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Computational modeling of cardiac cellular electrophysiology has a long history, and many models are now available for different species, cell types, and experimental preparations. This success brings with it a challenge: how do we assess and compare the underlying hypotheses and emergent behaviors so that we can choose a model as a suitable basis for a new(More)
MOTIVATION Only models that are accessible to researchers can be reused. As computational models evolve over time, a number of different but related versions of a model exist. Consequently, tools are required to manage not only well-curated models but also their associated versions. RESULTS In this work, we discuss conceptual requirements for model(More)
With the ever increasing use of computational models in the biosciences, the need to share models and reproduce the results of published studies efficiently and easily is becoming more important. To this end, various standards have been proposed that can be used to describe models, simulations, data or other essential information in a consistent fashion.(More)
MOTIVATION Repositories support the reuse of models and ensure transparency about results in publications linked to those models. With thousands of models available in repositories, such as the BioModels database or the Physiome Model Repository, a framework to track the differences between models and their versions is essential to compare and combine(More)
Background: With the ever increasing use of computational models in the biosciences, the need to share models and reproduce the results of published studies efficiently and easily is becoming more important. To this end, various standards have been proposed that can be used to describe models, simulations, data or other essential information in a consistent(More)
Sharing in silico experiments is essential for the advance of research in computational biology. Consequently, the COMBINE archive was designed as a digital container format. It eases the management of files related to a modelling result, fosters collaboration, and ultimately enables the exchange of reproducible simulation studies. However, manual handling(More)
COMBINE archives are standardised containers for data files related to a simulation study in computational biology. This manuscript describes a fully featured archive of a previously published simulation study, including (i) the original publication, (ii) the model, (iii) the analyses, and (iv) metadata describing the files and their origin. With the(More)
UNLABELLED The repeatedly reported effect of proteins on lipoprotein metabolism leaves the question if this is caused mainly by the amount of amino acid composition of the protein itself, by the accompanying fat of cholesterol content, or by the contemporary predominant kind of carbohydrate in the diet. The conducted experiments with male rats, feeding them(More)
The COMBINE archive is adigital container format for files related to avirtual experiment in computational biology.I teases the management of numerous files related to as imulation study,f osters collaboration, and ultimately enables the exchange of reproducible research results. The CombineArchive Toolkit is asoftware for creating, exploring, modifying,(More)