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The following two matters should be resolved in order for biosimulation tools to be accepted by users in biology/medicine: (1) remove issues which are irrelevant to biological importance, and (2) allow users to represent biopathways intuitively and understand/manage easily the details of representation and simulation mechanism. From these criteria, we(More)
Excellent book is always being the best friend for spending little time in your office, night time, bus, and everywhere. It will be a good way to just look, open, and read the book while in that time. As known, experience and skill don't always come with the much money to acquire them. Reading this book with the PDF foundations of systems biology using cell(More)
In many research projects on modeling and analyzing biological pathways, the Petri net has been recognized as a promising method for representing biological pathways. From the pioneering works by Reddy et al., 1993, and Hofestädt, 1994, that model metabolic pathways by traditional Petri net, several enhanced Petri nets such as colored Petri net, stochastic(More)
Genomic Object Net (GON) 1.0 is a software package for creating models and simulations of biopathways. Its core architecture employs the notion of a hybrid functional Petri net with extension (HFPNe). HFPNe can seamlessly handle discrete and continuous objects and events while keeping the model components themselves simple. With the feature and graphical(More)
To elucidate the mechanisms of antinociception mediated by the descending noradrenergic pathway in the spinal cord, the effects of noradrenaline (NA) on noxious synaptic responses of substantia gelatinosa (SG) neurones, and postsynaptic actions of NA were investigated in rats using an in vivo whole-cell patch-clamp technique. Under urethane anaesthesia, the(More)
All neuronal networks are modulated by multiple neuropeptides and biogenic amines. Yet, few studies investigate how different modulators interact to regulate network activity. Here we explored the state-dependent functional interactions between three excitatory neuromodulators acting on neurokinin1 (NK1), alpha1 noradrenergic (alpha1 NE), and 5-HT2(More)
The respiratory system is continuously modulated by numerous aminergic and peptidergic substances that act at all levels of integration: from the sensory level to the level of central networks and motor nuclei. The same neuronal networks receive inputs from multiple modulators released locally as well as from distal nuclei. All parameters of respiratory(More)
The research on modeling and simulation of complex biological systems is getting more important in Systems Biology. In this respect, we have developed Hybrid Function Petri net (HFPN) that was newly developed from existing Petri net because of their intuitive graphical representation and their capabilities for mathematical analyses. However, in the process(More)
One hundred twenty Salmonella enterica serotype Typhimurium strains, including 103 isolates from cattle gathered between 1977 and 1999 in the prefecture located on the northern-most island of Japan, were analyzed by using fluorescent amplified-fragment length polymorphism (FAFLP) and pulsed-field gel electrophoresis (PFGE) to examine the genotypic basis of(More)