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...

• Type: Journal
• Year: 2015
• Where: BTW
• Authors: Martin Scharm, Dagmar Waltemath
• Keywords: BTW 2015, Database