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Extracting reproducible simulation studies from model repositories using the combinearchive toolkit

3 years 6 months ago
Extracting reproducible simulation studies from model repositories using the combinearchive toolkit
: 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 CombineArchive Toolkit 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. 1 Reusability of simulation studies in systems biology A study by the pharmaceutical company Bayer in 201...
Martin Scharm, Dagmar Waltemath
Added 17 Apr 2016
Updated 17 Apr 2016
Type Journal
Year 2015
Where BTW
Authors Martin Scharm, Dagmar Waltemath
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