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HD Physiology Project-Japanese efforts to promote multilevel integrative systems biology and physiome research.
The HD Physiology Project is a Japanese research consortium that aimed to develop methods and a computational platform in which physiological and pathological information can be described in high-level definitions across multiple scales of time and size. During the 5 years of this project, an appropriate software platform for multilevel functional simulation was developed and a whole-heart model including pharmacokinetics for the assessment of the proarrhythmic risk of drugs was developed. In this article, we outline the description and scientific strategy of this project and present the achievements and influence on multilevel integrative systems biology and physiome research
Chaste: a test-driven approach to software development for biological modelling
Chaste (âCancer, heart and soft-tissue environmentâ) is a software library and a set of test suites for computational simulations in the domain of biology. Current functionality has arisen from modelling in the fields of cancer, cardiac physiology and soft-tissue mechanics. It is released under the LGPL 2.1 licence.\ud
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Chaste has been developed using agile programming methods. The project began in 2005 when it was reasoned that the modelling of a variety of physiological phenomena required both a generic mathematical modelling framework, and a generic computational/simulation framework. The Chaste project evolved from the Integrative Biology (IB) e-Science Project, an inter-institutional project aimed at developing a suitable IT infrastructure to support physiome-level computational modelling, with a primary focus on cardiac and cancer modelling
Quantitative Genetics and Functional-Structural Plant Growth Models: Simulation of Quantitative Trait Loci Detection for Model Parameters and Application to Potential Yield Optimization
Background and Aims: Prediction of phenotypic traits from new genotypes under
untested environmental conditions is crucial to build simulations of breeding
strategies to improve target traits. Although the plant response to
environmental stresses is characterized by both architectural and functional
plasticity, recent attempts to integrate biological knowledge into genetics
models have mainly concerned specific physiological processes or crop models
without architecture, and thus may prove limited when studying genotype x
environment interactions. Consequently, this paper presents a simulation study
introducing genetics into a functional-structural growth model, which gives
access to more fundamental traits for quantitative trait loci (QTL) detection
and thus to promising tools for yield optimization. Methods: The GreenLab model
was selected as a reasonable choice to link growth model parameters to QTL.
Virtual genes and virtual chromosomes were defined to build a simple genetic
model that drove the settings of the species-specific parameters of the model.
The QTL Cartographer software was used to study QTL detection of simulated
plant traits. A genetic algorithm was implemented to define the ideotype for
yield maximization based on the model parameters and the associated allelic
combination. Key Results and Conclusions: By keeping the environmental factors
constant and using a virtual population with a large number of individuals
generated by a Mendelian genetic model, results for an ideal case could be
simulated. Virtual QTL detection was compared in the case of phenotypic traits
- such as cob weight - and when traits were model parameters, and was found to
be more accurate in the latter case. The practical interest of this approach is
illustrated by calculating the parameters (and the corresponding genotype)
associated with yield optimization of a GreenLab maize model. The paper
discusses the potentials of GreenLab to represent environment x genotype
interactions, in particular through its main state variable, the ratio of
biomass supply over demand
The Virtual Runner Learning Game
A learning game has been developed which allows learners to study and learn about the significance of three important variables in human physiology (lactate, glycogen, and hydration) and their influence on sports performance during running. The player can control the speed of the runner, and as a consequence the resulting physiological processes are simulated in real-time. The performance degradation of the runner due to these processes requires that different strategies for pacing the running speed are applied by the player, depending on the total length of the run. The game has been positively evaluated in a real learning context of academic physiology teaching
From Models to Simulations
This book analyses the impact computerization has had on contemporary science and explains the origins, technical nature and epistemological consequences of the current decisive interplay between technology and science: an intertwining of formalism, computation, data acquisition, data and visualization and how these factors have led to the spread of simulation models since the 1950s.
Using historical, comparative and interpretative case studies from a range of disciplines, with a particular emphasis on the case of plant studies, the author shows how and why computers, data treatment devices and programming languages have occasioned a gradual but irresistible and massive shift from mathematical models to computer simulations
Integrative biological simulation praxis: Considerations from physics, philosophy, and data/model curation practices
Integrative biological simulations have a varied and controversial history in
the biological sciences. From computational models of organelles, cells, and
simple organisms, to physiological models of tissues, organ systems, and
ecosystems, a diverse array of biological systems have been the target of
large-scale computational modeling efforts. Nonetheless, these research agendas
have yet to prove decisively their value among the broader community of
theoretical and experimental biologists. In this commentary, we examine a range
of philosophical and practical issues relevant to understanding the potential
of integrative simulations. We discuss the role of theory and modeling in
different areas of physics and suggest that certain sub-disciplines of physics
provide useful cultural analogies for imagining the future role of simulations
in biological research. We examine philosophical issues related to modeling
which consistently arise in discussions about integrative simulations and
suggest a pragmatic viewpoint that balances a belief in philosophy with the
recognition of the relative infancy of our state of philosophical
understanding. Finally, we discuss community workflow and publication practices
to allow research to be readily discoverable and amenable to incorporation into
simulations. We argue that there are aligned incentives in widespread adoption
of practices which will both advance the needs of integrative simulation
efforts as well as other contemporary trends in the biological sciences,
ranging from open science and data sharing to improving reproducibility.Comment: 10 page
Multiphysics modeling for bone remodeling simulation: A methodological framework
In the present study an object oriented integrative modeling methodology is proposed for the construction of synthetic, computational models of bone-bone environment system that allow its simulation under in vivo conditions. The analytical mathematical approach to model and study ordinary materials will be outlined, indicating its limitations when dealing with biomaterials in physiological environments. The proposed object oriented integrative modeling will be explained emphasizing its advantages and possibilities. Finally, the architecture of the "in vivo" modeling and simulation software framework is shown, described and explained indicating further work based on this framework
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