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The COMBINE archive is a digital container format for files related to a virtual experiment in computational biology. It eases the management of numerous files related to a simulation study, fosters collaboration, and ultimately enables the exchange of reproducible research results. The CombineArchive Toolkit is a software for creating, exploring, modifying, and sharing COMBINE archives. Open model repositories such as BioModels Database are a valuable resource of models and associated simulation descriptions. However, so far no tool exists to export COMBINE archives for a given simulation study from such databases. Here we demonstrate how the CombineArchiveToolkit can be used to extract reproducible simulation studies from model repositories. We use the example of Masymos, a graph database with a sophisticated link concept to connect model-related files on the storage layer.
This article is submitted for the Workshop on Data Management for Life Sciences (DMforLS) 2015 at BTW 2015, Hamburg, Germany.