royal Society of London. Biological Sciences  
To bridge these vast difference in scales, biologists construct hierarchies of organization of cellular structures.  ...  I describe how systems biology provides an approach to bridge these different scales.  ...  The term 'modelling' describes the procedure to construct a model of a system, which can mimic observed behaviours.  ... 
doi:10.1098/rstb.2011.0074 pmid:22084389 pmcid:PMC3203457 fatcat:uixt2sgaznemxmdaxg5icdqkhq

Journal of Theoretical Biology

1961 Nature  
In the second case, by a simplification of the mechanisms for inter and intra-species competition, we construct a model without any explicit features and find that we are still able to grow model food  ...  Here we modify this scheme by firstly allowing for a richer structure and secondly by testing whether we are able to eliminate the need for an explicit choice of features altogether.  ...  C.A.L. acknowledges the award of a studentship from CONACYT (Mexico). A.J.M. wishes to thank the EPSRC (UK) for partial support under Grant no. GR/T11784/0.  ... 
doi:10.1038/189879a0 fatcat:rn24ubmeofhqtlibdoti5fbbhe

Perspectives on systems biology

Hiroaki Kitano
2000 New generation computing  
-Aim: to build a precise simulation model so that dynamical properties of system can be analyzed by changing parameters. 4.  ...  . • Emergence of molecular biology. • Rapid progress -complete sequencing of genome. • Identification of genes, elucidation of protein functions, linking genes, proteins and diseases. • However, understanding  ... 
doi:10.1007/bf03037529 fatcat:o7urcr7msvbh3fg6in42uxvdjm

Complex systems biology

Avi Ma'ayan
2017 Journal of the Royal Society Interface  
Systems biology, a more holistic approach to study molecules and cells in biology, has advanced rapidly in the past two decades.  ...  Considering concepts of complex systems theory in systems biology can illuminate our overall understanding of normal cell physiology and the alterations that lead to human disease. on November 3, 2017  ...  In combination, these forces can work in parallel, and sometimes counteract one another, to produce the final outcome behaviour of the system that is manifested as continual dynamical and functional structural  ... 
doi:10.1098/rsif.2017.0391 pmid:28931638 pmcid:PMC5636275 fatcat:qyjv2hvzbzccva4sbtlikmuzie

Open Problems in Mathematical Biology [article]

Sean T. Vittadello, Michael P.H. Stumpf
2022 arXiv   pre-print
Mathematical models allow us to test our understanding, make testable predictions about future behaviour, and gain insights into how we can control the behaviour of biological systems.  ...  Biology is data-rich, and it is equally rich in concepts and hypotheses.  ...  Acknowledgements The authors thank the members of the Theoretical Systems Biology group, past and present, for stimulating discussions that have shaped our view.  ... 
arXiv:2206.09516v1 fatcat:mowgnqqhzrdzbnap7ojrzk7tke

Systems biology: The reincarnation of systems theory applied in biology?

O. Wolkenhauer
2001 Briefings in Bioinformatics  
International conferences, research institutes and research groups concerned with systems biology have appeared in recent years and systems theory, the study of organisation and behaviour per se, is indeed  ...  Here we shall review the domain of systems theory, its application to biology and the lessons that can be learned from the work of Robert Rosen.  ...  Acknowledgements The author wishes to thank Allan Muir and Tim Porter for their interest and helpful comments.  ... 
doi:10.1093/bib/2.3.258 pmid:11589586 fatcat:n5xh5jvqs5cshaluhhffbsxakq

Systems biology

Karthik Raman, Nagasuma Chandra
2010 Resonance  
Her current research interests are in computational systems biology, cell modeling and structural bioinformatics and in applying these to address fundamental issues in drug discovery.  ...  Such a view of biological systems emanating from strong foundations of molecular level understanding of the individual components in terms of their form, function and interactions is promising to transform  ...  linked to each other, giving rise to behaviours that may not be described by simple models.  ... 
doi:10.1007/s12045-010-0015-7 fatcat:i7hbkuu35zhbbj2mltkoe6wmwq

Back to the biology in systems biology: What can we learn from biomolecular networks?

S. Huang
2004 Briefings in Functional Genomics & Proteomics  
Systems biology so far has emphasised the characterisation of large pathway maps. Now one has to ask: where is the actual biology in 'systems biology'?  ...  To study the function of genes, it is necessary not only to see them in the context of gene networks, but also to reach beyond describing network topology and to embrace the global dynamics of networks  ...  Acknowledgment This work was funded by the Air Force Office of Scientific Research (AFOSR/USAF) and the Patterson Trust. The author also wishes to thank Joy P.  ... 
doi:10.1093/bfgp/2.4.279 pmid:15163364 fatcat:pcr376nwmva5fiohwyiwvcmmn4

Systems Biology or just Biology? A report of the 11th International Conference on Systems Biology

Sergio Bordel, Intawat Nookaew
2010 Biotechnology Journal  
of intracellular dynamics, 5 th Biomedical Simulations, 6 th Understanding the Brain Function, 7 th Computational methods and tools, 8 th Cell signalling dynamics, 9 th Systems biology in health and diseases  ...  In our opinion, a reliable mathematical framework able to elucidate how the structure of a network of interacting elements constraints its behaviour could be a crucial step in establishing systems biology  ... 
doi:10.1002/biot.201000390 pmid:21154729 fatcat:vrktacazrvhuzknlos4p3ozvfe
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