Biochemical networks are the analog computers of life. They allow living cells to control a large number of biological processes, such as gene expression and cell signalling. In biochemical networks, the concentrations of the components are often low. This means that the discrete nature of the reactants and the stochastic character of their interactions have to be taken into account. Moreover, ...

Background: Cryopreservation of in vitro matured oocytes is a useful technique because the oocytes can be used for some assisted reproductive technologies. On the other hand, the cryopreservation of oocytes is an open problem as a result of their structural sensitivity to the freezing process. The purpose of this study was to evaluate the effect of vitrification on in vitro development of vitri...

MOTIVATION Most previous approaches to model biochemical networks have focused either on the characterization of a network structure with a number of components or on the estimation of kinetic parameters of a network with a relatively small number of components. For system-level understanding, however, we should examine both the interactions among the components and the dynamic behaviors of the...

A set of components (CMLReact) for managing chemical and biochemical reactions has been added to CML. These can be combined to support most of the strategies for the formal representation of reactions. The elements, attributes, and types are formally defined as XMLSchema components, and their semantics are developed. New syntax and semantics in CML are reported and illustrated with 10 examples.