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Recent studies have shown that the majority of published computational models in systems biology and physiology are not repeatable or reproducible. There are a variety of reasons for this. One of the most likely reasons is that given how busy modern researchers are and the fact that no credit is given to authors for publishing repeatable work, it is inevitable that this will be the case. The situation can only be rectified when government agencies, universities and other research institutions change policies and that journals begin to insist that published work is in fact at least repeatable if not reproducible. In this chapter guidelines are described that can be used by researchers to help make sure their work is repeatable. A scoring system is suggested that authors can use to determine how well they are doing.
Astrocytes affect neural transmission by a tight control via glutamate transporters on glutamate concentrations in direct vicinity to the synaptic cleft and by extracellular glutamate. Their relevance for information representation has been supported
Untargeted metabolomic studies are revealing large numbers of naturally occurring metabolites that cannot be characterized because their chemical structures and MS/MS spectra are not available in databases. Here we present iMet, a computational tool
The amount of mutual information contained in time series of two elements gives a measure of how well their activities are coordinated. In a large, complex network of interacting elements, such as a genetic regulatory network within a cell, the avera
Normal mode analysis offers an efficient way of modeling the conformational flexibility of protein structures. Simple models defined by contact topology, known as elastic network models, have been used to model a variety of systems, but the validatio
We study kinetic model of Nuclear Receptor Binding to Promoter Regions. This model is written as a system of ordinary differential equations. Model reduction techniques have been used to simplify chemical kinetics.In this case study, the technique of